The stained arrays were scanned on the Affymetrix GeneChip® Scanner 3000.

The data were analyzed with GeneSpring 12.5 GX using default analysis settings with RMA as the summerization algorithm.

Hybridization cocktails containing Affymetrix spike-in controls and 15.0ug of each fragmented, labeled cRNA were loaded onto Affymetrix GeneChip® Mouse 430 2.0 arrays.  The arrays were hybridized for 16 hours at 45°C with rotation at 60 rpm in the Affymetrix GeneChip® Hybridization Oven 640. The arrays were washed and stained with a streptavidin, R-phycoerythrin conjugate stain using the Affymetrix GeneChip® Fluidics Station 450 using fluidics protocol FS450_0001. Signal amplification was done using biotinylated antistreptavidin.

Samples were labeled using the standard Affymetrix linear amplification protocol using the 3’ IVT Express Kit.  250 ng of total RNA was reverse transcribed to produce double-stranded cDNA.  The cDNA product was used as a template for the vitro transcription reaction, producing biotin-labeled cRNA. The labeled cRNA was tested for integrity on the Agilent Bioanalyzer and quantified using the NanoDrop® ND-1000 spectrophotometer.  15.0 µg of the labeled cRNA was fragmented and re-checked for concentration and size.

The oriP/EBNA1-based pCEP4 episomal vectors pEP4EO2SCK2MEN2L (7.3 μg) (Addgene plasmid 20924) and pEP4EO2SET2K (3.2 μg) (Addgene plasmid 20927) were transfected into 106 human fibroblasts using nucleofection (NHDF - VPD-1001 with U020 program, Amaxa). After 2 days of culture in fibroblast medium, 50,000 fibroblasts were seeded onto MEF feeder plates and adapted to KOSR medium containing 100 ng ml b-FGF over a course of 3 days. The cultures were next supplemented with 20 mg/ml pifithrin-α and cultured for 3-4 weeks (first week with unconditioned KOSR + 100 ng/ml b-FGF and week 2-4 with MEF conditioned KOSR + 100 ng/ml b-FGF (Invitrogen)) under low oxygen (2%) conditions with daily medium changes. Subsequently 20 colonies of each line were manually picked and cultured on fresh MEF feeder plates for 4 weeks before bulk expansion by Collagenase IV (Gibco) passaging. Ultimately two iPSC clones from each fibroblast donor that conformed to the criteria of iPS cells were established.

Human ES cells and iPS cells were maintained on irradiated mouse embryonic fibroblasts (MEFs) in DMEM/F12 culture medium supplemented with 20% KnockOut serum replacement (KOSR), 0.1 mM non-essential amino acids, 1 mM L-glutamine, 0.1 mM ß-mercaptoethanol and 100 ng/mL human bFGF (all from Invitrogen). Feeder-free culture on Matrigel (BD Biosciences) with conditioned medium was carried out in the presence of 100 ng/ml human bFGF. Human male CRL2429 and female CRL1502 fibroblasts, and male DS CCL-54 fibroblasts (ATCC) were cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum (FBS), 0.1 mM non-essential amino acids and 2.0 mM Glutamax (all from Invitrogen).

For each probe, raw signal intensity was calculated using GenomeStudio software (Illumina). Normalization and statistical analysis of microarray data were performed in R using the Bioconductor packages Lumi and Limma.

Total RNA was extracted using the Qiagen RNeasy Mini RNA extraction kit (Qiagen) according to the manufacturer's protocols.

For microarray experiments cDNA was synthesized using the TotalPrep RNA Amplification Kit (Illumina) and cDNA was hybridized to Illumina HT12 v4 BeadChip microarrays according to manufacturer's instructions.

Samples were labelled using Illumina TotalPrep RNA Amplification Kit, following manufacturer's instructions.

5991413017_E
normal;induced pluripotent stem cell;CRL1502 C32;rep2

5991413017_D
normal;induced pluripotent stem cell;CRL1502 C32;rep1

5991413017_C
normal;induced pluripotent stem cell;CRL-2429 C11;rep6

5991413017_B
normal;induced pluripotent stem cell;CRL-2429 C11;rep5

5991413017_A
normal;induced pluripotent stem cell;CRL-2429 C11;rep4

At baseline, two biopsies were taken from each patient; one 6mm punch biopsy was obtained from lesional skin of each patient (involved sample) and the other from non-lesional skin (uninvolved sample). Non-lesional biopsies were taken from the buttocks or upper thighs. For each patient, lesional biopsies were then taken on days 1, 3, 7 and 14 following etanercept treatment. Biopsies were snap-frozen in liquid nitrogen, stored at -80°C. At processing the biopsy samples were homogenized while still frozen and total RNA isolation was performed using RNeasy kit protocol (Qiagen, Chatsworth, Ca, USA).

GeneChips were scanned using the Affymetrix GeneArray TM Scanner 3000.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 Human Genome Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

lesional skin bioposy obtained from patient after 7 days of treatment

lesional skin bioposy obtained from patient after 1 day of treatment

lesional skin bioposy obtained from patient after 3 days of treatment

lesional skin bioposy obtained from patient after 14 days of treatment

Images were quantified using Agilent Feature Extraction Software (version 9.5.1).

Agilent Feature Extraction Software (v 9.5.1) Pre-processing of data, quality checks, and significance analysis were all performed as described in: Fijneman et al,Pla2g2a attenuates colon tumorigenesis in azoxymethane-treated C57BL/6 mice; expression studies reveal Pla2g2a target genes and pathways. Cell Oncol 2009; 31: 345-56.  Please see readme.txt on the Series record for additional details from the reference above.
Two-channel arrays were analyzed as single-channel; comparison/ratios were not considered in the analysis of the data.  Raw data are linked as supplementary files on the Series record and each applies to two GEO Sample records as indicated in the description field above.

total RNA was isolated according to manufacturer's protocol , Qiagen

according to Agilent Gene Expression oligo microarrays protocol (version 5.0.1)

raw data file: US22502676_251486810270_S01_GE2-v5_95_Feb07_1_4.txt
ko_4_Cy5

raw data file: US22502676_251486810270_S01_GE2-v5_95_Feb07_1_3.txt
wt_3_Cy5

wt_8_Cy3

Dental pulp cells were grown in DMEM/F12 media supplemented with 1% non-essential aminoacids and 15% fetal bovine serum. iPSC cells were grown in mTeSR media (Stem cell Technologies). Embryonic cells were grown in human embryonic stem cells media (DMEM/F12 media supplemented with 20% knockout serum replacement; 50uM b-mercaptoethanol, 1% non-essential aminoacids; 10ng/ml FGF)

Biotinylated cDNA were prepared according to the standard Affymetrix protocol

gene expression data from induced pluripotent stem cells generated from dental pulp cells

Mice were housed under standard SPF conditions and according to the Ethical Committee for Animal Experimentation of the Government of Catalonia.

Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003)

Total RNA was isolated from FACS-sorted cells in Trizol by chloroform extraction, followed by the RNA clean-up protocol of RNeasy Micro or Mini Kit (Qiagen)

Affymetrix GeneChip Human Gene 1.0ST arrays were hybridized with 10 ug of labeled, amplified dsDNA, washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_007)

The indicated starting amount of total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and subsequently labeled using GeneChip Mapping 10K Xba Assay Kit (Affymetrix; catalog # 900441), according to manufacturer's instructions.

Gene expression data from purified clock positive Basal IFE stem cells

GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

Trizol extraction of total RNA followed by Rneasy column cleanup was performed according to the manufacturer's instructions.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scanning of Affymetrix chips were performed according manufacturer's instructions

The 19 CEL files were processed using Stratagene’s Array Lite 3.4 software using GC-RMA algorithm to calculate probeset intensity values and to calculate Absent/Present/Marginal flags.  These intensity values were log2 transformed.

RNA was isolated by first homogenizing the tissue with a Brinkmann homogenizer, passing it through a QIAshredder (Qiagen,) column and isolating the RNA by RNeasy miniprep kit (Qiagen).

hybridization of cRNAs to Affymetrix chips were performed according manufacturer's instructions

cRNA with biotin labeling was performed according to Affymetrix protocols

biopsy of normal esophagus from the same patient as a matched Barrett's esophagus biposy

HaCat cells are infected with an empty pLENTI6-EGFP vector or with a  pLENTI6-EGFP vector in which a BCL-3 cDNA was inserted

HaCat cells are maintained in DMEM supplemented with 10% FCS, glutamine and antibiotics.

The arrays have been scanned with the Affymetrix GeneChip Scanner 3000 7G with appropriate recommended protocols.

We used the BRB ArrayTools software in order to analyse the data. First, the data were normalized with RMA procedure included in the BRB Array tools software then filtered out based on the variance for the gene across the arrays, a feature included in the BRB Array tools software which allows to remove unexpressed or equally expressed transcripts. The variance of the log-ratios for each gene is compared to the median of all the variances. Those genes not significantly more variable than the median gene are filtered out. Specifically, the quantity (n-1) Vari / Varmed is computed for each gene i. Vari is the variance of the log intensity for gene i across the entire set of n arrays and Varmed is the median of these gene-specific variances. This quantity is compared to a percentile of the chi-square distribution with n-1 degrees of freedom. This is an approximate test of the hypothesis that gene i has the same variance as the median variance. In order to identify significant differentially expressed transcripts, we used the Class Comparison Tool (BRB Array Tools software). This tool computes the number of genes that are differentially expressed among the classes at the statistical significance level selected in the t-test menu and creates a gene list containing information about the significant genes. The Class Comparison Between Groups of Arrays Tool computes a t-test separately for each gene using the normalized log-intensities for one color oligonucleotide arrays.  The Class Comparison Tool also provides univariate permutation tests for the significance of individual genes. The univariate permutation tests are computed separately for each gene. The output gene list table is ordered by univariate p value with the most significant genes listed first. The false discovery rate (FDR) associated with a row of the table is an estimate of the proportion of the genes with univariate p values less than or equal to the one in that row that represent false positives. The method of Benjami and Hochberg is used for this FDR estimation. We used the t-test pvalue <0.001 threshold in our analysis.

Total RNAs were extracted from the resulting HaCat cells cultured in triplicate, using the RNeasy Mini kit from Qiagen (Valencia, CA). The integrity of the RNAs from those six distinct experimental conditions was checked with the Agilent Bioanalyzer using the RNA 6000 Nano kit (Agilent, Santa Clara, CA).

The arrays have been hybridized with 15 micrograms of fragmented aRNA as recommended. The Affymetrix GeneChip Hybridization, Wash, and Stain Kit has been used to hybridize and wash the arrays. The fluidics station 450 has been used following manufacturer's recommendations.

The Affymetrix GeneChip 3’ IVT Express Kit has been used to label targets from 100 nanograms of total RNA, following manufacturer's recommendations

empty vector;HaCaT;Immortalized keratinocytes;Immortalized cell line

HaCat cells infected with a control lentiviral construct. Replicat 2

biopsy of Barrett's esophagus from the same patient as a matched normal esophagus biposy

BCL-3 vector;HaCaT;Immortalized keratinocytes;Immortalized cell line

HaCat cells infected with a BCL-3-expressing  lentiviral construct. Replicat 1

HaCat cells infected with a BCL-3-expressing  lentiviral construct. Replicat 2

Mice used were Foxp3-GFP knock-in B6/129 F2's of 5-8 weeks of age. Single cell suspensions of cells from spleens and lymph nodes of 25 male mice were generated. Cell suspensions were enriched for CD4+ T cells by magnetic antibody mediated depletion using a cocktail of biotinylated antibodies specific for CD8, B220, CD11b, NK1.1, and DX5 followed by anti-biotin MACS beads. The remaining cells were labeled with CD4-PerCP, CD25-APC antibodies, and PE-conjugated streptavidin. CD4+PE- cells were sorted into four populations based on expression of GFP and CD25. Total RNA was isolated and biotinylated antisense cRNA was prepared using two cycles of in vitro amplification according to the Affymetrix Small Sample Labeling Protocol II. Biotinylated cRNA was fragmented and hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 arrays.
Keywords = regulatory T cells
Keywords = Foxp3

The data were analyzed (including normalization and modelling) with dChip

mRNA from isolated glomeruli from normal kidney
Keywords = kidney

Keywords = Kidney

mRNA from isolated glomeruli from kidneys with diabetic nephropathy

Cells were cultured in standard culture media conditions in 37⁰C/5% CO2 incubators

Raw data: The numerical results were extracted with GenomeStudio v. 2009.1 without any normalization or background subtraction.
Normalized data: Normalized using quantile normalisation with limma in R

total RNA was isolated with an Rneasy kit (Qiagen, Chatsworth, CA) with on-column Dnase treatment

For the Illumina gene expression analysis, 100 ng of purified total RNA was amplified and biotinylated in an overnight in vitro transcription reaction using the Illumina RNA TotalPrepTM amplification kit (Ambion, Applied Biosystems).

All iPSC lines were generated by retrovirus mediated cell reprogramming, and expanded in feeder-free Matrigel and mTesR conditions. No additonal treatment was performed before sample extraction.

Human fibroblasts were maintained in DMEM with 10% FBS. Human iPSC and ESC were cultured in Matrigel (BD Biosciences) with mTeSR medium (Stem Cell Technologies).

Expression signals were scanned on an Affymetrix GeneChip Scanner 3000 7G.

The statistical analysis of the data was performed using GenePattern platform from Broad Institute. Briefly, raw CEL files were imported into GenePattern platform and normalized using RMA algorithm. The Hierarchical Clustering analysis was performed using the HierarchicalClustering module of the software. The dendrograms and the heat map of the clustered gene expression data were visualized by the HierarchicalClusteringViewer module.

Total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA) and purified further using the Rneasy Mini Kit (Qiagen).

After hybridization cocktails preparation, the Affymetrix HG-U133A 2.0 arrays were hybridized with the fragmented labelled cRNA for 16 h at 45 °C as described in the Affymetrix Technical Analysis Manual.

The Affymetrix GeneChip microarray was performed by the Functional Genomics Core Facility at The Salk Institute for Biological Studies following the manufacturer’s protocol (Affymetrix, Santa Clara, CA). Briefly, 100 ng of total RNA of each sample were processed using Affymetrix GeneChip 3’ IVT Expression Kit following the manufacturer’s protocol. For each sample, 12.5 μg fragmented and labeled aRNA were hybridized to the Affymetrix HG-U133A 2.0 chips.

Human LRRK2 (G2019S) heterozygous induced pluripotent stem cells

Gene expression data from LRRK2 (G2019S) heterozygous fibroblasts

Cell were treated after plating into 6-well cell culture plates with the indicated cytokines (20 ng/ml M-CSF. 20 ng/ml IL-4 and vehicle (DMSO:ethanol) or 1 uM Rosiglitazone.

Bone marrow cells were isolated from the femur, washed twice with PBS and cultured in RPMI+10% FCS supplemented with glutamine, penicillin and streptomycin and 20 ng/ml M-CSF. Fresh media and cytokines were added every other day for 10 days.

Microarrays were scanned canned according to Affymetric standardized protocol.

The data were generated with GCOS, and cel files were analyzed in GeneSpring 7.3 using GC-RMA.

Qiagen extraction of total RNA was performed according to the manufacturer's instructions.

Following fragmentation, 10 ug of cRNA were hybridized on Mouse Genome 430 2.0  Affymetrix microarrays according to Affymetric standardized protocol.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

Gene expression data of IL-4+RSG-treated bone marrow-derived macrophages derived from C57Bl/6 wild type mouse
8_(Mouse430_2).CEL

2;C57Bl/6;Wild-type;bone marrow-derived macrophage;IL-4;Rosiglitazone;10 days

Gene expression data of IL-4-treated bone marrow-derived macrophages derived from C57Bl/6 wild-type mouse
7_(Mouse430_2).CEL

2;C57Bl/6;Wild-type;bone marrow-derived macrophage;IL-4;Control;10 days

Gene expression data of RSG-treated bone marrow-derived macrophages derived from C57Bl/6 wild-type mouse
6_(Mouse430_2).CEL

2;C57Bl/6;Wild-type;bone marrow-derived macrophage;Control;Rosiglitazone;10 days

Gene expression data of bone marrow-derived macrophages derived from C57Bl/6 wild-type mouse
5_(Mouse430_2).CEL

2;C57Bl/6;Wild-type;bone marrow-derived macrophage;Control;Control;10 days

4_(Mouse430_2).CEL

1;C57Bl/6;Wild-type;bone marrow-derived macrophage;IL-4;Rosiglitazone;10 days

3_(Mouse430_2).CEL

1;C57Bl/6;Wild-type;bone marrow-derived macrophage;IL-4;Control;10 days

Control bone marrow - Biological Replicate 5 - Technical Replicate 2

Slides were scanned on GenePix® 4200A instrument (Axon Instruments)
Images were quantified using GenePix Pro 6.0

LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. BRBArrayTools software was used.

Total RNA was extracted using Qiagen RNeasy Midi Kit following manufacturer's instructions

Labeled samples, diluted in Hybridization buffer (5X SSC; 50% Formamide; salmon sperm-DNA 100 ng/ul; 0.1% SDS), were applied to microarrays enclosed in Corning hybridization chambers - 42°C over night.

aRNA were obtained using the Ambion Amino Allyl MessageAmp™ II aRNA Amplification Kit, according to the manufacturer's instructions. 12 µg of aRNA were labeled with Amersham Cy5 (RNA samples) or Cy3 (Reference RNA)

Biological replicate 5 of 5. Technical Replicate 2 of 2. Control bone marrow cells, untreated

bone marrow cells;DBA/2;pool of untreated bone marrow cells;DBA/2;reference

Control bone marrow - Biological Replicate 5 - Technical Replicate 1

Biological replicate 5 of 5. Technical Replicate 1 of 2. Control bone marrow cells, untreated

Control bone marrow - Biological Replicate 4 - Technical Replicate 2

Biological replicate 4 of 5. Technical Replicate 2 of 2. Control bone marrow cells, untreated

Control bone marrow - Biological Replicate 4 - Technical Replicate 1

Biological replicate 4 of 5. Technical Replicate 1 of 2. Control bone marrow cells, untreated

Control bone marrow - Biological Replicate 3 - Technical Replicate 2

Biological replicate 3 of 5. Technical Replicate 2 of 2. Control bone marrow cells, untreated

Control bone marrow - Biological Replicate 3 - Technical Replicate 1

Biological replicate 3 of 5. Technical Replicate 1 of 2. Control bone marrow cells, untreated

Control bone marrow - Biological Replicate 2 - Technical Replicate 2

Biological replicate 2 of 5. Technical Replicate 2 of 2. Control bone marrow cells, untreated

Control bone marrow - Biological Replicate 2 - Technical Replicate 1

Biological replicate 2 of 5. Technical Replicate 1 of 2. Control bone marrow cells, untreated

Control bone marrow - Biological Replicate 1 - Technical Replicate 2

Biological replicate 1 of 5. Technical Replicate 2 of 2. Control bone marrow cells, untreated

Control bone marrow - Biological Replicate 1 - Technical Replicate 1

Biological replicate 1 of 5. Technical Replicate 1 of 2. Control bone marrow cells, untreated

Mice were housed in a temperature-controlled environment with a 12:12 hour light:dark cycle and free access to food and water. At 16 weeks of age, mice were euthanized and liver tissue was collected and stored at -80.

GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader.

Data was analyzed using the affy bioconductor package implemented in the R-statistical environment version 2.12.2. RMA was used to normalize the data and fit log2 transformed expression values.

RNA was extracted using the Trizol reagent (Invitrogen) from 100 mg of liver tissue according to the manufacturer's instructions. Quality of RNA was checked with the Agilent 2100 BioAnalyzer.

Following fragmentation, 16 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

Biotinylated aRNA were prepared according to the Affymetrix GeneChip 3’ IVT Express kit protocol from 250 ng total RNA (Affymetrix GeneChip 3’ IVT Express kit Instruction Manual, P/N 702646 Rev. 5).

PBMC was isolated from peripheral whole blood using Ficoll-Plaque Plus (Amersham Biosciences, USA) according to the manufacturer’s protocol. In brief, one ratio of diluted blood (1:1 ratio in PBS) sample was layered on 2 ratio of Ficoll-Plaque Plus (Amersham Biosciences, USA), pelleted (400g, 30 minutes at 18-20°C) and the buffy coat was collected, washed twice with PBS. PBMC with viability higher than 90% was subjected to RNA extraction.

Peripheral whole blood was collected in heparinized vacutainer tubes (Becton Dickinson) and subjected to PBMC isolation within 4 hours.

The data value(log2) were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

Trizol extraction of total RNA was performed according to the manufacturer's instructions.

Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA .

VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

Simple annotation: Stimulation, Jurkat cells
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14913.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14920.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14911.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16182.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14918.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14941.gif

To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).

To decide whether a signal was significantly above background, the MAS 5.0 algorithm was applied to calculate probe set detection calls. Robust Multichip Average (RMA) was applied to probe sets that had a present detection call in at least 4 out of 6 CCD samples. Using limma, the average expression value for each experimental condition was estimated. Based on these estimates, the contrasts CTC vs. T, CTC vs. P, CTC vs. G, T vs. P, T vs. G, and P vs. G were estimated. For each contrast it was tested whether it was significantly different from 0 using a moderated t-statistic (implemented in limma).

RNA was isolated using a protocol combining Trizol/chloroform extraction, followed by column chromatography with the RNeasy Mini kit (Qiagen).

Purified fragmented biotinylated cRNA and hybridization controls (Affymetrix) were mixed, hybridized on Affymetrix HG U133 Plus 2.0 arrays, and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).

Per sample, ideally an amount of 5-10 ng of total RNA spiked with four bacterial RNA transcripts (Affymetrix) was converted and amplified to double stranded cDNA in a 2-cycle cDNA reverse transcription reaction. Subsequently the sample was converted to antisense cRNA and labeled with biotin through an in vitro transcription reaction according to the manufacturer’s protocol (Affymetrix).

Gene expression data of original tumor tissue of pancreatic ductal adenocarcinoma patient

Gene expression data of circulating tumor cells of pancreatic ductal adenocarcinoma patient

Gene expression data of haematological cells of pancreatic ductal adenocarcinoma patient

Gene expression data of non-tumor pancreatic control tissue of pancreatic ductal adenocarcinoma patient

Cells were infected with TBK1- or GFP-specific lentivirally delivered shRNAs for 4 hours, puromycin selection was initiated 24 hours post-infection, then RNA was harvested 48 hours post-infection.

AALE cells (Lundberg et al., Oncogene 2002;21:4577) expressing oncogenic KRAS or vector alone were grown in serum free SABM media with supplements using standard culture conditions.

The data were analyzed with RMA (Gene Pattern's ExpressionFileCreator version 8). Parameters: method   RMA  quantile normalization  yes  background correct  yes  compute present absent calls  no  normalization method  none  value to scale to    clm file    annotate probes  yes

Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on U133A Human Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

Washing and staining of microarrays were performed on Affymetrix Fluidics Station 450 and scanned on Affymetrix GeneChip scanner 3000.

Data were collected using Affymetrix AGCC software. Basic statistical analysis was performed with Flexarray software as follows: Background correction (MAS5.0), array normalization (quantile normalization), probe set summarization technique (Tukey biweight [MAS5.0])

RNA was isolated using Trizol followed by clean up using Qiagen´s RNAeasy mini spin colomn according to manufacturer's instuctions.

Each sample was hybridized to Affymetrix mouse Gene ST 1.0 GeneChip in Affymetrix hybridization oven at 45C, 60rpm for 16 hrs.

RNA (200ng) was reverse transcribed using random hexamer primer, amplified and terminal labeled with biotin using Affymetrix Whole Transcript Sense Target Labeling kit according to manufacturer’s protocol.

All preprocessing of Affymetrix data was performed using the Bioconductor Package in the R statistical environment. Data set analysis done under the R statistical environment version 1.9.0 on i686-pc-linux-gnu. Bioconductor package 'affy' version 1.4.32, 'gcrma' version 1.1.0, 'siggenes'(R sam analysis) version 1.0.6.

Whole retinas were removed from 3, and 8 month old DBA/2J mice and rinsed in ice-cold 0.1 M phosphate buffered saline to remove blood. Three individual retinas at each age were homogenized in Qiagen RLT buffer using a micro pestle and pulled five times through a 22G needle, then flash frozen in liquid nitrogen.

Total RNA was isolated using a Qiagen RNeasy Kit. The quantity and quality of the RNA was assessed using a Nanodrop ND1000 spectrophotometer and an Agilent 2100 Bioanalyzer. 20ng of each retinal RNA sample was amplified, fractionated, and labeled with a NuGEN Ovation Biotin kit to generate probe for Affymetrix microarray analysis.

8 months, Sex: Female, Retina: left, Final IOP (mm Hg): 25.3, Strain:DBA/2J

8 months, Sex: Female, Retina: right, Final IOP (mm Hg): 26.5, Strain:DBA/2J

For osteoblast differentiation, growth medium was supplemented with 10 mM β-glycerophosphate, 0.2 mM ascorbate, 10^-8 M calcitriol, and 10^-7 M dexamethasone. For adipocyte differentiation, normal growth medium containing 15% BGS was supplemented with 2 X 10^-6 M insulin, 0.45 mM isobutylmethyl-xanthine, 10-5 M troglitazone, and 10^-7 M dexamethasone.

hMSC-Tert cells were cultured in low glucose, phenol red-free MEM (Invitrogen, Carlsbad, CA), supplemented with 10% bovine growth serum (BGS; HyClone, USA) and 1X penicillin/streptomycin (Invitrogen).

Log2 transformation of signal intensity, quantile normalization, R/Bioconductor, BeadStudio.

Total RNA was extracted using Qiazol (Qiagen) according to the manufacturer's instructions.

Illumina Whole-Genome Gene Expression Direct Hybridization Assay Guide (11286331).

Illumina TotalPrep RNA Amplification Kit (Ambion, Inc., Cat # IL1791); 200ng total RNA input.

human immortalized mesenchymal stem cells;control;2 days adipocyte differentiation

Data were analysed with the Affymetrix Microarray Suite 5.0 algorithm to generate a “signal” value and a “detection” label. Prior to normalisation, probes that generated an absent call in all cells were removed. Normalisation was calculated using a Global Scaling method based on the entire data set. Globally scaled values <10 were rounded up to 10.

Total RNA was extracted by RNA Isolation Kit (Stratagene) from the livers of Wistar and Kyoto rats at day 0 (Wistar n=3, Kyoto n=2), day 1 and 3 (Wistar n=2, Kyoto n=2), and day 14 (Wistar n=3, Kyoto n=2).

Biotinylated cRNA was fragmented and hybridised to RGU34A Affymetrix GeneChips according to standard Affymetrix protocols.

cDNA was generated from total RNA using SuperscriptTM Double-stranded cDNA Synthesis kit (Invitrogen, Life Technologies), cRNA was prepared by in vitro transcription (BioArray High Yield RNA transcript labelling kit Affymetrix, UK), and purified on an affinity resin column (RNeasy, Qiagen Ltd., UK).

Rats (Charles River UK Ltd.) were fed either standard laboratory chow, or chow supplemented with 1% orotic acid (Sigma Aldrich, UK) ad libitum. Orotic acid feeding is a well-characterised method for inducing reversible fatty liver disease in rodents. Rats were killed by cervical dislocation and the left lateral lobe of the liver excised. Tissues were snap frozen and stored in liquid nitrogen and/or at –80oC.

Keywords = orotic acid
Lot batch = 1

Kyoto rat liver tissue following animal exposure to orotic acid for 1 day

Ultrasound analysis was used to confirm viability and heart rate data in vivo immediately before isolation

Age- and size-matched E10.5 mouse hearts were isolated and total RNA was extracted

Performed by GeneLogic (Gaithersburg, MD). See Quality Control file from GeneLogic for more information.

Tcra-/- thymocytes were freshly harvested and positively selected for the DP subset over anti-CD4 magnetic columns (Miltenyi).

2-10 ug of total RNA was extracted using the Rneasy Kit (Qiagen). Total RNA integrity was assessed by analysis with an Agilent Bioanalyzer.

Hybridization was performed for 16 hrs per standard Affymetrix protocol

Morphine (morphine hydrochloride; Polfa, Kutno, Poland) was administered subcutaneously (s.c.). Experimental groups (control, acute and chronic morphine) consisted of 9 animals from each strain. To obtain the most reliable comparison, control and acute morphine groups received injections of saline for four days in the same time schedule as the chronic group received morphine. On the fifth day, acute treated animals were injected with a single dose of morphine (20 mg/kg) and killed by decapitation after 4 h. Chronically treated animals were injected with increasing doses of morphine for five days. Mice received morphine thrice daily (09:00 h, 13:00 h and 17:00 h) for four days using a dosing schedule of 10, 20, 40 and 40 mg/kg of morphine on days 1, 2, 3 and 4, respectively. On the last day, a final morphine dose of 40 mg/kg was administered and 4 h after the last injection, the animals were sacrificed. Mice in control groups were killed 4 h after the last injection of saline. The dose scheme and time schedule were used in order to maximize strains differences in response to morphine.

Adult male (8 to 10 weeks of age) 129P3/J (000690), DBA/2J (000671), C57BL/6J (000664) and SWR/J (000689) mice (The Jackson Laboratory, Bar Harbor, Maine, USA) were housed 6 per cage, under a 12 h dark/light cycle, with ad libitum access to food and water. Animals weighing from 20 to 30 g were used throughout the experiments. The animal protocols used in the study were approved by the local Bioethics Commission working at the Institute of Pharmacology, Polish Academy of Sciences (Krakow, Poland).

The arrays were scanned using the GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).

Trizol/RNeasy extraction of total RNA was performed according to the manufacturer's instructions.

Following labeling, samples were hybridized to the GeneChip Test3 array (Affymetrix, Santa Clara, CA) for quality control. Fragmented cRNA (15 μg) was used for hybridization to the GeneChip Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, CA). Arrays were washed and stained with streptavidin-phycoerythrin (Merck, Darmstadt, Germany) in Fluidic Station 400 (Affymetrix, Santa Clara, CA) according to standard protocol of the manufacturer.

C57BL/6J Chronic morphine treated, striatum, biological replicate 2

C57BL/6J Chronic morphine treated, striatum, biological replicate 1

Affymetrix GeneChip Scanner 3000 according to the manufacturer’s protocol

Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package affy.

Hybridization, staining, and scanning were performed in quadruplicate using the GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix)

Affymetrix GeneChip 3’ IVT Express Labeling Kit, manufacturer's protocol

C57BL/6J Chronic morphine treated, striatum, biological replicate 3

A total of 3 patch tests with 5% nickel sulfate was taken from each subject: i) the first patch test was exposed for 7h and a skin biopsy was taken immediately after removing the patch test ii) the second patch test was exposed for 48h immediately followed by a skin biopsy and iii) the third patch test was exposed for 48h and the skin biopsy was taken 48h after removing the patch test (the 96h biopsy). In addition, all participants were exposed to an empty patch test exposed for 48h followed by a skin biopsy.

The Affymetrix system was used and the protocols supplied by Affymetrix followed.

Log(2) transformed expression measures were calculated with the RMA procedure using the software from www.Bioconductor.org

For RNA extraction, the skin biopses were placed in a morter filled with liquid nitrogen and ground mechanically using a pistil. The tissue was transferred to a lysis buffer and RNA was extracted using the RNase Lipid Tissue Kit (Qiagen, Valencia; CA). The amount and quality of the extracted RNA was evaluated using a lab-on-a-chip Bioanalyzer (Agilent Technologies, CA, USA).

The Affymetrix GeneChip® Hybridization, Wash, and Stain kit was used according to the protocol supplied with the kit.

First strand cDNA was synthesized from 1 ug total RNA by incubation (42C, 1 hr) in a 20 ul reaction volume containing 2.5 mM T7-(dT)24 primer, 50 mM Tris-HCl pH 8.3, 75 mM KCL, 3 mM MgCl2, 10 mM DTT and 500 mM dNTP, 10 U/ml Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA, USA).Second strand cDNA was synthesized directly by adding 91 ul RNase free water, 30 ul 5 times second strand reaction buffer (Invitrogen), 3 ul 10 mM dNTP, 1 ul Escherichia coli DNA ligase (10 U/ml), 4 ul E. coli DNA polymerase I (10 U/ml), 1 ul E. coli RNase H (2 U/ml) followed by incubation (2 hr, 16C). The ends of the double-stranded cDNA were polished using T4 DNA polymerase (20 U, 5 min, 16C). The cDNA was purified and concentrated by phenol/ chloroform extraction and ethanol precipitation.

The sample is a part of an analysis of gene expression time-course in the human skin during elicitation of allergic contact dermatitis

Nickel allergic female (age range 33-49), skin biopsy from upper nates taken 48 hours after nickel exposure

Skin biopsy from upper nates taken 48 hours after exposure to 5% nickel sulfate

Nickel allergic female (age range 33-49), skin biopsy from upper nates taken 7 hours after nickel exposure

Skin biopsy from upper nates taken 7 hours after exposure to 5% nickel sulfate

Nickel allergic female (age range 33-49), skin biopsy from upper nates. No nickel exposure.

Nickel allergic female (age range 33-49), skin biopsy from upper nates taken 96 hours after nickel exposure

Skin biopsy from upper nates taken 96 hours after exposure to 5% nickel sulfate

Nickel allergic female (age range 33-49), skin biopsy from upper nates. No nickel exposure

normal section from mouse liver was dissected from Txnip deficient mice at 24 months of age.  RNA was extracted using TRIzol. Targets were produced using standard Affymetrix procedures.
This sample is also known as 3NA_signal.
Keywords = Mus musculus, liver tumor, hepatocellular carcinoma

tumor section from mouse liver was dissected from Txnip deficient mice at 24 months of age.  RNA was extracted using TRIzol. Targets were produced using standard Affymetrix procedures.
This sample is also known as 3TC_signal.

This sample is also known as 3TB_signal.

tumor section from liver was dissected from Txnip deficient mice at 24 months of age.  RNA was extracted using TRIzol. Targets were produced using standard Affymetrix procedures.
This sample is also known as 3TA_signal.

nontumor section from mouse liver was dissected from Txnip deficient mice at 22 months of age.  RNA was extracted using TRIzol. Targets were produced using standard Affymetrix procedures.
This sample is also known as 2NC_signal.

This sample is also known as 2NB_signal.

This sample is also known as 2NA_signal.

tumor section from mouse liver was dissected from Txnip deficient mice at 22 months of age.  RNA was extracted using TRIzol. Targets were produced using standard Affymetrix procedures.
This sample is also known as 2TC_signal.

This sample is also known as 3NC_signal.

This sample is also known as 3NB_signal.

The data were analyzed with Expressiojn Console 1.1 using default MAS5 method. The target intensity was 500.

About 1.0x10^3 PC-3 cells plated in a petri dish (diameter, 3.5 cm) were incubated at 35°C overnight, then gefitinib (iressa), luteolin and/or resveratrol dissolved in DMSO were added into the medium.

The PC-3 cells were provided by the Japanese Cancer Research Resources Bank (JCRB). The cells were maintained in 5% CO2 at 35°C in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (Hyclone Laboratory), penicillin (100U/mL), and streptomycin (100μg/mL).

Scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies). The array was scanned using Agilent G2505C DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

The Subio Platform and Subio Basic Plug-in (v1.15; Subio Inc., Aichi, Japan) was then used to calculate the between-sample fold change analyzed by one-sample t-test, Student T-test.

Total RNA was extracted from PC-3 cells 24h following treatment with DMSO, 60μM luteolin (Lut), 60μM gefitinib (Gef) or their co-administration (Lut+Gef) using an miRNeasy Mini kit according to the manufacturer's instructions (Qiagen). The quality of the RNAs was estimated by using the RNA 6000 Nano LabChip Kit (p/n 5065-4476) on the Agilent 2100 Bioanalyzer (G2940BA; Agilent Technologies, Santa Clara, CA).

Before hybridization, 1650 ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations to Agilent-014850 arrays were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual.

100 ng of total RNAs were independently reverse-transcribed using oligo-dT primers containing the T7 RNA polymerase promoter sequence to generate cDNAs and AffinityScript, RTase, which were then subjected to in vitro transcription using T7 RNA polymerase to label the cRNAs with Cy3-CTP (Amersham Pharmacia Biotech, Piscataway, NJ) using a Low input Quick-Amp Labeling Kit (Agilent Technologies).

PC-3 Luteolin_2
PC-3 cells treated for 24h with 60μM luteolin (Lut).

PC-3 L+G_2
PC-3 cells treated for 24h with 60μM luteolin (Lut) and 60μM gefitinib (Gef).

PC-3 Gefitinib_2
PC-3 cells treated for 24h with 60μM gefitinib (Gef).

immortalized human mammary epithelial cell line treated with 0.5 uM of Doxorubicin for 24 hours
Keywords = Breast Cancer, Chemotherapeutics, Gene expression, Microarray, Compugen

immortalized human mammary epithelial cell line treated with 0.2 uM of Doxorubicin for 24 hours

immortalized human mammary epithelial cell line treated with fresh medium for 24 hours

immortalized human mammary epithelial cell line treated with 0.5 uM of Doxorubicin for 36hours

breast cancer derived cell line treated with fresh medium for 36hours

Three sex-matched mice from each genotype (R6/1 and wild-type) were sacrificed at 18, 22 and 27 weeks of age. Brain samples were collected, snap frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted from one hemisphere for microarray analysis, as described previously (Morton et al., 2005). Microarray analysis of global gene expression was carried out using 10µg of total RNA and murine genome 430 2.0 Arrays

Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets.

in vitro Treatment: control, Treatment Time: 8, Units of Treatment Time: hour

Growth Media: DMEM 10%FBS,  Pen/Strep, Fungizone, Growth Conditions: 5% CO2, 37ïC

cells_ATCC 16Lu_human lung fibroblasts_JCB_0_8_33_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014

affylmGUI, The Walter and Eliza Hall Institute of Medical Research

JCB_0_8_33_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

Sample Type: cells, Cell Line: ATCC 16Lu, Cell Type: human lung fibroblasts, Harvest Time Point: 8 hour

cells_ATCC 16Lu_human lung fibroblasts_JCB_0_8_18_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014

JCB_0_8_18_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

in vitro Treatment: control, Treatment Time: 4, Units of Treatment Time: hour

cells_ATCC 16Lu_human lung fibroblasts_JCB_0_4_32_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014

JCB_0_4_32_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

Sample Type: cells, Cell Line: ATCC 16Lu, Cell Type: human lung fibroblasts, Harvest Time Point: 4 hour

cells_ATCC 16Lu_human lung fibroblasts_JCB_0_4_2_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014

JCB_0_4_2_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

in vitro Treatment: H2O2, Treatment Time: 12, Units of Treatment Time: hour, Dose or Concentration: 100, Units of Dose or Concentration: uM

cells_ATCC 16Lu_human lung fibroblasts_JCB_100_12_44_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

JCB_100_12_44_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

Sample Type: cells, Cell Line: ATCC 16Lu, Cell Type: human lung fibroblasts, Harvest Time Point: 12 hour

cells_ATCC 16Lu_human lung fibroblasts_JCB_100_12_29_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

JCB_100_12_29_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

cells_ATCC 16Lu_human lung fibroblasts_JCB_100_12_14_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

JCB_100_12_14_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

cells_ATCC 16Lu_human lung fibroblasts_JCB_0_8_3_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014

JCB_0_8_3_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

oct4 and  jhdm1b infected MEF  were cultured with or without vitamin C treatment. Media were changed everyday.

The data were analyzed with Robust Multichip Average (RMA) using Partek software.

Cells were trypsinized and feeder cells were eliminated. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

Following fragmentation and labeling, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip MoGene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Whole Transcript (WT) Sense Target   Labeling Assay Manual, 2007, Affymetrix).

Gene expression data from ICR MEF infected  with pMX-GFP retrovirus

in vitro Treatment: H2O2, Treatment Time: 1, Units of Treatment Time: hour, Dose or Concentration: 100, Units of Dose or Concentration: uM

cells_ATCC 16Lu_human lung fibroblasts_JCB_100_1_26_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

JCB_100_1_26_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

Sample Type: cells, Cell Line: ATCC 16Lu, Cell Type: human lung fibroblasts, Harvest Time Point: 1 hour

cells_ATCC 16Lu_human lung fibroblasts_JCB_100_1_11_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

JCB_100_1_11_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

Mouse embryos were dissected and then forelimbs were collected for further gene expression analysis.

Scanned on an Agilent scanner, images were processed using Agilent Feature Extraction software version 9.5.

Agilent Feature Extraction software version 9.5 was used for background subtraction and LOWESS normalization.

Total RNA extracted using Qiagen Rneasy kit following manufacturer's instructions.

Agilent In Situ Hybridization Kit Plus was used where Cy-dye labeled control and test samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, the arrays were washed twice, dried and then scanned.

Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Agilent’s Low RNA Input Fluorescent Linear Amplification Kit. 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal mouse reference (Stratagene, La Jolla, CA).

The data were analyzed with Bioconductor tools in R (http://www.r-project.org) using GC-RMA as normalization method. Next we employ a conservative probe-filtering step excluding those probe sets not reaching a log2 expression values of 5 in at least 1 sample.

Total RNA was extracted by Rneasy Kit (Qiagen) according to the manufacturer's instructions.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol

Gene expression data from human colon biopsies; non-inflammatory control

GeneChip Operating Software (GCOS) 1.2 software (Affymetrix, Inc.) using default values (scaling, target signal intensity = 500; normalization, all probe sets; parameters, all set at default values) was used to generate the data.

Age-matched wildtype littermates of glycerol kinase knockout mice.

Cells were transfected with Lonza 96-well Nucleofector system, using solution SF and program DN-100.  For each knockdown, 1 million cells were transfected with 50pmol of siRNA and total RNA was extracted 72 hours later.

Cells were grown at 37°C with 5% CO2 in RPMI-1640 (containing L-glutamine) supplemented with 15% FBS, 100 IU/ml penicilin and 100 µg/ml streptomycin.

First, probes overlapping SNPs were filtered out and the 3'-most probe for each gene was chosen. Then probes not meeting the detection threshold in at least one individual were filtered out. Intensity values were then log-transformed and quantile normalized using the 'lumi' package in R. Finally, the samples were corrected using the RUV-2 method.

Total RNA was extracted using the Qiagen RNeasy Plus 96 extraction kit. RNA quality was assessed with Agilent Bioanalyzer.

The stimulated CD3+ T-cells were grown at 37°C with 5% CO2 for 24 hrs. The unstimulated cells were after separation immediately used for RNA extraction.

The data were analyzed with dChip, invariant set normalization, model-based expression signal values, 5th percentile of region (PM-only) background subtraction

Total RNA was extracted with RNeasy Mini Kit (Qiagen, Valencia, CA, USA).

Following fragmentation, 100 ng of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA were prepared according to the two-cycle Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

Gene expression data from mouse CD4+ Wt T-cells without stimulation

Data were normalized using Robust Multi-Array Analysis (RMA). www.bioconductor.org

Following fragmentation cRNA were hybridized with HU133A arrays according to Affymetrix protocol.

Gene expression data from advanced human heart failure due to idiopathic dilated cardiomyopathy

Gene expression data from advanced human heart failure due to ischemic cardiomyopathy

GeneChip® Scanner 3000 with 1 number of scans per array with 2x image, pixel value 3 um and wavelenght 570 nm

Microarray data was pre-processed via the Robust Multichip Average (RMA) method, as implemented in the Bioconductor suite of programs (http://www.bioconductor.org/) implemented in the R statistical programming language. Analysis of differential expression was performed using bi-weight analysis.

Fragmented cRNA was  hybridized in the presence of BSA to an Affymetrix GeneChip™ following manufacture instructions. Volume for fragmented cRNA samples was 40 µl.

manufacture suggested biotin-labeled IVT reaction. 10 µg of total RNA was used in a maximum volume of 10 µl

Brown preadipocyte cell lines derived from newborn wildtype littermates of IRS-3 KO mice. Preadipocytes were grown to confluence (day 0) in differentiation medium (Dulbeco’s modified Earle’s medium containing 10% fetal bovine serum supplemented with 20 nM insulin and 1 nM T3). Brown preadipocytes were synchronized by overnight serum starvation. Total RNA was isolated with ULTRASPEC RNA Isolation System (Biotecx Laboratories, Inc., Houston, TX) following the manufacture’s instruction. 28 ug of total RNA were subjected to cDNA and cRNA preparations as previously described. 15 ug of adjusted cRNA were hybridised to Affymetrix U74A-v2 arrays (Santa Clara, CA). Intensity values were quantitated by MAS 5.0 software (Affymetrix). All chips were subjected to global scaling to a target intensity of 1,500 to take into account the inherent differences between the chips and their hybridization efficiencies.
Keywords = brown fat
Keywords = preadipocyte
Keywords = mouse
Lot batch = Joslin core 534

Flourescence was measured by confocal scanner (Agilent, Palo Alto, CA)

Signal intensity data was generated with Affymetrix Microarray Suite version 5.0 software with default parameters. Expression values were estimated with robust multi-array average (RMA) using standard background correction. RMA-normalized expression data is provided in log base 2 scale.

Total RNA was extracted by using Trizol (Invitrogen) per manufacturer's protocol

Gene expression from MEFs carrying a tet-inducible Pten transgene at 24 hrs after inducing PTEN

Pten-null (Ptenloxp/loxp), with doxycycline-inducible PTEN transgene;embryonic fibroblasts;tet-inducible Pten transgene;24 h;C57BL\6

MEFs carrying a tet-inducible Pten transgene, 24 hrs after inducing PTEN

Washing and scanning were performed using Fluidics Station 400 and
GeneChip Scanner (Affymetrix Inc.).

Expression value for each probe set was calculated using
RMAExpress program that uses RMA (robust multi-array
average) algorithm. For a first supervised analysis,
gene-filtering methods were applied following the detection
calls calculated using MAS 5.0 algorithm (Affymetrix). Probe sets
with absent calls as well as those showing minimal variation
across all samples (maximum–minimum log2 variation < 2.5)
were filtered out. In a second, more exhaustive analysis, the
complete set of microarrays without gene filtering was
introduced in a multivariable matrix where each of the six cell
states (NBL, WM-BL, CLL-BL, NPC, WM-PC and MM-PC) were
introduced to perform the differential expression analyses.

Total RNA was extracted from purified cell populations using the RNeasy Mini Kit (Qiagen, Valencia, CA,USA) according to the manufacturer’s instructions. The RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent,
Palo Alto, CA, USA).

Hybridizations were performed according to protocols from Affymetrix.
Labeled RNA was hybridized to Human Genome U133A microarray (Affymetrix),
after quality checking on GeneChips Test 3 Arrays.

Labeling were performed according to protocols from Affymetrix.
Briefly,100 ng of total RNA was amplified and labeled using the
GeneChip two-cycle cDNA synthesis kit and GeneChip IVT
labeling kit (Affymetrix Inc., Santa Clara, CA, USA)

Treatment: 2.8 mM HOCl in medium
Medium: see growth protocol below
Treatment Duration: 6 hrs
Cell Confluency upon Treatement: ~80-90%

RAW 264.7 macrophages (RAW Cells) were cultured in DMEM supplemented with 10% FBS, 10mM HEPES, 100 U penicillin/ml, and 100 ug streptomycin/ml

On day of experiment cells were either untreated, treated with 100 ng/ml EGF for 1 hr or treated with 100 ng/ml EGF for 3 hr.

Cells (SV40 immortalized primary human fibroblasts) were depleted of cavin-3 for 0, 3 or 8 days. This depletion was achieved by transfecting cavin-3 siRNA at day 0 and day 5 when cells were split. Media was replaced one day prior to the end of the experiment for cells that were serum starved.

RNA was isolated using RNeasy (Qiagen) according to the manufacturer's instructions. RNA quality was validated by BioAnalyzer Chip (Illumina)

Gene expression from MEFs carrying a tet-inducible Pten transgene

Pten-null (Ptenloxp/loxp), with doxycycline-inducible PTEN transgene;embryonic fibroblasts;tet-inducible Pten transgene;0 h;C57BL\6

Mice were either treated with control corn oil (100 micro L) or 2 micro gram estradiol in corn oil (100 micro L) subcutaneously.

GeneChips were scanned using the Affymetrix’s GeneChip® Scanner 3000 and the GeneChip Command Console software v3.0

The data were analyzed with dChip software using default analysis settings.

5000-7000 HSCs (CD150+ CD48- c-kit+ Sca-1+ lineage- cells) were sorted directly into Trizol reagent by flow cytometry.

2.5µg of labeled cDNA were hybridized to Affymetrix Mouse Gene ST 1.0 microarrays.

Biotinylated cDNA were prepared using Nugen Ovation Pico WTA V2 system and the Encore Biotin Module (NuGEN Technologies, San Carlos, CA)

Gene expression data from HSCs isolated from female mice treated with E2
FE3 HSC

FE2 HSC

Three individual siRNAs (Silencer Select, Ambion; Life Technologies, Grand Island, NY) were pooled and transfected into cells using the HiPerFect transfection reagent (Qiagen, Valencia, CA) following manufacturer’s instructions. Non-silencing siRNAs were used as controls.  siRNAs were used at a final concentration of  30nM per individual siRNA

LNCaP-abl cells were cultured in RPMI-1640 without phenol red media (Cellgro, Mediatech, Inc.  Manassas, VA) supplemented with 10% Charcoal-stripped fetal bovine serum (cFBS), 1% penicillin-streptomycin and 1% L-Glutamine

Robust Median Averaging, and quantile normalization using the espresso function form the affy package of R bioconductor

Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen, Valencia, CA)

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA

Microarray data was normalized with Expression Console software (Affymetrix, Santa Clara) using RMA algorithms for normalization.

RNA was isolated using Trizol 7 days after infection. RNA was further prepared by passage over an RNeasy column. cDNA synthesis, biotinylation of cRNA and hybridization to mouse Genechip 430_2 was performed according to the manufacturer’s instructions (Affymetrix, Santa Clara).

K-rasLSL-G12D MEFs were infected with adenoviral Cre to activate K-ras

Colitis was induced with 2.5% dextran sodium sulfate (DSS), 36,000–44,000 mol wt (ICN Biomedicals, Aurora, OH) in the drinking water.  After the DSS challenge mice were weighed on a daily basis and examined for clinical signs of disease associated with colitis (i.e., perianal soiling, rectal bleeding, diarrhea, and piloerection).  For the DSS challenge, the disease activity indices and rectal bleeding scores were calculated using a modification of a previously published compounded clinical score. Briefly, disease activity index consisted of a scoring for diarrhea and lethargy, whereas rectal bleeding consisted of a visual observation of blood in feces and the perianal area.  Mice in the DSS study were euthanized on day 7 of the DSS challenge by CO2 asphyxiation and blood was withdrawn from the heart.  Colons and spleens were scored based on size and macroscopic inflammatory lesions.

Six- to eight-week-old PPAR gamma flfl Cre+ mice, with a Cre recombinase targeted to the LysM promoter, and control Cre- littermates (n=20) were housed at the animal facilities at Virginia Polytechnic Institute and State University in a room maintained at 75 F, with a 12:12 h light-dark cycle starting from 6:00 AM.  All experimental procedures were approved by the Institutional Animal Care and Use Committee of Virginia Polytechnic Institute and State University and met or exceeded requirements of the Public Health Service/National Institutes of Health and the Animal Welfare Act.

colonic tissue from macrophage-specific PPARgamma-deficient mouse, biological rep3

gcRMA normalized by using Bioconductor package 'gcrma' in R 2.8.

Whole colonic tissue was collected from mice and preserved in RNAlater® (Applied Biosystems/Ambion Foster City, CA). After homogenization, total RNA was extracted and purified using the RNAeasy system according to manufacturer's instructions (Qiagen Valencia, CA). The QIAGEN RNase-free DNase supplement kit was used to ensure that the RNA was free from DNA contamination.

mut25
Gene expression data from colon of PPARr-deficient littermate mice.

C57BL/6;colon;PPAR g fl/fl; Lysozyme M cre+;PPAR gamma deficient;dextran sodium sulfate (DSS)

colonic tissue from macrophage-specific PPARgamma-deficient mouse, biological rep2

mut22

wild7
Gene expression data from colon of control littermate mice.

C57BL/6;colon;PPAR g fl/fl; Lysozyme M cre-;wild-type;dextran sodium sulfate (DSS)

wild4

colonic tissue from macrophage-specific PPARgamma-deficient mouse, biological rep1

mut14

wild8

Images were scanned using a GeneArray scanner [Agilent Technologies, Palo Alto, CA]

Processed with Microarray suite (Affymetrix) to generate .CEL files that were subject to RMAExpress 0.1 (Irizarry et al 2003) normalization.
Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
GeneSpring 7.0 (Agilent technologies Inc. Palo Alto, California) was used to normalization, Clustering and filtering. The Raw CEL files were processed using the RMA (Robust Multichip Average). All the samples were then normalized to the mean of the pooled control.

Total RNA was extracted from the ventricular tissue using Trizol kit (Invitrogen) and then purified two times using RNeasy columns (Qiagen)
Quality control steps:   RNA quality was assessed by using the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA) and only those samples with 28S/18S ratios between 1.3 and 2 were subsequently used

The protocol and conditions used during hybridization, blocking and washing:  Create a hybridization cocktail for a single probe array that contains 0.05 ug/uL fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 99°C for 5 minutes, to 45°C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 uL of 1X Hybridization Buffer. Incubate at 45°C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 uL of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization Oven rotating at 60 rpm

Labeling involved use of Genechip Expression 3’ Amplification One-Cycle Target Labeling and Control Reagents Kit (Affymetrix) to prepare biotin-labeled fragmented cRNA.

Samples used for hybridization consisted of pooled (P) and non-pooled (NP) RNA extracts from the three genotypic groups namely nontransgenic controls (NTG), alpha-TM175 and alpha-TM180. A total of ten hybridization experiments were performed in which each genotypic group was represented by two or more non-pooled (NP) individual RNA extracts and one pooled (P) sample that resulted from combining 20 individual heart extracts.

Placental biopsies were obtained during Caesarean section from late onset Preeclampsia. A mixture of 3 placentas from normal subjects were used for a template control.

Placental tissue from late onset Preeclampsia;A mixture of placental tissue from normal pregnancy

Cells were transfected with 3μM pcDNA3.1_GFP (Control) or 3μM pcDNA3.1_FoxA1 using Lipofectamine2000 (Invitrogen). Cells were harvested 48h later.

Cells were grown in RPMI + 10% FBS and standard antibiotics in a 37oC incubator with 5% CO2

The data were normalised using quantile normalisation with IlluminaGUI in R

RNA was extracted using Qiagen RNEasy with on column DNaseI digestion according the the manufacturer's instructions.Quality control was performed with Agilent Bioanalyser.

Biotinylated cRNA were prepared with Ambion MessageAmp kit for Illumina arrays

Control (GFP overexpressing) LNCaP prostate cancer cell line replicate 4

Control (GFP overexpressing) LNCaP prostate cancer cell line replicate 1

FOXA1 overexpressing LNCaP prostate cancer cell line replicate 3

Control (GFP overexpressing) LNCaP prostate cancer cell line replicate 6

FOXA1 overexpressing LNCaP prostate cancer cell line replicate 6

FOXA1 overexpressing LNCaP prostate cancer cell line replicate 2

Transmural sample taken from near the apex of the left ventricle

Transmural samples were taken from near the apex of the left ventricle and stored 4C for a maximum of 6 h from the time of coronary circulation loss. Samples were stored at -80C until the RNA extraction was performed.

GeneChips were scanned using the Gene Chip Scanner 7G System platform. GeneChip Comand Console software was used for initial image processing. Affymetrix Expression ConsoleTM software provided quality control and probe set summarization to attain gene-level signal data.

The data were analyzed with Partek Software, version 6,3 Copyright 2008, using Affymetrix default analysis settings.
Normalization and summarization of the data (background correction, normalization, log 2, and probe summarization with the RMA algorithm)

RNA was extracted using a RNeasy fibrous Tissue Mini kit from Qiagen according to the manufacturer´s intructions.

GeneChips were hybridized using the Gene Chip Scanner 7G System platform.

Biotinilated cRNA were prepared according to the standard Affymetrix protocol from Ambion WT Expression Sense Target Protocol kit.

male;heart;Transmural sample taken from near the apex of the left ventricle

The data were analyzed with R software. The MAS 5.0 normalization were performed using the justMAS function in the simpleaffy package from Bioconductor.

Total RNA was extracted by guanidine hydrochloride-phenol-chloroform method and transcribed to cDNA.

The labeled cDNA were then hybridized on Affimetrix gene chip and stained.

cDNA labeling was performed according to the manufacturer’s instructions.

Liver;GPR120 KO;normal diet ND;mixed 129/Sv and C57BL/6;mouse 718

NRK-52E cells were cultured to confluence on 6-well plates. Cells were then exposed to CHL dissolved in DMSO (0.1%) at the IC10 concentration at 72h (1.1 μM CHL) or DMSO only as control. After 6h, 24h and 72h the medium was removed and RNA was extracted from the cells. Three studies were conducted at each time point. All animal procedures were performed in accordance with a license issued under the animals (Scientific Procedures) Act, 1986.  Male rats (190-240g) 7-9 weeks of age were used, four rats being dosed with MON at 40mg/kg body weight on day 1 and 400mg/kg body weight on days 2 and 3, at 5ml/kg in corn oil. Four control animals were dosed with corn oil at 5ml/kg. Seventy two hours after the last dose all rats were killed by a rising concentration of carbon dioxide, the liver and kidneys quickly removed and immersed in RNAlater.

NRK-52E cells (DeLarco and Todaro, 1978) (ATCC, CRL-1571) were cultured in Dulbecco’s Modified Eagle Medium (DMEM) with 10% fetal calf serum, penicillin 100 I.U./ml, and streptomycin solution 100 µg/ml in a humidified 5% CO2 incubator at 370C. Wistar-derived rats where bred in the Life Science Support Unit at Liverpool John Moores University. The rats were housed in plastic cages in a room maintained at 20ºC ± 2ºC and a relative humidity of 50% ± 5% with a 12h light-dark cycle starting at 04.00h. Rats were allowed food (rat expanded diet), and water ad libitum.

Signal condensation and normalization was performed using GC-RMA (Robust Multiarray Analysis algorithm) using GeneSpring GX11.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

kidney epithelial proximal tubule cells;NRK-52E;Osborne-Mendel;monuron 72 hr

kidney epithelial proximal tubule cells;NRK-52E;Osborne-Mendel;DMSO 6 hr

kidney epithelial proximal tubule cells;NRK-52E;Osborne-Mendel;monuron 24 hr

kidney epithelial proximal tubule cells;NRK-52E;Osborne-Mendel;DMSO 24 hr

Laser Capture microscopy was used to dissect cancer cell from tumors or epithelium from normal endometria to provide material for RNA extractions. Approximately 5-8 slides (with tissue samples 10 microns thick) of LCM microdissection were required for each cancer case and 20 slides of LCM were required for each normal. Cancer samples were microdissected to provide >95% purity of cancer. Normal endometria were dissected to provide >95% purity of normal epithelial cells.

Fresh frozen cancer specimens from 91 stage I endometrial patients were examined. Normal endometrial samples from twelve age matched postmenopausal women were used for comparison. All tissues were collected under an IRB approved protocol at the corresponding institutions. Specimens were harvested by pathologists and frozen within one hour of excision and each uterine tumor was frozen until the time of analysis. Tissue specimens were evaluated by one of two board certified gynecologic pathologists using H&E staining to confirm the diagnosis.

Hybridized samples were washed, stained and scanned according to manufacterer's specifications (Affymetrix) for the HG-U133 plus 2.0 Gene Chip system, see protocol in GeneChip® Expression Wash, Stain and Scan User Manual.

All expression data were normalized to a target intensity of 500 using Affymetrix's MAS5.0 algorithm. Affymetrix .CEL files were processed with the program GCOS to generate signal valuses. All .CEL files were scaled to a global median intensity target intensity of 500. Hieracrchical clustering of samples was performed with Cluster 3.0 and the dendograms were visualized with Tree View (Eisen Lab, University of California, Berkeley). Clustering was performed with the entire gene list (unsupervised) to determine wheter there are groupings of samples and the same software was used to generate heat maps of the most differentially expressed genes. Differential gene expression betweeen groups of samples was performed using BRB array tools from the National Cancer Institute (http://linus.nci.nih.gov/BRB-ArrayTools.html). The biological annotation of differentially expressed gene lists were carried out by a number of methods including DAVID (http://david.abcc.ncifcrf.gov/), IPA (Ingenuity Systems, Redwood City, CA) and MetaCore (GeneGo, San Diego, CA).

Approximately 50ng of Total RNA was extracted from each sample with the Qiagen RNeasy® Micro Kit (Qiagen, 2003) by the manufacters suggested protocol for Total RNA Isolation from Microdissected Cryosections. See Rneasy® Micro Handbook Qiagen 4/2003.

Labeled RNAs were hybridized according to manufacterer's specifications (Affymetrix) for the HG-U133 plus 2.0 Gene Chip system, see Chapter 3 of Gene Chip® Expression Technical Manual (2005-2009 Affymetrix, Inc) for protocol.

Extracted RNA was processed using the GeneChip two cycle cDNA synthesis kit (Affymetrix), see Chapter 2 of Gene Chip® Expression Technical Manual (2005-2009 Affymetrix, Inc.) for protocol.

Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 200 uM Bis [(+)-tartrato] diantimonate (III) dipotassium trihydrate for 6h at  37 °C.

Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 °C and 5% CO2.

Probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).

The data were analyzed with MAS5 using Avadis 4.2 prophetic (Strand Genomics, Redwood City, CA).

The cells were were washed with phosphate buffered saline (PBS) and  lysed directly on culture dishes.  Total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany).

Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA).  Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate.  Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C.  After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).

Target preparation was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA).  cDNA was synthesized from the 5 ug of total RNA by using One-Cycle cDNA Synthesis kit (Invitrogen, Carlsbad, CA) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter.  cRNA was synthesized from the cDNA and biotin-labeled by in vitro transcription using IVT Labeling kit (Affymetrix, Santa Clara, CA).

RCB1648;Hep G2;male;15 years;liver;hepatocyte carcinoma;infinite;Transformed

Hep G2 treated with Bis [(+)-tartrato] diantimonate (III) dipotassium trihydrate

Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 6.5 mM Nickel (II) chloride hexahydrate for 6h at  37 °C.

Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA).  Labeled cRNA was fragmented by incubation at 94 °C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate.  Ten †g of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 °C.  After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).

GeneChips were scanned using the Affymetrix GeneChip Scanner 2500

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

Tissues were lysed in TRIzol (Invitrogen, Karlsruhe, Germany) and total cellular RNA was prepared using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U95Av2 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 13.5 ug total RNA (Expression Analysis Technical Manual v1, Affymetrix).

Analysis of gene expression in seminoma (pT1-pT3) vs. normal testis (NT)

Peripheral blood cells taken from survivors few horus after exposure to trauma. date: 2002
Keywords = Control
Keywords = ER
Keywords = D

Keywords = PTSD
Keywords = ND

Peripheral blood cells taken from survivors 4 months after exposure to trauma. date: 2001
Keywords = M4

Peripheral blood cells taken from survivors 4 months after exposure to trauma. date: 2002

Peripheral blood cells taken from survivors few hours after exposure to trauma. date: 2002

scanned with an Affymetrix Gene-Array Scanner according to Affymetrix GeneChip expression analysis technical manual

Total RNA was isolated from whole brains using TRI REAGENT (Sigma-Aldrich, St. Louis, MO) according to the manufacturer?s instructions, and further purified on a Qiagen RNeasy mini kit (Qiagen Sciences, Germantown, MD)

According to Affymetrix GeneChip expression analysis technical manual

whole brain from wild-type littermate of nicotinic acetylcholine receptor subunit mutant mice

whole brain, nicotinic acetylcholine receptor subunit mutant mice and littermate controls

The cells were treated with RLT lysis buffer (Qiagen) containing beta-mercaptoethanol to stabilize RNA.

LKS cells were isolated from JAK2V617F or WT mice using high-speed multiparameter flow cytometry.

Affymetrix GCS 3000 7G scanner using Affymetrix standard protocol

Signal normalization was performed by RMA method. RMA expression measure was computed using Bioconductor Affy package in R language (Bioconductor 2.5; R version 2.11.0).

RNA was extracted using Qiagen RNeasy Micro Kit according to manufacturers instruction. The RNA was amplified using a linear amplification protocol (Nugen Ovation V2 amplification system)

Total RNA was isolated from whole brains using TRI REAGENT (Sigma-Aldrich, St. Louis, MO) according to the manufacturer’s instructions, and further purified on a Qiagen RNeasy mini kit (Qiagen Sciences, Germantown, MD)

U-87 MG cells were grown in Eagle's minimum essential medium + 10% FBS + 100 U/mL penicllin + 100ug/mL streptomycin

Array d scanning wasperformed in the UCLA Bioinformatics Institute Core Laboratory Facility (Los Angeles, CA) according to Affymetrix (Sata Clara, CA) protocolsGeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

The raw data generated were processed using the Affymetrix Power Tools. The probe intensities were quantile normalized over all samples, summarized with the robust multi-array average (RMA) algorithm and log2 transformed with a median polish

Array hybridization was performed in the UCLA Bioinformatics Institute Core Laboratory Facility (Los Angeles, CA) according to Affymetrix (Sata Clara, CA) protocols. Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Gene expression data from U-87 MG cells after stable transfection with sh-p105 RNA and 16 hours of control DMSO treatment

U-87 cells transfected with sh-p105 RNA and treated with DMSO for 16 hours

IA, IB, II, IIIA, IIIB, or IV=IB;61;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=moderately differentiated;intestinal type, diffuse type, mixed type, or not determined=intestinal type;normal

IA, IB, II, IIIA, IIIB, or IV=IB;69;female, male:female;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=moderately differentiated;intestinal type, diffuse type, mixed type, or not determined=intestinal type;normal

Gene expression data from U-87 MG cells after stable transfection with sh-control RNA and 16 hours of control DMSO treatment

U-87 cells transfected with sh-control RNA and treated with DMSO for 16 hours

U-87 glioma cell line with shp105 and TMZ treatment, biological rep3

Gene expression data from U-87 MG cells after stable transfection with sh-p105 RNA and 16 hours of TMZ treatment

U-87 cells transfected with sh-p105 RNA and treated with TMZ for 16 hours

U-87 glioma cell line with shp105 and TMZ treatment, biological rep2

U-87 glioma cell line with shp105 and TMZ treatment, biological rep1

IA, IB, II, IIIA, IIIB, or IV=IA;45;female, male:male;early gastric cancer or advanced gastric cancer=early gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=IA;58;female, male:female;early gastric cancer or advanced gastric cancer=early gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=IA;64;female, male:male;early gastric cancer or advanced gastric cancer=early gastric cancer;moderately differentiated or poorly differentiated=moderately differentiated;intestinal type, diffuse type, mixed type, or not determined=intestinal type;normal

IA, IB, II, IIIA, IIIB, or IV=IA;56;female, male:male;early gastric cancer or advanced gastric cancer=early gastric cancer;moderately differentiated or poorly differentiated=moderately differentiated;intestinal type, diffuse type, mixed type, or not determined=intestinal type;normal

IA, IB, II, IIIA, IIIB, or IV=IB;39;female, male:male;early gastric cancer or advanced gastric cancer=early gastric cancer;moderately differentiated or poorly differentiated=moderately differentiated;intestinal type, diffuse type, mixed type, or not determined=intestinal type;normal

IA, IB, II, IIIA, IIIB, or IV=IA;41;female, male:female;early gastric cancer or advanced gastric cancer=early gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=IA;55;female, male:male;early gastric cancer or advanced gastric cancer=early gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=IA;68;female, male:male;early gastric cancer or advanced gastric cancer=early gastric cancer;moderately differentiated or poorly differentiated=moderately differentiated;intestinal type, diffuse type, mixed type, or not determined=intestinal type;normal

Images were scanned using an Affymetrix GeneArray Scanner, using default parameters.

The data were analyzed with MASv5 using Affymetrix default analysis settings and global scaling as normalization method.

Total RNA was extracted using TRIzol Reagent (Gibco), followed by clean up on RNeasy mini/midi columns (RNeasy Mini/Midi Kit, Qiagen).

12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA.

AML blasts from bone marrow;test;mutated;M5b;internal tandem duplication (ITD)

HMGA2 depletion were achieved by transducing the cells with HMGA2 shRNA in a pLKO.1 lentiviral vector, and were selected and maintained in 0.5 μg/ml puromycin. The inducible Tet1 or HOXA9 expressing cell line was generated by co-transducing the cells with pLVX-TRE3G-Flag-Tet1 (expressing inducible Tet1) or pLVX-TRE3G-HOXA9 (expressing inducible HOXA9) and pCMV-Tet3G (expressing Tet-On 3G) in the lentiviral vectors (Clontech, Mountain View, CA), and were selected in 0.5 μg/ml puromycin and 500 μg/ml G418.

Cells were cultured in complete medium consisting of DMEM supplemented with 10% FBS, 50 U/ml penicillin and 50 μg/ml streptomycin. For Tet1 or HOXA9 inducible cells, Tet System Approved FBS was used instead.

Using fluidics protocol FS450_0007, and scan with Fluidics Station 450.

Hybridization and background correction according to the standard protocols, the quantified signals were normalized using Robust Multi-array Average (RMA), an algorithm performing background adjustment, quantile normalization, and log-transformation using R version 2.11 and related packages from Bioconductor version 2.4 3 for analysis of the normalized data.

Total RNA was extracted using miRNeasy Mini Kit following the manufacturer’s instructions.

Following fragmentation, 5.5 ug cRNA were hybridized on GeneChip Hu-ST1.0 Array using GeneChip Hybridization, Wash and Stain Kit according to manufacturer's protocol. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug total RNA Using GeneChip WT terminal Labeling Kit.

AML blasts from bone marrow;test;mutated;M4;internal tandem duplication (ITD)

AML blasts from bone marrow;test;mutated;M4;internal tandem duplication (ITD)/D835 mutation

AML blasts from bone marrow;test;mutated;M5;internal tandem duplication (ITD)

AML blasts from bone marrow;test;mutated;M5a;internal tandem duplication (ITD)

Gene expression data from purified clock negative Basal IFE stem cells

Organ of Corti was immediately dissected from inner ear in phosphate-buffered saline, parted into apical and basal sections, and placed in lysis buffer on ice for immediate RNA extraction.

Genotyped mice were aged to postnatal day 16 and euthanized according to IACUC approved protocol.

The arrays were scanned using an Affymetrix High Resolution scanner 3000 7G.

The data were analyzed using Bioconductor (R) version 2.6.1 and the affy package version 1.26 using the mas5 function to obtain probe set expression values that correspond to those from MAS 5.0 Affymetrix default analysis settings and global scaling normalization method.

mirVana kit isolation of total RNA was performed according to the manufacturer's instructions.

15 ug of biotinylated target was hybridized and stained per standard protocols per manufacturer's suggestions in the Affymetrix hybridization oven model 640 and fluidics station model 450.

75 to 125 ng of total RNA was amplified and labeled using the Affymetrix 2-cycle labeling kit per the manufacturer's suggestions.

Gene expression data from mouse organ of Corti base, littermate control

Dicer1tm1Bdh (MGI:3589208) X Tg(Atoh1-cre)1Bfri (MGI:3775845);littermate control, Atoh1-Cre;Dicer1(flox/wt);organ of Corti from cochlea, basal half;postnatal day 16

Mouse organ of Corti from cochlea, basal half, littermate control

Gene expression data from mouse organ of Corti apex, littermate control

Dicer1tm1Bdh (MGI:3589208) X Tg(Atoh1-cre)1Bfri (MGI:3775845);littermate control, Atoh1-Cre;Dicer1(flox/wt);organ of Corti from cochlea, apical half;postnatal day 16

Mouse organ of Corti from cochlea, apical half, littermate control

regular insulin (Humulin, Eli Lily & Co., Indianapolis, IN) at a constant rate of 200 mU/m2/min

human skeletal muscle collected from 20 insulin sensitive, 20 insulin resistant, and 15 diabetic individuals

The arrays were scanned at a resolution of 3mm, using a specifically design confocal scanner (Affymetrix).

The data were normalized  by using quantile normalization and then obtained the probe set intensity using RMA or MAS5 as implemented in the affy package in Bioconductor. The present/absent calls for each probe set were generated based on Wilcoxon signed rank test using the mass5call function in the affy package.

Total RNA was extracted by Ultraspec RNA isolation Kit from Biotecx Laboratories, Inc according to the manufacturer's instructions.

The labeled cRNA were hybridized for 16 h at 45C on Affymetrix Hu95A chip. Affymetrix chips were washed and then stained with a streptavidin-phycoerythrin conjugate.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.

human skeletal muscle from insulin resistant individuals after insulin therapy

primary unilateral non-metastatic postmenopausal ERα-positive breast tumor

BRB Array tools (version 3.6.0 available on http://linus.nci.nih.gov/BRB-ArrayTools.html) were used to import CEL files applying the Robust Method Average (RMA) normalization and to analyze expression genes.

Total RNA was extracted from breast tissue samples by using acid-phenol guanidium method.

Gene expression data from ERα-positive breast tumor without PIK3CA mutation

primary unilateral non-metastatic postmenopausal ERα-positive breast tumor;woman;60 years

primary unilateral non-metastatic postmenopausal ERα-positive breast tumor;woman;65 years

Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-09/55553
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.72; Parameter Scan Time = 19:10:20; Parameter PMT Volts = 550; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 6576; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.72; Parameter Scan Time = 19:10:20; Parameter PMT Volts = 660; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 180117; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-09/55551
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.43; Parameter Scan Time = 20:53:17; Parameter PMT Volts = 550; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 6677; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.43; Parameter Scan Time = 20:53:17; Parameter PMT Volts = 660; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 180218; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56948
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.94; Parameter Scan Time = 21:03:30; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 13147; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.94; Parameter Scan Time = 21:03:30; Parameter PMT Volts = 670; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 186752; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.58; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56947
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.36; Parameter Scan Time = 20:14:39; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 13098; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.36; Parameter Scan Time = 20:14:39; Parameter PMT Volts = 670; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 186703; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.58; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56946
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.15; Parameter Scan Time = 21:27:29; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 13171; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.15; Parameter Scan Time = 21:27:29; Parameter PMT Volts = 670; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 186775; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56929
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.42; Parameter Scan Time = 19:35:08; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 12024; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.42; Parameter Scan Time = 19:35:08; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 185629; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.53; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56944
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.30; Parameter Scan Time = 21:54:05; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 13197; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.30; Parameter Scan Time = 21:54:05; Parameter PMT Volts = 670; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 186802; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.57; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56927
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.61; Parameter Scan Time = 20:25:51; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 12074; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.61; Parameter Scan Time = 20:25:51; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 185679; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.55; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56943
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.36; Parameter Scan Time = 22:06:17; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 13210; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.36; Parameter Scan Time = 22:06:17; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 186814; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.59; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56942
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.06; Parameter Scan Time = 21:15:40; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 13158; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.06; Parameter Scan Time = 21:15:40; Parameter PMT Volts = 670; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 186763; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.57; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

The tissue samples were immediately placed in RNAlater (Ambion) to stabilize intracellular RNA during transport.

Following washing, the specifically bound probe was detected by incubating the arrays with SAPE (streptavidin phycoerthryin, Molecular Probes) and scanning the chips using a Gene Array Scanner (Agilent).

The scanned images were analyzed using the Microarray Analysis Suite 5.0 (MAS5, Affymetrix). Data was extracted using MAS5 and filtered to exclude genes that were not expressed (taken to be equivalent to a MAS5 absent call) in all samples.

Biopsies were obtained from the sub-segmental and segmental bronchial carinae of the lower (3–5 biopsies) and upper (1–2 biopsies) lobes, as well as the lobar carinae of the middle (2 biopsies) and upper (1–2 biopsies) lobes to provide adequate samples of the large airways (3rd to 5th bronchial generation). When bronchoscopy was repeated after ICS treatment, biopsies were taken from the left lung at similar bronchial levels. The samples were mechanically homogenized (Rotor/Stator homogeniser, PowerGen) and total RNA was extracted using the RNEasy kit (Qiagen) according to the manufacturer's instructions.

Following fragmentation, 5 ug of cRNA were hybridized  at 45C overnight (16–20 hours). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated probe was prepared from the entire cDNA reaction mixture with the ENZO bioarray high-yield RNA transcript labeling kit (ENZO diagnostics).

Bronchial biopsies from lung tissue (pool of six bronchial biopsies)

Study participants were recruited under an institutional review board approved protocol and informed consent. A skin punch biopsy was used to establish a fibroblast cell culture. Unaffected control subjects were selected from patients visiting dermatology clinics. All of the cell strains (in the array group, between passage 2 and 6 and in the New Subject group, passage 2) were grown to confluence in SmGM2 +10% FBS + bullet kit containing recombinant EGF, FGF and insulin (BioWhittaker). After reaching confluence, the medium was modified to include ascorbic acid at 50-µg/ml [Jain MK, Layne MD, Watanabe M, Chin MT, Feinberg MW, Sibinga NE et al.: In vitro system for differentiating pluripotent neural crest cells into smooth muscle cells. J Biol Chem 1998, 273: 5993-5996]. Fresh medium was added after 24 hours.

Multiple exposures were collected on a Storm phosphorimager. Images were imported using Research Genetics Pathways 3 software.

See Yao et al., `A Marfan syndrome gene expression phenotype in cultured skin fibroblasts', submitted.  In outline, we do the following.  The median of log10-transformed expression values for each gene across all exposures of all arrays is calculated, and serves as a common baseline for comparison between experiments. Then, for each exposure, we compute a smooth `local' (loess) regression line between its log intensities and the median levels.  The resulting regression function transforms the expression values of each exposure to the scale of the common baseline while capturing nonlinear effects. Finally, we combine data from multiple exposures of an array by taking their medians. This technique builds on earlier work [Dozmorov I, Galecki A, Chang Y, Krzesicki R, Vergara M, Miller RA: Gene expression profile of long-lived snell dwarf mice. J Gerontol A Biol Sci Med Sci 2002, 57: B99-108], [Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J et al.: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 2002, 30: e15.] and more details are reported in [Mulvihill ER, Jaeger J, Sengupta R, Ruzzo WL, Reimer C, Lukito S et al.: Atherosclerotic plaque smooth muscle cells have a distinct phenotype. Arterioscler Thromb Vasc Biol 2004, 24: 1283-1289].   One innovation introduced here is the following:  to reduce the impact of outliers and differentially expressed genes on the inferred levels of other genes, the loess regression is based on only a `stable' subset of genes uniformly chosen across all intensity levels.  Specifically, for each gene we calculate the rank of its measured intensity in each exposure, and the median absolute deviation (MAD) of its rank across exposures.  We sort all n genes by increasing median intensity and partition them into n/5 groups of consecutive genes.  From each group of 5, the gene with the minimum MAD statistic is chosen. This selection of n/5 genes comprises the stable subset of genes on which our regression is based.  Other approaches to normalization based on stable genes have been proposed [Kepler TB, Crosby L, Morgan KT: Normalization and analysis of DNA microarray data by self-consistency and local regression. Genome Biol 2002, 3: RESEARCH0037.], [Schadt EE, Li C, Ellis B, Wong WH: Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data. J Cell Biochem Suppl 2001, Suppl 37: 120-125.] but those techniques seem more complex, and choose stable genes in ways that potentially yield sparse coverage of some regions of the intensity spectrum, consequently increasing the influence of anomalous or differentially expressed genes on the normalization in those regions.  As intensity-dependent non-linearity is a key concern in our normalization, uniform representation of intensities in the stable subset is valuable.

At 48h, total RNA was isolated using a guanidinium iso-thiocyanate-phenol-chloroform extraction protocol [Chomczynski P, Sacchi N: Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 1987, 162: 156-159].   Each sample was analyzed for quality and quantity by UV spectroscopy and gel electrophoresis.

Each sample was analyzed twice on duplicate arrays. The Research Genetics GF211 arrays were hybridized with 30-60 million cpm of probe/array for 18h then washed extensively at 50 degrees C in 0.5X SSC +0.1% SDS.

For hybridization to individual arrays, 1 µg of total RNA was used to synthesize 33P-dCTP labeled first strand cDNA with Invitrogen Superscript II.

Individual GF211 filters were stripped and reused several times; `Filter Number/Use Number' characteristic columns show which filter/which reuse corresponds to each hybridization.  Each hyb was exposed on the phosphoimager multiple times with varying durations; each exposure was scanned once; the `Exposures' characteristic shows how many exposures were combined to produce normalized intensity estimates.  This information is also encoded in the `Sample name'.  Un-normalized values from all exposures/scans of all hybridizations are provided in one of the two attached data files (one for normal fibroblast samples, one for MFS samples).  These two files do *not* use the GEO-defined gene ID's for platform GPL538; instead, correlate via GenBank Accession.

Mice were exposed in whole body exposure chambers to diluted mainstream cigarette smoke (CS) at a target concentration of 750 µg TPM/l for 2, 3, or 4 h/day or to conditioned fresh air (control) for 4 h/day. The CS exposure started with a dose adaptation period, i.e. 125 µg TPM/l on day 1 and gradually reached the target concentration on day 17.

Affymetrix.com:Protocol:Scan-M10, Agilent GeneArray® Scanner 3000 7G

.CEL files were processed using R/Biocondcutor packages affy and gcrma.

RNA was extracted from left lung lobes, which were deep-frozen in liquid N2 immediately after dissection and stored at -70°C, by using RNeasy Midi Kit (Qiagen, Hilden, Germany). RNA integrity was determined using Agilent 2100 Bioanalyzer

Ten µg of biotinylated fragmented cRNA was hybridized to GeneChip® Mouse Genome 430 2.0 for 16 hours at 60 rpm in a 45°C GeneChip® Hybridization Oven 640 (Affymetrix)

RNA isolated from lung tissue of CD-1 wildtype mouse, smoke treated
gene expression data

lung tissue;CD-1;13 weeks + 5 month + 1 day;2R4F whole mainstream smoke 750 µg/ml, treatment over 5 month + 1 day recovery, 3x1h exposure per day

lung tissue;CD-1;13 weeks + 5 month + 1 day;2R4F whole mainstream smoke 750 µg/ml, treatment over 5 month + 1 day recovery, 4x1h exposure per day

lung tissue;CD-1;13 weeks + 5 month + 1 day;2R4F whole mainstream smoke 750 µg/ml, treatment over 5 month + 1 day recovery, 2x1h exposure per day

RNA isolated from lung tissue of CD-1 wildtype mouse, control group

lung tissue;CD-1;13 weeks + 5 month + 1 day;fresh air, treatment over 5 month + 1 day recovery, 4x1h exposure per day

CD47 null mouse lung endothelial cells passaged for 6 months were seeded into 6-well tissue culture plates using basal Endothelial Basal  Medium (Lonza) without serum . Embryoid bodies appeared after 24-36 h.

WT and CD47 null Mouse lung endothelial cells were cultured at 37 °C with 5% CO2 using Endothelial Growth Medium-2 (EGM2) (Lonza).V6.5  mES cells were cultured in DMEM medium containing 15% fetal bovine serum and 1000 IU/ml LIF (Leukemia Inhibitory Factor.

An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays.

Gene expression intensities were calculated using GeneChip Command Console Software (AGCC version 3.2.4). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software (version 1.2.1) to generate an RMA normalized, log2 transformed and gene summarized matrix table.

The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix Mouse GeneChip 1.0 ST microarrays.  The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.

Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Human HuGene-1_0-st-v1 GeneChips (Affymetrix, Inc).  Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling.  300 ng of total RNA was used for labeling with theAmbion WT Expression Kit (cat#4411974)  and Affymetrix kit (Cat # 900652).After hybridization,  the probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).

GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1500.

Total RNA isolated from cell culture using RNeasy Midi Kit (Qiagen) according to the manufacturer's instructions.

Following fragmentation, 10 ug of cRNA were hybridized, washed and stained using the Affymetrix Fluidics Station 400 according to Affymetrix standard procedures

human skeletal muscle from insulin resistant individuals before insulin therapy

LAD was occluded for 30 min followed by reperfusion. Ventricle was collected after 7d of reperfusion.

DMEM + GlutaMAXTM-I (+ 4,5g/L D-Glucose + Pyruvate) (Gibco/invitrogen 31966)  + Penicillin/Streptomycin (1x) (100x Stock PAA)  +  50 µg/ml Zeocin (for the shRNA expression vector) (powder Cayla)  and 2 µg/ml Blasticidin (for the TR expression vector)(powder Invitrogen)

Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).

The data was analyzed in R statistical environment using Bioconductor packages. Normalization was done using the gcRMA algorithm

RNA was extrated using the Qiagen RNA extrction kit according to the manufacturer's instructions.

Following RNA purification, 20µg of cRNA were fragmented at 95°C using the Affymetrix fragmentation buffer, mixed with 200µl hybridization buffer containing hybridization controls and hybridized to U133-A2 microarrays. The arrays were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol

Target labelling and hybridization. For Affymetrix GeneChip analysis, 2.0µg total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer's protocols (Gene Expression Analysis, Technical Manual, Revison #4; Eukaryotic Target Preparation, Revison #3).

Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 96 hours, replica 1

1 ug/ml doxycyline;96 h;A673;doxycyclin  inducible EWS-FLI1 knockdown;Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown construct

Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown construct

J1 mouse ES cells were cultured in monolayer on gelatin-coated dishes containing ES medium (Dulbecco's Modified Eagle's Medium supplemented with 10% ES cell qualified fetal calf serum (Invitrogen, Carlsbad, CA), 2 mM glutamine, 100 units/ml penicillin, 100 µg/ml streptomycin, 1 mM sodium pyruvate, 100 µM MEM nonessential amino acids, and 0.1 mM ß-mercaptoethanol). 1 x 103 units/ml of leukemia inhibitory factor (LIF, Esgro, Invitrogen) were added prior to use to maintain undifferentiated ES cell growth.

Scanning of the chips was performed by the microarray core facility at Weil Cornell Medical College.

data from the chips were recorded as .cel files. Normalizaton was performed using the GC-RMA method.

Wild-type and Rex-1-/- ES cells were cultured for 12 hours in the absence of LIF, and total RNA was extracted using TRIzol (Invitrogen) as indicated by the manufacturer.

This mixture was hybridized to Mouse 430 2.0 microarray chips (cat# 900495, Affymetrix, San Diego, CA) for 16 h at 37 °C.  The hybridized microarray chips were washed and stained in a Fluidics station in the Microarray Core facility of the Weill Medical College of Cornell University.

cRNA was prepared by in vitro transcription of double strand cDNA with biotinylated ribonucleotides (Enzo Diagnostics, Farmingdale, NY). The cRNA was then fragmented by heating at 95 °C for 35 min and mixed with control oligonucleotide, control cRNA (composed of biotin B, biotin C, biotin D, and Cre), and herring sperm DNA.

The differential expression of putative Rex-1 target genes in wild type vs. Rex-1-/- ES cells was examined according to the Affymetrix microchip array protocol (Affymetrix, Santa Clara, CA).

Polymorphonuclear (PMN) leukocytes were obtained from healthy individuals (Healthy1, Healthy2, Healthy3, and Healthy4) or patients with X-linked chronic granulomatous disease (XCGD1, XCGD2, XCGD3, XCGD4, XCGD5, XCGD6). "time" indicates time at which transcript levels were analyzed. "treatment" indicates whether the polymorphonuclear leukocytes were resting (Control) or activated by phagocytosis (Stimulated)
Sample_PMN_treatment = Control
Affymetrix MAS version = MAS5
GeneSpring (version 5.0)normalization protocol:
1.  Data Transformation:  Set measurements less than 0.0 to 0.0
2.  Per Chip:  Normalize to a constant value of 150.0 (MAS scaling factor)
3.  Per Gene:  Normalize to median
Keywords = GENE PROFILING IN CHRONIC GRANULOMATOUS DISEASE NEUTROPHILS

Female mice were genotyped and necropsied at 2 month of age.  Uterine tissues were homogenized with Trizol reagent at collection and stored at-80C.

The data were processed in R (2.14.1) using limma (3.10.2) using the neqc function, which does a normexp background correction using negative control probes, quantile normalization using negative and positive control probes and log2 transformation.

RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit according to manufacturer's instructions.

C57BL/6;Cdh1 and P53 double knock-out; Cdh1-, P53-;2 months;female;uterus

Affymetrix MAS version = MAS4

Sample_PMN_treatment = Stimulated

The data were analyzed using the Gene Chip Operating Software Version 1.2 using the Affymetrix default settings and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

Trizol extraction of total RNA from whole tissue was performed according the manufacturer's instructions.

cRNA was fragmented and hybridized overnight to Affymetrix U133 Plus 2.0 Genechips.

biotinylated cRNA was generated from 5.0 ug total RNA using the Affymetrix labeling protocol.

Cyclophosphamide-treated spleen 2 days - Biological Replicate 2 - Technical Replicate 1

Biological replicate 2 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated splenocytes, day 2

splenocytes;DBA/2;pool of untreated bone marrow cells;DBA/2;reference

The data were analyzed for quality control with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Robust Multi-Chip Analysis (RMA) was used to generate signal intensity values using the standard settings in Bioconductor (2.2) operating in the R programming environment (R 2.7.1) with the 'justRMA' command.

RNA was extracted from each CA1 tissue block, as described previously (Blalock et al., 2003; Kadish et al., 2009; Rowe et al., 2007) using TRIzol (Invitrogen) followed by ethanol precipitation, and was reconstituted in RNase-free water (Standard Affymetrix)

Standard Affymetrix- 20 ug biotin-labeled cRNA was applied to a rat RGU34A GeneChip (Affymetrix) for hybridization (one chip per animal).

For each sample, 20 ug of biotin-labeled cRNA was generated from 5 ug of total RNA according to manufacturer’s instructions (Standard Affymetrix).

Fisher 344;male;18 months;hippocampal CA1 brain;Sham (intact) control

Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

Normalization was carried out by using the expression console (Affymetrix) with RMA algorithm which includes background correction, normalization and calculation of expression values (log2). Since myeloid contamination signature can be detected even in samples with high purity, those probes identifying genes exclusive of myeloid lineage were subtracted from the analysis from the out set.
Unsupervised analysis: In order to classify the samples, multidimensional scaling method (MDS) implemented with SIMFIT statistical package (version 6.4.1, available at http://www.simfit.manchester.ac.uk) was performed using Euclidean distance. In addition, an unsupervised hierarchical clustering with Euclidean distance as the distance measure, and group average as clustering method was carried out.
Supervised analysis: Significant Analysis of Microarrays (SAM) algorithm (http://www-stat.standford.edu/-tibs/SAM) was used to identify genes with statistically significant changes in expression between different classes(25). All data were permutated over 1,000 cycles by using the two-class and multiclass response format, without considering equal variances. Significant genes were selected based on the lowest q-value (q-value < 10-5).
Gene function analysis: The probe sets were functionally annotated and grouped according to their biological function using Gene Ontology biological process descriptions. The functional analysis to identify the most relevant biological mechanisms, pathways and functional categories in the data sets of genes selected by statistical analysis, was generated through the use of IPA (Ingenuity Systems, www.ingenuity.com).
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.r4.mps

In all the samples a CD138-positive PC isolation using the AutoMACs separation system (Miltenyi-Biotec) was carried out. Final purity was >95% in all MM and SMM cases, and >90% in MGUS patients and healthy donors. Total RNA was extracted from normal and tumor plasma cells using miRNEasy Mini Kit (Qiagen, Valencia, USA) following manufacturer's protocol. The RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

Labelling and hybridizations were performed according to protocols from Affymetrix. Briefly, 100-300 ng of total RNA were amplified and labeled using the WT Sense Target labelling and control reagents kit (Affymetrix Inc., Santa Clara, CA, USA)

RNA samples were labeled and hybridized by standard protocol to Affymetrix GeneChip Human Genome  U133+ Array Set HG-U133A array.

K562 (Iscoves + 10% FCS) and TF-1 (RPMI + 10%FCS + rhGM-CSF.  Cells were cultured at 37oC, 5% CO2 and split every 3 to 4 days.

Ovaries were treated with vehicle control medium (0.1% DMSO), VCD (50µM), MXC (50µM), or MEN (5µM). Xenobiotic culture concentrations were determined by pilot studies performed in our laboratory with the intention of inducing overt toxicity.

Swiss neonates were sacrificed by CO2 inhalation followed by decapitation. Ovaries were excised, trimmed of excess tissue and placed on culture plate inserts in 6-well tissue culture plate wells floating atop 1.5ml DMEM/F12 medium containing 5% (v/v) fetal calf serum, 1mg/ml bovine serum albumin, 50µg/ml ascorbic acid, 27.5μg/ml insulin–transferrin–selenium, 2.5 mM glutamine and 5U/ml penicillin/streptomycin. Media were supplemented with 40 ng/ml basic fibroblast growth factor, 50 ng/ml leukemia inhibitory factor, and 25 ng/ml stem cell factor. Using fine forceps a drop of medium was placed over the top of each ovary to prevent drying. Ovaries were cultured for 4 days at 37°C and 5% CO2 in air, with media changes every two days.

Upon completion of the washing, the chips are then scanned using the Affymetrix GeneChip Scanner 3000.  The scanner operating software, GCOS, converts the signal on the chip into a DAT file, which will then be used for generating subsequent CEL and CHP files for analysis.

The data were analyzed with Partek software  (Partek Genomics Suite) and were normalised using the Robust Multichip Average method using the DMSO treatment as a control.

Total RNA was isolated from ovaries using two rounds of a modified acid guanidinium thiocyanate–phenol–chloroform protocol: washed cells resuspended in lysis buffer (4 M guanidinium thiocyanate, 25 mM sodium citrate, 0.5% sarkosyl, 0.72% β-mercaptoethanol). RNA was isolated by phenol/chloroform extraction and isopropanol precipitated.

Samples that pass QC check are then prepared for hybridisation to the Mouse 430 version 2.0 GeneChip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that includes 1x Hybridisation Buffer (100mM MES, 1m NaCl, 20mM EDTA, 0.01% Tween-20), 0.1mg/ml Herring Sperm DNA, 0.5mg/ml BSA, and 7% DMSO. A total hybridisation volume of 300ul is prepared for each sample and 200ul loaded into a Mouse 430 version 2.0 GeneChip.  The chip is hybridised at 45C for 16 hours in an oven with a rotating wheel at 60rpm.  After hybridisation the chip is washed using the appropriate fluidics script in the Affymetrix Fluidics Station 450.

Mouse total RNA was quality ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol.  A total of 7ug was labelled using the Affymetrix One Cycle cDNA synthesis kit (Millenium Sciences cat no. 900431).  The subsequent cDNA was cleaned using the Affymetrix GeneChip Sample Cleanup kit (Millenium Sciences cat no. 900371).  Upon cleaning of the cDNA the next step was to incorporate biotin into the resultant cRNA using the Affymetrix IVT labelling kit (Millenium Sciences cat no. 900449).  After the IVT process the labelled cRNA was cleaned using the above GeneChip Sample Cleanup kit. The quantity of product was ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol.  A total of 20ug of labelled cRNA was then fragmented to the 50-200bp size range and quality control checked using the Bioanalyser 2100 using the NanoChip protocol.

GR-/- and GR+/+ embryo littermates were obtained by cesarean derivation at 18.5 days post-conception (the morning of the day that the vaginal plug was seen was considered as day 0.5).

Mice were housed in standard temperature and humidity conditions and animal experimentation was conducted with accepted standards of humane animal care in our animal facility (Instituto de Biomedicina de Valencia IBV-CSIC).

GeneChips were scanned using a GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA).

Probe set intensity values were summarized and normalized according to the RMA method using R and BioC.

Total RNA was obtained using the RNeasy RNA extraction kit (Qiagen, Valencia, CA).  RNA integrity was tested using the Bioanalyzer 2100 (Agilent Technologies).

15 mg of fragmented cRNA were used for each sample and hybridization performed as described on the webpage of the genomic platform at the Centro de Investigación del Cáncer de Salamanca (http://ubioinfo.cicancer.org).

Starting from an average of 5 mg total RNA, cDNA was synthesized and purified (one cycle cDNA synthesis Affy). cRNA was then biotin-labeled and purified (IVT Affy kit). After quantitation of the biotinylated cRNA, it was fragmented to perform the hybridization step as described on the webpage of the genomic platform at the Centro de Investigación del Cáncer de Salamanca (http://ubioinfo.cicancer.org).

Yolk sacs were isolated from E9.5 embryo without contaminating maternal tissue and placed in to RLT buffer.

standard Affymetrix procedures were done using GeneChip® Scanner 3000 7G

The data were analyzed with RMA normalization method (Expression Console 1.2.1.20).

RNA was prepared using RNAeasy Mini Kit  according manufacturer-suggested protocol

Following fragmentation, we used standard Affymetrix procedures for hybridization

For each sample, 100ng of total RNA were amplified using the WT sense strand Target Labelling kit (Affymetrix, Cat.no. 900223); 5.5μg of the resulting sense cDNA was fragmented by UDG (uracil DNA glycosylase) and APE 1 (apurinic/apyrimidic endonuclease 1) and biotin-labelled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip® WT Terminal labelling kit  (Affymetrix Cat.no. 900671)

HET3; Rnh1 Heterozygous-3
Gene expression data from Rnh1 heterzygous yolk sac at E 9.5 day

mixed (SV 129/C57BL/6);Rnh1 Heterozygous (Rnh1+/-);embryonic day E9.5;yolk sac

HET2; Rnh1 Heterozygous-2

KO2; Rnh1 Knock out-2
Gene expression data from Rnh1 knock out yolk sac at E 9.5 day

mixed (SV 129/C57BL/6);Rnh1 Knock out (Rnh1-/-);embryonic day E9.5;yolk sac

KO1; Rnh1 Knock out-1

KO3; Rnh1 Knock out-3

This sample is from Rotavirus infection convalescence phase of patient E31

This sample is from Rotavirus infection convalescence phase of patient E35

Image files were analyzed by use of GenePix Pro 4 image analysis software (Axon Instruments). The raw data was preprocessed using a pin-tip dependent normalization method as implemented in the limma package within Bioconductor. Calculated log2 ratio of Cy5/Cy3. VALUE column represents log2(test/ref) ratios.

Hybridization was performed at 50C and 35% formamide for 16 hours.

Direct incorporation of CyDye labeled dCTP by reverse transcription.

Scanning was carried out according to the manufacturer’s instructions

Data were normalized and analyzed using Illumina Beadstudio 3.1.3 (background correction and quantile normalization)
Expression profiles of each sample were imported into GeneSpringGX 7.3.1 (Agilent Technologies, USA).
In addition to expression values, Illumina BeadStudio software computes a detection p-value. Based on this, each probe was assigned a detection flag (P (present): p < 0.045; M (Marginal): p between 0.050 and 0.045, A (Absent): p>0.05). Expression values below a defined threshold (i.e. 20) are set to the threshold in order to remove negative values after background correction. To identify dysregulated genes in KO mice, t-test and/or ANOVA and additional steps of filtering were carried out.

8-12 weeks old mouse splenocytes from 3 KO and 3 littermate control C57/bl6-129sv mice were sorted by flow cytometry on the basis of IgM, IgD, CD21 and CD23 expression: T2-FP= IgMhiIgDhiCD21intCD23pos; FO=IgMlowIgDhiCD21intCD23pos. T2-FP and FO cell RNA was extracted by MirVana kit (Ambion) and treated with DNAse (Turbo DNA free kit, Ambion), following manufacturer instructions. Quality control for RNA integrity was performed by capillary electrophoresis on Agilent 2100 Bioanalyzer,

Hybridization on Mouse WG 6 v2 expression arrays (Illumina) was carried out according to the manufacturer’s instructions

100 ng of RNA was amplified and labeled using the Illumina TotalPrep RNA Amplification kit (Ambion)

The hematopoietic progenitor CD34+ cells were separated from the leukapheresis of normal donors stimulated with G-CSF using the immunonomagnetic MACS Miltenyi method. The cells harvested by apheresis were layered on a Ficoll-Paque gradient (specific gravity 1.077 g/ml; Nycomed Pharma AS, Oslo, Norway) in order to separate the low density mononuclear cells (LD-MNCs), and the samples were washed twice in Hanks' balanced salt solution (HBSS). The LD-MNCs were incubated with the QBEND10 monoclonal antibody directed against the CD34 antigen for 15 minutes at 4°C, and were then washed and incubated with immunomagnetic beads (Miltenyi Biotech, Bergisch Gladbach, Germany) against QBEND10 for a further 15 minutes at 4°C. For the flow cytometry analysis, CD34-phycoerythrin (CD34-PE) conjugated antibody (HPCA-2, Becton Dickinson, Mountain View, CA, USA) was added to the cells for 15 minutes at 4°C. At the end of the separation, the cells were counted and assessed for viability by means of trypan blue dye exclusion, and their purity was determined by means of flow cytometry. All of these steps were performed under aseptic conditions. The mean purity of the CD34+ cells after immunomagnetic separation was 96.0%.

The highly purified human CD34+ cells were exposed to 20 nM TCDD for 12h in vitro.

The HG-U133A arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix Inc., Santa Clara, CA).

The data were analyzed with GeneChip Operating Software (GCOS version 1.4) using Affymetrix default analysis settings and global scaling as normalization.

Trizol extraction of total RNA was performed according to the manufacturer's instructions (GibcoBRL). RNA was purified using the RNeasy® Mini Kit according to the manufacturer's instruction (Qiagen).

Following fragmentation, 15 micrograms of cRNA were hybridized for 16 hr 30 minutes at 45°C on GeneChip HG-U133A Array. The arrays were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 micrograms of total RNA.

Gene expression profiling data of highly purified CD34+ cells from normal donor 1 after in vitro TCDD exposure.

hematopoietic progenitor CD34+ cells;in vitro TCDD exposure;normal donor 1

Gene expression profiling data of highly purified CD34+ cells from untreated normal donor 1.

The data were analyzed with Microarray Suite GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

Trizol extraction of total RNA followed by RNEasy purification  was performed according to the manufacturer's instructions.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HGU133 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

After cleanup (Qiagen, Hilden, Germany), the biotin-labeled cRNA was fragmented by alkaline treatment (40 mmol/L Trisacetate (pH 8.2), 100 mmol//L potassium acetate, and 50 mmol//L magnesium acetate) at 94°C for 35 minutes. 15 µg of each cRNA sample was hybridized for 16 hours at 45°C to an Affymetrix Human Genome U133 Plus 2.0 GeneChip Array. Chips were washed and stained with streptavidin-phycoerythrin using a fluidics station according to protocolsrecommended by Affymetrix.

Starting with amounts below 1 µg, cRNA targets were generated using the small sample protocol (Affymetrix, vers. II). Briefly, in vitro transcribed unlabeled cRNA from the first round of amplification was subjected to a second round of amplification. cRNA was transcribed into cDNA using random primers. After RNAse H mediated removal of surplus cRNA a second strand was synthesized using a T7 primer. In detail, total RNA amounts of 50-200ng were used for first strand synthesis. cDNA was synthesized starting with the annealing to 5pmol/ul of a T7- (dT)24 primer that contains a promotor for DNA dependent RNA polymerase (TIB Molbiol, Berlin, Germany) at 70°C for 6 min. Reverse transcription (RT) was performed at 42°C for 1 hr in first strand buffer containing 50mM TRIS-HCl (pH=8.3), 75mM KCl, 3mM MgCl2, 10 mM dithiothreitol, 500 µM each dATP, dCTP, dGTP, and dTTP, and 20,000 U/ml of Superscript II reverse transcriptase (Invitrogen, Karlsruhe, Germany). Second-strand synthesis was carried out in 20-µl solutions, using the complete cDNA reaction mix and the MgCl2-, dNTP and enzyme solutions of the two cycle synthesis kit (Affymetrix) The mixture was incubated at 16°C for 2 hours, followed by a further incubation at 75°C for 10 minutes. Double strand cDNA was directly subjected to the first round of amplification using the MEGAScript T7 Kit (Ambion). Incubation was carried out at 37°C for 16hrs The amplified cRNA was purified with an affinity resin column (RNeasy, Qiagen, Hilden, Germany). 50-600ng of the yielded cRNA was used for the second round. For first strand synthesis random primers (final concentration 0.2 µg/µl) were used. After incubation at 42°C for 1h RNAse H was added at 37°C for 20min.and the reaction was stopped by heating at 95°C. After addition of 5pmol/ul of a T7- (dT)24-primer, the mix was heated at 70°C for 6 min. Then the second strand reaction mix was added. The mixture was incubated at 16°C for 2 h followed by a further incubation with 2 µl of T4 DNA polymerase (5 U/µl) (Invitrogen, Karlsruhe, Germany) for 10 min. The reaction was terminated by addition of 10 µl of 0.5 M EDTA. Cleanup of double stranded cDNA was performed using the cDNA-clean-up-modul of Affymetrix. Synthesis of biotin-labeled cRNA was performed using the GeneChip IVT labeling kit (Affymetrix, Santa  Clara, CA). The amplified cRNA was purified with an affinity resin column (RNeasy, Qiagen, Hilden, Germany) and fragmented by incubation at 94°C for 35 min. cRNA amounts were determined by UV-spectroscopy and distribution of cRNA fragment sizes of both, cRNA and fragmentation products, was checked by analyzing the samples on a LabChip (BioAnalyzer, AGILENT Technologies, Santa Clara, CA).

Cells were transfected with oligonucleotides using lipofectamine RNAiMAX.

The arrays are washed, stained, and scanned using the Affymetrix Model 450 Fluidics Station and Affymetrix Model 3000 scanner using the manufacturer’s recommended protocols, and the data collected using the GeneChip Operating Software (GCOS), v.1.4.

Data processing and analysis was performed using the Partek Genomics Suite v.6.3 (RMA normalization).

TriZOL and manufacturer's recommended protocol was followed to extract RNA from primary cultures

The resultant biotinylated cRNA is fragmented and then hybridized to The GeneChip® Porcine Genome Array. The GeneChip® Porcine Genome Array provides comprehensive coverage of the Sus scrofa transcriptome. The array contains 23,937 probe sets that interrogate approximately 23,256 transcripts from 20,201 S. scrofa genes.

Total RNA (5 μg) is processed using the Affymetrix GeneChip one-cycle target labeling kit (Affymetrix) according to the manufacturer’s recommended protocols.

Patients undergoing surgical resection of histologically proven primary colorectal adenocarcinomas were consented for participation in the study.  The patients enrolled in this study were randomized to receive either 400 mg celecoxib two times per day (n=11) or no COX-2 inhibitor (n=12) for 7 days prior to surgical resection.

Affymetrix .cel files were imported into GeneSpring GX 7.3 using GC-RMA File Preprocessor.  Data was normalized by (1) setting all expression measurements <0.01 to 0.01, (2) a per chip normalization to the 50th percentile, and (3) a per gene normalization to the median value across all chips.

Total RNA was isolated from surgically resected, histologically confirmed colorectal primary adenocarcinomas using a TRIzol RNA isolation kit (Invitrogen, Carlsbad, CA) according to the manufacturer’s recommended protocol at the Siteman Cancer Center Tissue Procurement Core (St. Louis, MO).

the data were extracted and normalized according to the default settings of Agilent Feature Extraction 7.5. LOWESS normalization, background subtraction, and ratio computation.

micro total RNA isolation from animal tissues protocol (Qiagen, Valencia, CA)

217;Asacol 1.2g daily;2/9/57;M;CAUCASIAN;1/1/79;1/10/79;FALSE;FALSE;FALSE;NO;FALSE;FALSE;11/26/04;1;0;0;0;0;0;0;0;TRUE;0;12;12;12;11;11;11;11;11;11;BOTH;unknown;unknown;unknown;unknown;11/26/04;BOTH;BOTH;BOTH;unknown;unknown;3/4/05;DISEASE IN REMISSION;never;unknown;None;UC;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

221;Prednisolone 7mg Asacol Adcal Seretide Fe SO4;1/29/86;F;CAUCASIAN;12/10/01;12/10/01;FALSE;FALSE;TRUE;NO;FALSE;FALSE;12/14/04;4;0;0;0;0;0;0;0;TRUE;0;BOTH;BOTH;BOTH;BOTH;BOTH;12/14/04;BOTH;BOTH;BOTH;BOTH;BOTH;3/7/05;FAILURE OF THERAPY;never;unknown;Asthma Eczema;UC;8-9-01;ascending colon;Inflamed;total RNA from 10 human cell lines

"Peripheral blood mononuclear cells were isolated 0, 30 min, 6 h, 24 h, and 7 day after intravenous endotoxin challenge using cell preparation tubes (Vacutainer® CPT). The PBMC layer was lysed with RLT buffer, homogenized, and then stored at –80°C. Total RNA was extracted as per RNeasy‚ Midi protocol (Qiagen). Double stranded cDNA was synthesized from total RNA (5 to 20 µg) using 7-d(T)24  primer and SuperScript‰ Double-Stranded cDNA Synthesis Kit and purified by phase lock gel-phenol/chloroform extraction followed by ethanol precipitation. Biotin-labeled cRNA was prepared by in vitro transcription using HighYield‰ RNA Transcript Labeling Kit followed by fragmentation with 5X fragmentation buffer.  Fragmented cRNA (10 µg) was hybridized to Affymetrix Hu95Av2 oligonucleotide probe arrays for 16 h at 45?C.  After removal of hybridization fluid, the arrays were washed, stained with streptavidin phycoerythrin (SAPE), and signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400.  Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix‚, Santa Clara, CA)."

"female subject, 18-45 yrs, peripheral blood mononuclear cells 168 h after intravenous endotoxin challenge"

HeLa cells were infected with retrovirus, and harvested for RNA 70 hours post-infection.

Scanning was performed at the DFCI microarray core facility (http://chip.dfci.harvard.edu).

Gene expression analysis was performed using dCHIP. Differentially expressed genes with at least 1.5 fold changes were obtained by normalization with either Quantile or Invariant Set method using dChip.

Total RNA was extracted by the method of Trizol. At the final step of purification, RNA was loaded onto an RNeasy column (Qiagen) and treated with RNAse free DNAse I.

Hybridization was performed per the manufacturer's instruction at the DFCI microarray core facility ( (http://chip.dfci.harvard.edu).

Biotinylated cRNA were prepared according to the standard Affymetrix protocol at the DFCI microarray core facility (http://chip.dfci.harvard.edu)

Gene expression data from HeLa cells infected with shLSD2 retrovirus

Gene expression data from HeLa cells infected with control retrovirus

Total RNA was isolated from skin, nevus and melanoma samples according to Standard Trizol protocol or Qiagen RNeasy Mini Kit protocol.

Approximately 5 µg of total RNA was processed to produce biotinylated cRNA targets.

Upon completion of the fluidics process, each sample was scanned using the Affymetrix GeneChip 3000 7Gplus scanner to create the image files (dat).  GeneChip Operating Software (GCOS v1.4) was then used to convert the image files to cel files

Data were collected using GeneChip Operating Software (GCOS v1.4). The robust multiarray average (RMA) and quantile normalization were performed.

Antibody stained spleen cells were sorted using FACS Aria Cell-Sorting System (Beckton-Dickinson, Franklin Lake, NJ) and either 104 Marginal zone (MZ) cells or 104 follicular (FO) B cells were directly collected into RLT buffer (Qiagen, Valencia, CA). lysates were thawed in room temperature and genomic DNA was fragmented to by spinning the samples through Qiashredder columns for 2 minutes at 21,000 x g.  To RLT buffer sample was added to 100% ethanol and RNAs were extracted using Qiagen RNeasy 96-well system as described previously (Virtaneva et al., 2005).  As contaminating gDNA will interfere with the downstream Nugen Ribo-SPIA™ technology, each RNA sample were treated with 27 units of DNAse I (Qiagen, Valencia, CA) for 15 minutes at room temperature during extraction.  RNA yield was estimated using Nanodrop (NanoDrop Technologies, Wilmington, DE) and 2100 Bioanalyzer (Agilent Technologies, Santa Clare, CA).

Five micrograms of labeled target from twenty-four submitted samples (received 2-10-09) was combined with 2X hybridization buffer, 3nM B2 control oligo (Affymetrix 900457), 20X spike in (Affymetrix 51214), and DMSO making a final volume of 100ul for the twenty-four individual hybridizations to the commercial Affymetrix GeneChip, mouse gene 1.0 ST containing the Mus musculus genome.  The hybridization cocktail, including the components listed above, was denatured for five minutes at 99◦C then transferred to a 45◦C heat block for an additional five minutes before transferring 80ul of the cocktail into the chip.  The hybridization was carried out at a constant temperature of 45◦C for approximately seventeen hours using the Affymetrix 640 oven 500k approved.

Total of 5 µg of double stranded cDNA was concentrated to 25 µL.  Each sample was combined with 5 µL fragmentation buffer mix (FL1) and 2 µL fragmentation enzyme mix (FL2).  DNA was digested at 37 °C for 30 minutes and enzyme was denatured at 95 °C for 2 minutes.  Fragmented ds cDNAs were biotin end-labeled using terminal transferase.  Each fragmented sample was combined with15 μl labeling buffer mix (FL3), 1.5 μl biotinylated nucleotides (FL4), 1.5 μl terminal transferase (FL5), incubated at 37 °C for 60 minutes, and heat inactivated.

Gene expression data spleen marginal zone B in WT
A combination of CD23, CD21 and CD19 markers was included in the sorting scheme. PE-labeled anti-CD23 Ab was used to give a satisfying separation of MZ and FO B cells. MZ B cells were sorted as B220+CD21BriCD23-. FO B cells were sorted as B220+CD21loCD23+

A total of 9x10(6) of lymphoblastoid cells were seeded in a T75 flask in 30 ml of fresh medium. Medium was RPMI1640 with 2 mM L glutamine and 25 mM HEPES and 10 percent fetal bovine serum and 1x Anitbiotic Antimicotic solution. After 24 hours total RNA was extracted.

Scanning of the microarray was done by Agilent DNA microarray scanner.

Scanner output image file was normalized and filtered using Feature Extraction Software ver 8.5. Normalization was performed so that overall intensity ratio of Cy5 to Cy3 was equal to one.

Total RNA was extracted from lymphoblastoid cells of AU010604 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

The generated cRNAs were mixed and subjected to hybridization to the Agilent Whole Human Genome Array G4112A according to the manufacture's protocol.

Target preparation was performed using a Low RNA Input Fluorescent Linear Amplification Kit (Agilent) according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;AU010604 is a male with autism and duplication of 15q11-13.

TER119- and TER119+ cells were purified from E14.5 fetal liver using Magnetic Activated Cell Sorting with Anti-TER119 MicroBeads (Miltenyi Biotech) by negative depletion (LD columns) and positive selection (MS columns) respectively as per supplier’s instructions.

Wildtype and Klf3 knockout mice were housed in standard University of NSW facilities, under SPF conditions

Arrays were scanned following manufacturers instructions, by the Ramaciotti Centre for Gene Function, UNSW, Sydney, Australia

Microarray data were analyzed using Partek Genomic Suite v6.5 (Partek Inc., St Louis, MO). Microarray CEL files were imported into Partek and normalized using RMA.

RNA extraction was performed using TRI-Reagent, according to manufacturer’s guidelines (Sigma-Aldrich). RNA samples were further purified using RNeasy columns (Qiagen) and by treating with DNase I (Ambion).

RNA was hybridized to Affymetrix Mouse Gene 1.0 ST arrays following manufacturers instructions, by the Ramaciotti Centre for Gene Function, UNSW, Sydney, Australia

According to established procedure at the Center for Expression Array. Seattle, WA

Sample isolated from wild type Foxp3 CD4+YFP+Ly5.2+ T cells following treatment with HR-MMPCreGFP and six week adoptive transfer.

Cells were seeded into matrigel and treatment with DMSO or 3 µM PLX4720 (Santa Cruz Biotechnology, CA, USA) was started at day 5. Medium was changed every 2-3 days. Cells were extracted from matrigel after the indicated period of time using the Becton Dickinson (BD) cell recovery solution and RNA was extracted as indicated.

DMEM medium containing 10% FCS was used to cultivate HT29 cells. Colo-205 cells were cultured in RPMI 1640 with 10% FCS. Matrigel 3D cultures were set-up as described for MCF-10A cells (Brummer et al., J Biol Chem. 2006), except that the aforementioned cell culture medium was used in place of the MCF-10A medium.

All arrays for the respective cell type Colo-205 and the HT29 were normalized together using the quantile normalization algorithm without background subtraction.

RNA was extracted with the QIAGEN RNeasy Plus Mini Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

Cell lines were transfected with 1 μg/μl (75 μM) of chemically synthesized anti-EVI1 siRNA or control siRNA.

Cells were cultured in RPMI-1640 medium supplemented with 10% FBS in the case of HTB-58 cells or with 20% FBS and 5-10 ng/ml recombinant GM-CSF in the case of TF-1.

GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.

The cells were harvested with TRIzol Reagent (Invitrogen)  and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133Plus2 chip according to the protocols provided by the manufacturer.

The cDNA was prepared from 2 microg total RNA using the One –Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthesizing the cRNA using the IVT labeling kit (Affymetrix). The synthesized cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).

The data were normalized using quantile normalization with Illumina BeadStudio. They were also batch normalized.

RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

cocaine addiction;Brain;Ventral midbrain;Postmortem;cocaine related

This is from a study of rat femoral fracture healing in 16 week old rats to compare intramedullary nailing, screw and plate fixation, and sham surgery.  This sample is the nail (intramedullary rod) collected 1 day after fracture.  Each sample is the pool of RNA from three rats.  The middle third of the femur was collected with the cortical bone, fracture callus and marrow elements.  Mid-diaphyseal, simple, transverse fractures were induced by a Gigli saw.
Keywords = rat
Keywords = fracture
Keywords = plate
Keywords = nail
Keywords = time
Keywords = femur

This is from a study of rat femoral fracture healing in 16 week old rats to compare intramedullary nailing, screw and plate fixation, and sham surgery.  This sample is the no fracture, 0 time control.  Each sample is the pool of RNA from three rats.  The middle third of the femor was collected with the cortical bone, fracture callus and marrow elements.  Mid-diaphyseal, simple, transverse fractures were induced by a Gigli saw.

GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

The data were analyzed with Partek Genomics Suite using the Affymetrix default analysis settings. RMA background correction and quantile normalization were applied with the median polish approach for summarizing probe sets.

Extraction of total RNA was performed using the Qiagen RNeasy Plus kit according to the manufacturer's instructions.
A custom, automated version of the NuGEN Ovation v2.0 WB amplification system was used for RNA extracted from blood.

The cDNA generated during the amplification step was used in a fragmentation and labeling reaction to generate target for hybridization to the Affymetrix Human GeneChip® HU133 Plus 2.0.

Sample isolated from loxP flanked Foxp3 CD4+YFP+Ly5.2+ T cells following treatment with HR-MMPCreGFP and six week adoptive transfer.

This is from a study of rat femoral fracture healing in rats 16 weeks old at fracture to compare intramedullary nailing, screw and plate fixation, and sham surgery.  This sample is from the nail (intramedullary rod) group collected 1 week after fracture.  Each sample is a pool of RNA from three rats.  The middle third of the femur was collected with the cortical bone, fracture callus, and marrow elements.  Mid-diaphyseal, simple, transverse fractures were induced by a Gigli saw.

This is from a study of rat femoral fracture healing in 16-week-old rats to compare intramedullary nailing, screw and plate fixation, and sham surgery.  This sample is from the nail (intramedullary rod) group collected 3 days after fracture.  Each sample is a pool of RNA from three rats.  The middle third of the femur was collected with the cortical bone, fracture callus, and marrow elements.  Mid-diaphyseal, simple, transverse fractures were induced by a Gigli saw.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 microg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 1 h.

Human SCC samples were obtained with Massachusetts General Hospital institutional approval as discarded material during Mohs micrographic surgery. For controls, normal skin was shaved very superficially with a #15 scalpel blade with minimal dermal contamination.

GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

Raw data were analyzed using the RMA package, available within Bioconductor.

15 μg total RNA from normal epidermis and  SCC lesions (all from different patients) were used for RNA probe preparation and hybridization to gene chips (Human Genome U133A 2.0 array; Affymetrix) according to the manufacturer’s recommendations

Biotin-labeled cRNA was hybridized on Human Genome U133A 2.0 array according to the manufacturer’s recommendation

The resulting cDNAs were used for preparation of biotin-labeled antisense cRNA

NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 4 h.

NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum.

NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 4 h. U0126 (20 uM) was added 30 min before stimulation.

Lymph node single cell suspension were obtained and the CD4+CD62L- resting T cells were sorted by flow cytometry.

Arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G

Software used: Genespring GX 9. Processing algorithm: MAS5. Intensity values were log2 transformed and median normalised

Cells were pelleted by centrifugation and lysed in RNAbee. Total RNA was then purified by phenol/chloroforme extraction according to manufacturer instructions.

Fragmented and labelled cDNA from three biological replicates was hybridised to GeneChip Mouse Gene 1.0 ST (Affymetrix).

GeneChip WT Terminal Labeling Kit (Affymetrix) for hybridization on MoGene 1.0 ST v1 arrays was used according to Affymetrix protocol.

The soman exposure paradigm utilized in this study was based on the model developed by Shih et al. (1991) and McDonough et al. (1998).  Animals were pretreated with the oxime HI-6 (125 mg/kg, ip, obtained from the Walter Reed Army Institute of Research, Rockville, MD) 30 min prior to challenge with soman (180 μg/kg, sc; diluted with 0.9% sodium chloride; soman was obtained from the Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD). One minute after soman challenge, animals were treated with atropine methyl nitrate (2.0 mg/kg, im, Sigma-Aldrich, St. Louis, MO). Vehicle control animals (n=4; 2 euthanized at 1h, 1 euthanized at 12h, and 1 euthanized at 24h) received an equivalent volume of vehicle (0.9% sodium chloride), HI-6 and atropine. Naïve animals (n=3) were also included in the study and received no treatments.

After scanning, array images were assessed by eye to confirm scanner alignment and the absence of significant bubbles or scratches on the chip surface. The 3'/5' ratios for GAPDH and B-actin were checked for quality. BioB, BioC, BioD and CreX spike controls were also examined to determine sample quality. All arrays were scaled to a target intensity of 150 using Affymetrix GeneChip Operating System (GCOS) software.

Raw signal intensities were imported into Partek Genomics Solutions v6.3 (Partek, St. Louis, MO) and normalized using the robust multi-array averaging (RMA) algorithm (Irizarry et al., 2003)

Frozen tissue was homogenized in Tri Reagent (Sigma Chemical Company, St. Louis, MO) and the RNA extracted according to the manufacturer's protocol. RNA was further purified using RNeasy columns (Qiagen, Valencia, CA). The quality and amount of RNA was monitored throughout processing with an Agilent Bioanalyzer (Agilent, Palo Alto, CA) and a NanoDrop® ND-1000 UV-Vis Spectrophotometer (Nanodrop Technologies, Rockland, DE).

Spike controls were added to 15 µg fragmented cRNA before hybridization (36h) using 10 µg of cRNA.  Arrays were washed and stained with streptavidin-phycoerythrin before being scanned on an Affymetrix GeneChip Scanner.

10 µg of mRNA was used to generate first-strand cDNA using a T7-linked oligo(dT) primer. After second-strand synthesis, in vitro transcription was performed with biotinylated UTP and CTP (Enzo Kits from Affymetrix).

Individually housed; controlled temperature and humidity;12h light/12h dark cycle; food and water ad libitum.

223;Prednisolone 20mg Asacol 2.4g;1/18/44;F;CAUCASIAN;3/1/04;3/15/04;FALSE;FALSE;FALSE;NO;FALSE;FALSE;12/16/04;2;0;0;0;0;0;0;0;TRUE;0;BOTH;BOTH;unknown;unknown;unknown;12/16/04;BOTH;BOTH;BOTH;unknown;unknown;5/31/05;DISEASE IN REMISSION;unknown;unknown;None;UC;5-25-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

224;Salazopyrin BFZ Losartan Thyroxine Doxazosin;2/21/38;F;CAUCASIAN;1/1/77;1/1/77;FALSE;FALSE;FALSE;NO;FALSE;FALSE;1/6/05;1;0;0;0;0;0;0;0;FALSE;0;12;12;12;12;12;11;12;11;11;BOTH;unknown;unknown;unknown;unknown;1/6/05;BOTH;BOTH;unknown;unknown;unknown;3/4/05;DISEASE IN REMISSION;never;unknown;Hypertension Hashimoto's Thyroditis;UC;5-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

225;Asacol;5/30/76;F;CAUCASIAN;1/1/03;6/2/03;FALSE;FALSE;FALSE;NO;FALSE;FALSE;1/6/05;3;0;0;0;0;0;0;0;TRUE;0;BOTH;unknown;unknown;unknown;unknown;1/6/05;BOTH;unknown;unknown;unknown;unknown;3/7/05;DISEASE IN REMISSION;ex;1/1/99;5-14;None;UC;5-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

206;Asacol 800mg BD;9/10/59;F;CAUCASIAN;1/1/79;1/1/80;FALSE;FALSE;TRUE;NO;FALSE;FALSE;10/8/04;3;0;0;0;0;0;0;0;FALSE;2;BOTH;unknown;unknown;unknown;unknown;10/8/04;BOTH;unknown;unknown;unknown;unknown;12/9/04;DISEASE IN REMISSION;ex;1/1/94;5-14;None;UC;6-2-01;terminal ileum;Uninflamed;total RNA from 10 human cell lines

217;Asacol 1.2g daily;2/9/57;M;CAUCASIAN;1/1/79;1/10/79;FALSE;FALSE;FALSE;NO;FALSE;FALSE;11/26/04;1;0;0;0;0;0;0;0;TRUE;0;12;12;12;11;11;11;11;11;11;BOTH;unknown;unknown;unknown;unknown;11/26/04;BOTH;BOTH;BOTH;unknown;unknown;3/4/05;DISEASE IN REMISSION;never;unknown;None;UC;5-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

218;Sulphasalazine Asprin Metoprolol Atorvastatin;9/27/24;F;CAUCASIAN;1/1/58;1/1/58;FALSE;FALSE;FALSE;NO;FALSE;FALSE;12/3/04;0;0;0;0;0;0;0;0;TRUE;0;BOTH;unknown;unknown;unknown;unknown;12/3/04;BOTH;unknown;unknown;unknown;unknown;3/4/05;DISEASE IN REMISSION;never;unknown;Breast cancer;UC;5-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

219;Sulphasalazine 1.2g Colifoam;1/5/43;F;CAUCASIAN;1/1/81;1/1/81;FALSE;FALSE;FALSE;NO;FALSE;FALSE;12/7/04;1;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;unknown;unknown;unknown;12/7/04;BOTH;BOTH;unknown;unknown;unknown;3/7/05;DISEASE IN REMISSION;never;unknown;None;UC;5-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

220;Asacol 800mg BFZ 2.5mg Metformin Simvastatin;6/28/48;M;CAUCASIAN;1/10/95;3/25/95;FALSE;FALSE;FALSE;NO;FALSE;FALSE;12/10/04;0;0;0;0;0;0;0;0;TRUE;0;BOTH;BOTH;BOTH;BOTH;BOTH;12/10/04;BOTH;BOTH;BOTH;BOTH;BOTH;3/7/05;DISEASE IN REMISSION;ex;1/1/90;5-14;Type 2 DM.;UC;5-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

210;Mesalazine 800mg B, Prednisolone Supps;6/28/56;M;CAUCASIAN;1/1/73;1/10/74;FALSE;TRUE;FALSE;NO;FALSE;FALSE;10/19/04;2;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;BOTH;unknown;unknown;10/14/04;BOTH;unknown;unknown;unknown;unknown;12/9/04;DISEASE IN REMISSION;never;unknown;Scarlet Fever 1964;UC;6-2-01;terminal ileum;Uninflamed;total RNA from 10 human cell lines

228;None;11/22/48;F;CAUCASIAN;1/1/80;1/1/82;FALSE;FALSE;FALSE;YES;TRUE;FALSE;1/14/05;2;0;0;0;0;0;0;0;FALSE;0;12;12;12;12;12;11;11;11;11;BOTH;BOTH;unknown;unknown;unknown;1/6/05;BOTH;BOTH;unknown;unknown;unknown;3/4/05;DISEASE IN REMISSION;never;unknown;Migraines;UC;6-2-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

BOEC were always harvested at passage 3, which comprised a nominal million-fold expansion since establishing culture and amounted to ~3x107 BOEC. They were always harvested 4 hours after the last change of culture medium, and always when they were at 85-90% confluent.

We obtained citrated fresh peripheral blood (50-100 ml) from each donor. For donors outside the Minneapolis metropolitan area, blood was shipped by same-day express delivery in Saf-T-Pak cartons that had been pre-equilibrated to room temperature. Samples were processed immediately upon arrival at the University of Minnesota. Blood buffy coat mononuclear cells were prepared and cultured on rat collagen I, in presence of endothelial cell growth factors, as previous described in detail 15,16. All samples were handled identically

An Affymetrix High Resolution Scanner was used according to the manufacturer's standard manual

For raw microarray data, we used the RMA (robust multi-array average) method to summarize expression values from probe pair values; data were background-adjusted, quantile normalized (global scaling across multiple arrays).

We prepared BOEC lysates by adding 10 ml trizol (Gibco) to each T75 flask to solubilize the sample. As necessary, trizol lysates were stored in liquid nitrogen. We then isolated total RNA, and cleaned it using an RNeasy kit (Qiagen, CA).

After we prepared biotin-labeled cRNA fragments, samples were turned over immediately to our Microarray Core Facility which used Gene Chip Hybridization Oven 640, Affymetrix FS4000 Fluidics Station for staining with a streptavidin-fluorochrome probe and washing,

We used the Invitrogen SuperScript Choice system to reverse transcribe and synthesize double-stranded cDNA. For in vitro transcription and biotin-labeling, we synthesized biotin-labeled cRNA using the Enzo Life Sciences BioArray High Yield RNA Transcript Labeling kit. Then fragmentation of cRNA was done by standard protocol, and fragmentation was verified by gel electrophoresis.

BOEC (blood outgrowth endothelial cells) from 20 subjects with sickle cell anemia shown to be either at-risk or not-at-risk for ischemic stroke

Medial gastrocnemius removed from 3-month old muscle glycogen synthase WT or knockout mouse. RNA was extracted using GibcoBRL TRIzol Reagent and a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA.

Cells were seeded 24 hours before drug treatment and incubated at 37°C and 5% CO2. Cells were seeded at 0.6–1.2 × 105 cells per well, in 6-well plates,using 4 mL of medium per well, with fresh drug added directly to the medium every 24 hours. At this seeding density, cells are30%–40%confluent at the start of drug treatments.

Biotin-labeled cRNA (10 μg) was fragmented and hybridized to each human U133A 2.0 genechip (Affymetrix, Santa Clara, CA).

Double-stranded cDNA and biotinlabeled cRNA were synthesized using 100 ng of total RNA with Ambion’s MessageAmp Premier RNA Amplification Kit (ABI, Foster City, CA).

azacitidine treated 48h
3210_A549_0.3 uM_Aza_1.CHP
A549 0.3A
3210_A549_0.3 uM_Aza_1.CEL

Liver removed from 3-month old muscle glycogen synthase WT or knockout mouse. RNA was extracted using GibcoBRL TRIzol Reagent and a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 10ug of total RNA.

3211_A549_0.3uM_Aza_2.CHP
A549 0.3A
3211_A549_0.3uM_Aza_2.CEL

3212_A549_1uM_Aza_1.CHP
A549 1A
3212_A549_1uM_Aza_1.CEL

GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

The data were analyzed with Microarray Suite version 5.0 (MAS5) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

Following fragmentation, 15 ug of cRNA were hybridized for 16-18 hr at 45C on GeneChip Mouse Genome 430A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2-5 ug total RNA

129/SVE;wild type;tibialis anterior;12-14 mo;129/SVE;50 eccentric contractions 12 hours

PAO1 was added to the apical side of monolayers at a multiplicity of infection (MOI) of 30:1 for 1 hour in the absence of antibiotics, and then planktonic PAO1 was removed by replacing the apical medium with MEM supplemented with 0.4% arginine. Control monolayers were treated identically except that vehicle only (medium used to grow PAO1, MEM supplemented with 0.4% arginine) was added to the apical side of cells.

CFBE41o- cells, a human bronchial epithelial cell line homozygous for the ∆F508-CFTR mutation, and CFBE41o- cells complemented with either ∆F508-CFTR (CFBE-∆F508-CFTR) or wt-CFTR (CFBE-wt-CFTR) were generously provided by Dr. J.P. Clancy (University of Alabama).  In all studies, we examined the effect of P. aeruginosa strain PAO1 on CFBE-∆F508-CFTR cells compared to CFBE-wt-CFTR cells, since both lines contain three copies of CFTR (either ∆F508/∆F508/∆F508 or ∆F508/∆F508/wt-CFTR).  Cells were grown as polarized monolayers in air-liquid interface culture on Transwell filters as described previously. Briefly, cells were seeded at 1 x 106 on 24 mm Transwell filters and grown for 8 days (to develop polarized monolayers) in minimal essential medium (MEM) (Mediatech, Herndon, VA) with 10% fetal bovine serum, 2 mM L-glutamine, 50 U/ml penicillin, and 50 g/ml streptomycin at 37°C and 5% CO2, balance air.

Arrays were washed and stained using the GeneChip® Fluidics Station 450 (Affymetrix). The chips were scanned with the 7G Affymetrix Gene Scanner (Affymetrix) according to manufacturer's procedures.

Raw fluorescence values were normalized and summarized raw gene array data using RMA as implemented in Bioconductor.

Cells were then homogenized with 600 μl RLT lysis buffer from the Qiagen  RNeasy kit, and the homogenate was vortexed for several seconds and drawn  through a 20-gauge needle 10 times. We then added 600 μl of 100% ethanol, and  applied samples to an RNeasy column for separation following manufacturer’s instructions.

Biotinylated cRNA products were hybridized to Affymetrix genechip HGU 133Plus2 arrays for 16 h at 40°C in a Gene Chip Hybridization oven 640 using the manufacturer's hybridization buffer (Affymetrix, Santa Clara, CA) in the Dartmouth Genomics and Microarray Laboratory (http://dms.dartmouth.edu/dgml/background/).

First-strand cDNA synthesis was conducted by priming the mRNA with a T7-(dT24) primer. Double-stranded cDNA was prepared using Life Technology Superscript cDNA Synthesis System (Invitrogen, Carlsbad, CA). From cDNA, cRNA was synthesized using the T7 MegaScript In Vitro Transcription kit (Ambion, Austin, TX). Synthesized cRNA was labeled during transcription (Megascript system; Ambion) with biotin-11–cytidine triphosphate and biotin-16–uridine triphosphate (Enzo Diagnostics, Farmingdale, NY).

129/SVE;Des(-/-);tibialis anterior;7-9 wk;Des(-/-)/129/SVE;50 eccentric contractions 12 hours

wild-type control (littermates) of "P32_exPKO_pancreas"; mixed genetic background; postnatal day 32; total pancreas; pooled two mouse cDNA samples equally to generate cRNA.

ES cells were transfected with either vector, SRFdM-VP16 control or SRF-VP16 expression plasmids. RNA was harvested 72 hours after transfection. Each experimental condition was performed in duplicate.

Scaling was used: All probe sets, target signal 150. Data parameters: Alpha1 (0.05), Alpha2 (0.065), Tau (0.015), Gamma1L (0.002), Gamma1H (0.002), Gamma2L (0.002667), Gamma2H (0.002667), Perturbation (1.1). Algorithm: Statistical, GCOS 1.1.

The aged mouse was injected intraperitoneal (ip) with saline (~100ul/mouse) and was killed 4 hours after injection by CO2 asphyxiation. Brain was removed, separated in half at the longitudinal fissure, frozen in liquid nitrogen and stored at -80C until use.

In-house BALB/c mice; Gender: Male; Age: 22 months old; Tissue: Brain; Treatment: 4 hours post saline ip.

The adult mouse was injected intraperitoneal (ip) with saline (~100ul/mouse) and was killed 4 hours after injection by CO2 asphyxiation. Brain was removed, separated in half at the longitudinal fissure, frozen in liquid nitrogen and stored at -80C until use.

In-house BALB/c mice; Gender: Male; Age: 4 months old; Tissue: Brain; Treatment: 4 hours post Saline ip.

The aged mouse was injected intraperitoneal (ip) with Escherichia coli lipopolysaccharide (LPS, 0.33mg/kg body weight (BW), ~10ug/mouse; serotype O127:B8, Sigma) and was killed 4 hours after injection by CO2 asphyxiation. Brain was removed, separated in half at the longitudinal fissure, frozen in liquid nitrogen and stored at -80C until use.

In-house BALB/c mice; Gender: Male; Age: 22 months old; Tissue: Brain; Treatment: 4 hours post LPS 0.33mg/kg BW ip.

129/SVE;Des(-/-);tibialis anterior;12-14 mo;Des(-/-)/129/SVE;50 eccentric contractions 12 hours

Effect of the absence of CCL3 and its injection in response to bilateral bulbectomy in the olfactory mucosa.

Carrier-injected C57BL/6, replicate 1

Mouse oocytes were derived from superovulated 5-10 week old females according to standard procedures. Fully-grown germinal vesicle (GV)-intact oocytes were collected 46 h after PMSG injection (5 U, Intervet) in M2 medium (Sigma) containing 2.5 μM milrinone (Sigma).

Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip® Scanner 3000 with autoloader.

Probesets were summarized and probeset-level values normalized with justRMA() function from R (version 2.10.0) / Bioconductor (version 2.5) package affy using the CDF environment MoGene-1_0-st-v1.r3.cdf (as provided by Bioconductor) and annotation from Netaffx (www.netaffx.com) (provided as a supplementary file on the Series record).

GV oocytes were pooled from several mice and RNA was isolated from batches of 50 oocytes, 3 biological replicates per genotype. RNA was isolated using the PicoPureTM RNA Isolation Kit (KIT0202) according to the manufacturer’s instructions (Stratagene). The quality of the RNA was assessed using the Agilent 2100 bioanalyzer and RNA 6000 Pico Chip. The extracted RNA was converted into OmniPlex WTA cDNA libraries and amplified by WTA PCR using reagents supplied with the TransPlex Whole Transcriptome Amplification kit (WTA1, Sigma, USA) following the manufacturer’s instructions with minor modifications. The obtained cDNA was purified using the GeneChip cDNA Sample Cleanup Module (Affymetrix).

Affymetrix GeneChip arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidics protocol FS450_0007 was used for washing.

RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix (GeneChip Whole Transcription Sense Target Labeling technical manual, Rev. 2).

GV oocyte;mixed 129/Sv and C57BL/6J;Ring1-/-Rnf2F/FZp3-cre (Ring1/Rnf2 double mutant)

.DAT files were generated using GCOS 1.2.1 software (Affymetrix). CEL files were generated using MAS 5.0 softare (Affymetrix) with target signals for probe sets scaled to 500. Log2 expression values for individual probe sets were generated from .CEL files via robust multi-array average (gcRMA).

Total RNA extracted using TRIzol reagent (Invitrogen, Carlsbad, CA)according to manufacturer's protocol.

Target was labeled with Enzo BioArray High Yield RNA Trascript Labeling Kit (Enzo Life TEchnologies, Farmingdale, NY) according to manufacturer's protocol.

GV oocyte;mixed 129/Sv and C57BL/6J;Ring1-/-Rnf2F/F (Ring1 mutant)

Stable overexpressed clones were generated by retroviral infection. siRNA was transfected by Dharmafect 4 transfection reagent. siRNA treatment  was performed for 5 days with the split after 2 days and retransfection of siRNA.

AtT20 pituitary gland cells were grown in DMEM with 10%FCS at 37C

GeneChips were scanned using the Affymetrix GeneChip scanner 3000.

RNA was isolated by TRIZOL following by RNeasy  clean up and DNAse treatment on the columns

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix mouse 430 2.0 GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using manufacturer-suggested script.

Biotinylated antisense cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA using One-cycle target labeling protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

Raw data generated from at least three independent experiments were further analyzed by the group of Dr. Ru-Fang Yeh at the Center for Informatics and Molecular Biostatistics, UCSF.

Total RNA was amplified with the WT-Ovation Pico RNA Amplification System, fragmented and labeled with the FL-Ovation cDNA Biotin Module V2 (Nugen).

YFP+ cells marking precardiac mesoderm were FACS-sorted (w/wo stabilized Beta-catenin), and their total RNA was isolated, amplified and labeled with the NUGENE pico kit for microarray analyses.  Mutant samples were obtained from YFP+ cells isolated from embryos with Isl1-cre, Rosa-YFP, Beta-catenin (loxP ex3). The mutants are conditional knockout mouse embryos that activates stable Beta-catenin in cardiac progenitors.

YFP+ cells marking precardiac mesoderm were FACS-sorted (w/wo stabilized Beta-catenin), and their total RNA was isolated, amplified and labeled with the NUGENE pico kit for microarray analyses. Mutant samples were obtained from YFP+ cells isolated from embryos with Isl1-cre, Rosa-YFP, Beta-catenin (loxP ex3). The mutants are conditional knockout mouse embryos that activates stable Beta-catenin in cardiac progenitors.

WT and Csbm/m mice were given daily injections of NR (500 mg/kg/d, ip) or saline for one week, after which the mice were sacrificed and the cerebellum was removed for further experiments.

Animal rooms were maintained at ~20°C and a 12-hour light/dark cycle. 4- or 18-month-old Csbm/m or WT male mice were maintained on house chow (Harlan Teklad, Madison WI).

Wt Mouse_cerebellum_Young_nicotinamide riboside treatment_Replicate-4

Arrays were scanned at a resolution of 0.8um using the BeadStation 500 X from Illumina.

Data was extracted using the Illumina GenomeStudio software (v1.9.0). Any spots at or below the background were filtered out using an Illumina detection Pvalue of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below. Z-score = (raw value - avg)/std. Complete data including detection scores are included in the supplemental file.

RNA was extracted from the cerebellum tissue using TRIzol® reagent (Invitrogen) using the standard manufacturer's protocol. Samples were assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Nano Chips (Agilent Technologies).

Standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix MouseRef-8 v2 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has ~24,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the biotin-labeled cRNA was detected by staining with streptavidin-Cy3.

Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791). In short, 0.5ug of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double-stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

Sample name: YOUNG-Wt_NR-9
Streptavidin-Cy3 bound to biotin-labeled cRNA.

C57BL/6;WT;male;cerebellum;4 months;daily injections of NR (500 mg/kg/d, ip) for one week

Wt Mouse_cerebellum_Young_nicotinamide riboside treatment_Replicate-3

Sample name: YOUNG-Wt_NR-4

Wt Mouse_cerebellum_Young_nicotinamide riboside treatment_Replicate-2

Sample name: YOUNG-Wt_NR-3

Wt Mouse_cerebellum_Young_nicotinamide riboside treatment_Replicate-1

Sample name: YOUNG-Wt_NR-13

Sample name: YOUNG-WT_ctrl-6

C57BL/6;WT;male;cerebellum;4 months;daily injections of saline for one week

Sample name: YOUNG-WT_ctrl-5

Sample name: YOUNG-WT_ctrl-14

Sample name: YOUNG-WT_ctrl-10

dChip expression analysis (PM only) of HepG2 human liver cell line following transfection of Hepatitis C Core protein - replicate 1

dChip expression analysis (PM only) of HepG2 human liver cell line following transfection of Hepatitis C Core protein - replicate 2

dChip expression analysis (PM only) of HepG2 human liver cell line following transfection of Hepatitis C Core protein - replicate 3

dChip expression analysis (PM only) of HepG2 human liver cell line untransfected - replicate 1

dChip expression analysis (PM only) of HepG2 human liver cell line untransfected - replicate 2

dChip expression analysis (PM only) of HepG2 human liver cell line untransfected - replicate 3

The data were analyzed with GeneChip Operating Software 1.1 (GCOS 1.1) using Affymetrix default analysis settings and global scaling to the same target intensity value

Total RNA was extracted using TOTALLY RNA kit (Ambion Inc.) according to the manufacturer's instructions.

cRNAs were hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 Array.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

Thymocytes were stained for CD4 and CD8, and DP thymocytes were sorted by flow cytometry.

Arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G.

Arrays were normalised using RMA function available in Affy Bioconductor package (R version 3.0.1).

Total RNA was isolated using RNA-Bee (Tel-Test). Total RNA was amplified using GeneChip WT cDNA Synthesis and Amplification Kit (Affymetrix).

cRNA from three biological replicates per condition was hybridised to GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix).

GeneChip IVT labelling kit (Affymetrix) for hybridization on Mouse 430 2.0 arrays according to Affymetrix protocol.

Control 3
Gene expression data from Dicer lox/lox control in DP thymocytes.

Control 2

Control 1

Dicer Knockout 3
Gene expression data from LckCre Dicer lox/lox KO in DP thymocytes.

mixed B6/129;thymus;CD4+CD8+ thymocytes;LckCre Dicer lox/lox knockout

Dicer Knockout 2

Control (air), smoke (10 puffs of cigarette smoke, delivered during 15 mins), dexamethasone (1 x 10-7M)  and dexamethasone + cigarette smoke.

GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.

Following fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on Rat 230_2 whole Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cDNA were prepared according to the NuGEN RNA Amplification System V2 protocol from 50 ug total RNA.

DS2_2h_39
Gene expression data from rat tracheal explants exposed to dexamethasone & cigarette smoke (treatment) at 2hrs.

Sprague-Dawley;tracheal explants;dexamethasone & cigarette smoke at 2hrs;2

DS1_2h_33

Sprague-Dawley;tracheal explants;dexamethasone & cigarette smoke at 2hrs;1

DS4_24h_15
Gene expression data from rat tracheal explants exposed to dexamethasone & cigarette smoke (treatment) at 24hrs.

Sprague-Dawley;tracheal explants;dexamethasone & cigarette smoke at 24hrs;4

DS3_24h_23

Sprague-Dawley;tracheal explants;dexamethasone & cigarette smoke at 24hrs;3

DS6_24h_21

Sprague-Dawley;tracheal explants;dexamethasone & cigarette smoke at 24hrs;6

DS5_24h_13

Sprague-Dawley;tracheal explants;dexamethasone & cigarette smoke at 24hrs;5

C6_2h_44
Gene expression data from rat tracheal explants exposed to air (control) at 2hrs.

C5_2h_11

DS2_24h_14

Sprague-Dawley;tracheal explants;dexamethasone & cigarette smoke at 24hrs;2

DS1_24h_29

Sprague-Dawley;tracheal explants;dexamethasone & cigarette smoke at 24hrs;1

Tissue Processing and Fluorescence Activated Cell Sorting (FACS) of Endometrial Cell Populations:
Tissue biopsies were divided into two fresh tissue samples processed separately for fluorescence activated cell sorting (FACS) and for histological examination in formalin-fixed, paraffin embedded tissue. Tissue processing for viable cell isolation and FACS analysis were performed as previously described (15). Briefly, enzymatically dissociated endometrial cells were incubated in blocking buffer (PBS with 40% human serum [HS] and 1% bovine serum albumin [BSA]) for 30min then labeled with the following fluorochrome-conjugated antibodies (BD Biosciences, San Jose, CA) in PBS containing 10% HS and 1% BSA: cluster of differentiation 45 (CD45, PE-Cy7 anti-CD45) at 1:20 dilution to label contaminating leukocytes for their removal; epithelial cell adhesion molecule (EPCAM, allophycocyanin anti-EPCAM) at 1:20 dilution to label eEP; cluster of differentiation 146 (CD146 or melanoma cell adhesion molecule [MCAM], CD146, fluorescein isothiocyanate anti-MCAM) at 1:5 dilution to label eEN/perivascular cells; beta-type platelet-derived growth factor receptor (PDGFRB, phycoerythrin (PE) anti-PDGFRB) at 1:5 dilution to label eSF. eMSCs were sorted using double labeling for CD146 and PDGFRB antibodies respectively, both at 1:5 dilutions. The cell suspension was sorted using a FACS Aria II with FACS Diva software (BD Biosciences). The FACS-sorted cell pellets were stored at -80C until RNA extraction.
FACS analyzed sorted cell populations were subject to RNA isolation and purification, with DNAse treatment, using Pico Pure RNA Isolation Kit

Microarrays were hybridized, washed, stained, and scanned according to the protocol described in WT Sense Target Labeling Assay Manual from Affymetrix (Version 4; FS450_0007) at the UCSF Gladstone Genomics Core Facility.

GeneSpringGX 11, Microarray Technology: Affymetrix.ExonExprChip.HuGene-1_0-st-v1, Summarization Algorithm: ExonRMA16, Normalization: Quantile, Baseline Transformation: median of all samples
Summarization Algorithm: RMA16. Transcript Level: Core. Baseline to median of all samples

Total RNA was isolated form FACS-sorted cell populations and purified using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems, Life Technologies Corporation, Carlsbad, CA) following manufacturer´s instructions. An additional DNase treatment was performed using the RNase-Free DNase Set (Qiagen, Valencia, CA).

Microarrays were hybridized, washed, stained, and scanned according to the protocol described in the WT sense target labeling assay manual from Affymetrix (version 4; FS450_0007).

Reverse transcription and amplification of isolated RNA into cDNA was performed using NuGEN WT-Ovation Exon FFPE System V2 (NuGen, San Carlos, CA). The integrity of resultant cDNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies), and individual samples meeting yield and quality standards were further processed and hybridized to Affymetrix Human Gene 1.0 ST arrays (Affymetrix, Cleveland, OH), probing 36,079 genes.

Diet induced changes in mouse liver mRNA profiles.
One of 3 replicates of LDL receptor deficient mice maintained for 12 weeks on high fat Western style diet.
Keywords = LDL receptor deficiency, high fat diet, atherosclerosis, liver

One of 3 replicates of C57BL/6 mice maintained for 12 weeks on low fat diet.

One of 3 replicates of C57BL/6 mice maintained for 12 weeks on a high fat Western style diet.

Gene Chip microarray scan protocol (Affymetrix Expression Analysis Technical Manual).

The RNAs extracted from microdissected tissue sections were pre-amplified prior to microarray hybridization using the Gene Chip Expression 3′-Amplification Two-Cycle cDNA Synthesis kit (Affymetrix, Santa Clara, CA, USA; #900432), the Gene Chip Sample Cleanup Module (Affymetrix #900371) and the MEGAscript T7 High Yield Transcription Kit (Ambion, Austin, TX, USA; #1334), according to Affymetrix instruction manual #701025 rev. 5.

Gene Chip microarray hybridization protocol (Affymetrix Expression Analysis Technical Manual).

Gene Chip microarray label protocol (Affymetrix Expression Analysis Technical Manual, http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

Laser Capture Microdissection (LCM) to isolate tissue sections of the hippocampus area of wild type mice brains

24B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; not assessable

Biopsies were snap-frozen after collection and stored in liquid nitrogen.  Frozen sections were taken prior to RNA extraction to confirm the presence of cancerous tissue within the specimens.  Only samples in which the malignant component comprised at least 20% of the section area were used in further analyses.  Immediately before RNA extraction the biopsies were pulverised using U2 micro-dismembranator U (Braun Biotech).  Total RNA was extracted from the resultant frozen tissue powder using TRI-reagent (Sigma) according to the manufacturer's recommendations.  Extracted RNA was additionally purified on RNeasy mini columns (Qiagen).  RNA quantity and quality was verified on Bioanalyser 2100 (Agilent).

standard Affymetrix procedures except for use of a custom 24-channel fluidics machine and GCS2500 scanner

Approximately 500 ng of total RNA was processed to produce biotinylated cRNA targets using protocol described in Biotechniques. 2003 Mar;34(3):546-50, 552-4, 556

23B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

27B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

25B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

Eight-week-old C57BL/6 mice were divided into three experimental groups and fed for 8 weeks as follows: a) normal chow (normal), b) methionine- and choline-deficient diet+ high fat diet (NASH), c) MCD + HF diet mixed with 0.1% metformin (nash metformin).

Hepatic tissues were obtained after the sacrifice and immediately frozen in liquid nitrogen and stored at −80°C until use.

The microarrays were subsequently scanned with the GeneChip Scanner 3000 MegAllele System (Affymetrix).

Data analysis was conducted with the GeneChip Operating System 1.1 (Affymetrix). Detection, signal, signal log ratio, and change were obtained from the GeneChip Operating System (GCOS) with default settings after global normalization was performed to make the average intensity of all probe sets equal to 100.

Total RNA was extracted from each liver using the RNeasy Mini kit (Qiagen, Tokyo, Japan).

After generating the hybridization cocktails, hybridization to the DNA microarray and fluorescent labelling were performed with a GeneChip Hybridization Wash and Stain kit (Affymetrix).

A total of 2 μg of total RNA was labelled according to the small sample labelling protocol recommended by the manufacturer.

Gene expression data from mouse liver.
Sample name: NASH3
GC1968new.CEL

C57BL/6;methionine- and choline-deficient diet+ high fat diet (NASH);liver

Sample name: NASH4
GC1969new.CEL

28B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

Sample name: NASH2
GC1967new.CEL

Sample name: Met3
GC1973new.CEL

C57BL/6;MCD + HF diet mixed with 0.1% metformin (nash metformin);liver

Sample name: Met4
GC1974new.CEL

Sample name: Met1
GC1971new.CEL

Sample name: Met2
GC1972new.CEL

Venous blood was collected in PAXgene (PreAnalytiX) tubes and immediately incubated at room temperature for 24 hours. RNA was then extracted following the PAXgene procedure including DNase treatment.

Approximately 4 µg of total RNA was processed to produce biotinylated cRNA targets.

MDA-MB231 Control shRNA and PIAS1 shRNA2 cells were cultured in DMEM plus 10% FBS (DMEM) or SCM for 30 h.

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Gene expression data from MDA-MB231 control shRNA cells grown in DMEM for 30 h.

Human lung adenocarcinoma cell lines of CL1-0 YWHAZ-transfected and CL1-0 vector control were grown in DMEM with 10% fetal bovine serum at 37¢XC, 20% O2, 5% CO2 and 1000 £gg/ml G418.

GeneChips from the hybridization experiments were read by the Affymetrix GeneChip scanner 3000.

The data were processed by GeneSpring GX software version 7.3.1 GC-RMA preprocessor to use on the CEL files

Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNAs extracted using TRIZOL reagent were quantified spectrophotometrically. The cDNA synthesis was carried out by using SUPERSCRIPTTM one-step RT-PCR kit (Invitrogen). For the reverse transcription step, the whole 5 ul of the resuspended RNAs were incubated for 60 min at 42oC, then 15 min at 72oC in 50 ul of reaction mixture containing 25 ul of 2x Reaction Mix (Invitrogen) and 1 ul of RT/PLANTINUM Taq Mix (Invitrogen). 28.5 ul of the cDNAs present in the 50 ul RT reaction mixture purified by Microarray Target Purification Kit (Roche Applied Science, Indianapolis, ID, USA, http://www.roche-applies-science.com) were used as templates to amplify cDNA by Microarray Target Amplification Kit. The amplified cDNAs were purified by Microarray Target Purification Kit, and complementary RNAs (cRNAs) were synthesized from 200 ng cDNA with Microarray RNA Target Synthesis Kit (Roche Applied Science).

Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr at 45oC on Affymetrix Human Genome U133 plus 2.0 GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms purified cRNA (Expression Analysis Technical Manual, 2004, Affymetrix).

The mRNA profiles from vector control transfectants and YWHAZ overexpressed transfectants were analyzed using Affymetrix Human Genome U133 plus 2.0 GeneChip according to the Manufacturer¡¦s protocols (Santa Clara, CA, USA, http://www.affymetrix.com).

Affymetrix Microarray Suite 5.0 was used to scan and quantitate the gene chips under default scan settings.

raw data processed by Affymetrix Microarray Suite 5.0 is provided

Alveolar type II cells were isolated from 8 weeks old sex age matched littermate control and Stat3∆/∆ mice using collagenase and differential plating. Type II cells from 3 mice were pooled to obtain one pellet. Two hours after isolation, type II cells were homogenized with TRIzol reagent (Invitrogen, Carlsbad, CA). RNA concentration was measured by spectrophotometer and normalized for cDNA synthesis.

The cRNA was then hybridized to the murine genome MOE430 (consists of ≈ 45000 gene entries) chips (Affymetrix, Santa Clara, CA) according to the manufacturer’s protocol.

SP-C-rtTA/(tetO)7CMV-Cre/Stat3flx/flx triple-transgenic mice, typeII cell

Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual, 2004.

Image analysis using GCOS 1.4, using MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 1.

16hrs at 45 C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual, 2004.

One round amplification protocol for total RNA following Affymetrix’ specifications using T7 promoter oligo dT primer for cDNA synthesis, and ENZO IVT kit (www.affymetrix.com, GeneChip Expression Analysis, Technical Manual, 2003).

WT and Nrf2 KO C57BL/6 mice (9 weeks old) were intraperitoneally injected with a single dose of cisplatin (15 mg/kg body weight) or vehicle (saline)

Animal were cared under the guidelines of the Institutional Animal Use and Care Committee at Seoul National University. Male C57BL/6 mice (9 weeks old) were purchased from Samtako Company (Osan, Korea), and housed at 20±2°C with 12-h light/dark cycles and a relative humidity of 50±5% (Tecniplast, Varese, Italy) under filtered, pathogen-free air, with food (Purina, Korea) and water available ad libitum.

The data were quantile normalized using R (version 2.9.1) with BeadArray (version 1.12.1).

RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

C57BL/6;WT;Male;9 weeks;kidney;intraperitoneally injected with a single dose of vehicle (saline)

Cells were transfected with siRNA using the recommended protocol for Lipofectamine2000 (Life Technologies)

Cells were maintained in normal growth medium for 48 h post transfection

The raw data was quantile normalized and Illumina control probes were removed from subsequent analysis using BASE (Vallon-Christersson et al., 2009). The data were exported to MeV, log2 transformed and gene and sample centred (Saeed et al., 2003).

RNA was extracted  QIAGEN RNeasy plus mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays; Modified Illumina TotalPrep-96 RNA Amplification Kit (Cat #4393543)

RNA was isolated from the sorted Ter119+CD71high population with RNeasy Plus (Qiagen).

Gene expression data from sorted Ter19+CD71high spleen cells from E2f8 KO mouse

Gene expression data from sorted Ter19+CD71high spleen cells from Rb;E2f8 KO mouse

Gene expression data from sorted Ter19+CD71high spleen cells from Rb KO mouse

normal growth; DMSO/0.375M 5-fluorouracil 12hrs; High/Low glucose DMEM media 24hrs; normoxia/1% O2 24hrs

Hct116 cells were plated in McCoys 5A medium supplemented with 10% fetal calf serum 24hrs prior to treatment as indicated

Differential gene expression was determined with Partek software using one-way ANOVA.

total RNA was extracted from cells using a Qiagen Rneasy kit according to manufacturer's instructions

software package R, version 1.9.1, libraries gcrma and limma of the Bioconductor Project

Total RNA was extracted from 1.5 x 107 CBMNC or APBMNC with RNeasy Kit (Qiagen). Quantity and purity of extracted RNA was checked by RNA LabChip® Kit (Agilent).

Biotinylated cRNA was heated for 5 min at 95°C, allowing RNA to breakdown to small fragments according to Affymetrix protocols. Fragmented cRNA (20 µg) was subjected to oligonucleotide hybridization (Hybridization Oven; Affymetrix) to the human Genome Focus Genechip (Affymetrix).

Biotinylated labeling cRNA was conducted by in vitro transcription using the BioArray High Yield RNA Transcript Labeling System (ENZO). cRNA was purified by GeneChip Sample Cleanup Module (Affymetrix).

to evaluate in vitro activation of the neonatal and adult immune system, gene expression patterns were compared in mononuclear cells from cord and adult peripheral blood without and after incubation with 5 µg/ml Lipopolysaccharide (LPS).

Peripheral blood was obtained by venipuncture from healthy adult volunteers. Blood samples from umbilical cords of the placentas of healthy, full-term infants after scheduled caesarean section or vaginal delivery were obtained by puncture of the cord immediately after delivery

Total retinal RNA extracted from six total retinas from three mice who have had experimentally induced diabetes for 3-4 weeks.

Total retinal RNA extracted from four retinas from two mice who are age-matched with the diabetic mice but have not undergone treatment and have normal blood-glucose levels.

Total retinal RNA extracted from four total retinas from two mice who have had streptozotocin-induced diabetes for 5 weeks.

Total retinal RNA extracted from four retinas from two mice who have had streptozotocin-induced diabetes for 5 weeks.

Total RNA (Trizol + RNeasy cleanup) extracted from E14.5 ganglionic eminence (left and right, medial and lateral) from Arx-/Y Brn4Cre+ SRY+ mouse.

Total RNA (Trizol + RNeasy cleanup) extracted from E14.5 ganglionic eminence (left and right, medial and lateral) from Arx+/Y Brn4Cre+ SRY+ (wild-type control) mouse.

Qiagen RNeasy Fibrous Tissue Mini Kit extraction of total RNA was performed according to the manufacturer's instructions.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HGU133 Plus 2.0 Array. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

2_(Mouse430_2).CEL

1;C57Bl/6;Wild-type;bone marrow-derived macrophage;Control;Rosiglitazone;10 days

1_(Mouse430_2).CEL

1;C57Bl/6;Wild-type;bone marrow-derived macrophage;Control;Control;10 days

Data were imported into GeneSpring 7.3 with RMA preprocessing and normalized to median of all samples.  Normalized data were exported and subjected to Distance Weighted Discrimination (DWD) to account for any batch effects then reimported into Gene Spring and analyzed.

Peripheral blood was drawn and PBMC were isolated over Ficoll.  Samples were stored in Trizol at -80oC until extracted according to manufacturer's directions.

Peripheral blood mononuclear cells;RF- polyarticular JIA;GTE6;105min;White;Female

Peripheral blood mononuclear cells;RF- polyarticular JIA;GTE6;145min;White;Female

Peripheral blood mononuclear cells;RF- polyarticular JIA;GTE6;120min;White;Male

Peripheral blood mononuclear cells;RF- polyarticular JIA;GTE6;111min;White;Male

Peripheral blood mononuclear cells;RF- polyarticular JIA;LT6;82min;White;Female

Peripheral blood mononuclear cells;RF- polyarticular JIA;GTE6;100min;Black/African American;Male

Peripheral blood mononuclear cells;RF- polyarticular JIA;LT6;195min;White;Female

Peripheral blood mononuclear cells;RF- polyarticular JIA;LT6;170min;White;Female

10_(Mouse430_2).CEL

3;C57Bl/6;Wild-type;bone marrow-derived macrophage;Control;Rosiglitazone;10 days

9_(Mouse430_2).CEL

3;C57Bl/6;Wild-type;bone marrow-derived macrophage;Control;Control;10 days

Data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples. This was performed in R (v 3.0.2) with aroma.affymetrix and bioconductor packages.

Sample was hybridized to Affymetrix Mouse Gene 1.0 ST array using a Affymetrix GeneChip Hybridization Oven 645

100ng of total RNA from each sample was processed, labelled according to the Affymetrix GeneChip® Whole Transcript Sense Target Labelling Assay

The AML cell lines, MOLM-14, U937, THP-1 and HL-60, were infected with a scrambled control hairpin (shControl), two shRNAs directed against GSK-3B (shGSK3B_1 and shGSK3B_2), and two shRNAs directed against GSK-3A (shGSK3A_5 and shGSK3A_6). Cells were selected 48 hours post-infection with 1 µg/mL of puromycin. RNA and protein were extracted 48 hours later. Knockdown of GSK-3A and GSK-3B was confirmed by western blot.

All cell lines were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin (Cellgro) and 10% fetal bovine serum (Sigma Aldrich) at 37°C with 5% CO2.

Raw expression values were normalized using Robust Multiarray Averaging (RMA) method in Bioconductor.
The ABS_CALL values were generated in R with the MAS5 algorithm.

RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).

Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.

First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.

MOLM-14 cell line infected with scrambled control shRNA, biological rep1
Sample name: MOLM14_CTRL-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C01_596616.CEL

For all experiments involving transgenic mice, experimental and control animals were genotyped at weaning using PCR, and development of psoriasiform lesions was spontaneous and not induced by wounding (e.g., tape stripping). For the IMQ-generated phenotype, the treatment protocol was to apply a daily topical dose of 62.5 mg IMQ cream (5% Aldara; 3M Pharmaceuticals) to the shaved back region of 8-10 week old C57BL/6 mice. This treatment was carried out for six consecutive days, and during this time, control animals were treated with a vehicle cream (Vaseline Lanette cream; Fagron). In all experiments, adult mice were euthanized at 10-20 weeks of age at which time ear, tail or back skin samples were flash frozen and stored at -80C prior to the isolation of total RNA.

Laboratory animals were maintained under standard conditions in accordance with protocols approved by animal welfare committees at each participating institution

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

MOLM-14 cell line infected with scrambled control shRNA, biological rep2
Sample name: MOLM14_CTRL-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C02_596656.CEL

SK-MEL-2 cells treated with Ad-E2F-1 at MOI 2 plus doxorubicin (sample 1)

SK-MEL-2 cells treated with Ad-E2F-1 at an MOI of 2 plus doxorubicin 0.1 uM(sample1)

Total RNA was isolated from D2 K14deltaNB-cateninER transgenic mice treated for 1 day with 4-hydroxytamoxifen (4OHT; Sigma) using Trizol reagent (Gibco BRL). Double stranded cDNA was generated from 10 ug total RNA and used to generate biotinylated cRNA using the Enzo BioArray High Yield Transcription Labelling Kit (Affymetrix). The cRNA was fragmented using the GeneChip Sample Cleanup Module (Affymetrix) and 10 ug were hybridized to GeneChip Mouse Expression Set 430 A oligonucleotide arrays (Affymetrix). Hybridizations were performed according to the manufacturers instructions using an Affymetrix Gene Chip Instrument System. The arrays were scanned on an Affymetrix GeneChip scanner.
Keywords = Mouse
Keywords = Affymetrix
Keywords = Skin
Keywords = Hair
Keywords = Epidermis
Keywords = Keratinocyte
Keywords = B-catenin
Keywords = Stem Cell

Total RNA was isolated from D2 K14deltaNB-cateninER transgenic mice treated for 0 days with 4-hydroxytamoxifen (4OHT; Sigma) using Trizol reagent (Gibco BRL). Double stranded cDNA was generated from 10 ug total RNA and used to generate biotinylated cRNA using the Enzo BioArray High Yield Transcription Labelling Kit (Affymetrix). The cRNA was fragmented using the GeneChip Sample Cleanup Module (Affymetrix) and 10 ug were hybridized to GeneChip Mouse Expression Set 430 A oligonucleotide arrays (Affymetrix). Hybridizations were performed according to the manufacturers instructions using an Affymetrix Gene Chip Instrument System. The arrays were scanned on an Affymetrix GeneChip scanner.

CD8+ cells were isolated and purified from the spleen of wild type (C57BL/6) or Elf-/-  knock out mice and cultured in vitro.  CD8 T cells were left untreated or activated in vitro by culturing on anti-CD3 coated plates and anti-CD28 in media (RPMI 10% FBS supplemented with 5% T-stim) for 3.5 days

CD8+ T cells were left untreated or activated in vitro by culturing on anti-CD3 coated plates and anti-CD28 in media (RPMI 10% FBS supplemented with 5% T-stim) for 3.5 days

Affymetrix One Cycle Target and Labeling Protocol Hybridization and Staining, as described in Expression Analysis Technical Manual with following exception(s):  Hybridization volume increased to 250.0µL.  Fluidics Script: EukGE ws2v5.

Affymetrix One Cycle Target and Labeling Protocol, exactly as described in Affymetrix Expression Analysis Technical Manual

Affymetrix One Cycle Target and Labeling Protocol Hybridization and Staining, as described in Expression Analysis Technical Manual with following exception(s):  Hybridization volume increased to 250.0ÂµL.  Fluidics Script: EukGE ws2v5

A standard percutaneous kidney biopsy was performed under ultrasound guidance using an 18G-biopsy needle. Biopsy specimens prepared for light microscopy (LM) were formalin-fixed, paraffin-embedded and stained with hematoxylin-eosin and Periodic Acid Schiff reagents. Glutaraldehyde-fixed tissue was processed for electron microscopy (EM). Direct immunofluorescence (IF) studies used polyclonal antibodies for IgA, IgG, IgM, and C3 and C1q components of complement. All biopsies were reviewed by a single experienced renal pathologist at our institution.

GeneChips were scanned using the Affymetrix Gene Chip 3000 7G scanner, software AGCC v2.0

Probe intensities were extracted from Affymetrix CEL files, normalized and summarized at the transcript cluster level using the Robust Multiarray Average method from the R/Bioconductor (http://bioconductor.org) oligo package. Array quality control was performed to remove arrays that significantly differed in initial overall probe intensity. Expression values were analyzed on the log base 2 scale. Significance testing was performed by fitting gene-wise linear models using the limma Bioconductor package, and genes were ranked for differential expression using Benjamini & Hochberg adjusted p-values and log-posterior odds of differential expression. Gene set analysis was performed using the limma romer method. Gene set used were taken from the Molecular Signatures Database (MSigDB) Pathogenesis Based Transcripts (PBT; http://transplants.med.ualberta.ca/Nephlab/data/gene_lists.html) gene sets from the University of Alberta, Edmonton. Analysis for changes in gene expression of Gene Ontology (GO) categories was performed using the GOstats Bioconductor package to calculate Hypergeomtric p-values for over or under-representation of each GO term. Biopsy and blood sample were processed separately.

Biopsy cores were immediately placed into a vial containing 1ml of RNALater® (Ambion, Catalog Number AM7023), stored at -20°C for 24 hours and then transferred to -70°C until RNA isolation.  Renal tissue content in all cores was verified using a dissecting microscope and non-renal tissue was removed. Total RNA was isolated using the QIAGEN RNeasy Mini Kit (Catalog Number 74104, Qiagen, USA)

Total RNA samples hybridized to the Affymetrix Hugene 1.0 st chip according to the protocols provided by the manufacturer.

Labelled as per manufacturer's instruction in Ambion Whole Transcript Expression Kit (Catalog Number 4425209, Ambion, Austin, TX) and Affymetix Genechip Whole Transcript Terminal Labeling Kit (Catalog Number 900671, Affymetrix, Santa Clara, CA)

L16
Gene expression data from kidney biopsy of liver disease patient

alive;White;M;60;HCV;1.3;57;50;0;1;1;1;neg;POS;0;NEG;5.1;11;UN;ATN, mild IFTA, moderate arterisclerosis;0;0;1;0;0;1;1;1;1;1;0;0;3;0;0;0;12;0;0.7;moderate intimal fibrois;IGG+IGA+;A;Kidney_Biopsy_Liver_disease

L17

alive;Hispanic;F;58;HCV;1.4;41;39;0;0;1;1;102;POS;1;POS;7;15;NEG;MESANGAIL PROLIFEATION,Ig A nephropathy;1;0;0;1;1;2;2;2;1;3;2;0;2;1;0;0;31;0.13;0.5;intimal fibrosis,duplication n widening;IGG+IGM+IGA+++C1Q+ mesangial only IgG and focal capillary walls;A;Kidney_Biopsy_Liver_disease

L12

alive;Hispanic;M;48;ETOH;1.9;38;63;1.2;1;1;1;52;NEG;0;NEG;5.1;19;POS;Mesangial Immune complex deposit, lupus class II;1;0;1;0;0;0;1;1;1;2;1;2;NA;NA;NA;P;7;0;0.95;intimal fibrosis, thickening;IGM+IGG+IGA++C3++C1Q+mesangial;ACMG;Kidney_Biopsy_Liver_disease

L13

alive;African American;M;61;HCV;1.7;47;UN;3;1;1;1;1420;POS;0;NEG;5.7;14;POS;Mild mesangial immune complex glomerulonephritis, Severe tubular atrophy;1;0;1;0;0;2;2;0;1;0;1;1;1;0;0;1;9;0.11;0.3;intimal duplication;IGM+IGG+C3+C1Q++mesangial;MGC;Kidney_Biopsy_Liver_disease

HDC-deficient (HDC-KO) and HDC-EGFP mice were injected intraperitoneally with one dose of a genotoxic colonic carcinogen, azoxymethane (AOM), followed by 10 days of a non-genotoxic carcinogen, dextran sodium sulfate (DSS) oral exposure. 22-24 weeks later colon tumors were collected and CD11b+Gr-1+ myeloid cells were sorted.

Histidine decarboxylase null myeloid-derived suppressor cell from colon tumor, rep2

Arrays were scanned on an Affymetrix Scanner 3000-7G scanner with GCOS software. Scanning was peformed according to the protocol described in the Affymetrix GeneChip® Expression Analysis Technical Manual, November 2004 Edition.

Data was normalized using the GCRMA algorithm as implemented in Bioconductor/R.

12 μg of RNA dissolved in 300 μL of buffer was hybridized to Mouse Genome 430. 2.0 GeneChips (Affymetrix). All samples were prepared with the standard protocol recommended by the manufacturer.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

MDSC HDCKO-colon tumor-R
Technical replicate 2 of 2.

Differentially expressed genes of CD11b+Gr-1+ IMCs in the colonic tumors of HDC-EGFP/HDC-KO mice.

C57BL/6J;HDC-EGFP/HDC-KO;7 months;colon tumor;CD11b+Gr-1+ myeloid cells in the tumor stroma

CD11b+Gr-1+ myeloid cells sorted from the colon tumors of HDC-EGFP/HDC-KO transgenic mice induced with AOM/DSS

U2OS cells were transfected with siRNA against NT (non-targeting) or CDK9 at 10 nM using Hi-Perfect (Qiagen) and harvested 72 hours after transfection.

GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 7G

The primary microarray data was normalized using RMA method in Affymetrix Expression Console 1.1 and annotated using latest annotation file based on genome version hg19.  The analysis was done in R using LIMMA package.

Total RNA was isolated from the cell lines using Qiagen RNeasy Mini kit as directed (Qiagen, Valencia, CA). The quality and quantity of the RNA was determined using the Agilent RNA 6000 NanoLabChip kit and Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

Following fragmentation, the RNA was loaded on to the Affymetrix HuGene-1_0-st-v1 GeneChip as directed (Affymetrix, Santa Clara, CA).

The RNA was labeled with GeneChipR One-Cycle Target Labeling and Control Reagents.

Fear conditioning in rats leads to long term memory (LTM) formation. A central substrate for this type of LTM is the basolateral amygdala. We sought expression changes specific to LTM at 6 h following conditioning. The effect of isoflurane, an effective amnestic agent, was also assessed.
Keywords = Rampil
Keywords = anesthesia
Keywords = memory
Keywords = amygdala
Lot batch = rat 29

Lot batch = rat 26

Lot batch = rat 32

Lot batch = rat 30

Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets

THP-1 cell line infected with GSK3A Construct 5 shRNA, biological rep2
Sample name: THP1_GSK3A_5-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B10_596686.CEL

Following fragmentation, 15 ug of cRNA were hybridized according to the standardized protocol from Affymetrix.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

Pulmonary Arterial Hypertension PBMC sample
Sample_series_id: GSE703
Keywords = Pulmonary Arterial Hypertension
Keywords = PBMC

Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14923.gif

Gene expression data from sorted Ter19+CD71high spleen cells from WT mouse

After plating, PPAR WT and PPAR KO macrophages were incubated for 24hrs in RPMI medium supplemented with 0,5% FBS and antibiotics

Thioglycollate-elicited macrophages were isolated by peritoneal lavage 3 days after peritoneal injection of 2.5 ml of 3% thioglycollate (Difco). Cells were plated in RPMI and 10% FBS and washed after 5 h, the medium was removed, and cells were fed with fresh medium containing 0.5% FBS.

Data were analyzed with the MICROARRAY suite (Affymetrix), GENESPRING (Silicon Genetics), and in-house software developed by Sasik et al. 2002 (Bioinformatics).

Cells were lysed with TRIzol (Invitrogen),and total RNA was purified by using RNeasy columns (Qiagen, Valencia, CA).

Fragmented cRNA was hybridized to Affymetrix (Santa Clara, CA) arrays according to the manufacturer’s instructions.

cRNA was generated from 10 ug of total RNAby using the SuperScript kit (Invitrogen) and the High Yield RNA transcription labeling kit (Enzo Diagnostics).

Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16199.gif

Total RNA was isolated from tyII cells by RNeasy Mini Kit according to the manufacturers protocol (Cat. 74104, Qiagen, Valencia, CA).

lung;Insig1 flox/flox /Insig2 -/- ( AT2 cells obtained from 2 months old SpC-rTTA / Otet-CRE / Insig1 flox/flox / Insig2-/- mice treated with doxycycline from E6.5 to E12.5. Control animals lacked either SpC-rtTA or Otet-CRE);Alveolar Type II

RNA was extracted and purified as described in Khodarev et.al., Biotechniques, 2002, 32:316
Keywords = Barrett's esophagus
Keywords = Barrett's-associated adenocarcinomas
Keywords = epidermal differentiation

CD34+ cells from imanitib-treated patients
Keywords = CD34+
Keywords = bone marrow
Keywords = Imatinib
Lot batch = 3001955

Normal CD34+ cells

Lot batch = 3001789

Arrays were scanned with an Illumina BeadArray Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the manufacturer's instructions.

Array data processing was performed on Illumina BeadStudio software. We normalized gene expression data using quantile normalization and log2 transformation. To export to a data matrix, the Sample Gene Profile option of this software was used.

Total RNA was isolated from tissues with the mirVana RNA Isolation labeling kit (Ambion, Inc.) according to the manufacturer's protocol. RNA quality and integrity were confirmed by the ExperionTM Automated Electrophoresis System (BIO-RAD).

Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V4.0 expression BeadChip according to the manufacturer's instructions (Illumina, Inc., San Diego, CA).

Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 750 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion, Inc., Austin, TX). cRNA concentrations were determined using a spectrophotometer (Nanodrop, ND-1000).

To export gene expression data based on unique genes, we used the Sample Gene Profile option of Illumina BeadStudio software. All 47231 probes on the Human-12 BeadChip ver.4 were used.

Cells were transduced with H1P, shNANOG, shOCT4 or shSOX2 lentivirus in the presence of polybrene for 8 days.

Cells were cultured on Matrigel-coated plates in mTeSR medium (Stem Cell Technologies).

RNA was isolated using Trizol, treated with DNase I (Ambion) to remove genomic DNA, extracted with phenol:chloroform (1:1), precipitated and diluted in water.

Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit according to the manufacturer's protocol.

Microarray raw data were normalized using robust multi-array average16 (RMA) implemented in Bioconductor's “affy”-package. Probe sets with “absent” calls (as defined by Bioconductor’s affy-package) in more than 50% of tissue samples in either group (NF and DCM) were excluded

10 µg of total RNA was processed to produce biotinylated cRNA targets

Cell Culture, 100 mm dishes, minimum essential medium (Sigma) plus 10% fetal bovine serum (Life Technologies, Rockville, MD) and 2 mM glutamine in a 5% CO2 atmosphere.

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 1000.

Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133 plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.

Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 10 microg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

MOLM-14 cell line infected with GSK3B Construct 1 shRNA, biological rep2
Sample name: MOLM14_GSK3B_1-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C08_596612.CEL

Hybridization signal on the chip was scanned using an HP GeneArray scanner (Hewlett-Packard).

The data were normalized by median centering by GeneSpring software (Agilent)

Biotin-labeled cRNA sample was hybridized according to manufacture's instruction.

Arf1 SMART Pool siRNA was purchased from Dharmacon (catalog #M-011580-01-0005). On the day prior to transfection, cells were plated at a density of 1x105 cells/well in a 6-well plate. Cells were transfected with 100nM siRNA (final concentration) using Oligofectamine according to the manufacturer’s instructions.

MDA231 cells were obtained from ATCC (Manassas, Virginia) and were cultured in RPMI1640 and DMEM media, respectively, supplemented with 10% FBS and penicillin/streptomycin.

Beadstudio v.2.3.47 was used for processing the raw data and the Average method was used for normalization. Averaged data were filtered for probes with detection pvalue < 0.01 in at least one sample.

Total RNA was isolated using Purelink™ RNA isolation kit (Invitrogen®) as per the manufacturer's recommended protocol. RNA quantity and quality was assessed on a Bioanalyzer™ 2100 instrument (Agilent®). The RNA preparations had 260 nm/280 nm absorbance ratios in the 1.9-2.0 range, 260 nm/230 nm absorbance ratios >1.8, and RNA integrity numbers >7

Illumina® TotalPrep RNA Amplification kit (Ambion®) was used to convert 500 ng of RNA to cDNA which was then transcribed in vitro to generate biotin-labeled RNA.

MOLM-14 cell line infected with GSK3B Construct 2 shRNA, biological rep1
Sample name: MOLM14_GSK3B_2-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C04_596732.CEL

The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037

Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133  Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients

PBMC were isolated, tagged with fluorochrome-conjugated antibodies to CD3, CD4, CD19 and CD33 for 30 min. PBMC were sorted into subsets on a Cytomation MoFlo cytometer into individual subsets. Purity of the populations was confirmed after sorting.

Affymetrix arrays were scanned using the Affymetrix GeneChip Scanner 3000 System

Data was analyzed with Microarray Suite version 5.0 (MAS 5.0) software using the Affymetrix default analysis settings and global scaling normalization methods.

Qiagen Rneasy mini column; only high quality RNA samples as assessed by BioAnalyzer were hybridized to the GeneChips

Following fragmentation, hybridization was carried out according to the Affymetrix Expression Analysis Technical Manual; only samples passing stringent quality control guidelines were assessed

Biotinylated cRNA was prepared according to the Affymetrix protocol from at least 5 ug of high quality RNA

MCF-7 human breast cancer cells were transfected with 20 nM of siGENOME ctrl (siGL3),ERK1 or ERK2 (Thermo Scientific) using Dharmafect1 following the manufacturer’s instructions. After 60 h of transfection, cells were treated with 0.1% control ethanol vehicle or 10 nM E2 for 4h or 24h

GeneChips were scanned using the Hewlett-Packard GeneArray Scanner GCS 3000.

The data were analyzed with  GCOS2.1 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix [HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

2649_E_1_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siCtrl treatment 60h, 0.1%EtOH for 4h

Mouse embryonic fibroblasts (MEF) cells were harvested as described. Briefly, timed pregnancies were set up; E12.5 to E14.5 fetuses were harvested. After carefully removing the embryo’s head, liver and blood clots, the rest of the tissues were washed with PBS, minced and digested with Trypsin at 37?C for 10 min. After digestion, fetal tissues were vigorously pipetted until it is a single cell suspension. The cells were spun down and cultured in DMEM supplemented with Gentamicin, Glutamine, non-essential amino acids, 2-mercaptoethanol and 10% FBS at 37 ?C in a 5% CO2 incubator.  MEFs with 3 different genotypes were treated with or without 5 ng/mL TGF-b1 (R&D systems) for indicated times.

Total RNA was isolated from cell pellets using the RNeasy kit (Qiagen, Valencia, CA, USA).

2 ug total RNA was used in a standard Affymetrix single amplification protocol.

2657_E_3_(HG-U133A_2).CEL

2663_E_2_(HG-U133A_2).CEL

GeneChips were scanned using an Affymetrix GeneChip Scanner (Agilent).

log2 expression values estimated using GC RMA with Array analyzer software

Following fragmentation, 5 ug of cRNA were hybridized on U133A GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-2v4.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

H2.3hrSFM
MCF-7 cells were plated in 10cm dishes and then switched to SFM on the next day.
Reanalysis of GSM183422.

H4.3hrE2
MCF-7 cells were plated in 10cm dishes and then switched to SFM on the next day.  Following overnight starvation, cells were treated in triplicate with E2 (10nM) for 3hr.

H1.3hrSFM
Reanalysis of GSM183421.

H5.3hrE2

H6.3hrE2

The R statistical software was applied for data analysis. The RMA method was used for global background correction and constant normalization was used for normalization. Gene expression index calculation was done using model based index calculation (MBEI). Only perfect match probes were included in data analysis. Welch two sample t-test for paired data was used to calculate p-values

Frozen muscle tissue was homogenized in Trizol with a Polytron Homogenizer and total RNA was purified using TRIzol Reagent including an extra step after phase separation with chloroform. Briefly, 1 volume of phenol-chloroform-isoamylalcohol (25-24-1) was added to the aqueous phase and spun at 10.000 x g for 10 minutes at 4˚C. Then, 1 volume of chloroform was added to the aqueous phase and spun at 12.000 x g for 20 minutes at 4˚C before RNA precipitation.

One µg purified total RNA was converted to biotin-labeled aRNA using the MessageAmpTM II-Biotin single round aRNA amplification kit.

Chronic Myelogenous Leukemia
type: cd34
blast count: NaN
Center code: 1
Note: Center code == 5 not used for disease phase analysis
imatinib analysis: 0

H1299 cells were treated with buffer, PTD-DRBD GAPDH siRNA or Lipofection GAPDH siRNA for 6 h, washed with medium twice and recovered after 12 or 24 h post-treatment.

Preliminary data analysis and QC was carried out using the BeadStudio Software (Illumina).
Simultaneous normalization of multiple microarrays was done using the mloess method.

RNA was extracted with DNase I treatment using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

non-small cell lung carcinoma cell line H1299;PTD-DRBD-mediated siRNA delivery;24hr

non-small cell lung carcinoma cell line H1299;Lipofection-mediated siRNA delivery;24hr

Arrays were washed using an Affymetrix fluidics stations and scanned using the Gene Chip Scanner 3000

CEL files were produced using the Affymetrix® GeneChip® Command Console® Software (AGCC)

Total RNA was extracted from tumor cells using the AbsolutelyRNA microprep kit (Stratagene, Agilent Technologies, Santa Clara, CA, USA)

Hybridization was performed according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA).

Affymetrix GeneChip® WT Terminal Labelling and Hybridization was performed according to the manufacturer’s protocol

DLBCL cell lines were grown in RPMI 1640 with 10% fetal calf serum and 2mM glutamine with R406 (1 micromolar) or  vehicle (DMSO) alone.

The raw .CEL files were converted into probeset-specific expression values using the RMA summarization method as implemented in the BioConductor package 'affy' (Gentleman et al. 2004).

Cell samples were homogenized in Trizol and RNA was extracted according to standard protocols.

cRNA was biotinylated according to the standard Affymetrix protocol.

Mice were kept on standard laboratory chow diet and had free access to water. Hepatic expression profiles of the four genotypes (wild type, and the three knockouts) was performed on male mice, that were all aged between 8-9 weeks.

We generated mice carrying the loxP-site-flanked NEMO gene as described before (Beraza et al., 2009, J Exp Med; PMID: 19635861). From NemoΔhepa, we generated double knockout animals by crossing NemoΔhepa with constitutive TRAIL-/- and TNFR1-/- animals.

Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.14.0).

Total RNA was purified from liver tissue using Trizol reagent (Invitrogen, Karlsruhe, Germany) andpurified using RNeasy microkit (Qiagen, Venlo, The Netherlands). RNA quality was assessed on a Agilent 2100 Bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 fluidics station using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

The Ambion WT Expression kit (Life Technologies, Carlsbad, CA; P/N 4411974) in conjunction with the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix, Santa Clara, CA; P/N 900671) was used for the preparation of labeled cDNA from 100ng of total RNA without rRNA reduction.

C57/BL6;NEMO-TNFR1 double knockout (NemoΔhepa/TNFR1-/-);male;8-9 weeks;liver

Animals were grown to postnatal day 2, 4, 6 or 8 where eyes were enucleaded and retinas isolated.  8-14 retinas were combined per sample.

GeneChips were scanned using the Affymetric GeneArray 2500 scanner.

Expression scores were obtained using Robust Multichip Average to do background correction, quantile normalization and summarization. Normalized data  was subjected to a two-stage analysis based on FDR-CI.

Total RNA was isolated from retinas using TRIzol reagent according to manufacture's protocol.

Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip MOE430A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

C57/BL6;NEMO-TRAIL double knockout (NemoΔhepa/TRAIL-/-);male;8-9 weeks;liver

siRNA transfections were performed using the siPORT® Amine transfection agent according to manufacturers instructions.  siRNAs used were against SRC-1 (Ambion product code: AM16706, working concentration 40nM) and scrambled control (Ambion product code 4390644  working concentration 40nM).  Transfected cells were then incubated at 37oC for 24 hours prior to treatments to allow sufficient knockdown. Cells were treated with 10-7M 4-hydroxytamoxifen (treated) or vehicle control (untreated: 0.01% ethanol) for a period of 2 hours prior to RNA extraction.

LY2 breast cancer cells were propogated in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum and 10-8M 4-hydroxytamoxifen. Prior to treatment cells were sub-cultured for 72 hours in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum without 4-hydroxytamoxifen.

The array was washed and stained on the GeneChip® Fluidics Station 450 Human Genome U133 Plus 2.0 GeneChip® and scanned using the GeneChip® Scanner 3000.

The data were analyzed by using R/bioconductor (R version 2.9.2) packages for differential expression genes, and ComBat.R script was used to adjust the batch effects.

RNA extraction was peformed using the RNeasy® RNA extraction kit (Qiagen) according to manufacturers instructions.The RNA samples were DNase-I treated.

Fragmented and labelled cDNA was added to the hybridisation cocktail in accordance with the NuGEN™ guidelines and hybridised to Human Genome U133 Plus 2.0 GeneChip® for 16-18 hours at 45°C in an Affymetrix GeneChip® Hybridisation Oven 640.

Total RNA was amplified using the NuGEN™ Ovation™ RNA Amplification System V2. The amplified single-stranded cDNA was purified for accurate quantitation of the cDNA and to ensure optimal performance during the fragmentation and labelling process.  The appropriate amount of amplified single-stranded cDNA was fragmented and labelled using the FL-Ovation™ cDNA Biotin Module V2.

Gene expression data from endocrine resistant breast cancer cell line LY14

Gene expression data from endocrine resistant breast cancer cell line LY15

Gene expression data from endocrine resistant breast cancer cell line LY12

Gene expression data from endocrine resistant breast cancer cell line LY13

Gene expression data from endocrine resistant breast cancer cell line LY10

Gene expression data from endocrine resistant breast cancer cell line LY11

Gene expression data from endocrine resistant breast cancer cell line LY8

Gene expression data from endocrine resistant breast cancer cell line LY9

The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).

Total RNA was isolated from laser-capture microdissected tissue using the Picopure RNA isolation kit from Arcturus.

For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases.  15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm.  Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).

A dual-round amplification procedure was performed on 100 nanograms total RNAusing the MessageAMP aRNA kit from Ambion.  In the second round, biotin-labeled cRNA was generated from the double-stranded cDNA template using a nucleotide mix that contained biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY).  The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).

reduction mammoplasty histologically normal breast epithlieum patient 357

Hearts were put into liquid nitrogen immediately after mice euthanization

Mice were maintained on normal chow and the normal 24-hr light/dark cycle

GeneChips were scanned using the Hewlett-Packard GeneArray Scanner GCS3000.

Microarray image analysis was carried out using Partek Genomics Suite software. Subsequent analysis was carried out using BioConductor. Data from the 8 samples were subjected to background subtraction, quantile normalization, log2 transformation and probeset summarization using the RMA (Robust Multichip Average) algorithm. Only the probe sets that interrogate genes were retained and those meant for QC and normalization purposes were excluded from further analysis. The SAM procedure was then used to obtain multiple test corrected q-values for differential expression of genes between the hearts from MCH3-KO mice and control.

RNA were hybridized to the Mouse Gene 1.0 ST Array (Affymetrix).

Affymetrix® GeneChip® Scanner 3000 with GCOS software according to manufactuer's protocol (GeneChip® Expression Analysis Technical Manual 701021 Rev. 5)

TRIzol (Invitrogen) following the manufacturer's protocol, followed by RNeasy column cleanup and ethanol precipitation.

Affymetrix Eukaryotic Target Hybridization protocol (GeneChip® Expression Analysis Technical Manual 701021 Rev. 5)

Affymetrix GeneChip® IVT Labeling Kit, according to manufacturer's protocol (GeneChip® Expression Analysis Technical Manual 701021 Rev. 5)

HD patient; Gender: male; Age: 62; Tissue: lymphocytes (blood); IT15 CAG repeats: 17/47

HD patient; Gender: male; Age: 59; Tissue: lymphocytes (blood); IT15 CAG repeats: 21/45

HD patient; Gender: male; Age: 55; Tissue: lymphocytes (blood); IT15 CAG repeats: 25/43

HD patient; Gender: male; Age: 51; Tissue: lymphocytes (blood); IT15 CAG repeats: 17/45

HD patient; Gender: female; Age: 61; Tissue: lymphocytes (blood); IT15 CAG repeats: 19/44

HD patient; Gender: female; Age: 56; Tissue: lymphocytes (blood); IT15 CAG repeats: 18/43

HD patient; Gender: female; Age: 50; Tissue: lymphocytes (blood); IT15 CAG repeats: N/A

HD patient; Gender: female; Age: 44; Tissue: lymphocytes (blood); IT15 CAG repeats: 17/48

The data were analyzed with GeneChip Operating Software (GCOS) using Affymetrix default analysis settings and global scaling as normalization method.

Trizol extraction of total RNA followed by purification using Rneasy kit was performed according to the manufacturer's instructions.

Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

1AAV-Galgt2 and 2AAV-Galgt2 were mdx mice whose gastrocnemius muscle was treated with AAV carrying the Galgt2 gene. 3mdxPBS and 4mdxPBS were contralateral muscles mock-treated with phosphate-buffered saline.

All mice were maintained in the institute animal facility following the IACUC guidelines

GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA).

CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA) and probe set signals were generated using the RMA algorithm in ArrayAssist 3.4 (Stratagene).

Trizol extraction of total RNA was performed according to the manufacturer's instructions followed by further purification on a silica-gel-based membrane (RNeasy-Mini; Qiagen, Valencia, CA).

For each array, 2.2 µg of fragmented and labeled cDNA was hybridized onto 430 2.0 GeneChips® (Affymetrix Inc., USA), for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).

The Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from 25 ng of total RNA from gastrocnemius muscle following manufacturer’s instructions.

Gene expression data from C2CT myoblasts - C2C12 myoblasts stably transfected with Galgt2

RNA was isolated using Trizol 7 days after infection.  RNA was further prepared by passage over an RNeasy column.  cDNA synthesis, biotinylation of cRNA and hybridization to mouse Genechip 430_2 was performed according to the manufacturer’s instructions (Affymetrix, Santa Clara).

Local background correction and intrachip LOWESS normalization was accomplished by Genespring® 7.3.1 (Agilent Tech., CA)

Oligoarray control targets and hybridization buffer for 16 hrs at 60 degree celcius

Microarray labeling was performed using Micromax Tyramide Signal Amplification (TSA) Labeling and Detection Kit (Perkin Elmer, Inc., MA)

The mice were exposed to 4% dextran sulfate sodium (DSS) in the drinking water for 6 days followed by 4 days of water or 1% L-arginine in the drinking water (10-day protocol). The mice were assigned to one of the following groups: Control (Ctrl), Ctrl + L-Arg, DSS, or DSS + L-Arg

7-week-old male wild-type C57BL/6 mice were used in our experiment. Animals were maintained on a 12 h light/12 h dark cycle under biosafety level 2 conditions. The mice had ad libitum access to a standard diet and water until reaching the desired age for experiments.

Data were processed using the Affymetrix Expression Console v. 1.1 using an RMA normalization algorithm producing log base 2 results
probe group file: MoEx-1_0-st-v1.r2.pgf
probe group file: MoEx-1_0-st-v1.r2.dt1.mm9.mps

At the time sacrifice (day 10 of protocol), a piece of the colon was obtained, cleaned, and placed in RNALater. The following day, the RNALater was removed and the RNA was isolated from the tissue using a Qiagen Rneasy kit per manufacturer's protocol. The samples were submitted to the Vanderbilt Genomic Sciences Resource for first strand cDNA synthesis, 2nd strand cDNA synthesis and IVT-cRNA synthesis. Reactions were performed with Ambion's WT-Expression target preparation kit .

Samples were hybridized using Affymetrix hybridization kit materials. A total of 2 μg of fragmented, labeled target was hybridized to the array. The cartridge array was washed and stained per standard Affymetrix Protocols using Affymetrix Hybridization Wash and Stain kit reagents on the Affymetrix Fluidics Station 450, using script FS450_0007

Samples were enzymatically fragmented and biotinylated using the Whole Transcript Terminal Labeling Kit (Affymetrix)

24 h later, after having grown to a subconfluent layer, cell cultures were incubated with doxorubicin (0.5 ug/ml) for 24 h or an equal volume of PBS as control

Primary human liposarcoma cultures were isolated by dissecting the tumor and digesting the minced samples enzymatically with 10 ml each of collagenase and dispase (10 mg/ml). The single cell suspension was depleted of red blood cells and cellular debris by centrifugation through a Ficoll-Hypaque density gradient. Liposarcioma cells were diluted and cultured during the whole experiment with Leibovitz's L-15 medium, supplemented with 2.0 mM glutamine and 10% fetal bovine serum in a humidified atmosphere in free air exchange with atmospheric air. Cells were seeded at a density of 2.00E+06 in 25 cm2 flasks.

The data were analyzed with GCOS 1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133A  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Gene expression data from primary liposarcom cultures incubated with doxorubicin (0.5 µg/ml) for 24 h

male;70 years;thigh;9x3x6;atypical lipoma;medium;G1;primary tumor;no;no

Mice were housed in Type II L cages (365x207x140 mm, floor area 530 cm2; IVC-based)at an environmental temperature 20-24°C, humidity: 55±10%and under 12/12 h light/dark cycle with food and water ad libitum.

The data were analysed using Bioconductor package 'oligo' 1.18.0 under R-2.14.0. Background correction, normalization and probe summarization was performed with RMA.

RNA  was extracted by using RNeasy Midi Kit (Qiagen) following manufacturers instructions for animal tissues.

Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HT MG-430 PM Array Plates. Hybridization, washing, staining and scanning was performed fully automated on a Gene Titan instrument.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA using the 3'IVT Express Kit (Ambion).

Autoimmune pancreatic islets, no cyclophosphamide treatment, rep 8

Infiltrated pancreatic islets of an autoimmune BDC2.5/NOD mouse. Time course of diabetes induction with Cyclophosphamide (day0 to day3). RNA prepared from purified islets (collagenase digestion, density separation, hand picking), amplified using Ambion protocol.
Keywords = type I diabetes
Keywords = cyclophosphamide
Keywords = BDC2.5
Keywords = NOD
Keywords = pancreas
Keywords = islets
Lot batch = jos1216

Autoimmune pancreatic islets, day 1 cyclophosphamide treatment, rep 1

Lot batch = jos1061

Autoimmune pancreatic islets, no cyclophosphamide treatment, rep 6

Lot batch = jos1149

Autoimmune pancreatic islets, no cyclophosphamide treatment, rep 7

Lot batch = jos1170

Autoimmune pancreatic islets before cyclophosphamide treatment, rep 4

Lot batch = jos1060

Autoimmune pancreatic islets, no cyclophosphamide treatment, rep 5

Autoimmune pancreatic islets before cyclophosphamide treatment, rep 2

Lot batch = jos1072

Autoimmune pancreatic islets before cyclophosphamide treatment, rep3

Lot batch = jos1073

Blood samples were collected in EDTA tubes within 48-hours of acute myocardial infarction or following recruitment into the study. Nucleated cells were fractionated from 5 mL of heparinized blood.

The study samples consisted of whole blood collected from first-time AMI patients within 48-hours post-MI and controls with a normal echocardiogram.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array (HG-U133_Plus_2). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

Autoimmune pancreatic islets, day 1 cyclophosphamide treatment, rep 2

Lot batch = jos1150

Autoimmune pancreatic islets, day 1 cyclophosphamide treatment, rep 3

Lot batch = jos1171

Liver samples from each mouse were ground into a fine powder in a mortar cooled by liquid nitrogen, and 100 mg was added to 1 ml prechilled Trizol reagent (Invitrogen, Carlsbad, CA). Total RNA extractions were performed according to the manufacturer’s directions, and the RNA was further puri-fied by passage through RNeasy mini-columns (QIAGEN, Valencia, CA) according to the manufacturer’s protocols for RNA clean-up. Final RNA preparations were resuspended in RNase-free water and stored at –80°C. The RNA samples were quantified spectrophotometrically, and purity and integrity were assessed by agarose gel electrophoresis. All samples exhib-ited 260/280 absorbance ratios of approximately 2.0, and all showed intact ribosomal 28S and 18S RNA bands in an approximate ratio of 2:1 as visu-alized by ethidium bromide staining.

a time series of ConA injections was administered and  20 mg/kg ConA was injected through the mouse caudal vein at one of 4 time points (0 hr, 1 hr, 3 hr, 6 hr),here is  hepatic gene expression at "0 hr" (rep3)

Z score transformation for normalization was performed for each Illumina sample/array as previously described (Cheadle et al. J Mol Diagn, 5:73-81).

RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

C57BL/6x129Sv/B6 hybrid;Prkar1a+/- Prkaca+/-;9 months;caudal vertebral bone lesion

RNA samples (60ug) were extracted from the mouse heart and retrotranscribed to cDNA labeled with Cy5 (male) and Cy3 (female) individually. The cDNAs were co-hybridized with the 27K mouse microarray slide.

heart of female mouse subjected 1 week to chronic constant hypoxia

Keywords = Hypoxia
Keywords = Heart
Keywords = Microarray

heart of female mouse subjected 2 week to chronic constant hypoxia

DBA/2J Chronic morphine treated, striatum, biological replicate 1

Affymetrix One Cycle Target and Labeling Protocol Hybridization and Staining, as described in Expression Analysis Technical Manual with following exception(s):  Hybridization volume increased to 250.0µL.  Fluidics Script: EukGE ws2v5

C57BL/6x129Sv/B6 hybrid;Prkar1a+/-;9 months;caudal vertebral bone lesion

The data was preprocessed by Bioconductor lumi package (version 1.7.18). It was vst transformed and quantile normalized.

Total RNA was extracted from U2OS PRC shRNA1 cells using TRIzol reagent (Invitrogen) and purified further using the RNeasy MinElute Cleanup kit (Qiagen).

Illumina TotalPrep RNA amplification kit (Ambion) per manufacturer's instructions

Total RNA was isolated from U2OS PRC shRNA1 transductants using TRIzol (Invitrogen) and DNase treated with the TURBO DNA-free kit (Ambion). RNA samples were further purified using the RNeasy MinElute Cleanup kit (Qiagen). Integrity of the RNA was evaluated using the Agilent 2100 BioAnalyzer. 500 ng of RNA was used to perform in vitro transcription in the presence of biotin UTP with the Illumina TotalPrep RNA amplification kit (Ambion). The amplified, labeled RNA (1.5 _g) was then hybridized in triplicate to an Illumina Whole-Genome Sentrix Human-6 v2 Expression BeadChip, and detected according to the Illumina user manual.

U2OS, Treatment: infected with PRC shRNA1_pLenti, blasticidin selection

Ramos cells were transfected in triplicates with pRTS-GFP or pRTS-CA-IKK2, selected with hygromycin and transgene expression was induced with doxycycline (0,5mg/ml) for 48hrs. RNA was isolated with RNeasy mini kit (Qiagen, Venlo, Netherlands)

Imaging on an Affymetrix GeneChip (3000) scanner. Raw data were generated using the GCOS 1.4 software (Affymetrix). Probe level data were obtained using the Robust Multichip Average (RMA) normalization algorithm [Bolstad, B.M.,
Irizarry, R.A., Astrand, M. & Speed, T.P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185?193 (2003)]

Data pre-processed with RMA.
Data analysis was performed using the BRB-ARRAYTOOLS software package (available at http://linus.nci.nih.gov/BRB-ArrayTools.html)

extraction with RNeasy Mini Kit (QIAGEN) according to manufacturer´s instructions

Hybridization on a Hybridization Oven 640 (Affymetrix).
Arrays were stained and washed in a FS 450 Fluidics station (Affymetrix)

2 µg of total RNA were labeled using the GeneChip® One-Cycle Target Labeling assay kit (Affymetrix), according to the manufacturer´s instructions

pRTS-CA-IKK2;human Burkitt lymphoma;ACC 603;established from the ascitic fluid of a 3-year-old boy with American-type Burkitt lymphoma in 1972; cells were described to be EBV-negative but EBV infectible, to carry the (8;14) translocation and p53 mutations

Total RNA was extracted from U2OS control shRNA cells using TRIzol reagent (Invitrogen) and purified further using the RNeasy MinElute Cleanup kit (Qiagen).

Total RNA was isolated from U2OS control shRNA transductants using TRIzol (Invitrogen) and DNase treated with the TURBO DNA-free kit (Ambion). RNA samples were further purified using the RNeasy MinElute Cleanup kit (Qiagen). Integrity of the RNA was evaluated using the Agilent 2100 BioAnalyzer. 500 ng of RNA was used to perform in vitro transcription in the presence of biotin UTP with the Illumina TotalPrep RNA amplification kit (Ambion). The amplified, labeled RNA (1.5 _g) was then hybridized in triplicate to an Illumina Whole-Genome Sentrix Human-6 v2 Expression BeadChip, and detected according to the Illumina user manual.

U2OS, Treatment: infected with control shRNA_pLenti, blasticidin selection

Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44K array slides

Total RNA extracted using Trizol according to the manufacturer's instructions.

Labeled RNA was hybridized for 17 hr at 65C on Agilent gene expression array. Arrays were washed according to the manufacturer's protocol.

Cy3-CTP  labeled RNA was prepared according to the standard Agilent protocol from 50ng total RNA

Freshly isolated  Bronchial Epithelial Cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011). The bronchial brushings generally comprised >90% epithelial cells and were placed into Trizol for mRNA analysis.

Moderate Asthma;Fresh Bronchial Epithelial Cells;female;46.25205

Moderate Asthma;Fresh Bronchial Epithelial Cells;female;42.93699

Moderate Asthma;Fresh Bronchial Epithelial Cells;female;24.77534

Moderate Asthma;Fresh Bronchial Epithelial Cells;female;43.23288

Moderate Asthma;Fresh Bronchial Epithelial Cells;female;29.04384

Moderate Asthma;Fresh Bronchial Epithelial Cells;female;24.32603

The HepG2 transformant pools expressing ectopic wildtype THRA, THRB, an HCC-TR mutant (αΙ or βN), a RCCC-TR mutant (6α or 15β), or the empty plasmid control were treated with 100 nM T3 or with ethanol carrier alone for 6h in DMEM containing 10% hormone-stripped fetal bovine serum.

HepG2 cells were maintained at 37°C in Dulbecco's Modified Eagle's Medium (DME) supplemented with 10% fetal bovine serum using bicarbonate buffer and a 5% CO2 atmosphere.

The purified RNA was provided to the University of California, Davis, Cancer Center Gene Expression Resource for subsequent cDNA probe generation and hybridization to Affymetrix GeneChip Human Gene 1.0 ST microarrays (Affymetrix Incorporated, Santa Clara CA).

The raw microarray data was normalized by the Robust Multichip Array (RMA) method using R software.

The cells were harvested and the RNA was isolated using an RNeasy kit (Qiagen, Valencia CA).

HepG2 cells stably expressing HCC-THRA mutant al treated with vehicle for 6h.

HepG2 cells stably expressing HCC-THRA mutant al treated with 100 nM T3 for 6h

HepG2 cells stably expressing wild-type THRB and treated with 100 nM T3 for 6h

HepG2 cells stably expressing wild-type THRB and treated with vehicle for 6h.

The data were analyzed in the R/Bioconductor statistical programming environment. Summarization and MAS5.0 normalization were obtained via the affy package

Peritoneal cells were recovered by lavage with 5ml of ice-cold 5 mM EDTA in PBS. Lavage from mice were pooled, stained and sorted on a FACSAria III (BD biosciences)

RNA was extracted using RNeasy mini kit (QIAgen) according to the manufacturer's instructions.

Gata6-KO;Peritoneal resident (CD11b-high, MHCII-low/negative) macrophages

Gata6-WT;Peritoneal resident (CD11b-high, MHCII-low/negative) macrophages

Mononuclear cells were separated using Histopaque density gradient centrifugation, labelled with CD34 MicroBeads, and then CD34+ cells were isolated using MACS magnetic cell separation columns according to the manufacturer’s recommendations.

GeneChips were scanned using an Affymetrix GeneChip Scanner 3000.

Affymetrix CEL files were pre-processed using Robust MultiChip Analysis (RMA) using GeneSpring 7.3.1.

Total RNA was extracted using TRIZOL following the manufacturer’s protocol

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

50 ng of total RNA were amplified and biotin-labelled with the Two-Cycle cDNA Synthesis and the Two-Cycle Target Labelling and Control Reagent packages according to the standard Affymetrix protocol.

bone marrow;CD34+ hematopoietic stem cells (HSC);myelodysplastic syndromes (MDS);refractory anemia with ringed sideroblasts (RARS);normal

bone marrow;CD34+ hematopoietic stem cells (HSC);myelodysplastic syndromes (MDS);refractory anemia with excess blasts 2 (RAEB2);normal

bone marrow;CD34+ hematopoietic stem cells (HSC);myelodysplastic syndromes (MDS);refractory anemia (RA);other

bone marrow;CD34+ hematopoietic stem cells (HSC);myelodysplastic syndromes (MDS);refractory anemia with excess blasts 1 (RAEB1);other

bone marrow;CD34+ hematopoietic stem cells (HSC);myelodysplastic syndromes (MDS);refractory anemia with ringed sideroblasts (RARS);other

bone marrow;CD34+ hematopoietic stem cells (HSC);myelodysplastic syndromes (MDS);refractory anemia (RA);del5q

The chips were scanned using an Affymetrix genechip scanner as per manufacturer's instructions

Expression values were estimated using the GCRMA algorithm implemented in Genedata's Refiner 4.5. Further data anaylsis was performed using Genedata's Analyst 4.5

RNA was purified using the Qiagen RNA easy protocol according to the manufacturer's insructions

RNA was hybridised using the standard Affymetrix hybridisation protocol as per manufacturer's instructions (45°C over night)

RNA was amplified and labelled using the Affymetrix 1-cycle 3'IVT protocol

female Spargue-Dawley rats, diet only for 7 days,  tissue: liver

female Spargue-Dawley rats, 4-hydroxyphenylretinamide, 782 mg/kg diet for 7 days, tissue: mammary gland

female Spargue-Dawley rats, 4-hydroxyphenylretinamide, 782 mg/kg diet for 7 days, tissue: lung

female Spargue-Dawley rats, 4-hydroxyphenylretinamide, 782 mg/kg diet for 7 days, tissue: liver

female Spargue-Dawley rats, diet only for 7 days,  tissue: mammary gland

The data were normalized by median centering by GeneSpring software (Agilent).

No treatment done, but samples were taken in WT and VMH-specific FoxO1 KO mice.

The data were normalised using quantile normalisation with Partek Genomic Suite V6.5

RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

Mixed;VMH-specific FoxO1 Knockout;ventromedial hypothalamus (VMH)

101;Paracetamol;10/5/63;M;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;11/2/04;Weight loss, altered bowel habbit.;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;1-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

103;None;6/30/65;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;11/9/04;Diarrhoea, now settled, Mum has UC;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;1-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

102;Movicol 1 sachet daily;9/5/62;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;11/2/04;RIF pain, persistent anaemia.;0;TRUE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;1-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

105;None;7/29/84;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;11/15/04;IBS type symptoms;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;1-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

Epididymal adipose;GPR120 KO;normal diet ND;mixed 129/Sv and C57BL/6;mouse 720

Liver;GPR120 KO;normal diet ND;mixed 129/Sv and C57BL/6;mouse 719

Epididymal adipose;wild-type;normal diet ND;mixed 129/Sv and C57BL/6;mouse 686

Liver;GPR120 KO;normal diet ND;mixed 129/Sv and C57BL/6;mouse 720

vastus lateralis biopsy,63 year-old sedentary COPD patient (male #20).

Needle biopsies were obtained from the vastus lateralis muscle of 6 COPD patients,72±2 year-old males before and after 3 months of training.  RNA was extracted using Trizol. Targets were produced using standard Affymetrix procedures from about 4ug of total RNA.
Keywords = COPD, microarray, exercise, skeletal muscle, training effect

Probe arrays were then scanned in the Affymetrix GeneChip scanner.

Total RNA from mouse spinal cords (4)was prepared with the Trizol method (Invitrogen 15596-018).  PolyA RNA was isolated using an Oligotex mRNA kit.

15 micrograms of cRNA were added to 300 microliters of hybridization buffer containing 0.1 mg/mL of herring sperm DNA, 0.5 mg/mL acetylated bovine serum albumin, and MES hybridization buffer (Sigma). Standard Affymetrix controls were added and 200 microliters of this mixture hybridized to the chip (MG-U74v2A) for 16 hr. Probe arrays were washed and stained in an Affymetrix Fluidics station using preprogrammed methods.  The arrays were then stained with streptavidin phycoerythrin and the signal amplified with biotinylated antibody

First strand synthesis was done using Superscipt choice system kit (Life technologies). A T7(N)24 primer was used starting with 1 microgram of polyA RNA and 400 units of Superscript II reverse transcriptase.  Second strand synthesis was done with DNA ligase/DNA polymerase mix and RNAase H in the two step reaction following the manufacturer's instructions. cDNA was purified by phenol-chloroform extraction and ethanol precipitation. In vitro transcription and biotin labeling of the purified cDNA was performed using the Affymetrix IVT kit.  cRNA was purified using an RNeasy spin column (Qiagen) followed by ethanol preciptitation. Twenty micrograms of cRNA was fragmented accoriding to the kit instructions.

Calculated using the MAS5 algorithm where sc=1500, tau=0.015, alpha1=0.05, and alpha2=0.065

This sample was analyzed as part of aproject aiming to identify PTHrP-responsive genes. Cells were either transfected with siPTHrP or control siRNA (siLuc) and harvested 3 days later for RNA isolation. The RNA of this samples derived from cells treated with siPTHrP (3).

Subjects were instructed to take one capsule (75 mg resveratrol or placebo) in the morning with breakfast for 12 weeks. Subjects randomized to the calorie restriction weight loss group participated in a lifestyle intervention calorie restriction program that included weekly ~1 h long dietary and behavioural education sessions led by an experienced weight management dietician.

We assigned non-obese women with normal glucose tolerance to 1) the placebo, 2) the resveratrol supplementation, and 3) calorie restriction group.

Scanning of the arrays was done on an Affymetrix scanner 3000 and the Command Console Software was used to monitor scanning and to convert raw data into cell intensity files.

Gene expression microarray data were analyzed by using using R/Bioconductor.  The quality of all expression microarray data were examined for comparable scale factor, similar average background and percent present calls, and RNA integrity using R package ‘simpleaffy’.

Total RNA was extracted from the frozen tissue samples (subcutaneous adipose tissue and skeletal muscle (vastus lateralis) biopsy samples) using Trizol.

Prepare the hybridization cocktail containing fragmented and labeled aRNA. Heat the hybridization cocktail to 99 degree for 5 minutes. Incubate the probe array filled with Pre-hybridization mix at 45 degree for 10 minutes with rotation. Transfer the Hybridization Cocktail that has been heated at 99 degree to a 45 degree heat block for 5 minutes. Hybridize at 45 degree for 16 hours.

Biotinylated cRNA were prepared according to 3`IVT Express Kit (Lot: 1004019).

GeneChips were scanned using the Affymetrix GeneChip 3000 7G scanner.

cRNA was hybridized for 16 hr at 45C on the Affymetrix Human U133A array.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

GeneChips were scanned by using the Hewlett-Packard GeneArray Scanner G2500A.

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as a normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

Following fragmentation, 10 microgram of cRNA was hybridized at 45C for 16 hr on GeneChip Murine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA was prepared  from 12 microgram of total RNA according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

Human neuroblastoma cells IMR-32 (ATCC) were grown in DMEM medium supplemented with 10% FBS and treated as described above.  RNA was isolated using the RNeasy Kit from Qiagen.

standard Affymetrix procedures using the GeneChip Fluidics Station 450

cDNA synthesis and amplification employed the Affymetrix 3' IVT protocol.

RNA was extracted using Qiagen RNeasy Midi Kit according to manufacturer guidelines

Mouse embryonic fibroblast derived from MyoD-/-/Myf5-/- animals transduced with ER-MyoD wt in differentiation media for 6hrs

Male Fisher 344 rats aged 11-12 weeks were treated with various doses (0, 5, 20, 50, 200 & 500 mg/kg) of d-serine and terminally sacrificed 96 hours post-exposure.  An approximate 30mg-section of the forebrain was processed for total RNA isolation.

GeneChips were scanned in the Affymetrix GeneChip Scanner 3000 using the Affymetrix GeneChip Operating Software (GCOS, version 1.2).

Data obtained from the Affymetrix GeneChip Scanner 3000 was processed using the statistical algorithm of the Affymetrix GCOS.  The gene expression signal was scaled using "All Probe Sets Scaling" with a target intensity of 500.

Total RNA was isolated from brain tissue using Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA).  Frozen tissues were homogenized in lysis buffer containing guanidinium thiocyanate and -mercaptoethanol.  Extraction and purification of total RNA from tissue

Hybridization was performed at 45°C for 16 h in an Affymetrix hybridization oven with constant end over end rotation at 60 RPM.

Microarrays were stained in the Affymetrix GeneChip Fluidics Station 450 using the EukGE_Ws2v5 protocol.

Gene expression data from male F344 rats treated with a single dose of 200mg/kg D-Serine for 96 hours

Brain tissue from Fisher 344 male rat, Animal #253, 200mg/kg D-Serine

Brain tissue from Fisher 344 male rat, Animal #254, 200mg/kg D-Serine

Brain tissue from Fisher 344 male rat, Animal #255, 200mg/kg D-Serine

Morning leukopheresis, 100ml, followed by standard Ficoll protocol, buffy coat separation and isolation of CD4+ T cells using negative selection kit from StemCell (StemSep Human CD4+ T Cell Enrichment Cocktail).

GeneArray Scanner (Agilent) was used for scans. Initial image processing was performed using GCOS ver. 1.2 (Affymetrix) with the following settings Alpha1: 0.05, Alpha2: 0.065, Tau: 0.015, Gamma1H: 0.0045, Gamma1L: 0.0045, Gamma2H: 0.006, Gamma2L: 0.006, Target: 500, NF: 1.

MAS5 algorithm, Alpha1: 0.05, Alpha2: 0.065, Tau: 0.015, Gamma1H: 0.0045, Gamma1L: 0.0045, Gamma2H: 0.006, Gamma2L: 0.006, Target: 500, NF: 1.

20 µg of biotin-labeled cRNA was fragmented following GeneChip Sample Cleanup Module protocol (cat. # 900371, Affymetrix). Fragmented cRNA was hybridized to Hu133A microarrays (Affymetrix) for 16hr in GeneChip Hybridization Oven 640 (Affymetrix) in hybridization cocktail. Washing, staining and scanning were performed on-site using Fluidics Station 400 (Affymetrix) for washes.

5-6 µg of total RNA was reverse-transcribed using SuperScript II reverse transcriptase (Invitrogen) and second strand synthesis was performed using SuperScript Double-Stranded cDNA Synthesis Kit (cat. # 11917-010, Invitrogen) per manufacturer’s instructions. cDNA was purified using cDNA cleanup columns of the GeneChip Sample Cleanup Module (cat. # 900371, Affymetrix). In vitro transcription of biotin-labeled cRNA was performed with the BioArray HighYield RNA Transcript Labeling kit (cat. # 900182, Enzo Life Sciences) following manufacturer’s instructions. cRNA was purified using IVT cleanup columns of the GeneChip Sample Cleanup Module (cat. # 900371, Affymetrix)

CD4+ T cells derived by negative selection from leukopheresed blood sample

Gene expression data from male F344 rats treated with a single dose of 500mg/kg D-Serine for 96 hours

Brain tissue from Fisher 344 male rat, Animal #247, 500mg/kg D-Serine

Brain tissue from Fisher 344 male rat, Animal #248, 500mg/kg D-Serine

Brain tissue from Fisher 344 male rat, Animal #249, 500mg/kg D-Serine

Brain tissue from Fisher 344 male rat, Animal #251, 500mg/kg D-Serine

GeneArray Scanner (Agilent) was used for scans. Initial image processing was performed using GCOS ver. 1.2 (Affymetrix) with the following settings Alpha1: 0.05, Alpha2: 0.065, Tau: 0.015, Gamma1H: 0.0045, Gamma1L: 0.0045, Gamma2H: 0.006, Gamma2L: 0.006, Target: 500, NF: 1. Scaling factors ranged from 1.2 to 4.8

MAS5 algorithm, Alpha1: 0.05, Alpha2: 0.065, Tau: 0.015, Gamma1H: 0.0045, Gamma1L: 0.0045, Gamma2H: 0.006, Gamma2L: 0.006, Target: 500, NF: 1. Scaling factors ranged from 1.2 to 4.8

Morning leukopheresis, 100ml, followed by standard Ficoll protocol, buffy coat separation and isolation of CD8+ T cells using negative selection kit from StemCell (StemSep Human CD8+ T Cell Enrichment Cocktail).

CD8+ T cells derived by negative selection from leukopheresed blood sample

MCF7/BUS cells were inoculated in a plastic dish in DMEM (phenol red-free, 5% stripped fetal calf serum) and incubated for 16 hours. Cells were then washed and cultued in DMEM supplemented with 17beta-estradiol (E2) at the indicated concentration. Total RNA was isolated 48 hours after E2 treatment.

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

QIAGEN RNeasy extraction of total RNA was performed according to the manufacturer's instructions.

Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Gene expression data from MCF7 (BUS stock) exposed to 10 pM 17beta-estradiol for 48 hours.

MCF7/BUS cells, human breast adenocarcinoma cell line, estrogen receptor-positive

Gene expression data from MCF7 (BUS stock) exposed to 30 pM 17beta-estradiol for 48 hours.

Gene expression data from MCF7 (BUS stock) exposed to 60 pM 17beta-estradiol for 48 hours.

Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used.

Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V3.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48697 probes on the Human-6 beadChip ver. 2 were used.

Protocol from BioArray High Yield RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY

Hai, M., Muja, N., DeVries, G.H., Quarles, R.H. and Patel, P.I.;497–.508.

RT4D6 Schwannoma cells, treated with mutant siRNA for Sox 10, 48 hours

RT4D6 Schwannoma cells, treated with wild type siRNA for Sox 10, 48 hours

On the next day the cells were transfected with 60 pmol of siRNA per well using Lipofectamine RNAiMAX (Invitrogen) using manufacturer’s protocol. After 2 days (24hr time point), or 3 days (2 hr and 4 hr timepoints) cells were treated with Dex for the indicated times. All treatment groups were harvested at the same time.

A clonal line of U2OS cells that stably express wild-type rat GRα were plated in 6-well dishes with medium supplemented with 5% fetal bovine serum.

The data were normalized using neqc with limma (v.3.14.4) in R (v.2.15.3).
The non-normalized data matrix contains 48,210 data rows (with extra 887 rows for control probes). Control probes do not have Illumina IDs but have Probe IDs, were used in normalization, and thus removed in the dataset after normalization.

Total RNA was isolated using QIAshredder and RNeasy mini columns (Qiagen). The quality of RNA samples was evaluated by A260/A280 ratio which was at least 1.9 and the integrity was analyzed using electrophoresis on an Agilent Bioanalyzer using the Experion RNA Stdsens analysis kit (Biorad). For each experimental condition 5 ug of high quality total RNA was submitted to the Southern California Genotyping Consortium at the University of California, Los Angeles.

Labeling, hybridization and scanning was performed by the Southern California Genotyping Consortium at UCLA as per their standard protocol.

U2OS;osteosarcoma cells;none (non-infected control);dexamethasone (Dex) for 4h

Cells were seeded in 96-well plates at an optimal density (ranges 4,000 ~ 12,000; 80% confluency). Following an overnight incubation, cells were treated with GI50 concentrations of cisplatin for 48 h.

Data were normalized by Robust Multichip Average (RMA) using Affymetrix Powertools.

Total RNA was extracted by Qiagen RNeasy kit according to the manufacturer's instructions.

Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA.

SMhu183
Gene expression data from cultured ovarian cancer cell line.

SMhu184

SMhu185

SMhu186

PC-3 cells were mock transfected or transfected with a pool of control siRNAs (siControl) or Ago1 siRNAs (siAgo1) at 10 nM total concentration for 48 hrs

Total cellular RNA was isolated using RNeasy kit. The resulting total RNA concentration and quality were assessed by the Agilent™ Bioanalyzer

Hybridization, washes, and scanning were performed by following the GeneChip Expression Analysis Technical Manual 702232 Rev. 3

Ovation Pico WTA V2 & Encore Biotin Module (NuGen) were used to prepare probes for hybridization to Affymetrix GeneChip Human Gene 1.0 ST Arrays

SMhu049

SMhu050

SMhu041

SMhu042

SMhu039

SMhu040

SMhu037

SMhu038

WT C57BL/6 mice and IL-22 KO mice were infected with the ME49 strain of Toxoplasma gondii (100 cysts in 0.3ml of PBS by gavage). Ileum of these mice was harvested at day 5 post-infection

The method for array schanning was provided by Affymetrix. Arrays were washed and stained in Fluidics station and scanned on Affymterix scanner.

Raw data were processed using the RMA algorithm using the affy Bioconductor package (affy_1.42.3).

The method for hybridization of the arrays was provided by Affymetrix. Twenty micrograms of cRNA was fragmented and then hybridized to the arrays at 45°C for 19 hours in a rotisserie oven set at 60 rpm.

The method for prepartation of cRNA was provided by Affymetrix. Briefly, 5 ug of total RNA was converted into double-stranded cDNA using a cDNA synthesis kit SuperScript Choice and a T7-(dT)24 oligomer primer. Double-stranded cDNA was purified on an affinity resin and ethanol precipitation. Following second-strand cDNA synthesis, labeled cRNA was generated using a T7 RNA polymerase and biotin-labeled nucleotide in an in vitro transcription reaction (Enzo Diagnostics). The labeled cRNA was purified on an affinity resin.

Gene expression data from wild type mouse ileum after infection with T. gondii

C57BL/6;WT;ME49 strain of T. gondii;at day 5 post-infection;ileum

Gene expression data from IL-22 knockout mouse ileum after infection with T. gondii

C57BL/6;IL-22-/-;ME49 strain of T. gondii;at day 5 post-infection;ileum

SMhu051

SMhu052

Fluorescence intensities were captured with an Affimetrix GeneArray 2500 Scanner and quantified with Affymetrix Microarray Suite 5.0.

Data were normalized and analyzed using dChip2004 (Li and Wong, 2001).

RNA was isolated with Trizol (Invitrogen) and purified using RNeasy columns (Qiagen).

Samples were hybridized to MG U74Av2 arrays (Affymetrix), and stained with streptavidin-phycoerythrin.

Samples were labeled with biotinylated nucleotides by reverse transcription.

ES cells were cultured as described in the corresponding Materials and Methods section

labeling, hybridization, and primary data processing were performend by Atlas Biolabs, Berlin

Ring1B/Eed double mutant ES cell line generated by gene targeting of Ring1B in Eed deficient ES cells;ES

At 3 weeks of age, Gnmt knockout and wild-type mice from the same litter were intraperitoneally injected with 10 mg AFB1/kg of body weight

The data were normalised using quantile normalisation with Bioconductor (v2.5) Lumi package.

Biotinylated cDNA were prepared with the Illumina® TotalPrep™ RNA Amplification Kit (Ambion)

Oker_1(tube3)
We isolated a cell line derived from a hepatic tumour of GNMT-KO mice, OKER cells.

Stable cell populations with silenced CCM3 or control were obtained via puromycin selection after lentiviral transduction using MISSION lentiviral shRNA transduction particles against human CCM3 or MISSION lentiviral non-target shRNA transduction particles, from Sigma-Aldrich (TRC).

Human Coronary Artery Endothelial Cells (HCAEC) were obtained from European Collection of Cell Cultures, and were grown as recommended.

GeneChips were scanned using a GeneChip Scanner 3000 (Affimetrix).

Microarray data were normalized using the Affimetrix Expression Console. Subsequent analysis was made using the MeV software. Cutoff intensity was set on 6. Sample comparisons between late and early passage control cells were made using SAM algorithm with delta2 as a cutoff. Genes that were considered overexpressed when log2 (shNTp11/shNTp7)>0.5 (senescence genes).

RNA extracts were obtained using Trizol reagent and quantified with a Nanodrop 2000 (Thermo Scientific). RNA quality was assesed using a RNA 6000 Nano kit (Agilent Biotechnologies).

Hybridization was performed as recommended in GeneChip Hybridization, Wash and Stain kit (Affimetrix), incubating the samples for 17 h at 45º C in a GeneChip Hybridization Oven 640 (Affimetrix). GeneChips were washed and stained in the GeneChip Fluidics Station 450 (Affimetrix).

Single-stranded cDNA was obtained from 250 ng total RNA using Ambion WT Expression kit (Life Technologies). Then, ss cDNA was fragmented and labeled using the Affimetrix GeneChip WT Terminal Labeling and Hybridization kit.

CUTLL1 cells were cultured in RPMI 1640 medium (Invitrogen) supplemented with 10% fetal bovine serum, 2 mM L-glutamine, penicillin and streptomycin.

Affymetrix expression data were normalized using the standard robust multichip average (RMA) package in R.

Total RNA prepared with RNeasy Mini kit (Qiagen) was subjected to expression profiling in triplicate on Affymetrix human genome U133 plus 2.0 arrays.

Hybridization was performed according to standard protocols for Affymetrix HG-U133 plus 2.0 arrays.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7-10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

Gene expression data from CUTLL1 cells treated with compound E for 3days and washouted compound E and treated with cycloheximide for 4 hours

Gene expression data from CUTLL1 cells treated with compound E for 3days and washouted compound E for 4 hours

Gene expression data from CUTLL1 cells treated with compound E for 3days and washouted compound E and treated with cycloheximide for 2 hours

No treatment. Samples are from SIRT3 WT or KO littermate mice of approximately 1 year of age on a 129 background.

The data were analyzed with Robust Multi-array Average (RMA) with PM only models as normalization method.

Trizol extraction of total RNA was performed according to manufacturer instructions (Invitrogen). RNA was cleaned using RNeasy MiniKit from Qiagen.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse Genome Array Mouse430_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Gene expression data from CUTLL1 cells treated with compound E for 3days

Using institutionally approved animal protocols, mice were given 0.5 ml TMPD intraperitoneally, and grow for 3 and 18 days. Animals untreated were prepared at the same time and used as the control

The data were analyzed with GeneChip® Operating Software (GCOS) using MAS5 Statistical algorithm.
The data in the matrix table are normalized by global scaling, and the mean target signal was set to 500.

total RNA was extracted from mesentery of experimental/control animals, using TRIzol (Invitrogen), and followed by a cleanup using Qiagen Rneasy kit.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on mouse genome 430 2.0 array chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Labeled aRNA prepared from 1 µg of RNA using MessageAmpII aRNA Amplification kit ( Ambion) following manufactory instruction.

Timed-pregnant CD-1 mice were dosed by oral gavage from gestation day (GD)1 through GD 17 with PFOA (ammonium salt) prepared fresh each day in deionized water.  The presence of a sperm plug was considered GD 0.   On GD18, dams were euthanized by CO2 asphyxiation and three fetuses per litter were collected for preparation of total RNA from a portion of the liver and lung.

The arrays were washed and stained using an Affymetrix 450 fluidics station as recommended by the manufacturer, and scanned on an Affymetrix Model 3000 scanner.

Probe set data were summarized, background adjusted, and quantile normalized using Robust Multichip Average methodology (Irizarry et al., 2003) as provided by RMA Express (version 0.4).

Collected tissue was immediately homogenized in TRI reagent and processed on the same day through alcohol precipitation according to the manufacturer’s directions. RNA pellets were then washed in cold 80% ethanol and stored at -80?C until further use.  Following resuspension in nuclease-free water, the RNA was quantified and evaluated for purity (260nm/280nm ratio) using a NanoDrop ND-1000 spectrophotometer. 100 ug of each sample was then further purified using RNeasy spin columns according to the manufacturer’s directions. Approximately 250 ng of each sample was evaluated for quality using an Agilent 2100 Bioanalyzer.  RNA samples were used only if they were found to have an RNA Integrity Number of at least 8.0.

Following fragmentation, samples were hybridized overnight at 45C according to the protocols recommended by the manufacturer in an Affymetrix Model 640 GeneChip hybridization oven

Biotin-labeled cRNA was produced from 2 ug total RNA using an Affymetrix “one-way” labeling kit (cat# 900493).

Fetal lung gene expression data from full term pups exposed to PFOA throughout gestation.

Pooled litter samples were collected 24 hrs after the final compound dose.

Collected tissue was immediately homogenized in TRI reagent and processed on the same day through alcohol precipitation according to the manufacturerÆs directions. RNA pellets were then washed in cold 80% ethanol and stored at -80?C until further use.  Following resuspension in nuclease-free water, the RNA was quantified and evaluated for purity (260nm/280nm ratio) using a NanoDrop ND-1000 spectrophotometer. 100 ug of each sample was then further purified using RNeasy spin columns according to the manufacturerÆs directions. Approximately 250 ng of each sample was evaluated for quality using an Agilent 2100 Bioanalyzer.  RNA samples were used only if they were found to have an RNA Integrity Number of at least 8.0.

Biotin-labeled cRNA was produced from 2 ug total RNA using an Affymetrix ôone-wayö labeling kit (cat# 900493).

Fetal liver gene expression data from full term pups exposed to PFOA throughout gestation.

primary unilateral non-metastatic postmenopausal ERα-positive breast tumor;woman;70 years

GeneChips were scanned using the Affymetrix Gene Titan instrument  with AGCC 3.0 software.

The data were analysed using Bioconductor package 'oligo' under R-2.14.0. Background correction, normalization and probe summarization was performed with RMA.

Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HT MG-430 PM Array Plates. Plates were hybridized, washed and stained in the Affymetrix Gene Titan.

Biotinylated cRNA were prepared using the 3'IVT Express Kit (Ambion) from 100ng total RNA according to the manufacturer.

0.5mM VPA or 0.2mM NaBu were added to the cell medium in the indicated samples for 16 hrs.

Cells were grown on mitomycin-C-treated primary embryonic fibroblasts, with ES cell medium with 15% FBS and leukemia inhibitory factor.

GeneChip Scanner 3000 7G according to manufacturer's instructions at the Genomics Center at the Life Sciences Institute, The Hebrew University of Jerusalem.

RMA signal intensity calculation using Affymetrix Expression Console, version 1.1.

RNeasy extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

According to manufacturer's instructions at the Genomics Center at the Life Sciences Institute, The Hebrew University of Jerusalem.

Sca+/Kit+/AA4.1+/Lin- HSC were isolated from the livers of 12.5-14.5 day old embryos.  RNA was isolated from 50,000-100,000 FACS sorted cells and subjected to two round of T7 based linear amplification using Ambion's Message Amp kit.  Two replicates were analyzed.
Keywords = HSC
Keywords = proliferation
Keywords = fetal liver

HSC (Sca+ SP) were isolated from 8-12 week C57B6 mice at various time points after treatment with 5-Fluorouracil.  RNA was isolated from 50,000-100,000 FACS sorted cells and subjected to two round of T7 based linear amplification using Ambion's Message Amp kit.  Two replicates from each time point were analyzed.
Keywords = 5-FU

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual. 2001. Affymetrix).

Quantile normalization and RMA (using GeneTraffic Uno version 3.2-11)

Expression profiles generated from the white portion of the gastrocnemicus muscle from AMPK gamma3 mutant (R225Q) transgenic mice

C57BL/6;AMPK gamma3 mutant (R225Q) transgenic;F5;male;white portion of the gastrocnemius muscle;fasted

Expression profiles generated from the white portion of the gastrocnemicus muscle from wild type littermates to AMPK gamma3 mutant (R225Q) transgenic mice

C57BL/6;wild type;F5;male;white portion of the gastrocnemius muscle;fasted

bone marrow;CD34+ hematopoietic stem cells (HSC);myelodysplastic syndromes (MDS);refractory anemia with excess blasts 1 (RAEB1);normal

THP-1 cell line infected with GSK3B Construct 1 shRNA, biological rep2
Sample name: THP1_GSK3B_1-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B08_596590.CEL

THP-1 cell line infected with GSK3B Construct 1 shRNA, biological rep1
Sample name: THP1_GSK3B_1-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B03_596576.CEL

HL-60 cell line infected with GSK3A Construct 6 shRNA, biological rep2
Sample name: HL60_GSK3A_6-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A11_596684.CEL

bone marrow;CD34+ hematopoietic stem cells (HSC);myelodysplastic syndromes (MDS);refractory anemia with excess blasts 1 (RAEB1);trisomy8

bone marrow;CD34+ hematopoietic stem cells (HSC);myelodysplastic syndromes (MDS);refractory anemia with excess blasts 1 (RAEB1);del5q plus other

bone marrow;CD34+ hematopoietic stem cells (HSC);myelodysplastic syndromes (MDS);refractory anemia with excess blasts 2 (RAEB2);other

bone marrow;CD34+ hematopoietic stem cells (HSC);myelodysplastic syndromes (MDS);refractory anemia with excess blasts 2 (RAEB2);del5q plus other

Each group of mice (n=4 for wild type mice analysis and n=3 for CAR decficient mice analysis) was fed Lieber's isocaloric diet (Oriental yeast, Japan) containing water, containing ethanol, containing ethanol and ellagic acid (Fluka Biochemika, Switzerland), or containing ethanol and trans-resveratrol (Sigma, USA) (Supplementary Table 1) for one week at 10:00 ad libitum. Then, the mice were fed each diet at 12 g / day for four weeks (Supplementary Fig. 1A). The approximate intake of each polyphenol was 50 mg / kg body weight / day. At 10:00 of the final day of the experimental period, the animals were anesthetized by diethyl ether, sacrificed by cervial fracture, and the heart blood, and the liver were collected.

Five-week-old C3H/HeN female mice (CLEA, Japan) were acclimated to the maintenance condition (25°C, 8:00-20:00 day / 20:00-8:00 night cycle and 35~40 % humidity), fed a CE-2 diet (CLEA, Japan), and given water ad libitum for one week.

The chip was washed, stained, and scanned with Affymetrix GeneChip Command Console software (Affymetrix, Japan).

The probe signals were normalized by the Factor Analysis for Robust Microarray Summarization (qFARMS) on the R 2.12. platform, and the probes were selected according to the false discovery rate (FDR) values obtained by comparisons of expression levels among the experimental groups. The selected gene sets were analyzed by the Database for Annotation, Visualization, and Integrated Discovery (DAVID; http//david.abcc.ncifcrf.gov/) for their significant representation in certain Gene Ontology (GO) terms.

Total RNA was isolated from 50 mg of mouse liver using ISOGEN (Nippon gene, Japan) and purified using an RNeasy Mini Kit (Qiagen, USA). The quality of the purified RNA was examined by the Agilent RNA 6000 Nano Assay protocol (Agilent technologies, Japan) and reverse-transcribed into cDNA using a One-Cycle cDNA Synthesis Kit (Affymetrix, Japan).

anti-sense RNA probe was fragmented, and hybridized with GeneChip® Mouse Genome 430 2.0 Array (Affymetrix, Japan) for 16 hr.

A biotin-labeled anti-sense RNA probe was synthesized from cDNA using a GeneChip® 3' IVT Express Kit (Affymetrix, Japan),

The generation of Smad3-/- mice have been described in Yang, X., et al. Targeted disruption of SMAD3 results in impaired mucosal immunity and diminished T cell responsiveness to TGF-beta. Embo J 18, 1280-1291 (1999). Mice were fed with high fat diet (55% high fat diet) and antibodies (IgG and Anti-TGF-beta) were injected through intra-peritoneal route three times in a week for 8 weeks.

All animal studies were approved by the NIDDK/NIH Animal Care and Use Committee.

Smad3-/-;mixed strains of C57BL/6 and NIH Black Swiss females (Taconic);high fat diet

Smad3-/-;mixed strains of C57BL/6 and NIH Black Swiss females (Taconic);regular diet

Cells were transfected with either scrambled control or MLL2 siRNA (Ambion) by reverse transcription using RNAi Max (Life Technologies). 24 hours post-transfection medium was changed to DermaLife containing 1.8mM Calcium.

NHEK cells were grown in DermaLife medium (LifeLine Cell Technologies) at 37C, 5%CO2

Arrays were scanned using GeneChip Scanner 3000 7G and Command Console Software v. 3.2.3 to produce .CEL intensity files.

The probe cell intensity files (*.CEL) were analyzed in Affymetrix Expression Console software v1.1.1 using the PLIER algorithm to generate probe level summarization files (*.CHP).  The settings used were algorithm-PLIER v2.0; quantification scale-Linear; quantification type-signal and detection p-value; background-PM-GCBG; normalization method-sketch-quantile.

Isolated total RNA samples were processed as recommended by Affymetrix, Inc.  (Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay Manual, Affymetrix, Inc., Santa Clara, CA).  In brief, total RNA was initially isolated using TRIzol Reagent (Gibco BRL Life Technologies, Rockville, MD), and then put through an RNeasy spin column (Qiagen, Chatsworth, CA) for further clean up.  Eluted total RNAs were quantified by NanoDrop (ThermoScientific, Wilmington, DE) and the concentrations of sample aliquots were adjusted to 100ng/ul.  Total RNA samples were assessed for quality prior to performing target preparation/processing steps by loading approximately 25-250ng of each sample onto a RNA 6000 Nano LabChip and evaluated on an Agilent Biolanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

2ug of the labeled, fragmented single-stranded cDNA is hybridized at 45oC with rotation for 17 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix GeneChip 1.0ST array.  The GeneChip arrays were washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 450 (Fluidics protocol FS450_007).

The Ambion WT expression kit (Life Technologies, Carlsbad, CA) was used to prepare RNA samples for whole transcriptome microarray analysis.  Briefly, random hexamers that are tagged with a T7 promoter are used in first strand synthesis of cDNA.   Then using the T7 promoter, second strand synthesis is performed and the double stranded cDNA is subsequently used as a template in an in vitro transcription reaction to generate many copies of antisense cRNA.  10ug of antisense cRNA is input into a second cycle cDNA reaction using reverse transcriptase and random hexamers to produce single stranded DNA in the sense orientation.  The single-stranded DNA is fragmented to an average length of 70 bases and then labeled using a recombinant terminal deoxynucleotidyl transferase (TdT) and an Affymetrix proprietary DNA labeling reagent that is covalently linked to biotin.

Normal Human Epidermal Keratinocytes (NHEK);scrambled siRNA (control)

The arrays were scanned by a GeneArray Scanner and patterns of hybridization detected as light emitted from the fluorescent reporter groups incorporated into the target and hybridized to oligonucleotide probes.

The data were analyzed with Agilent Gene Spring GX 7.3 version using Affymetrix default analysis settings and GC-RMA as normalization method.

RNA extraction was performed as Affymetrix GeneChip expression technical manual (Affymetrix, Inc., Santa Clara, CA). Briefly, total RNA samples were extracted, followed by measurement of the A2260/a280 ratio with at least 1.8 for pure RNA. Quality of the RNA was checked by an Agilent 2100 Bioanalyzer.  The Bioanalyzer gel profile exhibited a 28S band that is 2 times more intense than 18S ribosomal RNA. The quality of RNA was assessed by agarose gel electrophoresis.

The targets for Affymetrix DNA microarray analysis were prepared according to the manufacturer’s instructions. Biotin-labeled cRNA, produced by in vitro transcription, was fragmented and hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays at 45°C for 16 hr and then washed and stained using the GeneChip Fluidics.

Lableing was performed according to Affymetrix Gene Chip technical manual

5 ug total RNA,  was labeled with Cy3 and hybridized to the microRNA microarray.  Cy3 median intensities were background subtracted, filtered to remove genes that did not have cy3> 2x background.  Log cy3 values were median center normalized and are represented by the ref_value.
Keywords = microRNA, miRNA

NIH-3T3 cells transduced with either EBF1-, PPARg2- or empty vector were stimulated with hormones to initiate adipocyte differentiation. RNA extraction was done using TriZol at d0, d2, d4 and d10 after stimulation. Samples were handled according to standard affymetrix protocols. 7 independent stimulation experiments were analysed.
Keywords = Adipogenesis, early B-cell factor 1 (EBF1), commitment, differentiation, NIH-3T3, pparg

Log2 transformation and Quantile normalization uzing the R Lumi package.
The normalized data file contains log2 transformed and quantile normalized data for all probes that fulfilled the robust expression criteria (i.e detection pvalue<0.05 for at least half of the samples). Expression data for cortex and cerebellum are listed separately as the two datasets were normalized separately and contain different number of probes that fulfilled the expression criteria.

Total RNA was isolated using the RNeasy Mini kit  according to the protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

After overnight seeding, cells were treated with or without doxycycline (1 μg/ml) for 48 hr before RNA extraction.

RT112 cells expressing doxycline-inducible shRNAs targeting FGFR3 or EGFP were grown in 1%FBS medium with or without doxycycline (1 μg/ml) for 48 hr.

HGU 133 plus 2.0 arrays were scanned according to the Affymetrix protocol

Affymetrix HGU 133 plus 2.0 intensity signal CEL files were processed using the RMA algorithm as implemented in the 'affy' package from Bioconductor.

Total cellular RNA was prepared with a RNeasy Plus kit (Qiagen) and subject to DNAse I digestion.

HGU 133 plus 2.0 arrays were hybridized according to the Affymetrix protocol

skeletal muscle;insulin resistant;untreated;0.85;180;78;1650;78;24.6;57;1918.8

Affymetrix Microarray Suite version 5.0, dchip PM-MM Difference Model

T47D cells were grown in DMEM medium (Gibco Life Technologies, Paisley, UK) supplemented with 10% v/v heat-inactivated fetal calf serum, sodium pyruvate and a mixture of antibiotics (penicillin and streptomycin) at 37 °C and 5% CO2. Cells were then infected with lentiviral particles carrying the indicated shRNA particles at MOI=5 in the presence of 8mg/ml of polybrene. Cells were thereafter selected using puromycin and their RNA was extracted.

Vldlr-/- mice and wild type (WT) B6129SF2/J mice received intranasal challenges of house dust mite (25 ucg) or saline, both in a volume of 10 ul, five days a week for 6 weeks.

Gene-level intensity values for each of the chips were collected using Affymetrix Expression Console (EC) Software (Affymetrix, Santa Clara, CA).  The RMA-sketch workflow was applied for raw data preprocessing, which included global background correction, quantile normalization and median polish summarization.

Biotin-labeled sense targets were prepared from samples of total lung RNA using the Affymetrix Whole-Transcript (WT) Sense Target Labeling Protocol without rRNA reduction.  Double-stranded cDNA templates were synthesized from 50 ng of total RNA using random hexamers coupled with a T7 promoter sequence and amplified by in vitro transcription (IVT) with T7 RNA polymerase to produce multiple copies of cRNAs.  Random hexamers were utilized to prepare sense strand cDNA.

Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

10 µg of sense strand cDNA was fragmented, labeled with biotin using terminal deoxynucleotidyl transferase.

Mice underwent 85% liver resection and were sacrificed 2 hours later.

Mice were maintained at all times on a 12-hour light-dark cycle in a pathogen-free environment with free access to rodent chow and water.

Data was normalized using the GCRMA algorithm (version 2.16) as implemented in Bioconductor (version 2.40) / R (version 2.16).

RNA was isolated from ~1000 isolated glomeruli per mouse using the RNaqueous kit (Ambion, Austin, TX) including a DNase step. Total RNA concentration was assessed by NanoDrop Spectrophotometer (NanoDrop Technologies) and quality was assessed on a 2100 Bioanalyzer system (Agilent Technologies) using the Agilent RNA 6000 Nano kit. All of our samples had an RNA integrity score >8, and there was no indication of RNA degradation or contamination with DNA.

10 μg of RNA dissolved in 300 μL of buffer was hybridized to Mouse Genome 430. 2.0 GeneChips (Affymetrix). All samples were prepared with the standard protocol recommended by the manufacturer.

RNA was amplified, biotin labeled and fragmented using the Gene Chip 3’IVT Express Kit (Affymetrix). Yield of fragmented samples was tested by Nanodrop and RNA size was assessed by Bioanalyzer using the Agilent RNA 6000 Pico kit.

B2RKOS1407

Gene expression of livers from 10-12 week-old mice, sacrificed 2 hours after liver resection.

Ager/Rage null C57BL/6 mice, liver, 10-12 weeks old, sacrificed 2 hours after 85% liver resection

Total RNA was extracted using the GenElute Mammalian Total RNA Purification Kit (Sigma-Aldrich)

Lungs of the hyperresponsive AJ strain of mice 24 hours post aspiration with PBS

C1MKOS312

Myd88 null C57BL/6 mice, liver, 10-12 weeks old, sacrificed 2 hours after 85% liver resection

The data were normalised using standard normalization procedures recommended for the GeneSpring GX version 11.5.1 software for Illumina single-color array. Probes were filtered based on their flag values using P (present) and M (marginal) flags using standard GeneSpring GX software settings for Illumina single color arrays.

Biotinylated cRNA were prepared with the Ambion Total Prep RNA amplification kit (Cat. No. IL1791) for Illumina arrays.

patient with AAA undergoing open surgery to treat AAA;non-aneurysmal AAA neck tissue

Cyclophosphamide-treated spleen 1 day - Biological Replicate 4 - Technical Replicate 2

Biological replicate 4 of 4. Technical Replicate 2 of 2.Cyclophosphamide-treated splenocytes, day1

Cyclophosphamide-treated spleen 1 day - Biological Replicate 4 - Technical Replicate 1

Biological replicate 4 of 4. Technical Replicate 1 of 2. Cyclophosphamide-treated splenocytes, day1

Cyclophosphamide-treated spleen 1 day - Biological Replicate 3 - Technical Replicate 2

Biological replicate 3 of 4. Technical Replicate 2 of 2. Cyclophosphamide-treated splenocytes, day1

Cyclophosphamide-treated spleen 1 day - Biological Replicate 3 - Technical Replicate 1

Biological replicate 3 of 4. Technical Replicate 1 of 2. Cyclophosphamide-treated splenocytes, day1

Cyclophosphamide-treated spleen 1 day - Biological Replicate 2 - Technical Replicate 2

Biological replicate 2 of 4. Technical Replicate 2 of 2. Cyclophosphamide-treated splenocytes, day1

Cyclophosphamide-treated spleen 1 day - Biological Replicate 2 - Technical Replicate 1

Biological replicate 2 of 4. Technical Replicate 1 of 2. Cyclophosphamide-treated splenocytes, day1

Cyclophosphamide-treated spleen 1 day - Biological Replicate 1 - Technical Replicate 2

Biological replicate 1 of 4. Technical Replicate 2 of 2. Cyclophosphamide-treated splenocytes, day1

Cyclophosphamide-treated spleen 1 day - Biological Replicate 1 - Technical Replicate 1

Biological replicate 1 of 4. Technical Replicate 1 of 2. Cyclophosphamide-treated splenocytes, day1

Cyclophosphamide-treated spleen 2 days - Biological Replicate 1 - Technical Replicate 2

Biological replicate 1 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated splenocytes, day 2

Cyclophosphamide-treated spleen 2 days - Biological Replicate 1 - Technical Replicate 1

Biological replicate 1 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated splenocytes, day 2

HEK293 cells were  transfected 72h with siRNA BAHD1 or siRNA control (Ambion) using lipofectamine RNAi max (Invitrogen)

HEK293 cells(ATCC #CRL 1573) were grown in DMEM supplemented with Glutamax (Gibco) and 10% FCS

CEL files were generated using GCOS software and preprocessed using GC-RMA method

Total RNA from cells  was extracted and purified by using the RNeasy kit according to the manufacturer's instructions.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133Plus2.0  Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

RT on 5 μg of total RNA using oligo(dT) primers and « in vitro » transcription of the cDNA in presence of biotin were performed by using a GeneChip Amplification One-Cycle Target Labeling kit according to Affymetrix (Santa Clara, CA) standard protocols  Labeling kit according to Affymetrix (Santa Clara, CA) standard protocols.

Gene expression data from HEK293 cells transfected with control  siRNA

15 ACBP-/- and 15 +/+ mice were divided into 6 groups with 5 individuals in each. Thus, each sample is made from a pool of equal amounts of RNA from 5 ACBP-/- or +/+ individuals, respectively.

Fed state 21 days old mice were taken away from their mother at 8-11am, euthanized and dissected. Livers were snap frozen in liquid N2.

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was cleaned up on Qiagen RNeasy columns to remove traces of organic solvents.

After hybridization the hybridization mixture is removed and the GeneChips® are washed, stained with phycoerythrin-labeled Streptavidin, washed, incubated with biotinylated anti-streptavidin, and then restained with phycoerythrin-labeled Streptavidin to amplify the signals; these steps are carried out using the Affymetrix Fluidics Station.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA isolated from mouse liver

Injured Rat Rat retinas from male Sprague-Dawley. Injuries were induced by a single scrape of retina.  Retinas from two animas were pooled.
Keywords = Retina
Keywords = Injury
Keywords = Gliosis
Lot batch = EEG093

Lot batch = EEG012

Lot batch = EEG077

Lot batch = EEG018

Lot batch = EEG019

Treated with 10uM Motexafin gadolinium for 4 hrs -- replicate #3

Treated with 10uM Motexafin gadolinium and 25uM Zinc for 4 hrs -- replicate #1

Treated with 10uM Motexafin gadolinium for 4 hrs -- replicate #1

Treated with 10uM Motexafin gadolinium for 4 hrs -- replicate #2

in vitro Treatment: siHSF1_#2 (Sense 5’-rArCrArGrCUUrCrCrArCrGUrGUUrCrGrGTT-3’ Antisense 5’-UrCrGrArArCrArCrGUrGrGrArArGrCUrGUTT-3’), Treatment Repeat: 1, Units of Treatment Repeat: dose, Treatment Duration: 52, Units of Duration: hours, Treatment Time: -48, Units of Treatment Time: hrs, Vehicle for Chemical: Lipofectamine 2000, Amount of Vehicle: 0.44, Route of Exposure: transfection, Units of Amount of Vehicle: ul, Dose or Concentration: 3.3, Units of Dose or Concentration: nM
Treatment_2: in vitro Treatment: Heat, 43ºC, Treatment Repeat: 1, Units of Treatment Repeat: exposure, Treatment Duration: 1.5, Units of Duration: hours, Treatment Time: 0, Units of Treatment Time: hrs, Route of Exposure: convection, Dose or Concentration: 43, Units of Dose or Concentration: degrees Celcius

Growth Media: DMEM_10%FBS_P/S
Amount of Media: 5
Units of Media: ml
Growth Conditions: 37 C 5% CO2

01-04-05 TP11_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2: These samples were previously hybridized on HG-U133A version 1 chips.  This experiment repeats these samples on HG-133A version 2 chips.  HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

Sample Type: Cells, Cell Line: HeLa, ATCC Number: CCL-2, Number of Cells Seeded: 2.20E+05, Cell Type: cervical carcinoma, Separation Type: Trypsin, Harvest Time Point: 4, Units of Harvest Time Point: hr

01-04-05 TP10_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2: These samples were previously hybridized on HG-U133A version 1 chips.  This experiment repeats these samples on HG-133A version 2 chips.  HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

in vitro Treatment: siHSF1_#1 (Sense 5’-rGUrCrGUrCrArArCrArArGrCUrCrAUUrATT-3' Antisense 5’rGrArAUrGrArGrCUUrGUUrGrArCrGrArCTT-3’), Treatment Repeat: 1, Units of Treatment Repeat: dose, Treatment Duration: 48, Units of Duration: hours, Treatment Time: -48, Units of Treatment Time: hrs, Vehicle for Chemical: Lipofectamine 2000, Amount of Vehicle: 0.44, Route of Exposure: transfection, Units of Amount of Vehicle: ul, Dose or Concentration: 3.3, Units of Dose or Concentration: nM
Treatment_2: in vitro Treatment: Heat, 43ºC, Treatment Repeat: 1, Units of Treatment Repeat: exposure, Treatment Duration: 0, Units of Duration: hours, Treatment Time: 0, Units of Treatment Time: hrs, Route of Exposure: convection, Dose or Concentration: 43, Units of Dose or Concentration: degrees Celcius

06_21_04 TP-3: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

Sample Type: Cells, Cell Line: HeLa, ATCC Number: CCL-2, Number of Cells Seeded: 2.20E+05, Cell Type: cervical carcinoma, Separation Type: Trypsin, Harvest Time Point: 0, Units of Harvest Time Point: hr

06_21_04 TP-2: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

in vitro Treatment: siHSF1_#1 (Sense 5’-rGUrCrGUrCrArArCrArArGrCUrCrAUUrATT-3' Antisense 5’rGrArAUrGrArGrCUUrGUUrGrArCrGrArCTT-3’), Treatment Repeat: 1, Units of Treatment Repeat: dose, Treatment Duration: 48.5, Units of Duration: hours, Treatment Time: -48, Units of Treatment Time: hrs, Vehicle for Chemical: Lipofectamine 2000, Amount of Vehicle: 0.44, Route of Exposure: transfection, Units of Amount of Vehicle: ul, Dose or Concentration: 3.3, Units of Dose or Concentration: nM
Treatment_2: in vitro Treatment: Heat, 43ºC, Treatment Repeat: 1, Units of Treatment Repeat: exposure, Treatment Duration: 0.5, Units of Duration: hours, Treatment Time: 0, Units of Treatment Time: hrs, Route of Exposure: convection, Dose or Concentration: 43, Units of Dose or Concentration: degrees Celcius

06_21_04 TP-5: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

Sample Type: Cells, Cell Line: HeLa, ATCC Number: CCL-2, Number of Cells Seeded: 2.20E+05, Cell Type: cervical carcinoma, Separation Type: Trypsin, Harvest Time Point: 0.5, Units of Harvest Time Point: hr

06_21_04 TP-4: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

in vitro Treatment: siHSF1_#1 (Sense 5’-rGUrCrGUrCrArArCrArArGrCUrCrAUUrATT-3' Antisense 5’rGrArAUrGrArGrCUUrGUUrGrArCrGrArCTT-3’), Treatment Repeat: 1, Units of Treatment Repeat: dose, Treatment Duration: 50, Units of Duration: hours, Treatment Time: -48, Units of Treatment Time: hrs, Vehicle for Chemical: Lipofectamine 2000, Amount of Vehicle: 0.44, Route of Exposure: transfection, Units of Amount of Vehicle: ul, Dose or Concentration: 3.3, Units of Dose or Concentration: nM

06_21_04 TP-7: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

Sample Type: Cells, Cell Line: HeLa, ATCC Number: CCL-2, Number of Cells Seeded: 2.20E+05, Cell Type: cervical carcinoma, Separation Type: Trypsin, Harvest Time Point: 2, Units of Harvest Time Point: hr

06_21_04 TP-6: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

06_21_04 TP-9: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

06_21_04 TP-8: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

Mice used were B6/129 F2's, 3-5 weeks of age, with both copies of the autoimmune regulator gene (aire, GenBank #AF079536) disrupted. Thymi from five of these mice of both sexes were removed and pooled. After collagenase/dispase digestion, density gradient fractionation, and fluorescent antibody staining, cells with the phenotype CD45-, G8.8+, CDR1int and B7.1hi were FACS-sorted and total RNA was made from them. RNA was twice-amplified using a T7 polymerase-based method.

Mice used were wild type B6/129 F2's of 3-5 weeks of age. Thymi from five of these mice of both sexes were removed and pooled. After collagenase/dispase digestion, density gradient fractionation, and fluorescent antibody staining, cells with the phenotype CD45-, G8.8+, CDR1int and B7.1hi were FACS-sorted and total RNA was made from them. RNA was twice-amplified using a T7 polymerase-based method.

Mice used were wild type B6/129 F2's of 3-5 weeks of age.  Thymi from five of these mice of both sexes were removed and pooled.  After collagenase/dispase digestion, density gradient fractionation, and fluorescent antibody staining, cells with the phenotype CD45-, G8.8+, CDR1int and B7.1hi were FACS-sorted and total RNA was made from them.  RNA was twice-amplified using a T7 polymerase-based method.

Bone marrow cells were cultured in RPMI growth media containing 10% Fetal bovine serum and in the presence of GM-CSF (20 ng/ml). Cell culture medium was replenished with fresh medium every two days. On day 7 cells were used for isolation of RNA using the Trizol method.

Bone marrow cells were isolated from the femurs of mice and in vitro cultured for seven days. Cell were induced to differentiate into BMDCs using 20ng/ml of GM-CSF for seven days.

Probe level normalization and signal summarization was performed using the Robust Multi-chip Algorithm (RMA) as implemented in the Affymetrix Expression Console software version 1.1

Following fragmentation, 5 micrograms of cRNA was hybridized for 16 hr at 45C on each array. GeneChips were washed and stained in the Affymetrix GeneTitan system.

Biotinylated cRNA was prepared according to the Affymetrix 3' IVT Express protocol starting with 100 ng of total RNA (GeneChip 3’ IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix)

R1 ESCs were cultured at 37°C and 5% CO2, in ESC media consisting of Dulbecco modified eagle serum (DMEM) supplemented with 15% FBS (North Bio, Lot SF30408), 0.1 mM nonessential amino acids, 1 mM sodium pyruvate, 2 mM L-glutamine (all from Gibco), 1000 U/mL leukemia inhibitory factor (LIF) (ESGRO, from Chemicon, batch 11061065) and 100 µM b-mercaptoethanol (Sigma).  Differentiation media consisted of either ESC media without LIF, or ESC media without LIF and supplemented with 0.1 uM retinoic acid.  Selection media consisted of ESC media supplemented with 150 ug/mL G418 (Gibco).  ESCs were passaged every two days at a ratio of 1:5 by washing with PBS (Gibco), dissociating with 0.05% trypsin (Gibco) for 5 minutes at 37°C and resuspending in ESC media. Media was changed daily.

Total RNA was extracted from Pcl2 mismatch controls and one Pcl2 shRNA clone with RNeasy columns (Qiagen). RNA quality was tested using an Agilent Bioanalyzer before performing standard cDNA synthesis (Invitrogen Superscript) and in vitro transcription (IVT) (Enzo IVT kit). 10 ug of RNA was used for IVT and 15 ug of cRNA was used for hybridization (EukGEWS2v4 kit) to the Mouse Genome 430 2.0 GeneChip. Scanning was performed using the Affymetrix GeneChip Scanner 3000 and analysis done using GCOS1.4 to obtain signal-log ratios of the control to the sample. Hybridizations of three biological replicates for both the control and Pcl2 shRNA clone were performed.

R1 mouse embryonic stem cells stably transfected with Pcl2 shRNA sequence

Cells were stably expressing shRNA mismatch control sequence for comparision with Pcl2 shRNA knockdown cells.

R1 mouse embryonic stem cells stably transfected with shRNA mismatch control sequence

Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA).
More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining.
MRI-lytic-lesion sample
Keywords = multiple myeloma, osteolytic lesions, MRI, osteoblast, mesenchymal stem cell, Wnt signaling, DKK1

Cervical cancer, squamous cell carcinoma, microdissected, age 47, stage IIB, HPV 16

Cervical cancer, squamous cell carcinoma, microdissected, age 40, stage IA, HPV 45

Cervical cancer, squamous cell carcinoma, microdissected, age 58, stage IIA, HPV 16

animals were trained in the water maze. SIT = control rats stayed in cages, YOKE=swam with no platform, VIS= were trained with visible platform, HID= animals were trained in the hidden version of the paradigm

Fisher-344 male rats, 3 and 24 month old, were housed (2 per cage) in a 12:12 light-dark cycle with ad libitum access to food and water.  Behavioral testing occurred during the light phase of the cycle.

Animals were sacrificed 24 hours after the last behavioral trial by decapitation, following a lethal dose of pentobarbital (100 mg/kg), and the brains were extracted from the skull and washed with ice-cold PBS.  The brains were sectioned into 1 mm slices and placed in RNAlater (Ambion).  The brain slices were stored at -20°C until ready for further dissection and RNA isolation.  The RNAlater gave the tissue a “fixed” consistency and allowed for clear visualization of the hippocampal cellular layers.  Three main anatomical areas of the hippocampus were dissected.  Using a 300 µm micro punch (Electron Microscopy Sciences), the main cell layer of the CA1 region from each animal was dissected out and placed in tubes containing 50 µl of RNAlater.  RNA was isolated using the Qiagen RNeasy protocol (Qiagen).  The tissue was homogenized in 400 µl of RLT buffer and 1% mercaptoethanol, and treated with 200 µg/ml proteinase K for 10 minutes at 55ºC.  After RNA isolation with the Qiagen RNeasy kit we assessed the quality of the RNA using an Agilent 2100 bioanalyzer using the RNA 6000 Nanochips assay kit (Agilent Technologies).  The RNA was stored at -80°C until further use.

two rounds of RNA  amplification were performed following the Affymetrix Small Sample Target Labeling version I protocol, which consists of two cycles of cDNA synthesis.  (The detailed protocol can be obtained at the Affymetrix website: http://www.affymetrix.com/index.affx).

A HID U_B089
The first letter refers to the age of the animal (Y= young, 3month old rat; or A=aged, 24 month old rat). The second word refers to the treatment, as described in sample treatment protocol. The third descriptor, eg, B003, B refers to the region of the hippocampus (CA1 region) animal number 3. In addition, aged animals who underwent the hidden platform (HID), can either be learning impaired (I) or hidden unimpaired (U)

A HID B_B041

A HID B_B043

A YOKE_B063

A SIT_B099

A HID U_B016

A HID U_B020

A HID U_B042

Y SIT_B070

Y SIT_B074

Fresh Atypical ductal hyperplasia tissue collected from breast of a women who had no prior history of breast cancer and had not developed breast cancer in five years after diagnosis
Keywords = Homo sapiens, Atypical Ductal Hyperplasia

Whole blood was collected PAXgene tubes (PreAnalytiX, Feldbachstrasse, Switzerland), incubated at room temperature for 2 hours and stored frozen at -80 degrees celcius until extraction

Arrays were scanned on an Agilent G2565C DNA Scanner.
Images were quantified using Agilent Feature Extraction Software (version 10.5) extraction protocol GE2_105_Dec08.

R/Bioconductor package limma was used for background correction, quantile and loess normalization.

RNA was extracted using the PAXgene Blood RNA Kit following the manufacturer's instructions (PreAnalytiX, Feldbachstrasse, Switzerland). RNA quality was assessed by Agilent 2100 Bioanalyzer and all samples had RIN>7.

Total RNA was labelled and hybridized following Agilent's Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7, using the Low RNA Input Linear Amplification Kit, 2-colour, QuickAmp Lot #006043422, Hybridization Kit Lot #0006044567.

whole blood;Psoriatic arthritis;Male;2;38.0;7;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Psoriatic arthritis;Male;3;24.0;31;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

Biopsy samples were embedded in Tissue Tek OCT compound and snap-frozen in liquid nitrogen. Samples cut into 10 μm thick sections and placed on membrane-covered glass slides (PALM Membrane Slides, PALM Microlaser Technologies, Bernried, Germany). Laser capture microdissection was then carried out using a PALM® microlaser system (PALM GmbH, Bernried, Germany). Epithelium only was used in further analysis.

Standard Illumina scanning protocol using the iScan System: iScan Reader, iScan PC, iScan Control Software

GenomeStudio software was used to export probe summary profiles (probe profile and control probe profile). Intensities was exported from GenomeStudio without background correction or normalization. Then the Illumina data was background corrected and normalized using the neqc functions in LIMMA (linear models and differential expression for microarray data) package which is available in R through Bioconductor.

Standard Illumina hybridization protocol: Illumina whole-genome gene expression direct hybridization assay

Biotinylated cRNA were prepared with the TargetAmp Nano Labeling Kit for Illumina Expression BeadChip (epicentre)

whole blood;Psoriatic arthritis;Female;4;48.0;19;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Psoriatic arthritis;Female;3;37.0;11;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Psoriatic arthritis;Male;3;22.0;23;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Psoriatic arthritis;Male;3;13.0;31;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Psoriatic arthritis;Male;3;33.0;26;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Psoriatic arthritis;Male;2;18.0;29;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

Gene expression data from DN-MAML transduced CUTLL1 cells treated with compound E for 3days and washout compund E for 4 hours

A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factors can be identified. This entry corresponds to the RNA isolated from tet-induced INS-1 cell line #1a containing hepatocyte nuclear factor-1b (HNF1b).
Keywords = INS-1
Keywords = beta-cell
Keywords = HNF1b
Keywords = tetracycline
Keywords = FRT

Experiments were performed in 2-3 month old animals and in all cases the mice used as control were littermates of the mutant mice. Standard housing consisted of 30x15x11 cm clear cages occupied by up to 5 mice. The environmental enrichment boxes were large white plexiglass boxes (>1m2) and were occupied by a maximum of 20 mice. We used natural materials, plastic tubing, running wheels and toys to create an enriched environment whose configuration was modified every 48h shortly before the start of the dark cycle. The samples were obtained at least 16 h afther the last modification in the enviromental enrichment box to prevent any interference between the response to novelty and to environmental enrichment. The brains were immediately removed, and hippocampi rapidly dissected and placed in RNAlater solution (Qiagen, Venlo, The Netherlands) until total RNA extraction.

CBP deficient heterozygous mice were maintained in a mixed background (F2 of C57BL/6J and DBA) (Alarcon et al., 2004). Mice were group-housed in single-sex cages on a light:dark cycle (12/12 h) with food and water available ad limitum. The wild type mice used as control were, in all cases, littermates of the mutant mice.

GeneSpring GX software (Agilent Technologies Inc) was used. RMA algorithm was uset to background correction, data normalization and probe sumarization.

Total RNA was extracted separately from individual hippocampi using Trizol Reagent (Invitrogen, Carlsbad, CA, USA) per manufacturers instructions followed by DNaseI treatment (Qiagen, Valencia, CA, USA) and a clean-up step using RNeasy RNA purification columns (Qiagen, Valencia, CA, USA). Equal amounts of total RNA from four animals were pooled, processed, and hybridized to GeneChIP Mouse Gene 1.0 ST Arrays (Affymetrix, Santa Clara, CA) according to the manufacture's protocol. Three to five independent biological replicates were prepared for each genotype and condtition (wild-type and crebbp deficient mice (cbp+/-; standar housing and environmental enrichment). GeneChIP® Mouse Gene 1.0 ST Arrays were hybridized, stained, washed and screened for quality according to the manufacturer's protocol. Microarray data were processed, normalized and statistically analyzed using GeneSpring GX (Agilent Technologies, Santa Clara, CA).

Pseudomonas aeruginosa (PA51673) was exposed to cells at a MOI of 5 for 1 to 24 h

Primary mouse airway epithelial cells were cultured at an air liquid interface

Chips were treated with phycoerythyrin-conjugated streptavidin and scnned for hybridized targets with the GeneChip Scanner 3000

The data were inspected visually and with the Affymetrix quality control metrics in the GeneChip Operating Software. Two replicates were discarded from futher analysis (WT-24h-rep1 and M10-24h-rep2) due to high background and high scale factor. Cel files were extracted using GCOS and normalized in Bioconductor in the R environment. All samples were normalized using RMA and mean centered by genotype using the RMA function in the Affymetrix package and the scale function of the base R environment.

Qiagen Rneasy total RNA extraction was performed according to manufacturer's specifications

cRNA were hybridized overnight to Mouse 430 2.0 Arrays then washed in the Affymetrix Fluidics Station.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2-8 ug total RNA by the Center for Array Technologies at the University of Washington (Seattle, WA)

Gene expression data for airway epithlium exposed to Pseudomonas aeruginosa

C57BL/6, Tissue: Airway Epithlium, Culture: Organotypic Air Liquid Interface

Standard Affymetrix protocols (see GeneChip Expression Analysis Technical Manual)

Standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocal can be found manufacturer's web site.

C57Bl6;4 weeks;BCR-ABL1 transformed pre-B cells;BCR-ABL1-driven ALL;Wild-type

F2 of C57BL/6J and DBA;female;cbp+/-  (CBP deficient, heterozygous);3 months;hippocampus

pRTS-GFP;human Burkitt lymphoma;ACC 603;established from the ascitic fluid of a 3-year-old boy with American-type Burkitt lymphoma in 1972; cells were described to be EBV-negative but EBV infectible, to carry the (8;14) translocation and p53 mutations

A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factors can be identified. This entry corresponds to the RNA isolated from tet-induced INS-1 cell line #2b containing hepatocyte nuclear factor-1b (HNF1b).

Mutant mice were given 2mg 4-hydroxytamoxifen (4-OHT) at 5 weeks of age for 3 days

Mice were housed in pathogen-free animal facilities  at Harvard Medical School and   Dana-Farber Cancer Institute

Raw expression values were normalized using Robust Multiarray Averaging (RMA) using quantile normalization

Total RNA was extracted using Trizol (Invitrogen) followed by RNA cleanup (QIAGEN)

Following fragmentation, cRNA were hybridized on Affymetrix MoGene-1_0-st-v1. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

control;Brain;Ventral midbrain;Postmortem;arteriosclerotic cardiovascular disease

Trypsin-treated cells were re-suspended in DME/F12 medium supplemented with 2% horse serum, insulin, cholera toxin and hydrocortisone. Eight-chambered plates (BD Biosciences) were coated with 35 µl MatrigelTM per well. The cells were mixed 1:1 with assay medium containing MatrigelTM (4%) and EGF (20 ng/ml), and 400 µl added to each chamber.

Data was normalized by RMA method using Command Console CHP file version 1.

Cells were lysed and RNA isolated using a Versagene kit (Gentra Systems, Minneapolis).

control;Brain;Ventral midbrain;Postmortem;multiple gunshot wounds

Full description found in Eliezer Masiliah, Eleanor S. Roberts, Dianne Langford, Ian Everall, Leslie Crews, Anthony Adame, Edward Rockenstein, and Howard S. Fox.  (2004) Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis.

Total RNA from 20 embryos was extracted and purified using an Picopure kit (Arcturus).

total RNA from 20 embryos was processed to produce biotinylated cRNA targets using Affy Small Sample Target Labeling Assay Version II.

Affymetrix GCOS 1.2 with default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

Peripheral blood from individuals with systemic lupus erythematosus

Mice were placed in individual stainless-steel wire cages within a Hazelton 1000 chamber (Lab Products, Maywood, NJ) equipped with a charcoal and high-efficiency particulate air–filtered air supply.  Mice were exposed to 0.3 ppm O3 or filtered air for 24, 48 or 72 hr (23.5 hr/day) as described previously (Cho et al, 2007).

We provided mice with water and pelleted open-formula rodent diet NIH-31 (Zeigler Brothers, Gardners, PA) ad libitum.  All experimental procedures were conducted in accordance with approved National Institutes of Health Humane Care and Use of Laboratory Animals guidelines and the American Physiological Society’s “Guiding Principles in the Care and Use of Animals.”  Animals were treated humanely and with regard for alleviation of suffering.

Left lobes of mouse lung tissue were harvested, flash frozen in liquid nitrogen, and stored at -80oC.  For RNA extraction, the lung tissue was homogenized in 2ml Trizol (Invitrogen, Calsbad, CA) with a Tekmar Tissumizer and saw-tooth generator.  One ml of homogenate was subsequently processed according to the manufacturer’s (Invitrogen) protocol with the following minor modifications.  Two µl of 5 mg/ml glycogen was used as a carrier for the isopropanol precipitation, duration of the isopropanol precipitation was increased to overnight, and all centrifugation times were increased to 15 minutes.  RNA pellets were resuspended in nuclease-free water.  RNA quality was tested using a Beckman DU680 spectrophotometer, and quality assessment was determined by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100.  A Qiagen RNeasy total RNA cleanup protocol was subsequently performed followed by re-quantitation by spectophotometry.

A fragmentation buffer (250mM Tris acetate pH 8.1, 150 mM MgOAc, 500mM KOAc) was used to fragment 15µg of cRNA.  The fragmented cRNA was then hybridized to GeneChips (Affymetrix Mouse Genome 430A 2.0).

Double stranded cDNA was synthesized from 4µg of total RNA using the GeneChip Expression 3’ amplification reagents one-cycle cDNA synthesis kit (Affymetrix).  The resultant double-stranded cDNA was column-purified using the GeneChip Sample Cleanup Module.  Biotinylated cRNA was synthesized from the double-stranded cDNA by in vitro transcription (IVT) using the GeneChip Expression 3’ amplification reagents for IVT labeling (Affymetrix), and was subsequently purified by column purification with the GeneChip Sample Cleanup Module (Affymetrix), and quantified.  Quality of biotinylated cRNAs was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100.

Gene expression data from left lung samples from B6.129P2-Il10tmlCgn/J male mice exposed to 0 ppm O3  for 48 hours

B6.129P2-Il10tmlCgn/J;Il10-/-;6-8 weeks;Male;Left lung;Jackson Labs, Bar Harbor, ME;48 hours;air;0 ppm O3

Gene expression data from left lung samples from C57BL/6 male mice exposed to 0.3 ppm O3  for 48 hours

C57BL/6;Il10+/+;6-8 weeks;Male;Left lung;Jackson Labs, Bar Harbor, ME;48 hours;ozone;0.3 ppm O3;10028-15-6

Gene expression data from left lung samples from C57BL/6 male mice exposed to 0 ppm O3  for 48 hours

C57BL/6;Il10+/+;6-8 weeks;Male;Left lung;Jackson Labs, Bar Harbor, ME;48 hours;air;0 ppm O3

Whole blood was collected into sodium heparin tubes.  PBMCs were separated and placed in Trizol within 4 hrs of blood collection and stored frozen at -80 degree celsius.

Expression values were derived using RMA preprocessing methods.  Each probe set was then normalized to the median expression of the control samples.

RNA extraction using Trizol reagent was performed according to the manufacturer protocol.

Labeled cDNA was hybridized to Affymetrix U133plus2.0 Gene Chips

Biotio-labeled cDNA was generated using the Nugen Ovation Biotin RNA Amplification and Labeling System

Gene expression data from ICR MEF infected  with pMX-Oct4 retrovirus

The cells were treated by the drug or by the solvent control, tripsinized and lysed in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

Approximately 8 ?g of total RNA was processed to produce biotinylated cRNA targets.

male;CABG patient, atrial tissue, sevoflurane anesthesia, after CABG surgery

training: mice were put into a 30 x 50, 20 cm deep container filled with warm (35 C) water equipped with a floating rotating wheel. Swimming duration was continously increased from 5 minutes to 90 minutes daily (6 times per week) swimming. Mice were stimulated to swim as sonn as they began floating to maximize activity in the water.

15 ug of each cRNA sample was hybridized for 16 hours at 45°C to Affymetrix GeneChip arrays. Following the hybridization arrays were washed and stained with streptavidin-phycoerythrin using a fluidics station in accordance with the Affymetrix protocol.

The amplification and labeling of the RNA samples were carried out according to the manufacturer's instructions (Affymetrix, Santa Clara, CA). Briefly, total RNA was quantified by UV-spectroscopy and its quality was checked by analysis on a LabChip (BioAnalyzer, AGILENT Technologies, Santa Clara, CA). In the presence of an oligo(dT)24 primer containing a T7 RNA polymerase promoter (TIBMOL Biol, Berlin, Germany) one to three micrograms of total RNA were used for the synthesis of double-stranded cDNA (SuperScript transcriptase, Life Technologies, Inc., Carlsbad, CA). Labeled complementary RNA (cRNA) was prepared from double-stranded cDNA by in vitro transcription using the GeneChip RNA transcript labeling kit (Affymetrix, Santa Clara, CA). After cleanup (Qiagen, Hilden, Germany), the biotin-labeled cRNA was fragmented by alkaline treatment [40 mmol/L Tris-acetate (pH 8.2), 100 mmol//L potassium acetate, and 50 mmol//L magnesium acetate] at 94°C for 35 minutes.

trained plakoglobin (+/-) animal for the identification of genotype specific training induced gene expression response

male;CABG patient, atrial tissue, propofol anesthesia, after CABG surgery

trained wt animal for the identification of genotype specific training induced gene expression response

cultured in RPMI 1640 with 10% FBS as described previously (Liu and Tseng, 1979), infected with Jag1 nonreplicative retrovirus

cultured in RPMI 1640 with 10% FBS as described previously (Liu and Tseng, 1979), harvested for mRNAs analysis on day-3 post-infection

Standard Affymetrix protocol performed at SUNY DNA Microarray Facility (Stony Brook University, NY),

MAS 5 protocol performed at SUNY DNA Microarray Facility (Stony Brook University, NY),

DNA-free total RNA was isolated from cell cultures (day-3 post-infection) using RNAqueous-4PCR Kit (Ambion)

Standard Affymetrix protocol performed at SUNY DNA Microarray Facility (Stony Brook University, NY)

endometrial stromal cell - Jag1 retrovirus infected3, 3 days post infection

cultured in RPMI 1640 with 10% FBS as described previously (Liu and Tseng, 1979), infected with control nonreplicative retrovirus (vector)

endometrial stromal cell - control/vector1, 3 days post infection

For gene expression profiling studies three clones of each line (see above), PFR3 or PFR3K650E cells, were plated in 150-mm plates and the following day induced for 24 hr.  Total RNA was isolated separately for each clone using Trizol Reagent according to the manufacturer (Invitrogen).  RNA was quantitated spectrophotometrically and integrity tested by capillary electrophoresis (Agilent 2100 Bioanalyzer).  Equal amounts of RNA from each clone of mutant and wild type lines were pooled and a total of 25 µg total RNA was used to generate target cRNAs for hybridization to Affymetrix Rat Genome U34A oligonculeotide arrays (UCI DNA Array Core Facility).  Three separate cell growths were done for each clone and cRNAs were synthesized from the pooled RNAs separately and triplicate GeneChips were done.  Gene expression profiling is described in Supplemental Text.

endometrial stromal cell - control/vector2, 3 days post infection

The raw data from 180 microarrays were processed using the Robust Multichip Average (RMA) method. The expression values in the table were after adjustment of RMA expression values (on the log scale) to account for batch and sex effects.

Two biopsies were taken from each patient; one 6mm punch biopsy was obtained from lesional skin of each patient (involved sample) and the other from non-lesional skin (uninvolved sample), taken at least 10 cm away from any active plaque. One biopsy was obtained from each healty control. The non-lesional and control biopsies were taken from the buttocks or upper thighs.
Biopsies were snap-frozen in liquid nitrogen, stored at -80°C.  At processing the biopsy samples were homogenized while still frozen and total RNA isolation was performed using RNeasy kit protocol (Qiagen, Chatsworth, Ca, USA).

15µM,2,4-benzenetriol was added to the cell suspension in one plate. Untreated cells in the second plate served as a control for basal levels of gene expression.

BBMC cells were suspended at 1 x 106 cells/ml in complete RPMI supplemented with 10% heat-inactivated fetal bovine serum, 100 units/mL penicillin, and 100 µg/mL streptomycin. 107 cells were placed in two 10 cm tissue culture plates. Cells were incubated at 37°C in humidified air containing 8% CO2 for 18 hours.

Total cellular RNA was isolated by using Trizol® Reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.

Clear cell sarcoma of the kidney (CCSK), the second most common renal tumor in children, poses significant diagnostic challenges.  No diagnostic positive markers are available, and the pathogenesis of CCSK remains an enigma.  To address these challenges, the gene expression patterns of fourteen CCSKs were compared to fifteen Wilms tumors (WT) and three fetal kidney samples using oligonucleotide arrays.

Microarray scanning and data acquisition were done at the gene expression facility, Roswell Park Cancer Institute, following their routine standard procedure.

Data were median-normalized for comparison. Medium normalization were done by our collaborators at Roswell Park cancer institute and verified using MS Excel2003.

Samples were stored in RNAlater at -80 freezer before total RNA extraction with Qiagen RNeasy kit.

1, Fragmentation of cRNA.
2, Denature cRNA at 90C for 5 min.
3, Hybridization was performed at 37 C, for 18-24 hours.
4, Detection with Cy5-streptavidin conjugate.

Complementary DNA was prepared from total RNA.
In vitro transcription was then performed with biotin labeled substrate to produce biotin labeled cRNA.

Total RNA purchased from ADMET Technologies (Durham, NC), extracted from healthy liver tissue.

CD4 or CD8 T cells were isolated using negative selection magnetic labeled antibody mix.

Each cRNA bound at its complementary oligonucleotide was excited using confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured. These measures provided the basis of subsequent analysis.

The data were analysed using dCHIP (C Li and W Wong, Proc. Natl. Acad. Sci. Vol. 98, 31-36, 2001a. ).

Following fragmentation, cRNA were hybridized for overnight at 45C on Affymetrix hu133A microarray chip.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

Dicer-heterozygous and Dicer KO cells were grown to confluence in T25s and harvested for extraction of total RNA.

Cells were cultured in DMEM supplemented with penicillin/streptomycin, L-glutamine, and 10% FBS.

R version 2.11.1 (x86_64-pc-linux-gnu), affyPLM_1.24.0, preprocessCore_1.10.0, gcrma_2.20.0, affy_1.26.0, Biobase_2.8.0

Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was DNAseI treated and further purified using the QIAgen Rneasy mini columns

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse 430_2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA according to the Affymetrix Expression Analysis Technical Manual.

animals were housed in Brown University's accredited animal care facility

10 ucg of  c RNA were hybridized for 17 hours at 45 degrees Celsius, 60rpm, FS450_0007

expression profile pre-treatment a 62 year-old patient with clinical diagnosis of dermatomyositis

expression profile pre-treatment a 49 year-old patient with clinical diagnosis of dermatomyositis

Total mRNA was extracted from the frozen heart tissue using the RNeasy fibrous tissue Kit from QIAGEN (Chatsworth, CA).  Contaminating DNA was removed by deoxyribonuclease I digestion of the RNA preparation when still bound to the column. An average of 27ug of total RNA was obtained from 20mg of frozen mouse heart tissue.

Cell lines were cultured in DMEM medium supplemented with 10%FBS, 0.08% Fungizone and 100units/mL penicillin/streptomycin, and maintained at 37ºC in 5% CO2.

Microarrays were scanned using an Agilent DNA microarray scanner.

Agilent Feature Extraction software (version 9.5.3) was run on all array datasets using the GE2-v5_95_Feb07 protocol.  Lowess  and quantiles were applied for intra-array and between array normalization, respectively.

Total RNA was extracted from cell lines using Trizol (Invitrogen) according to the instructions of the manufacturer.

For each hybridization, 1 μg Cyanine 3 labeled cRNA (reference) and 1 μg of Cyanine 5 labeled cRNA (samples) were mixed, fragmented, and hybridized at 65°C for 17 hours to an Agilent 4 × 44 K Whole Human Genome Oligo Microarray.

500 ng of total RNA from samples and Universal Human Reference RNA (Stratagene, Catalog #740000) were used for amplification and labeling using the Low RNA Input Linear Amplification Kit (Agilent) following the detailed protocol described in the kit manual.

pool of total RNA from 10 human cell lines;HCC1937;breast cancer cells;no

average) algorithm For a first supervised analysis,

Total RNA was extracted from purified cell
populations using the RNeasy Mini Kit (Qiagen, Valencia, CA,
USA) according to the manufacturer’s instructions. The RNA
integrity was assessed using Agilent 2100 Bioanalyzer (Agilent,

PC from WM patient, isolated using Kappa or Lambda-fluorescein isothiocyanate, CD10-PE, CD38-PerCPCy5.5,CD19-PE-Cy7, CD34-APC and CD45-APC-Cy7.

pool of total RNA from 10 human cell lines;BRCA1-transfected HCC1937;breast cancer cells;yes

in vivo Treatment: MEHP, Treatment Duration: 6, Units of Duration: hours, Treatment Time: 10:05, Units of Treatment Time: am, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.265, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

Extraction Method: Trizol
Additional Purification Method: Qiagen RNeasy Maxi Kit

KJ_1_6_32_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

Crohn's Disease subject (42 year old black female, SAK_1287526311)

PBMCs from Crohn's Disease subject
Subject Disease : Crohn's Disease
Subject Age : 42
Subject Race : BLACK
Subject Gender : FEMALE

Expression values were estimated using the RMA algorithm implemented in Bioconductor. Further data anaylsis was performed using GeneSpring 4

Levitiracetam brainstem 4
Treatment, type=compound_based_treatment, description=Male Wistar rats receive levetiracetam (150 mg/kg x 2) through a gastric tube twice daily for 90 days.

Cubic spline normalization using Illumina BeadStudio Version "BSGX Version3.2.3"

Illumina TotalPrep RNA amplification kit (Ambion Catalog#IL1791)

As described in the illumina Human-6 chip processing protocol. Briefly, generation of biotin labelled cRNA from the product of RT cDNA synthesis and 2nd strand cDNA synthesis.

HEK293 human embryonic kidney cell line;MIF depletion, siRNA-mediated;siRNA concentration = 100pmol/ml

Animals were sacrificed by cervical dislocation. Dissected brains were stored at -20°C in RNAlater (Qiagen). Subsequently, prefrontal cortices were dissected.

Animals were kept under specific pathogen free housing conditions (SPF unit) according to the guidelines of the German Council on Animal Care.

GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.

The data was processed in R using the RMA algorithm including RMA background correction, quantile normalization, and median polish as summarization method implemented in the affy package and provided by Bioconductor.

Total RNA was prepared using the RNAeasy kit from Qiagen and following the manufacturer's recommendations. RNA quality was assessed with the Bioanalyzer 2100 (Agilent) to ensure high sample quality across all samples.

Following fragmentation, 15µg cRNA were hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1µg total RNA (Expression Analysis Technical Manual, Affymetrix).

prefrontal cortex from adult wild-type mouse;back-crossed to C57BL/6 for 6 generations;male

Levitiracetam brainstem 3

normal tissue collected during removal of head and neck cancer, snap frozen with lq N2 in operating room, stored at -80 until RNA isolation

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. CEL files were normalized with RMA and signal intensity of probe sets were computed with GeneTraffic v3.2 (Iobion Informatics).

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on  Affymetrix human U95A.v2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from `10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

Phenytoin hippocampus 7
Treatment, type=compound_based_treatment, description=Male Wistar rats receive phenytoin (75 mg/kg x 2) through a gastric tube twice daily for 90 days.

Phenytoin hippocampus 6

The arrays were scanned with a GeneChipTM  Scanner 3000 laser confocal slide scanner

The images were quantified using GeneChipTM Operating Software (GCOS) v1.2.  Probe level data were imported into the R statistical software environment (http://www.r-project.org) and expression values for each probe set on the array were summarized using the Robust MultiChip Average (RMA) method with quantile normalization in the R/affy package

For tissue harvesting, mice were anesthetized and the left eye was dissected free, and the cornea and lens removed. The optic nerve was cut close to the back of the eye. The optic nerve head was excised using a sharpened 1mm glass capillary centered over the optic nerve and immediately placed in RNAlater® (Qiagen). A small portion of central retina as well as a small portion of choroid and sclera are included in this tissue. This tissue is substantially enriched for the glial lamina. The retina (containing no optic nerve head) was then dissected free from the back of the eye and placed in a separate vial containing RNAlater (Ambion, Austin TX) and stored at 4oC until required. The process was repeated for the right eye. Dissection of each eye was completed in ≤5 minutes (10 minutes per mouse)

Hybridization and post-hybridization staining and washing were performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).

Biotin-labeled cDNA was synthesized separately from 20ng of each total RNA sample per the manufacturer’s protocols (Ovation™ Biotin System (NuGEN, San Carlos, CA). 2.5 μg of each biotin-labeled and fragmented cDNA sample was then hybridized onto Mouse Genome 430 v2.0 GeneChip™ arrays (Affymetrix, Santa Clara, CA).

Following washing and staining, the chips were scanned using a GeneChip Scanner 3,000 6 G in the UNMC microarray core facility.

1) Place freshly isolated tissue directly in TriReagent (1ml/50-100mg of tissue).
2) Immediately homogenize tissue and transfer to a sterile 50 ml centrifuge tube.
3) Cap the tube securely, shake, vortex vigorously, and incubate at room temperature 5 min. to assure dissociation of nucleoproteins.
4) Add 0.1 ml BCP/ ml of TriReagent used. Cap the tube, shake, and vortex. Incubate at RT for 10 min. Centrifuge at 3200 rpm in Sorvall tabletop centrifuge or equivalent (1800 g) for 30 min. at 40 C.
5) Of the three phases seen, RNA remains in the topmost aqueous phase. Transfer the aqueous layer to a fresh tube being careful not to disturb the protein-rich interface.
6) Precipitate the RNA by adding isopropanol (molecular biology grade) at 0.5 ml / ml TriReagent used. Shake vigorously, vortex, and leave at room temperature 10-15 min.
7) Centrifuge at 3200 rpm for 45 min. to one hour at 40 C.
8) Decant the isopropanol and wash the pellet gently with 10ml ice cold 75% ethanol (made with 100% ethanol (molecular biology grade) and HPLC grade-H2O). Centrifuge at 3200rpm for 20 min. at 4ºC.
9) Carefully decant the ETOH. Draw off the last with a pipet and allow excess ethanol to evaporate 5-10 min. Do not permit the pellet to completely dry as this will decrease its solubility.
10) Bring the volume of the sample up to 250ul (or appropriate volume) with HPLC-H20. Transfer the RNA sample to a 1.5ml microfuge tube.
11) Add 625μl (2.5X original volume) 100% ice cold ethanol.
12) Add 25μl (0.1X original volume) 3M sodium acetate, pH 5.2.
13) Mix well and place in -200C freezer for 30-60 minutes.
14) Microcentrifuge at top speed for 20-30 min. at 4º C.
15) Decant the ethanol mixture and wash the RNA pellet with 100μl 75% ethanol. Spin at top speed of microfuge for 10 minutes at room temperature. Draw off the supernatant with pipet and repeat the wash step. After drawing off the second 75% wash, invert the tube 5-10 min. to partially dry the sample. Do not completely dry the RNA pellet as this will decrease its solubility.
16) Resuspend in an appropriate amount of HPLC-H2O, depending on the size of the pellet.

Resultant cRNA probes were hybridized to the Affymetrix (Santa Clara, CA) Mouse Genome MG_U74Av2 Array per manufacturer's suggestion.

2.5 ug of total RNA was reverse-transcribed and cRNA generated per Affymetrix instructions using the Affymetrix 1-cycle Target Labeling Kit.

Cells were transfected with pCDNA3-Flag-SIRT6 WT, pCDNA3-Flag-SIRT6 H133W mutant, pCDNA3 alone or no DNA. Cells were grown in media containing transfection complexes for 24h prior to stimulation. Growth media was removed and replaced with fresh media containing TNFα (10ng/ml, R&D systems) or media containing equivalent volume of PBS/0.1% BSA as a control.

HEK293 cells were plated at 0.4 x 106 cells per well in 6-well plates (Costar)

Fluorescence raw data of the hybridization were computed, RMA normalized, log2 transformed and statistically analyzed using ArrayStudio v4.0 (Omicsoft).

Total cellular RNA was isolated, processed, and hybridized to the oligonucleotide microarray HG 133A Plus 2.0 Gene Chip arrays (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions.

Following fragmentation, 3.75 ug of cRNA were hybridized for 16-18 hr at 45C on GeneChip U133 Plus2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

A mouse testicular Sertoli cell line, TTE3, derived from transgenic mice harboring a temperature-sensitive simian virus 40 large T-antigen was used. TTE3 cells were treated with 0.2 mM bisphenol A (BPA) for 12 h.

5-FU-primed mononuclear bone marrow cells harvested from C57/B6 mice were retrovirally transduced with Evi1-GFP or GFP and cultured in Methocult 3434 for 48 hrs. GFP positive cells were sorted and subjected to the analysis.

Washing was performed using an automated fluidics workstation, and the array was immediately scanned with GeneChip Scanner 3000 7G.

Expression  data  were  extracted  from  image  files produced  on  Affymetrix®  GeneChip  Operating  Software  1.0®  (GCOS®).
Background subtraction, normalization and expression values of our data were calculated using the rma algorithm, available as a part of the Affymetrix package of the Bioconductor open-source software library for the statistical language R (http://www.bioconductor.org).

Biotin-labeled cDNA was hybridized to the Mouse Genome 430 2.0 Array® (Affymetrix®) for 16 h at 45°C as recommended by the manufacturer.

Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system.

C57BL/6;mononuclear bone marrow cells;mock retroviral transduction

Arrays were scanned using the GeneChip Scanner 3000 7G and GeneChip Operating Software v. 1.4 to produce .CEL intensity files.

These probe cell intensity files (*.CEL) were analyzed in Affymetrix Expression Console software v1.1 using the PLIER algorithm to generate probe level summarization files (*.CHP). (Algorithm: PLIER v 2.0; Quantification Scale: Linear; Quantification Type: Signal and Detection P-Value; Background: PM-GCBG; Normalization Method: Sketch-Quantile)

Total RNA was initially isolated using TRIzol Reagent (Gibco BRL Life Technologies, Rockville, MD), and passed through an RNeasy spin column (Qiagen, Chatsworth, CA) for further clean up.  Eluted total RNAs were quantified (Nanodrop) with a portion of the recovered total RNA adjust to a final concentration of 100ng/ul.

0.54 ug of single-stranded cDNA was hybridized at 45c with rotation for 17 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on an Affymetrix (GeneChip® Mouse Gene 1.0 ST) array.  The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fludics Station 450 (Fluidics protocol FS450_007)

Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+mRNA present in the isolated total RNA (typically 100ng total RNA starting material each sample reaction) using the GeneChip® WT cDNA synthesis Kit (Affymetrix, Inc., Santa Clara, CA) and random hexamers tagged with a T7 promoter sequence.  The double-stranded cDNA is then used as a template to generate many copies of antisense cRNA from an in vitro transcription reaction (IVT) of 16hrs in the presence of T7 RNA Polymerase using the Affymetrix GenechipÒ WT cDNA Amplification Kit.  10 ug of cRNA were input into the second cycle cDNA reaction with random hexamers that are used to reverse transcribe the cRNA from the first cycle to produce single-stranded DNA in the sense orientation. The single-stranded DNA sample is fragmented (WT Terminal Labeling Kit, Affymetrix, Inc, Santa Clara, CA) to an average strand length of 60 bases (range 40-70bp) following prescribed protocols (Affymetrix GeneChipÒ WT Sense Target Labeling Assay Manual).  The fragmented single-stranded DNA is subsequently labeled with recombinant terminal deoxynucleotidyl transferase (TdT) and the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.

Cells were treated in triplicate in either 0.1% DMSO or 1 μM Imatinib for 8 hours

After washing  and staining with streptavidin-Cy3, the chip was scanned using Illumina  BeadArray Reader. The scanning was done using standard DirectHyb Gene  Expression protocol with the following settings: Factor=1, PMT=587,  Filter=100%.

The raw data was extracted using Illumina BeadStudio  software without normalization. Raw data was imported into Genespring 10.0.2 for normalization. Detection P-value >0.8 is called present and <0.6 is called absent. Raw signal is threhold to 1.0. The signal is log2 transformed and quartile normalized between samples.

RNA is extracted using Rneasy per protocol. RNA quality was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano kit (Agilent Technologies Inc., Palo Alto, CA).

The  amplified, biotin-labeled antisense RNA (aRNA) was purified and quality  was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano  kit. 750 ng of aRNA in 5 ul was mixed with 10 ul of hybridization  reagents and heated at 65C for 10min. After cooled to room temperature,  total 15 ul of the hyb solution was applied to Illumina HumanHT-12 v3  chip. The chip was incubated for about 18 hours at 58C.

~500 ng of total RNA was used to prepare biotin-labeled RNA using Ambion Illumina TotalPrep RNA Amplification Kit (Cat# AMIL1791,  Applied Biosystems, Foster City, CA).  Briefly, 500 ng of total RNA was used to synthesize the first strand of  cDNA using ArrayScript reverse transcriptase and an oligo(dT) primer  bearing a T7 promoter. The single-stranded cDNA was then converted into  a double-stranded DNA (dsDNA) by DNA polymerase^ I in the presence of  /E. coli/ RNase H and DNA ligase. After column purification, the dsDNA  was served as a template for in vitro transcription in a reaction  containing biotin-labeled UTP, unlabeled NTPs and T7 RNA Polymerase.

C57BL/6;mononuclear bone marrow cells;Evi1 retroviral transduction

Total RNA from whole kidney was hybridized
Keywords = diabetes mouse models diabetic nephropathy streptozotocin db/db

Performed at the Affymetrix microarray unit at the Institute of Molecular Oncology of the Italian Foundation for Cancer Research-European Institute of Oncology campus, Milan, Italy, according to the manufacturer’s instructions.

Data were processed using standard procedures: Programmatic identifier: GeneChip.CallGEBaseCall.1; Algorithm: ExpressionStat 5.0

Total RNA was extracted independently from three Suz12 and three Suz12 ES cell clones. RNA was quantified, and equal amounts fromthe three Suz12 WT and the three Suz12 KO samples were pooled into one sample to reduce the experimental variation.

Targets for microarray hybridization were synthesized according to the supplier’s instructions (Affymetrix).

Cells were treated with either 15 nm Cetuximab or PBS during 13 hours

All HNSCC cell lines were grown as monolayers in Dulbecco's Modified Eagle's Medium (DMEM), supplemented with 10% fetal calf serum, 2 mM glutamine and 1% penicillin/streptomycin. All media and supplements were obtained from Life Technologies (Merelbeke, Belgium). Cultures were maintained in exponential growth in a humidified 5% CO2/95% air atmosphere at 37 °C. Cells were confirmed free of mycoplasma infection through regular testing (MycoAlertTM, Plus Mycoplasma detection kit, Lonza, Verviers, Belgium).

RNA was isolated using the TRIzol-based method (Invitrogen, Merelbeke, Belgium). Concentration and purity were measured by Nanodrop ND-1000 spectrophotometry (Isogen, Sint-Pieters-Leeuw, Belgium). The RNA quality was assessed by capillary electrophoresis with an Agilent 2100 Bioanalyzer Series Nano kits (Agilent Technologies).

Biotinylated cRNA were prepared with the Illumina Totalprep RNA amplification kit (Life technologies)

Gift Prof Dr Sandra Nuyts (University Hospital Leuven, Leuven, Belgium)

Data was processed in Affymetrix GeneChip Operating Software (GCOS) 1.2.  Values shown are not normalized to the median of each array.

PC-3 prostate cancer cells were either untreated (0hr) or incubated with 5 µg/mL arachidonic acid (AA) in RPMI media containing 0.25 mg/mL albumin for 2 hours.  Albumin alone was added to untreated cells which remained inactivated.

Gene expression data from late passage CCM3-knockdown endothelial cells.

Total RNA was extracted and purified from the liver, lung, kidney, and heart of WT and Cmah-null mice using RNeasy columns (Qiagen; Valencia, CA, USA) according to the manufacturer’s protocol.

Biotinylated cRNA were prepared with Ambion's Illumina RNA Amplification kit for Illumina arrays

Gift Prof Dr Olivier De Wever, Ghent University Hospital, Ghent, Belgium)

GeneChips were scanned using the Affymetrix GeneChip scanner 3000 at 2.5 μm resolution.

The data were analyzed with Probe Logarithmic Intensity Error (PLIER) estimation method using Affymetrix Power Tools.

The cRNA was quantified (using A260) and fragmented. Fragmented cRNA was hybridized on the GeneChips according to the manufacturer's standard protocol.

A total of 250 ng was processed using established Affymetrix protocols for the generation of biotin-labeled cRNA.

The RNA (10 µg) was a total RNA mix that was assessed for quality with an Agilent Lab-on-a-Chip 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

Fluorescent array images were collected for both Cy3 and Cy5 with a Axon GenePix Pro 4000A scanner and image intensity data were extracted and analyzed with Microarray Analysis Suite (MAS) 5.0 software.

VALUE column is the log2 ratio of normalized Cy5:Cy3 signal after Intensity-Dependent normalization.

RNA isolation was accomplished by homogenizing liver in liquid nitrogen, then extracting RNA using TriReagent (Molecular Research Center, Inc.). The RNA (10 µg) was purified using an RNeasy Kit (Qiagen) and assessed for quality with an Agilent Lab-on-a-Chip 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

Hybridization of a Cy labeled cDNA probe (mix of Cy3 and Cy5) onto coated slide spotted with oligonucleotides (70mers) was performed as described in detail at http://mgm.duke.edu/genome/dna_micro/core/protocols/SOP_hyb.doc.

The RNA from murine liver was directly labeled with Cy dyes using oligo dT primers, for complete details see http://mgm.duke.edu/genome/dna_micro/core/protocols/ for detailed labeling and hybridization protocols.

Sample is murine liver RNA extract after infected with 1st generation LacZ adenovirus (1.5x10E11 particles per mouse) at 6 hpi.

C57/BL6 murine Liver RNA- 6 hours post-injection with a 1st generation (E1-E3-CMVLacZ) vector.;Murine Universal RNA (Stratagene, La Jolla, CA) which is a mixture of RNA from 10 control cell lines approximating the expression profile of the majority of murine genes was used.

Embryos were harvested at 8.5 dpc in chilled DEPC-PBS, dissected out of the yolk sac, the allantois was removed, somites counted for the purposes of stage-matching, then flash frozen in liquid nitrogen.

Female Cited2+/— mice were fed with Beekay Rat and Mouse Diet (BK002P) between weaning and 6 weeks of age, and then were randomly assigned to specially formulated high-fat or control diets, which were provided ad libitum. At baseline and after 8 weeks on the diet, the mice were weighed and a 6-hour fasting blood sample was collected. Blood glucose and plasma insulin were measured. Following 8 weeks on diet, Cited2+/— female mice were mated with Cited2+/— males, and the diet continued through pregnancy.

Data generated from scanning was imported into Illumina BeadStudio version 3.2.6 to generate signal values for each bead type. These data were exported to the R statistical computing language where it was background corrected, and transformed and normalised using the BioConductor package, vsn2 (Huber et al. 2002).

Qiagen Rneasy Micro Kit was used as per manufacturer's instructions.  Quality control was performed with Agilent Bioanalyser.

Samples were hybridised for 16 hours to an Illumina Sentrix Mouse Whole Genome Ref 6 v2 chip.  Washing, staining and scanning was performed according to the manufacturer’s protocol

Standard Illumina labelling protocol was used to prepare biotinylated cRNA

Following pathological verification, a serous papillary epithelial cancer sample was embedded in cryomatrix (Shandon).  Seven micron frozen sections were cut and attached to uncharged microscope slides for each sample.  Immediately following dehydration and staining (HistoGene, LCM Frozen Section Staining Kit, Arcturus), slides were processed in an Autopix‘ instrument (Arcturus) for laser capture microdissection (LCM) of cells to CapSure Macro LCM Caps.  Approximately 30,000 epithelia were collected from each cancer sample.

MAS 5.0 via Affymetrix Expression Console (TM) Software Version 1.1

RNA was isolated with Trizol (Invitrogen) and purified with PicoPure RNA Isolation Kit (Arcturus). RNA quality was verified on the Bioanalyzer RNA Pico Chip (Agilent Technologies).

Labeled mRNA was hybridized to GeneChip Human Genome U133 Plus 2.0 Arrays in the GeneChip Hybridization oven 640, further processed with the GeneChip Fluidics Station 450 and scanned with the GeneChip Scanner.

Total RNA from the above extractions was processed using the RiboAmp OA or HS kit (Arcturus) in conjunction with the IVT Labeling Kit from Affymetrix, to produce an amplified, biotin-labeled mRNA suitable for hybridizing to GeneChip Probe Arrays (Affymetrix).

Serous ovarian tumor tissues were placed in cryotubes and immediately (<1 minute) frozen in liquid nitrogen following resection.

Normal ovarian surface epithelial (OSE) cells were collected from ovaries at time of surgery using a Cytobrush ® Plus (Medscand) and immediately stabilized in RNAlater (Ambion) and stored at –20 degrees C.

Ovarian surface epithelia brushing from ovaries described by pathology as within normal limits.

Scans were imported into Rosetta Resolver and pre-processed using the 'Resolver Affymetrix Rosetta Intensity Profile Builder (saves reporters)' pipeline

Total RNA was reverse-transcribed and amplified using the NuGen Ovation™ RNA amplification system V2 with Ovation™WB reagent. Amplified RNA was fragmented and labeled using the NuGen FL-Ovation™ cDNA Biotin Module V2. Amplification and labeling were performed on a Beckman-Coulter ArrayPlex.

Arrays were scanned on a GeneChip Scanner 3000 and fluorescence intensity for each feature of the array was obtained by using GeneChip Operating Software (Affymetrix).

Total RNA was extracted from frozen BA10 using a Polytron type homogenizer (YellowLine DI 25 Basic) and TriZol reagent (Invitrogen, Paisley, UK) in a ratio of 1 ml of TriZol to 20 mg of tissue. RNA was further purified using RNeasy mini-columns (Qiagen, Valencia, CA, USA) including on-column DNAse-1 step and elution in water. Although pH was analysed in brain lysates using a pH meter, this was not considered to be rigorous enough to exclude or include samples and instead the RNA integrity number (RIN) was used to assess the quality of the RNA as the primary inclusion criterion. The quantity of extracted RNA was determined by spectrophotometry and quality was assessed using an Agilent 2100 Bioanalyzer (South Plainfield, NJ, USA) to determine the RIN. Based on the RIN, samples were classified into three quality groups—pass (RIN >7.0); borderline (RIN 6.0–7.0); fail (RIN<6.0). Following classification, there were 41 pass (RIN range of samples 7.0–9.0: average=7.7), 16 borderline (RIN range of samples 6.0–6.9; average=6.4) and 5 fail samples. Samples in the fail category were excluded from the study, and the remaining samples were randomized into four batches, containing an equal number of schizophrenic/control and male/female samples, for target generation and hybridization.

For each batch, 10ug total RNA was processed to Biotin-labeled cRNA and hybridized to HG-U133_Plus_2.0 GeneChips in accordance with the Affymetrix protocol (Affymetrix, Santa Clara, CA, USA,).

Ten milliliters of sterile saline was instilled into a lung subsegment (either the right middle lobe or lingula) followed by instillation of LPS (in 10 ml saline) from Escherichia coli (United States Pharmacopeial Convention, Lot G, Bureau of Biologics, United States Food and Drug Administration, Rockville, MD) into the contralateral lung, using a flexible video bronchoscope. The subjects were randomized to left or right lungs for saline or LPS instillation. The subjects received LPS at a dose of 4 ng/kg body weight. A bilateral bronchoalveolar lavage (BAL) was performed 6 hours post-challenge; seven successive 20 ml aliquots of pre-warmed 0.9% saline were instilled in the saline-challenged subsegment of the lung and each aspirated immediately with low suction. This procedure was repeated in the LPS-challenged subsegment of the contralateral lung.

GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000. Affymetrix GeneChip Operating Software version 1.4 (GCOS) was used to manage Affymetrix GeneChip array data and to automate the control of GeneChip fluidics stations and scanners.

Expression data were generated using the Robust Multi-array Average (RMA) method implemented in the Affy package of the Bioconductor microarray analysis environment.  Before the analysis of differentially expressed genes, a filter was applied to minimize the technical noise. In both groups, the genes with an expression level under a threshold value corresponding to the overall median value from all microarrays were removed. Linear model for microarray, as implemented in the LIMMA package available on the Bioconductor environment, was selected to identify differentially expressed genes

BAL fluid (BALF) was immediately centrifuged for 10 min at 1200 rpm at 4°C. BALF cells were passed over a 40 µm nylon filter (BD Falcon, Bedford, MA) and resuspended in ice-cold sterile automated magnetic cell sorting and separation (autoMACS) buffer (PBS, 0.5% bovine serum albumin, 2 mM EDTA; pH = 7.4). Subsequently, cells were incubated for 15 min with CD71 microbeads (Miltenyi Biotec, Bergisch Gladbach, Germany) at 4°C. Cells were washed again in autoMACS buffer and purified by autoMACS (Miltenyi Biotec). Total and viable cell counts were determined before and after the isolation procedure using a Burker-Turk haemocytometer and trypan blue (Emergo, Landsmeer, the Netherlands). Additionally, cytospins were prepared before and after autoMACS and stained with Giemsa. Total and differential cell counts revealed a recovery of 35-40% macrophages and a purity of isolated macrophages of >95% in all groups. After isolation, alveolar macrophages were dissolved in RNAeasy lysis Buffer (buffer RLT, QIAGEN, Hilden, Germany) and stored at -80°C until used for RNA isolation with RNeasy Mini kit (QIAGEN, Hilden, Germany).  Hence, in each subject alveolar macrophages were harvested from a lung segment instilled with LPS and from a contralateral lung segment instilled with sterile saline.

Fragmented and labeled cDNA was hybridized for 18 h at 50°C in a hybridization solution containing 7% DMSO. Hybridization was performed using GeneChip Human Genome U133 Plus 2.0 arrays (Affymetrix). After washing, chips were stained with streptavidin-phycoerythrin according to Affymetrix EukGE-WS2v4 protocol using the Fluidic FS450 station.

cDNA was synthesized from 50 ng of total RNA using the WT-OvationTM System (NuGEN, San Carlos, CA, USA) powered by Ribo-SPIATM technology. Fragmented cDNA was end labeled with a biotin-conjugated nucleotide analog (DLR-1a; Affymetrix, Santa Clara, CA, USA) using terminal transferase (Roche Diagnostics, Mannheim, Germany).

Macrophages obtained from a contralateral lung segment challenged with saline

Macrophages obtained from a contralateral lung segment challenged with LPS

Probeset intensities were extracted from CEL-files using GeneChip Operating Software (GCOS) (Affymetrix). Probe intensities were normalized. Differentially expressed genes between mixed lineage leukemia translocation (tMLL) and MLL-partial tandem duplication (MLL-PTD) subgroups were calculated using the Student t-test.

Trizol extraction of total RNA was performed according to the manufacturer's instructions. The integrity of the RNA was assessed using the RNA 6000 Nano assay kit on a Bioanalyzer (Agilent Technologies).

Mouse embryonic fibroblasts (MEFs) were generated from 13.5-day-old embryos obtained from heterozygous PKBa mice intercrosses (Yang et al., 2003). Briefly, after dissection of head and visceral organs for genotyping, embryos were minced and trypsinized for 30 min at 37°C. Embryonic fibroblasts were then plated and maintained in Dulbecco’s Modified Eagle Medium (DMEM) with 10% foetal calf serum (FCS) (Life Technologies), 100 units/ml of penicillin and 100 mg/ml of streptomycin at 37°C in an atmosphere of 5% CO2. All experiments were performed with wild-type and PKBa-/- MEFs between 15-20 passages. To induce adipocyte differentiation, 2-day-postconfluent cells (day 0) were treated with DMEM supplemented with 10% FCS, 8 mg/ml biotin, 4 mg/ml pantothenate, 0.5 mM 3-isobutyl-1-methylxanthine, 1 mM dexamethasone and 10 mg/ml insulin (all from Sigma). Total RNA was extracted from cells using TRIzol (Invitrogen) according to the manufacturer’s instructions.

Approximately 8 µg of total RNA was processed to produce biotinylated cRNA targets.

PKBa -/- mouse embryonic fibroblasts (MEFs) were generated from 13.5-day-old embryos

Human neuroblastoma SH-SY5Y cells (ATCC) were maintained in culture as suggested by vendors.

Neuroblastoma SH-SY5Y cells_cloneB_stably transfected with RNAi against DJ-1_replicate1

Cell intensity values and probe detection calls were computed from the raw microarray data using the Affymetrix GeneChip Operating Software (GCOS). Further data processing was performed in the R computing environment (http://www.r-project.org/) using packages from the BioConductor software project (http://www.bioconductor.org/). Robust Multi-Array Average (RMA) normalization was applied. Normalized data were then filtered based on the Affymetrix detection call, so that only probes with a Present call in at least one of the arrays were retained. Data were then imported in the MultiExperiment Viewer (MeV) software, and statistical analysis was performed using SAM (Significance Analysis of Microarrays). Additionally, an expression fold-change cutoff of 2 was applied to detect significantly differentially expressed genes.

Total RNA was isolated using the TRIZOL reagent (Invitrogen) following the manufacturer’s instructions, and purified using the RNeasy mini kit (Qiagen). The quality of total RNA was assessed using a bioanalyzer (Agilent 2100; Agilent Technologies) and RNA was quantified using a ND-1000 Nanodrop spectrophotometer.

Labeled cRNA was hybridized on Affymetrix GeneChip Human U133A 2.0 Arrays containing over 14,500 transcripts. Hybridized GeneChips were stained and washed (GeneChip Fluidics Station 450).

10 micrograms of each total RNA sample was labeled according to the standard one-cycle amplification and labeling protocol developed by Affymetrix (Santa Clara, CA).

human neuroblastoma cells;SH-SY5Y;B;stably transfected with RNAi against DJ-1

Neuroblastoma SH-SY5Y cells, stably transfected with RNAi against DJ-1

astrocytes from second trimester (14-19 weeks) human fetal brains

1: PBMCs were isolated after the blood draw and kept in RPMI and 10% FBS overnight in 37°C incubator. 2: Next day, cells were stained and sorted by flow cytometry.

Quantile normalization followed log2 transformation using Partek Genomics Suite (v.6.6).; Only the probes with average signal intensity value greater than 0.1 and a detection p value less than 0.05 were considered present in this study. The raw data was then filtered by this cretieria.  Of the 44,589 probes on the bead-arrays, 38,932 probes were present in at least one of 208 samples (the PALO list). Thus the raw data from these 38,932 probes had been processed and analyzed in present study.

African-American (AA);Female;Systemic lupus erythematosus (SLE) patient;Peripheral blood;CD20-APC;CD20 positive B cells

The Pdx1-cre/Kras*A is a standart genetic mouse model based on cre lox recombination, therefore no treatment was utilized.

30 day old bitransgenic Pdx1-cre/Kras*A mice and their wild type siblings were sacrificed and their pancreata were excized for total RNA  extraction.

DNA microarray analyses were performed with R. MAS5.0 normalization and log2 transformation was used. Differentially expressed genes were called if FC ≥1.5 and p<0.05.
MAS5.0 raw intenisty and ABS_CALL (Flag). Probes with raw intensity below 50 were considered 'Absent'. Probes with 'Marginal' or 'Present' flag were considered 'Present'

Trizol extraction of total RNA was performed according to the manufacturer's instructions and further purified with the RNAeasy kit from QIAGEN

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

WT3.CEL (unavailable due to loss from servers)
WT pancreatic cells

WT4.CEL (unavailable due to loss from servers)

WT2.CEL (unavailable due to loss from servers)

WT5.CEL (unavailable due to loss from servers)

Wild type mouse embryonic fibroblasts (MEFs) were generated from 13.5-day-old embryos

RNA was extracted with the RNeasy 96 kit (QIAGEN) per the manufacturer’s instructions.

H295R adrenocortical carcinoma cells;Cells derived from Adrenal gland;DMSO (control);n/a;3 hr

H295R adrenocortical carcinoma cells;Cells derived from Adrenal gland;angiotensin II;100 nM;3 hr

H295R adrenocortical carcinoma cells;Cells derived from Adrenal gland;test compound CP-529414 (CETP+ /BP+ THQ+);100 nM;3 hr

Transduced (GFP+) cells were sorted using FACS AriaII and re-stimulated with anti-CD3 and anti-CD28 antibodies for 2 days.

Naive CD8 T cells were activated by anti-CD3/CD28 antibodies for 1 day followed by spinoculation of empty, AP4-, or Myc-expressing retrovirus. Deletion of Myc was achieved by culturing the activated CD8 T cells in media containing 500nM 4OHT and IL-7 for 2 days.

GeneChips were scanned using the Affymetrix GeneChip 7G 3000 Scanner

The data was analyzed with the Affymetrix GeneChip Command Console. Microarray expression data was processed using Command Console (Affymetrix, Inc) and the raw (.CEL) files generated were analyzed using Arraystar version 4 (DNAStar) software with Robust Multichip Analysis ( RMA).

Total cellular RNA was extracted using Nucleospin RNA XS kit (Macherey-Nagel) according to the manufacturer's instructions.

Following fragmentation with NuGen Encore Biotin Module,2.5 ug of cDNA were hybridized into the GeneChip Hybridization Oven 640 for 18 hr at 45C on Gene 1.0 ST Array. GeneChip were washed and stained in the Affymetrix Fluidics Station 450

Biotinylated cDNA were prepared according to the standard NuGen WT-Ovation Pico RNA Amplification system

In vitro activated Myc-deficient CD8 T cells transduced with Myc-expressing retrovirus

DAOY M2.1 MB cells (70-80% confluent) were transfected using either “SMARTpool siRNA” specific for c-myc or “siCONTROL Non-targeting siRNA Pool” as a control, both purchased from Dharmacon (Thermo Fisher Scientific, Waltham, MA 02454 USA). Each pool of small interfering RNA (siRNA) was used at a final total concentration of 50 nM, in combination with Dharmafect 4 as transfection reagent (Dharmacon), according to the manufacturers’ instructions optimized for adherent cell lines. After 24, 48, and 72 h, cells were harvested for both mRNA and protein extraction to assess gene expression by quantitative real-time PCR (qRT-PCR) and protein content by immunoblotting, respectively.

DAOY cells were obtained as reported elsewhere and maintained in culture as previously described (von Bueren, Shalaby et al. 2007). DAOY cells were grown in GIBCO improved MEM Zinc option 1X, 10% FCS and penicillin-streptomycin. The stable clones DAOY V11 (empty vector-transfected), DAOY M2.1 (c-Myc-overexpressing), and DAOY M14 (c-Myc-overexpressing) (Stearns, Chaudhry et al. 2006) were maintained under selective pressure by supplementing the medium with 500 μg/ml G418.

An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescent intensity emitted by the labeled targets. Generated raw data were processed using the Affymetrix AGCC software.

Data was preprocessed and analysed with Affymetrix AGCC software. Data were then RMA normalized in R and statistical significance was tested with t-tests (with R).

Total RNA was extracted using the RNeasy columns-Mini Kit (Qiagen, Basel, Switzerland) following the manual’s instructions. After DNA enzymatic digestion (by using RNase-free DNase, Qiagen), 0.5-1 μg of total RNA was used as template for reverse-transcription, triggered by random hexamer primers and performed by using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystem). Next, qRT-PCR was performed under conditions previously optimized for the ABI7900HT instrument, using Gene Expression Master Mix (Applied Biosystems) and probes/primers specific for c-Myc (Hs00153408_m1), BMP-2 (Hs00154192_m1), BMP-6 (Hs01099594_m1), BMP-7 (Hs00233476_m1) (Applied Biosystems). Normal human cerebellum was used as a reference (Clontech-Takara Bio Europe, Saint-Germain-en-Laye, France).

Biotin-labeled single-stranded cDNA was used for hybridization to GeneChip Human Genome U133 Plus 2.0 arrays for 18h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450.

This single-stranded cDNA was fragmented and labeled with biotin using FL-Ovation Biotin Module V2 (NuGEN).

Cell strain 1 of cyclin D1KO 3T3 cells obtained by serial passaging MEFs from E14 embryos, stably infected with MSCV murine stem cell virus expressing cyclin D1a.

Cells maintained in DMEM supplemented with 10% fetal bovine serum/ 100u/ml of Penicillin-Streptomycin and cultured at 37oC in 5% carbon dioxide.

Sample from retroviral MSCV-D1a infected cyclin D1 knockout 3T3 cells (line 1).

Mouse 430 2.0 chips scanned using Gene chip scanner 3000 with autoloader following Affymetrix guidelines. Image aquired using Gene Chip Operating Sofware version 1.4.

The data were analyzed and normalized by Robust Multi-array Average (RMA) algorithm.

Total RNA extracted using Trizol reagent (Invitrogen) as per manufacturers' guidelines.

The hybridization protocol was followed for single probe array 49 format (standard)/64 format array outlined in genechip expression analysis technical manual provided by Affymetrix. This was also true for washing, staining and scanning procedures.

Total RNA (5µg of RNeasy purified) was reverse transcribed using Superscript III First-Strand Synthesis System (Invitrogen) using a HPLC purified T7-dT24 primer (Sigma Genosys) which contains the T7 polymerase promoter sequence. The single stranded cDNA was converted to double stranded cDNA using DNA polymerase I (promega) and purified by cDNA spin column purification using GeneChip Sample Cleanup Module (Affymetrix). The double stranded cDNA was used as a template to generate biotinylated cRNA using Bioarray HighYield RNA Transcription Labeling Kit (Enzo) and the labeled cRNA purified by GeneChip Sample Cleanup Module (Affymetrix). 15µg of cRNA was fractionated to produce fragments between 35–200 bp using 5x Fragmentation buffer provided in the Cleanup Module.

Gene expression data from cyclin D1 knockout 3T3s (cell line 1) infected with full length cyclin D1 (variant D1a) using Murine Stem Cell Virus (MSCV) system.

Arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix).

Interslide norm. : none, Intraslide norm. : none, Background norm. : rma, Software used : expr_console --> VALUE data obtained from log2 normalized expression signal.

Frozen tissues were homogenized in Trizol (Invitrogen Life Technologies, Gaithersburg, MD, USA). After extraction with isopropanol, total RNAs were purified on RNeasy Qiagen columns (Qiagen Inc., Valencia, CA, USA).

Liver; day 14 postnatal_liver
Keywords = mouse gene expression database

type: accelerated phase
blast count: 5
Center code: 4

Peripheral blood was collected using PAXgene tubes, and then stored immediately to -80 degree freezer until ready for RNA extraction. Cells were not grown or cultured.

All probe arrays were scanned using the GeneChip scanner 3000, and operating software (MAS 5.0) was used to scan the images and for data acquisition.

Total RNA was isolated using Trizol (Invitrogen) and purified using an RNeasy mini kit (Qiagen, Valencia, CA).

A total of 15 µg of fragmented cRNA was hybridized on an Affymetrix GeneChip (human U133A) at 45ºC for 16 hours at 60 rpm followed by washing/staining procedures.

A total of 5 µg of purified RNA was reverse-transcribed into cDNA using T7-oligo (dT) primer (Affymetrix, Santa Clara, CA) and SuperScript II RT (Invitrogen). The biotin-labeled cRNA was synthesized from cDNA using the BioArray RNA transcript labeling kit (Enzo, Farmingdale, NY) and was followed by fragmentation.

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D7;P1

Kidney; Day 2 postnatal

Kidney; Fetal Day 18.5

Kidney; FVB/N Folic Acid toxic injury

Scanning was done on an Affymetrix GeneChip Scanner 7G and hybridization quality control were assessed using RACE (Psarros et al., 2005), a web service based on Bioconductor “affy” and “affyPLM” packages (Gautier et al., 2004).

Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003).

Total RNA was prepared using TRIzol (Invitrogen) and purified on Qiagen RNeasy Mini columns (Qiagen), according to manufacturers' instructions.

Twelve micrograms of biotinylated cRNA from each sample were fragmented and hybridized to GeneChip Mouse 430 2.0 arrays, according to standard procedures. Washing and staining was performed using the EuGE-WS2v5 protocol.

Target preparations were performed as described by the Affymetrix GeneChip Expression Analysis Technical Manual (http://www.affymetrix.com), and were conducted at the DNA array facility of the University of Lausanne (Switzerland). 3 ug of each pool was used to perform the chiparray experiment according to the Affymetrix Gene Expression procedure.

Mature (day 6- 8 differentiation) adipocytes were infected with adenovirus expressing sXBP1 or GFP.  After 4-6 days of infection cells were harvested for analysis.

F442A preadipocytes were differentiated according to standard adipogenesis protocol. (see Gregor et al., Cell Reports 2013)

The samples were hybridized and scanned according to Affymetrix protocol for Mouse 430A 2.0 chips. (Affymetrix GeneChip Manual (rev.1.3))

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) as normalization method. Genome profiling was performed at Harvard Medical School-Partners Healthcare Center for Genetics and Genomics using an Affymetrics platform (Cambridge, MA).

Biotinylated cRNA were prepared according to the standard Affymetrix protocol. (Affymetrix GeneChip Manual (rev.1.3))

Groups of 6 mice were administered, daily for 7 consecutive days, with 50, 200, and 400 mg/kg vancomycin, delivered via the iv and ip routes. Six control mice were administered a similar volume of 0.9% saline solution using both routes.

BALB/c mice were maintained on Purina Certified Rodent Chow 5002 (Richmond, IN, USA) and purified tap water ad libitum in microisolator cages under controlled lighting (12 h light/dark cycle).

Scaning was performed using a TGT value = 500 using the protocol described in the Affymetrix Genechip Expression Analysis Technical Manual, revision 5 (http://www.affymetrix.com/support/technical/manual/expression_manual.affx)

The Affymetrix CEL files were loaded into GeneSpring GX version 7.3.1 (Agilent technologies, Santa Clara, CA, USA) and preprocessed using GenChip Robust Multi-Array analysis (GC-RMA).

Approximately 15-20 mg of each kidney to analyze was transferred into 1 ml Trizol reagent (Invitrogen, Carlsbad, CA, USA) along with a stainless steel bead (Qiagen, Valencia, CA, USA) and homogenized with a TissueLyser (Qiagen). Total RNA was extracted with 200 µl chloroform, precipitated with 500 µl 100% ethanol, and transferred to a RNeasy mini spin column (Qiagen) for purification according to the manufacturer’s instructions. Total RNA was subsequently precipitated with ethanol, resuspended in water and stored at –70°C.

The cRNA was fragmented before hybridizing to the GeneChip Mouse Genome 430 2.0 Array (Affymetrix). Hybridization was performed according to the manufacturer’s instructions, as described in the Affymetrix Genechip Expression Analysis Technical Manual, revision 5 (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

cDNA was prepared and cleaned from 10 µg total RNA using the One-Cycle cDNA Synthesis and Clean-up module kits (Affymetrix, Santa Clara, CA, USA). The cDNA was further processed to biotin-labeled cRNA using the IVT labeling kit (Affymetrix). Labeling protocol was performed according to the manufacturer’s instructions, as described in the Affymetrix Genechip Expression Analysis Technical Manual, revision 5 (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

Gene expression analysis of the kidney of mouse treated with 7 repeat daily doses of vancomycin at 50 mg/kg administered via the intraperitoneal route (ip)

Kidney from mice treated with 7 daily ip injections of vancomycin at 50 mg/kg

Gene expression analysis of the kidney of mouse treated with 7 repeat daily doses of saline, administered via the intraperitoneal route (ip)

Gene expression analysis of the kidney of mouse treated with 7 repeat daily doses of vancomycin at 400 mg/kg administered via the intravenous route (iv)

Kidney from mice treated with 7 daily iv injections of vancomycin at 400 mg/kg

Exposures of 24 hours in duration were initiated once flasks were confluent using the test chemicals CoCl2.

MH1C1 and H4-II-E-C3 cells (ATCC, Manassas, VA) were grown in Dulbecco's Modified Eagle's Medium (DMEM; Lonza, Walkersville, MD) containing 10% fetal bovine serum (Invitrogen, Carlsbad, CA) and 10 mL Glutamax (Invitrogen) in T75 flasks incubated at 37 °C with 5% carbon dioxide.

Microarrays were scanned on an Affymetrix GeneChip Scanner following the manufacturer's instructions.

Microarray data was processed for background adjustment, normalization, and summarization using the Robust Multi-Array Averaging method (RMA) using Partek Genomic Suite (GS) software (Version 6.6, St. Louis, MO).

Samples were hybridized on the GeneChip Rat Genome 230 2.0 Array using Affymetrix instrumentation according to the manufacturer’s instructions.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D42;13

type: blast crisis
blast count: 71
Center code: 3

Cells were exposed to 1 nmol/L 17β-estradiol or its vehicle (0.1% ethanol) for 24 hours. Meduem was discarded, cells washed with PBS and then collected in Trizol.

Primary HUVEC were isolated and grown in human endothelial cell-specific Medium EBM-2 supplemented with EGM-2 (Lonza), in an incubator at 37 ºC with 5% CO2

GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.

Files obtained from GCOS (.cel) were used to analyze significant changes in expression profiles of different experimental groups using the dCHIP Analysis Software and the SpotFire Decision Site software. Data were normalized using the Invariant Set Method and modeled using the PM/MM model

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133A plus 2.0 microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station EukGene_ws_2v5.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 µg total RNA.

Age-related macular degeneration has a strong epidemiological association with cardiovascular disease. One pathogenic hypothesis that applies to both diseases is the concept of an abnormal cellular response to injury resulting in a disease phenotype. It has been hypothesized that this phenotype is also present in dermal fibroblasts. This study tests this hypothesis by examination of the expression profiles of fibroblasts obtained from diseased patients and subjected to sublethal cell injury.

type: blast crisis remission

blast count: 95

ESCs were transfected with plasmids by LipofectAMIN 2000 (Invitrogen) and extracted RNA by Trizol

Foxd3 conditional knockout cells treated with DMSO, biological rep1

Following fragmentation, 10 ug of mRNA were hybridized for 16 hr at 45C on  Mouse 430 2.0 gene expression array chip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated mRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

embryonic stem cells;CGR8;Foxd3 conditional knockout cells treated with DMSO

Foxd3 conditional knockout cells treated with DMSO, biological rep2

Foxd3 conditional knockout cells treated with DMSO, biological rep3

Foxd3 conditional knockout cells treated with Tamoxifen, biological rep1

embryonic stem cells;CGR8;Foxd3 conditional knockout cells treated with Tamoxifen

Tumors were harvested from nude mice hosts. Skin was trimmed off of the tumors and a small piece (~50mg) of tumor parenchyma was placed into RNA Later preservation reagent, refrigerated overnight at 4C, then stored at -80C. Samples were later placed into Trizol after minimal thawing and homogenized using a hand-held electric tissue homogenizer.

The iNRAS-475 mouse melanoma cell line was injected intradermally into nude mice which were fed 2mg/ml doxycycline water. Tumors were allowed to reach 200-500mm3 after 6 weeks. Mice were then treated with vehicle or 100mg/kg of the AZD6244 MEK inhibitor, or doxycyline was withdrawn from the diet.

Raw image files were converted to probe set data (.cel files) in Microarray Suite (MAS 5.0). The 18 probe set data files were normalized together, and expression values were determined, using the Robust Multi-chip Average (RMA) method as implemented in RMAExpress (Bolstad/Berkeley).

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

nude mice;iNRAS-475 mouse melanoma cells;Melanoma allograft;Doxycycline withdrawal 4 days

nude mice;iNRAS-475 mouse melanoma cells;Melanoma allograft;vehicle

scanned on Affymetrix GeneChip scanner 3000.  Data were collected using Affymetrix GCOS software.

Statistical and clustering analysis was performed with Partek Genomics Suite software using RMA normalization algorithm.  Differentially expressed genes were identified with ANOVA analysis.  Genes that are up- or down-regulated more than 2 fold and with a p<0.001 were considered significant.  Significant genes were analyzed for enrichment for pathways using DAVID bioinformatics database (http://david.abcc.ncifcrf.gov/) and Ingenuity Pathway Analysis software.

Total RNA was isolated with RNAeasy kit from Qiagen RNeasy. RNA quality was checked on Agilent Bioanalyzer.  All samples used for microarray analysis have high quality score (RIN >9).

Four replicates of each group were prepared, labeled, and hybridized to Affymetrix mouse Gene ST 1.0 GeneChip

200 ng of RNA was reverse transcribed with random hexamer primer, amplified and terminal labeled with biotin using Affymetrix Whole Transcript Sense Target Labeling kit according to manufacturer's protocol.

Total RNA (TRNA) was isolated from heart samples utilizing Trizol Reagent (GIBCO/BRL) following the manufacturer's protocol. The quality of TRNA was assessed using the Agilent 2100 Bioanalyzer (version A.02.01S1232, Agilent Technologies). Only RNA with the OD ratio of 1.99-2.0 at 260/280 was used for microarray analysis.

BMMCs were purified by negative selection with MicroBeads (Miltenyi Biotec) after 4 weeks in culture. The cells were further rested in cytokine free medium for 4h.

Bone marrow derived mast cells (BMMCs) from AhR null, AhR_d and normal control mice were cultured in 30% WEHI-3-conditioned medium

All signal intensity quantification was performed using an Illumina iScan scanner, using the standard Illumina scanning protocol.

A single intensity (expression) value for each Illumina probe on the array was obtained using Illumina GenomeStudio software with standard settings and no background correction.  The expression values for all the probes for each sample were scaled to have median 256 and then log (base 2) transformed.

RNA was extracted with RNeasy mini kits with DNase I treatment (Qiagen) in accordance with the prescribed protocol provided with the kit and stored at -80°C.  The quality of total RNA samples was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

cRNA was hybridized to Illumina Sentrix® Murine Ref8_v2_R3 Expression BeadChips, and signal was detected with streptavidin-Cy3, using the standard Illumina hybridization protocol

Biotin-labeled, complementary RNA (cRNA) was prepared from total RNA according to the chip manufacturer’s protocol (Illumina, San Diego, CA).

The Gene Chips were scanned using the GeneChip Scanner 3000 (Affymetrix).

The analysis was performed with GeneSpring software package (Agilent Technologies, Santa Clara, CA).  All samples were subject to per-chip normalization. Data were filtered twice, a fold change filter (2 fold up or down), and the Statistical Analysis of Microarray software (http://www-stat.stanford.edu/~tibs/SAM/), to find all genes with a < 10% false positive q-score.

Lung tissues were homogenized in the presence of TRI reagent (MRC Molecular Research Center, Cincinnati, OH). Total RNA was isolated using the 1-bromo-3-chloropropane (BCP) phase separation reagent (MRC Molecular Research Center). RNA was precipitated by 2-propanol and washed with 75% ethanol.

Biotin-labeled cRNA was purified (GeneChip Sample Cleanup Module, Affymetrix), and 20 mg of the labeled cRNA was fragmented. The cRNA and fragmented cRNA quality was assessed by the Agilent 2100 Bioanalyzer (Agilent; Foster City, CA) and the RNA 6000 Nano LabChip kit (Agilent). The labeled fragmented cRNA was hybridized to Affymetrix GeneChip Rat 230 2.0 arrays for 16 h at 45oC following the Affymetrix protocol specific to this array type. Washing and staining were performed on the Affymetrix fluidics (450) station according to the antibody amplification protocol (Fluidics script: EukGE-WS2v5).

Biotinylated cRNA was synthesized by in vitro transcription using the GeneChip IVT Labeling kit (Affymetrix).

Dorsal root ganglia were incubated in 5 ml MEM containing collagenase P (Roche, Penzberg, DE) (0.1 U/ml, 1 h, 37°C, 5% CO2), dissociated by trituration with fire-polished Pasteur pipettes, and then treated with the solvent DMSO (0.1%) or RTX (100 nM). The cells were spun down (100 g, 5 min), resuspended in 1 ml Hanks buffered salt solution (pH 8.0) containing 0.025% EDTA and 245 U/ml trypsin (Worthington, Lakewood, NJ), and incubated for 4 min at 37°C in a water bath. Trypsination was stopped by the addition MgSO4 (400 µM final conc.). The cell suspension was then loaded onto BSA gradients (15% BSA in Hanks buffered salt solution) and centrifuged (120 g, 8 min). The pellet was frozen in liquid nitrogen and stored at -80°C for RNA isolation.

Lumbar dorsal root ganglia were isolated from 8 weeks old Spargue Dawley rats

Raw fluorescence intensities were background corrected and exported from the Illumina Genome studio software. Background corrected data were log2 transformed and normalized (quantile method) using the R package lummi. The data were filtered for expressed genes (detection p < 0.01) and differentially expressed transcripts were identified with the R package limma. P-values were adjusted for multiple testing with Benjamini and Hochberg's method.

RNA isolation was performed with NucleoSpin RNA/Protein kits from Macherey-Nagel including on column DNase treatment. The RNA concentration and quality was measured with spectroscopy (Nanodrop, Thermo Fisher Scientific) and capillary electrophoresis (Agilent 2100 Bioanalyzer, 28S:18S rRNA ratio > 1.7, RNA integrity number (RIN) > 8.2).

Dissociated dorsal root ganglia treated for 30 min with capsaicin

mESCs (D3, siSCR, siPRMT1 and siPRMT8) were cultured as described in the article. ES medium contained 15% ES qualified FBS.  For induction of EB formation mES cells were aggregated in 100-mm bacteriological dishes (Greiner) at a specific density (4x106 cells/ 15 ml) in the abscence of LIF.  Protocol details described Bibel et al., 2007

GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.

The data were analyzed with GeneSpring GX12 Software (Agilent). Cel files were imported using RMA16 algorithm and median normalization was performed.

RNeasy mini kit was used to extract total RNA (according to the manufacturer's instructions).

10 ug of ss cDNA was fragmented and labeled with biotin and were hybridized for 16 hr at 45C on GeneChip  1.0 ST Mouse Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated ss cDNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA using WT Expression kit (Ambion).

Total RNA from the tissues of 3 male mice were pooled into a single sample and hybridized to the Affymetrix 430A GeneChip. The colon was defined as the tissue below the caecum and above the rectum. The small intestine was defined as the tissue below the stomach and above the caecum, and was divided into three equal parts corresponding to the duodenum, jejunum, and ileum. The epithelial layer of intestinal tissues was scraped off for RNA processing. Whole liver was extracted. All tissues were rinsed with PBS.

C57BL/6,;Male,;between 6-8 weeks,;RM3 (E) 801710 Soya-free powdered diet from B.S & S.,;Liver

C57BL/6,;Male,;between 6-8 weeks,;RM3 (E) 801710 Soya-free powdered diet + 7mg quercetin from B.S & S.,;Jejunum

C57BL/6,;Male,;between 6-8 weeks,;RM3 (E) 801710 Soya-free powdered diet from B.S & S.,;Jejunum

A transfection mix containing 2.5µl of RNAiMAX transfection reagent (Invitrogen) and 5nM siRNA in 500µl of OptiMEM media (Invitrogen) was incubated for 20 min at room temperature before added dropwise to 5.0 x 105 cells in 2.5ml of antibiotic-free media per well in a 6-well plate. The cells were incubated at 37°C for 24 h and harvested in 1ml of TRIzol Reagent (Invitrogen).

MCF7 cells were grown in DMEM medium containing 10% fetal bovine serum, 1 mM sodium pyruvate, 0.01 mg/ml bovine insulin, 2 mM L-Glutamine, 1 U/ml penicillin G and 1 ug/ml streptomycin sulfate, at 37˚C in a fully humidified atmosphere containing 5% CO2.

Data was analyzed with R using Affymetrix default analysis settings and RMA as the normalization method.

Total RNA was isolated from Trizol homogenate using chloroform and purified using RNA affinity mini columns according to the manufacturers’ protocol (Invitrogen). RNA yields were determined by spectrophotometry using the NanoDrop (NanoDrop Technologies Inc, USA), and RNA integrity was assessed by capillary electrophoresis using the Experion (Bio-Rad Laboratories, CA, USA).

Following fragmentation, 15 ug of labelled cRNA was hybridized for 16 h at 45°C @ 60 RPM on Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA was prepared from 1 ug total RNA according to the standard Affymetrix protocols (Expression Analysis Technical Manual, 2001, Affymetrix).

Gene expression profile of MCF7 cells analyzed using Affymetrix Human Genome U133 plus 2.0 microarrays, 24 h after the corresponding gene was knocked down using siRNA.
ESR1_KD_AM0009

MCF7 breast cancer cells;estrogen receptor alpha (ESR1) knockdown

MCF7 cells that were transfected by siRNA targeting estrogen receptor alpha (ESR1).

ESR1_KD_AM0003

ESR1_KD_AM0006

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and  as quantile normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

Gene expression data from muscle of 4 weeks old altered in glucose and steroid metabolism

CONTROL_AM0002

CONTROL_AM0004

C57BL/6,;Male,;between 6-8 weeks,;RM3 (E) 801710 Soya-free powdered diet + 7mg quercetin from B.S & S.,;Liver

Mouse was rendered diabetic at six weeks by administration of 5 daily intraperitoneal injections of streptozotocin, 65 mg/kg in citrate buffer (0.05 mol/L; pH 4.5) (Sigma Aldrich).
Serum glucose was measured from tail vein blood using a glucometer. Mice with a glucose concentration greater than 250 mg/ml were considered diabetic. All nondiabetic mice had a glucose concentration well below 200 mg/ml. Beginning at age 9 weeks, certain diabetic and nondiabetic mice were euthanized. Serum glucose was measured again before euthanization. Total Aortic segments from root to bifurcation) were snap-frozen for further analysis. Aortic roots were embedded into OCT (Tissue-Tek) and further sectioned for histological and immuohistochemical analysis.

Total aortic RNA was isolated from the indicated mice by using TRIzol (Invitrogen) and RNeasy MinElute Cleanup (QIAGEN Inc.) including a DNase step. Total RNA concentration and quality were assessed on a 2100 Bioanalyzer system (Agilent Technologies). All of our samples had an RNA integrity score >8, and there was no indication of RNA degradation or contamination with DNA.

1 μg of RNA was hybridized to Mouse Genome 430. 2.0 GeneChips (Affymetrix). All samples were prepared with the two-cycle protocol recommended by the manufacturer.

After purification, cDNA was in vitro transcribed into biotin labeled antisense cRNA using an Affymetrix kit according to the standard kit protocol.

ApoE-/-;C57BL/6;Jackson labs (backcrossed >10 generations against C57BL/6 background).;Male;9 weeks;Total aorta from root to bifurcation.;diabetic

16 embryonic stem cell (ESC) samples (8 groups in duplicate) were processed for microarray analysis using the Affymetrix Mouse Genome 430 2.0 GeneChip.  The samples included the parental Ainv15 ESC line (1) undifferentiated (Ainv15 ESC), (2) differentiated for 3 days as embryoid bodies (Ainv15 EB3) or (3) for 10 days as embryoid bodies (Ainv15 EB10).  The remaining samples included tetracycline inducible Ngn3 ESC line derived from the parental Ainv15 ESC line (4) after differentiation and addition of doxycycline for 3 days without embryoid body formation (Ngn3 ES3 ON), (5 and 6) after differentiation as embryoid bodies for 3 days with (Ngn3 EB3 ON) or without (Ngn3 EB3 OFF) doxycycline, and (7 and 8) after differentiation as embryoid bodies for 10 days with (Ngn3 EB10 ON) or without (Ngn3 EB10 OFF) doxycycline.

Overexpression experiment: control human primary myoblasts were transduced with lentivirus carrying DUX4-fl, DUX4-s or GFP (MOI = 15) for 24h.
Defensin experiment: cultured control myoblasts were grown at 50% confluence and treated with 1 µM human β-defensin 3. Equivalent volume of vehicle (water) was added to myoblasts for the control condition.

Primary human myoblasts were collected and cultured as previously described (Snider et al., 2010, PubMed ID 21060811).

Probe intensities were corrected, normalized, and summarized by the Lumi package of Bioconductor (Du et al., 2008). Differentially expressed genes were identified by the LIMMA package of Bioconductor (Wettenhall and Smyth, 2004).
Data from the DUX-overexpression and the defensin experiments were normalized separately.

RNA was extracted with Qiagen RNeasy kit according to manufacturer's instruction. Quality control was performed with Agilent Bioanalyzer.

Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit (Applied Biosystems) for Illumina arrays

myotubes grown in media containing human beta-defensin 3 peptide

75% C57BL/6, 25% CBAJ;Female;9 weeks (Moderate Stage);Mutant huntingtin

The PBMCs were counted and stained with a cocktail of fluorochrome-conjugated monoclonal antibodies in PBS (APC-aCD4 (clone RPA-T4), APC-Cy7-aCD25 (clone M-A251), FITC-aCD14 (clone M5E2), FITC-aCD32 (clone FL18.26), FITC-aCD116 (cloneM5D12), PE-Cy7-aCD8 (clone RPA-T8) all from BD Pharmingen, San Diego, CA) and sorted on a FACSAria (BD Biosciences, San Diego, CA). Cells were first gated on the live lymphocyte population, eliminating dead cells and debris. Two additional gates were set up to eliminate non-CD4 T cells (FITC-stained cells and CD8-PE-Cy7 stained cells). CD4+ T cells were further gated as CD4+25- and CD4+CD25+high using the Fluorochrome Minus One (FMO) method, which allows for a more precise definition of cells having fluorescence above the background level. The 1% of cells expressing the highest level of CD25 were collected and defined as CD4+25+high T cells, known to be enriched for Tregs.

Peripheral blood mononuclear cells (PBMCs) were collected using vacutainers with ACD solution B of trisodium citrate and isolated using Ficoll-Hypaque density centrifugation according to the recommended protocol (Amersham Pharmacia, Uppsala, Sweden).

After hybridization arrays were washed, stained with PE-conjugated streptavidin (Molecular Probes, Eugene, OR) and scanned on a GeneChip® Scanner 3000.

Bayesian Hierarchical Analysis (using the BGX: R package) was used to find differentially expressed genes across 12 T1D and 15 controls. Details are in the supplementary notes to the accompanying paper.  For SAM analysis, we used RMA normalised intensity values as input. For analysis of 10 T1D and 10 Controls, we used adaptive MCMC methods and probe affinity effects.

Total RNA was extracted from T cells using TRIzol Reagent (Invitrogen) according to the recommended protocol. The GeneChip® Human Genome U133 Plus 2.0 array was selected for this study which interrogates more than 47,000 probe sets, representing roughly 39,000 unique UniGenes.

Purified total RNA (~50ng) was amplified using the two-cycle cDNA synthesis kit (Affymetrix, 900432) and cRNA was synthesized, labeled, fragmented and hybridized to the arrays in accordance to standard Affymetrix protocols (Affymetrix, Santa Clara, CA).

Gene expression data from unstimulated Tregs from a recent-onset T1D subject

Medium;162.5 cm;53.4 kg;20.2;13.03 years;Female;White;81 mg/dl;7.8%

Medium;151.2 cm;42.9 kg;18.4;11.22 years;Female;White;230 mg/dl;6.8%

Low;147.2 cm;35.2 kg;16.2;11.45 years;Female;White;247 mg/dl;6.7%

High;147.8 cm;52.9 kg;24.1;12.2 years;Female;White;83 mg/dl;8.1%

Medium;166.3 cm;64.5 kg;23.2;18.16 years;Female;Other;114 mg/dl;7.4%

High;145.1 cm;32.1 kg;15.2;10.16 years;Female;White;188 mg/dl;6.1%

Medium;124.8 cm;26 kg;16.9;7.21 years;Female;White;180 mg/dl;7.5%

Primary monolayer chondrocytes were treated with 10-7 M dexamethasone (DEX) or the DMSO control (vehicle) diluted in fresh media supplemented with 0.25 mM ascorbic acid (Sigma) and 1 mM beta-glycerophosphate (Sigma) and incubated for up to 24 hrs

Tibiae, femurs and humeri were isolated from E15.5 mouse embryos and placed in alpha-MEM media (Invitrogen) containing 0.2% Bovine Serum Albumin (BSA), 1 mM beta-glycerophosphate, 0.05 mg/ml ascorbic acid and penicillin/streptomycin incubated at 37°C in a humidified 5% CO2 incubator overnight. The following morning media was removed and the bones placed in 4 ml of 0.25% trypsin-EDTA (Invitrogen) for 15 min at 37oC. Trypsin was subsequently replaced with 1 mg/ml collagenase P (Roche) in DMEM / 10% fetal bovine serum (Invitrogen), and cells were incubated at 37°C with rotation at 100 rpm for 90 min. Following digestion, the cell suspension was centrifuged for 5 min at 1000 rpm, and the collagenase containing supernatant was decanted. Chondrocytes were resuspended in media containing 2:3 DMEM:F12, 10% fetal bovine serum, 0.5 mM L-glutamine, and penicillin/streptomycin (25 units/ml). Cells were seeded in 6-well NUNC plates at a density of 2.5X104 cells per ml and incubated overnight.

According to standard protocols used in London Regional Genomics Centre. Ontario, Canada

Microarray data were pre-processed using the GC-RMA algorithm in Genespring GX* Expression values were further filtered by retaining only those  probe sets with expression values of at least 50 in at least 25% of all conditions,
thus generating a list of 22 091 probe sets. To assess differential gene expression between treatments at both the 6 and 24 hr time points, a Welch ANOVA test with a p-value cut-off of 0.01 and a 5% false discovery rate (FDR)
reduced the data to 1158 probe sets. Subsequent 1.5-, 5- and 10-fold change filters produced lists of 162, 21 and 7 probe sets for the 6 hr time point and 399, 53 and 19 probe sets for the 24 hr time point, respectively.
The same data set was normalized in parallel using Robust Multichip Analysis using RMAEXPRESS software v.0.4.1 developed by B. Bolstad, University of California, Berkeley. Background adjustment and quantile
normalization parameters were selected for data processing. Logarithmically transformed expression values were used to implement Gene Set Enrichment Analysis (GSEA).

Completed according to the London Regional Genomics Centre (LRGC): http://www.lrgc.ca/

DEX-treated embryonic primary chondrocyte cultures, incubated for 6hr

DMSO-treated embryonic primary chondrocyte cultures, incubated for 6hr

Hepatocyte-specific excision of the Socs3 gene was achieved by breeding Socs3 fl/fl mice with mice expressing the Cre recombinase transgene under control of the albumin promoter (Alb-Cre+), yielding Socs3 h-KO mice (SOCS3 Cre plus). Socs3 fl/fl, Alb-Cre- littermates were used as controls for all experiments, and are referred to as SOCS3 Cre minus. All mice (C57BL/6) were free of Helicobacter species, housed in a specific pathogen free facility with 12-h light/dark cycles with free access to standard food and water. 2/3 partial hepatectomies (PH) were performed as previously described.

Total RNA was isolated from whole liver tissue harvested 18h after PH, as described in Supplemental materials and methods.

The standard hybridization protocol was used as recommended by Affymterix.

Total RNA (2 ug) was labeled and hybridized to the Mouse Genome 430 2.0 arrays and hybridized according to manufacurer’s instructions.

All mice (C57BL/6) were free of Helicobacter species, housed in a specific pathogen free facility with 12-h light/dark cycles with free access to standard food and water.

analysis of RNA from kidneys of wild-type (WT) and AT1A receptor-deficient mice (KOs) at baseline and after 2 days of angiotensin II  (ANG II) infusion (1 μg/kg/min)

Gene Chips were scanned using GeneChip® Scanner 3000 7G (Affymetrix)

The expression data were processed with robust multiarray analysis (RMA) algorithms with GeneSpring GX version 7.3.1 (Agilent Technologies, Santa Clara, CA) and per-gene normalization to the median was applied with using cross-error model to enhance the statistical power of  the analysis.

Total RNA from snap-frozen kidneys was extracted with RNeasy Mini Kit (Qiagen) according to manufacturer’s protocols

20 micrograms of  biotin-labeled target complementary RNA (cRNA) were fragmented and hybridized for 16 hr at 45 C to each GeneChip Mouse Genome 430 2.0 Arrays  according to the manufacturer's instructions

Data analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as the normalization method

Tissue RNA was isolated using Qiagen RNeasy kits (Qiagen, Inc., Valencia, CA).  Biotinylated-cRNA made from pooled RNA preparations (RNA from two rats per preparation) was used to probe Affymetrix Rat Expression 230A GeneChips (Affymetrix) as per the Invitrogen protocol (Invitrogen, Inc., Carlsbad, CA), three arrays per group.

Biotin-labeled cRNA probes were in vitro transcribed using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Life Sciences).

adipose tissue (epididymal);male;Zucker;fatty (fa/fa);normal chow

adipose tissue (epididymal);male;Zucker;fatty (fa/fa);Pioglitazone

standard affymetrix protocol-GeneChip Scanner 3000 using the protocol http://www.affymetrix.com/support/downloads/manuals/10k_manual.pdf

Affymetrix MAS5.0 gene expressions are normalized with median invariant method.  To filter out significant genes, we adapted two approaches. A primary filtering method we used the standard two samples t-test in pair-wise comparisons involving gender (male or female), animal types (control, JNK, RAS, p38) and different time points (0, 1, 3, 4, 5, 9, 14). The selection criteria are as follows: |the fold change >2, |difference|>100, and p-value < 0.05

RNA extration was accomplished using TRIzol reagent(http://www.invitrogen.com/content/sfs/manuals/15596026.pdf) and purified using Qiagen Rneasy Mini Kit (http://www1.qiagen.com/literature/protocols/pdf/RY20.pdf)

standard affymetrix protocol http://www.affymetrix.com/support/downloads/manuals/10k_manual.pdf

The mouse strains for all the transgenic lines are C57black background and established after nearly 2 years of cross-breeding between the floxed alleles and the MCM strain. ?MHC-floxed-HRas-v12/MKK3bE/MKK7D transgenic mice were established as reported previously(19, 20, 36, 37, 40). They were bred with ?MHC-Mer-Cre-Mer (MCM) mice (from Dr. J. Molkentin, Cincinnati Children’s Hospital)(32) to generate double transgenic animals harboring both floxed transgenes and Mer-Cre-Mer transgene.  At 12 weeks of age the double transgenic mice and non-transgenic littermate controls were treated via i.p. injection of tamoxifen at a dosage of 20mg/kgBW once a day for 3 consecutive days as reported.  The hearts were harvested at an early (4-7 days post first tamoxifen injection) and a late (2-4 weeks) time point.  Left ventricles were dissected and rapidly frozen in liquid nitrogen and stored at -80?C prior to protein and RNA analysis.

adipose tissue (epididymal);male;Zucker;fatty (fa/fa);Rosiglitazone

CD4+CD25+Foxp3-YFP+ Treg cells from WT and Ptenfl/flFoxp3-Cre mice were purified from spleen and peripheral lymph nodes by flow cytometry

HT MG-430PM arrays were scanned using the Affymetrix GeneTitan system

Probe signals were quantile normalized and summarized by the RMA algorithm using Partek Genomics Suite software v6.5

RNA was extracted using Qiagen's RNAeasy kit, with on-column DNase digestion included.

Six (6) micrograms of cRNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix HT MG-430 PM array. Following hybridization, arrays were washed and stained using the GeneTitan system

Biotinylated cRNA were prepared according to the standard Affymetrix 3’IVT Express protocol starting with 100 ng of total RNA (GeneChip 3’ IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix)

Mice were given a single dose of 1mg/kg Aplidin and 50mg/kg AraC.

Mice were kept in CINJ vivarium under standard condition. SKI-DLCL cells were injected s.c.

Washing, Staining, and Scanning

Water, Molecular Biology Grade
Distilled water
Acetylated Bovine Serum Albumin (BSA) solution (50 mg/mL)
R-Phycoerythrin Streptavidin
20X SSPE (3M NaCl, 0.2M NaH2PO4, 0.02M EDTA)
Goat IgG, Reagent Grade
Anti-streptavidin antibody (goat), biotinylated
10% surfact-Amps 20 (Tween-20)

Hybridization

Water, Molecular Biology Grade or DEPC-treated
Herring Sperm DNA
GeneChip Eukaryotic Hybridization Control Kit
5M NaCl, RNase-free, DNase-free
MES Free Acid Monohydrate
MES Sodium Salt
EDTA Disodium Salt

Miscellaneous Reagents/Supplies

Surfact-Amps 20 (Tween-20), 10%
Hybridization Oven 640
Sterile, RNase-free, microcentrifuge tubes, 1.5mL
Micropipettors
Sterile-barrier pipette tips and non-barrier tips
Heatblock

Synthesis of Biotin-Labeled cRNA/Purification

ENZO BioArray RNA Transcript Labeling Kit
GeneChip Sample Cleanup Module

100% ethanol room temperature
80%   ethanol room temperature
Ethidium Bromide
Sterile-barrier, RNase-free pipette tips
Mini agarose gel electrophoresis unit with appropriate buffers
UV Spectrophotometer
Cooling water bath

Sample processed by CINJ core expression array facility according to Affymetrix protocol.

SKI-DLCL tumor grown in CB-17 scid/scid mice. Tumor was harvested on day eight following the treatment. Total RNA was extracted using RNeasy kit.

RNA isolated from SKI-DLCL tumor harvested from mice treated with Aplidin and AraC

Cells were grown under standard cell culture condition (95% air, 5%CO2, 37 C)

100% ethanol ? room temperature
80%   ethanol ? room temperature

RMA normalization, log2 transformed, probe value mean-centered, mean=0, stdv=1

Mouse skin tissue, obtained after birth, was preserved in RNAlater (Ambion), and disrupted and homogenized using Mixer Mill MM301 (Retsch). Total RNA was extracted and purified from 30 mg of skin using RNeasy Fibrous Tissue Mini kit (Qiagen) following manufacturers' recommendations

SKI-DLCL cells untreated, cultured for 24h, total RNA was isolated using RNeasy kit

Cells were treated with vehicle (DMSO/ethanol). Ligands or vehicle were added to the cell culture starting from the first day.

Monocytes were cultured for 5 days with 500 U/ml IL-4 and 800 U/ml GM-CSF, cytokine treatment was repeated at day 3.

Total RNA was isolated using Trizol Reagent (Invitrogen) and further purified by using the RNeasy kit (Quiagen).

cRNA was generated from 5 μg of total RNA by using the SuperScript Choice kit (Invitrogen) and the High Yield RNA transcription labeling kit (Enzo Diagnostics).

Monocytes (98% CD14+) were obtained from Buffy coats by Ficoll gradient centrifugation and magnetic cell separation using anti-CD14-conjugated microbeads (VarioMACS; Miltenyi Biotec)

freshly isolated human monocyte;female; age: 19 yr; weight: 65 kg

SLM2, VMM39, and DM331 cells were plated and incubated overnight before being treated, in duplicate, with inhibitors or vehicle control in phenol red-free RPMI Medium 1640 without fetal bovine serum for 8 hours at 37°C. Cells were placed on ice and rinsed with cold 1x PBS.

Cell line VMM39, mutant status Ras, condition Treated with Sorafenib 2

The gene array was performed using Illumina 3’IVT human HT-12 BeadChip arrays by Gene Analysis (Durham, NC).

Cells were collected and RNA was isolated using the Qiashredder (Qiagen, Valencia, CA) and RNeasy Mini Kit (Qiagen, Valencia, CA).

RNA from Cell line VMM39, mutant status Ras, condition Treated with Sorafenib

Cell line VMM39, mutant status Ras, condition Treated with Diclofenac 2

RNA from Cell line VMM39, mutant status Ras, condition Treated with Diclofenac

Cell line VMM39, mutant status Ras, condition Treated with Sorafenib+Diclofenac 1

RNA from Cell line VMM39, mutant status Ras, condition Treated with Sorafenib+Diclofenac

Cell line VMM39, mutant status Ras, condition Treated with Sorafenib 1

Cell line VMM39, mutant status Ras, condition Treated with Diclofenac 1

Male mice of C57BL/6J background with or without IL10 gene knockout were kept in conventional conditions (not germ-free or specific-pathogen-free) from approximately 5 weeks of age and inoculated with a mixture of Enteroccocus strains and complex intestinal flora harvested from C57BL/6J mice kept in conventional conditions. Mice were fed AIN76A diet and euthanased by CO2 followed by cervical dislocation.

Scanned on an Agilent G2565AA scanner and images were quantified using Agilent Feature Extraction Software (version 8.5.1.1 (samples 1-24) or 10.10.1.1 (samples 24-47)).

Cy5 and Cy3 intensity ratios for all microarray spots were normalized using a global loess algorithm using the limma package in R 2.14.1.  No background correction was applied. Spots that did not pass quality control metrics were flagged and removed from the normalisation calculations.
Note that samples 1-24 were analysed as one experiment, and samples 25-47 were analysed as another up to generation of differentially expressed gene lists. These two sets of arrays cannot be directly compared due to the different amplification procedure required for samples 25-48 due to starting material limitations.

Total RNA was extracted from frozen colon samples using Trizol according to the manufacturer instructions followed by cleanup with Qiagen RNeasy columns according to manufacturer instructions for all channel 1 samples and samples 1-24 of channel 2. Total RNA was extracted from frozen microdissected colon epithelial cells using the Arcturus Picopure RNA extraction kit for channel 2 samples 25-48.

Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed. All steps were performed according to the manufacturer instructions - protocol G4140-90050_Hyb_Label_two-colour_GE_v5.5.

For channel 1, all samples, and channel 2, samples 1-24, 500 ng total RNA was amplified according to the Agilent protocol protocol G4140-90050_Hyb_Label_two-colour_GE_v5.5. For channel 2 samples 25-47, 30 ng total RNA was amplified using 2 rounds of amplification by the Arcturus RiboAmp Plus kit and labelled using the Arcturus Turbo Labelling kit.

Swiss;adult mouse intestine, kidney, and liver plus fetus tissue;C57BL/6J;IL10-/-;12 weeks;colon

Swiss;adult mouse intestine, kidney, and liver plus fetus tissue;C57BL/6J;wildtype;6 weeks;colon

Swiss;adult mouse intestine, kidney, and liver plus fetus tissue;C57BL/6J;IL10-/-;6 weeks;colon

Pancreata from e10.5, e15.5, or p23 pancreata were dissected and dissociated with collagenase B and trypsin, if necessary, to create single cell suspensions that were subjected to FACS.  Cells expressing high levels of GFP were collected for analysis for each population. For the Sox9-EGFPneg_p23 samples, the GFP negative cell population was also collected. Multiple animals were pooled before sorting for each population to achieve sufficient cell numbers.

All animal experiments described herein were approved by the University of California, Irvine and San Diego Institutional Animal Care and Use Committees. Sox9-EGFP or Ngn3-EGFP males were crossed with CD1 (Charles River) wild-type females and embryos were harvested at e10.5 or e15.5.  Alternatively, pancreata were harvested from Sox9-EGFP pups at p23. For timed matings, noon on the day of vaginal plug appearance was designated e0.5.

Gene chips were scanned on an Affymetrix GeneChip 3000 Scanner 7G.

The results were quantified and analyzed using Expression Console ver.1.1 software (Affymetrix, Inc.) using the PLIER Algorithm default values (Quantification Scale: Linear; Quantification Type: Signal and Detection P-Value; Background: PM-GCBG; Normalization Method: Sketch-Quantile).

Total RNA isolation was performed with the Qiagen Micro RNA kit according to the manufacturer's instructions.  The optional on column DNAse digestion was performed. Using the NuGEN Ovation RNA Amplification System V2 (NuGEN Technologies, San Carlos, CA) first strand cDNA was synthesized from the poly(A)+ mRNA present within the isolated total RNA (20 ng total RNA starting material used in each sample reaction). Fragmentation of the mRNA within the resulting cDNA/mRNA complexes created priming sites for DNA polymerase to synthesize DNA complementary to the first strand cDNAs. The resulting double stranded (ds) cDNAs have a unique DNA/RNA heteroduplex at one end. These ds DNA templates were used to perform linear isothermal DNA amplification (SPIA, NuGEN Technologies, San Carlos, CA).

After labeling the resulting fragmented, biotin-tagged cDNA (2.2 μg) was placed into a hybridization cocktail (220 μL), with 200 μL actually hybridized at 45°C with rotation for 18 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix Mouse Gene 1.0 ST array. The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450 using the FS450_0004 fluidics protocol.

Biotinylated cDNA were prepared according to the NuGEN FL-Ovation cDNA Biotin Module V2 protocol after fragmentation of 3.75 ug of the amplified cDNA (NuGEN Technologies, San Carlos CA).

The algorithm, implanted in Affymetrix Suite Version 5.0 (MAS5) generates signal value (which designates a relative measure of the abundance of the transcript), a detection p-value (which indicates the reliability of the transcript’s detection call) and detection call (present, absent or marginal). For interarray comparisons, the data from each array was scaled using MAS5. The bioinformatics analysis was carried out using GeneSpring® version7 software (Silicon Genetics, Redwood City, CA, USA). Normalization procedure: Values below 0.01 were set to 0.01.  Each measurement was divided by the 50.0th percentile of all measurements in that sample (per chip normalization). Each gene was divided by the median of its measurements in all samples (per gene normalization). Genes were filtered out if appearing present in only none or 1 of the 8 samples.

RNA was extracted from cells as described before and quality was assessed on Agilent 2100 Bioanalyzer device (Agilent Technologies, Palo Alto, CA) from the indicated cell lines and clones. If MAB treatment is indicated, cells were exposed for 1:40 SWA11 MAB for 72h. RNA was labeled and hybridized as described before (8), only this time, using the human (HG-U133A) Genechip® (Affymetrix Inc., Santa Clara, CA).

HT29 derived clone with 2 vectorS expressing CD24 directed shRNA

At 30 months of age mice were euthanized via cervical dislocation; organs were dissected, flash-forzen in liquid nitrogen and stored at -80C for future analysis

B6C3F1 hybrid mice were individually housed and fed on of the following three diets from 14 to 30 months of age: control AIN93M diet, 40% calorie restricted diet, or a control diet supplemented with resveratrol to achieve a dose of 4.9 mg resveratrol per kg bodyweight

The data were analyzed with GeneChip Operating System 1.2 (GCOS 1.2) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

The data were normalized using RMA method with arrays on the plate.  Batch correction was done using ComBat.

mRNA was isolated from SN in accordance with the protocol outlined in RNAqueous-Micro kit (Ambion, Austin, TX) according to manufacturer's recommendations.

Following fragmentation, 5 microgram of cRNA were hybridized for 16 hr at 45C on HT MG-430 PM array plate.  Arrays were washed and stained in the Affymetrix GeneTitan.

Biotinylated cRNA were prepared according to the standard Affymetrix expression protocol from 100 nanograms total RNA (GeneChip 3' IVT Expression Kit, P/N 702646 Rev. 5).

Gene expression data from mRNA of substantia nigra from saline-treated mouse

gastrocnemius-30 months of age-control diet-biological replicate1

gastrocnemius-30 months of age-control diet-biological replicate2

gastrocnemius-5 months of age-control diet-biological replicate4

gastrocnemius-30 months of age-control diet-biological replicate5

gastrocnemius-30 months of age-control diet-biological replicate3

gastrocnemius-30 months of age-control diet-biological replicate4

The data were analyzed using the RMA algorithm and then SAM was applied to calculate significant differential expression between samples

Sample was hybridized to Human Gene 1.0 ST Array (Affymetrix) using a GeneChip Hybridization Oven 640

100-300 ng of total RNA were amplified and labeled using the WT Sense Target labeling system and control reagents (Affymetrix)

Total RNA from MDA-MB-231 cells infected with a lentivirus shLOXL2

Cells were transduced with vector or Cebpa shRNA, puromycin selected, and cultured in IMDM plus 10% FBS and containing 10 ng/mL IL3, 10 ng/mL IL6, and 50ng/ml SCF for 2 days.

Lineage negative bone marrow cells were cultured in IMDM plus 10% FBS and containing 50 ng/mL murine stem cell factor (SCF), 100 ng/mL murine FLT3 ligand (FL), and 10 ng/mL murine thrombopoietin (TPO, Peprotech) for 24 hrs.

Dried arrays were stored in a dark box until scanned with iScan System.

Data were extracted with Gene Expression Module in GenomeStudio Software.

Total RNA was prepared using the NucleoSpin RNA II kit with on-column DNase digestion. RNA quality was confirmed via Nanodrop-1000 spectrometric analysis and via a Bioanalyzer.

750 ng biotin-labeled cRNA was combined with hybridization buffer and hybridized to the array at 58°C for 16-20 hours. After hybridization, the hybridization cartridge was disassembled and the array was washed with buffer at 55C and blocked at room temperature. Bound biotinylated cRNA was stained with streptavidin-Cy3 and then washed.

500 ng total RNA from each sample was amplified and labeled using the Illumina TotalPrep RNA Amplification Kit (AMIL1791, Ambion, Austin, TX) as described in the instruction manual.

Standard Affymetrix Protocol
Keywords = microarray
Keywords = extraocular muscle

Cells were transiently transfected with MED1 expression vector or empty vector control using Lipofectamine.

GeneChips were scanned using the Affymetrix G7  GeneArray Scanner.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChips. The arrays were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA  (Affymetrix).

Gene expression data from LNCap cells transfected with MED1 expression vector

In one well of a 24-well dish, 7X10^4 cells were transfected with 100 ng esiRNA using Lipofectamine 2000. After 12-15 hours, the media was replaced and cells were cultured until 48 hours post-transfection.

Feeder-free growth on gelatin coated dishes in standatd ES medium: KO DMEM + 10% FBS, glutamine, LIF, non-essential amino acids, beta-mercaptoethanol.

Slides were scanned on the Agilent scanner immediately after washing.

The scanned images were analyzed with Feature Extraction Software 10.1 (Agilent) using default parameters. We used quantile normalization.

Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

Mice 42 h of age received an intracranial inoculation of 4x10(4) PFU Edmonston MeV (infected) or an equivalent volume of phosphate-buffered saline (uninfected) in the left cerebral hemisphere.

H-2(d) congenic C57BL/6 mice, with (TG) or without (NT) the human hsp70 transgene driven by the neuron-specific enolase promoter, were used in these studies.

Affymetrix GeneChip Scanner 3000 7G using GCOS (GeneChip Operating Software).

Raw data were analyzed through Bioconductor package affy. The RMA method was used as the background-correction, normalization, and probe summarization method.

Total brain RNA was isolated from the right cerebral hemisphere, 5 or 10 d.p.i., using the RNeasy lipid tissue mini-kit (Qiagen).

Samples were hybridized using Herring sperm DNA, acetylated BSA (50mg/mL), BioArray Eukaryotic Hybridization Controls (Enzo Life Sciences); heat 65C for 5 min, 90C for 5 min, 45C for 5 min, centrifuge top speed for 5 min; hybridize 16 h at 45C, 60rpm; Fluidics script EukGE-WS2v4_450.

2ug RNA was enzymatically labeled using the BioArray High Yield RNA Transcript Labeling kit (Enzo).

MO-B10-Tg 9
Gene expression data from MeV-infected TG mice brain at 10 d.p.i.

C57BL/6;hsp70 transgenic;brain (right cerebral hemisphere);12 days;measles virus (MeV);10

MO-B10-Tg 8

The chips were scanned using the Affymetrix GeneChip Scanner 3000 using defalt settings and a target intensity of 250 for scaling.

Microarray analysis was performed in dChip. There was information available on 22,690 genes for each array. Normalization was performed using the invariant set method by Wong and Li (2001). ANOVA filtering criterion was used, with a cutoff of p<=0.02. Groups were compared using the following criteria: ratio greater than 2.0, p-value for testing Experimental=Baseline less than 0.05, P call of either Baseline or Experimental greater than 20%.

Total RNA was extracted from cell pellets using Qiagen microcolumns

Arrays were hybridized using standard Affymetrix protocol as described in Lockhart et al, 1996. (http://affymetrix.com)

Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle target labeling protocol  (Affymetrix P/N 900494).

C57BL/6;control mice (Runx1floxed/floxedMxCre-/-);bone marrow;sorted c-Kit+/Sca-1+/Lin-/IL7Ra- (KSL) cells;3 months after poly IC treatment

Test Compound:  Deltamethrin
Test Compound CAS#:  52918-63-5
Isomer Composition:  100 % (1R, 3R, alpha-S)
Purity:  98.9 %
Vehicle:  Corn Oil
Vehicle CAS #:  8001-30-07
Administration Route:  Oral Gavage
Test Compound Concentration:  0.3 mg/mL
Delivery Volume:  1 mL / kg body weight
Expsoure Duration:  Single, Acute
Sampling Time:  6 Hours post-exposure

Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding.  Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment.  Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%.  Purina 5001 Rat Chow and tap water were provided ad libitum.

GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.

Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions.  Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour.  DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7.  Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min.  Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min.  Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH = 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min.  Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.

Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).

First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021).  Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol.  Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol.  Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.

This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.

Test Compound:  Permethrin
Test Compound CAS#:  52645-53-1
Isomer Composition:  40%-cis, 60%-trans, 1:1 ratio of 1R, 1S
Purity:  92.0 %
Test Compound Concentration:  100 mg/mL
Delivery Volume:  1 mL/kg body weight

Technical duplicate of pooled soleus muscle from five female mice, age 6 months

MO-B10-Tg 2
Gene expression data from MeV-infected TG mice brain at 5 d.p.i.

C57BL/6;hsp70 transgenic;brain (right cerebral hemisphere);7 days;measles virus (MeV);5

disease modifying antirheumatic drugs (DMARD), non-steroidal anti-inflammatory drugs (NSAID), steroids

Total RNA was isolated using TRIzol Reagent (Invitrogen) followed by column based clean up (RNeasy, Qiagen).

Fifteen micrograms of each cRNA sample was hybridized for 16 hours at 45°C to human expression Affymetrix HG U95Av2 GeneChip arrays. Following the hybridization arrays were washed and stained with streptavidin-phycoerythrin using a fluidics station in accordance with the Affymetrix protocol.

The amplification and labeling of the RNA samples were carried out according to the manufacturer's instructions (Affymetrix, Santa Clara, CA). Briefly, total RNA was quantified by UV-spectroscopy and its quality evaluated by analysis on a LabChip (BioAnalyzer, AGILENT Technologies, Santa Clara, CA). In the presence of an oligo(dT)24 primer containing a T7 RNA polymerase promoter (Operon Biotechnology, Huntsville, AL, USA) five micrograms of total RNA were used for double-stranded cDNA synthesis (SuperScript transcriptase, Life Technologies, Inc., Carlsbad, CA). Labeled complementary RNA (cRNA) was prepared from double-stranded cDNA by in vitro transcription using the bioarray high yield RNA transcription kit (Enzo Diagnostics, Farmindale, N.Y., USA). After cleanup (Qiagen, Hilden, Germany), the biotin-labeled cRNA was fragmented by alkaline treatment (40 mM Tris-acetate (pH 8.2), 100 mM potassium acetate, and 50 mM magnesium acetate) at 94°C for 35 minutes.

Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6µm cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). EBV-harboring cells were identified by detecting EBV-encoded small RNAs (EBERs) using the EBV Probe In Situ Hybridization Kit (NCL-EBV-K, Novocastra laboratories, Newcastle upon Tyne, UK). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens, using an Arcturus Pixcell-II LCM microscope and CapSure Macro LCM caps (Arcturus Bioscience, Mt. View, CA). Typically, from one to a few thousand cells per sample were captured.

Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of National Taiwan University, UW-Madison, and U.S. NCI. After resection, specimens were immediately flash frozen and stored in liquid nitrogen. Histopathology and tumor staging definitions and information are provided in Sengupta et al, 2006, Cancer Research 66(16): 7999-8006.

Microarray scanning and data acquisition was carried out at the University of Wisconsin-Madison Gene Expression Center using Affymetrix-recommended equipment and procedures.

Detailed description of data analyses and statistical methods used are provided in two primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006; Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225.

RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.

Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.

Polyadenylated RNA was amplified twice using Affymetrix’s Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring β-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).

Total RNA extracted from laser-captured epithelium from 31 nasopharyngeal carcinomas and 10 normal healthy nasopharyngeal tissue specimens.

According to Affymetrix Gene expression Analysis Technical manual REV.3

Affymetrix CEL files were used for Robust MultiChip Analysis (RMA)

Trizol extraction of total RNA was performed according to the manufacturer's instructions

Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

Biotinylated cRNA were prepared according to the Two-cycle Affymetrix protocol from 50 nanograms total RNA

Following fragmentation. 10 micrograms of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

Following fragmentation 10 micrograms of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

When indicated, cells were grown in DMEM supplemented with either 10 nm farnesyltransferase inhibitor L-744832 (Biomol, Plymouth Meeting, PA, USA) or DMSO and 15% fetal bovine serum, 2 mm l-glutamine, 100 U mL−1 penicillin and 100 µg mL−1 streptomycin at 37 °C in 5% CO2, and 3% O2. Media was changed every 4 days.

Primary dermal fibroblast cell line (GM00038) from healthy individual was obtained from the Coriell Cell Repository. Cells were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 15% fetal bovine serum, 2 mm l-glutamine, 100 U mL−1 penicillin and 100 µg mL−1 streptomycin at 37 °C in 5% CO2, and 3% O2. Cells seeded at 1.4 × 10exp5 per 100-mm-diameter dish were passaged when cultures reached 85% confluency.

A Fluidics Station 400 (Affymetrix) was used to wash and stain the chips and fluorescence was detected using a G2500 GeneArray Scanner (Hewlett-Packard).

Raw data were analyzed initially using Microarray Suite version 5.0 (MAS 5.0, Affymetrix)

Total RNA was isolated from each fibroblast line at passage 10 using RNeasy kit from QIAGEN according to the manufacture’s protocol and quantitated by assessing absorbance at 260 and 280 nm using a NanoDropTM 1000 spectrophotometer.

Three micrograms of total RNA was then submitted to the University of Southern California Affymetrix MicroArray Core Facility at Children's Hospital Los Angeles for processing, chip hybridization, and scanning. Gene expression was analyzed on an Affimetrix gene chip Human Genome U133 Plus 2.0 Array,

Ero1α expression was either not induced or induced for 24 h using 1 mg/mL doxycline (Sigma).

Doxycline-inducible Flp-In T-REx HEK-293 cell lines were grown in a-minimal essential medium (Invitrogen), supplemented with 10% FCS, 100 mg/mL hygromycin B (Invitrogen) and 15 mg/mL blasticidin (Invivogen) at 37°C, 5% CO2.

The arrays were scanned in the Affymetrix GeneArray® 3000 scanner to generate fluorescent images, as described in the Affymetrix GeneChip® protocol.

Cell intensity files (CEL files) were generated in the GeneChip® CommandConsole® Software (AGCC) (Affymetrix, Santa Clara, CA, USA). The raw data was RMA-normalized using the R Bioconductor package 'affy' and used for a 2-way ANOVA with the cell line and induction status used as factors.

RNA was extracted using TRI Reagent (Sigma) according to the manufacturer’s instructions.

The labeled samples were hybridized to the Human Gene 1.0 ST GeneChip array (Affymetrix, Santa Clara, CA, USA). The arrays were washed and stained with phycoerytrin conjugated streptavidin (SAPE) using the Affymetrix Fluidics Station® 450.

Biotinylated cDNA were prepared by amplifying and labeling 250 ng RNA using the Ambion WT Expression Kit (Applied Biosystems) according to manufacturer’s guidelines.

Inducible stable HEK 293 Flp-In T-REx Ero1alpha-C104A/C131A cells, expression induced with doxycycline for 24 h

10;fibroblast;overexpressing prelamin A treated with FTI;GM00038

Subjects infected with HPV-16 rhinovirus or sham-infected prior to nasal epithelial scraping.  Only subjects exhibiting rhinovirus infection were used for collection.

Total RNA was extracted from nasal scrapings using Trizol Reagent and protocol provided by supplier.  Extracted RNA was further purified using Qiagen RNEasy Micro columns and protocol provided by supplier.

Following fragmentation, cDNA was hybridized for 16 hr at 45C on GeneChip Human U133plus2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Purified RNA was converted to biotinylated cDNA target using NuGEN Ovation Biotin kit and protocol provided by supplier.

Standard Trizol protocol extraction. Total RNA pools from 3-5 mice were processed and hybridized to each microarray.

Wild type, snap frozen, tibialis anterior muscle, 10 month age animal

Transgenic for alpha tropomyosin slow, snap frozen, tibialis anterior muscle, 7month age animal

Transgenic, snap frozen, tibialis anterior muscle, 7month age animal

Transgenic for alpha tropomyosin slow, snap frozen, plantaris muscle, 7month age animal

Wild type, snap frozen, tibialis anterior muscle, 7month age animal

Transgenic for alpha tropomyosin slow, snap frozen, plantaris muscle, 10 month age animal

The arrays were scanned using the Affymetrix GeneChip® Scanner 7G. Scanned image files was visually inspected for artefacts and then analyzed, each image being scaled to the same target value for comparison between chips. The GeneChip® Operating Software (GCOS) was used to control the fluidics station and the scanner, to capture probe array data and to analyze hybridization intensity data.

Array data was normalized using scaling or per-chip normalization to adjust the total or average intensity of each array to be approximately the same.
Microarray chips were analyzed by the GCOS (GeneChip Operating Software) from Affymetrix with the default settings except that the target signal was set to 500 and used to generate a microarray quality control and data report.
CEL files exported from GCOS were uploaded into ArrayTrack software (National Center for Toxicological Research, U.S. FDA, Jefferson, AR, USA (NCTR/FDA)) and normalized using Total Intensity Normalization after subtracting backgrounds for data management and analysis. ArrayTrack software includes some tools common to other bioinformatics software (e.g., ANOVA, T-test and SAM).To compare the normalized data from dysplasia, normal lung tissue from transgenic mouse, tumor cells and non-transgenic of different mice, we used the Significance Analysis of Microarrays (SAM) algorithm (ArrayTrack), which contains a sliding scale for false discovery rate (FDR) of significantly up- and down-regulated genes [70]. All data were permuted 100 cycles by using the two classes, unpaired data mode of the algorithm. As cut-off for significance an estimated FDR of 0.001 was chosen. Moreover, a cut-off for fold-change of differential expression of 2 was used.
Two clustering approaches were used to determine components of variation in the data in this study as follows.
A) Principal-component analysis (PCA) that was used to obtain a simplified visualization of entire datasets. PCA is a useful linear approach to obtain a simplified visualization of entire datasets, without losing experimental information (variance). PCA allowed the dimension of complex data to be reduced and highlights the most relevant features of a given dataset to be highlighted.
B) Hierarchical gene clustering (HCA) where the data points were organized in a phylogenetic tree in which the branch lengths represent the degree of similarity between the values.

From each frozen lung tissue 10-µm thick sections were prepared and transferred on polyethylene napthalate foil-covered slides (Zeiss, P.A.L.M. Microlaser Technologies GmbH, Bernried, Germany).
The sections were fixed in methanol / acetic acid and stained in hematoxylin. The desired cells were microdissected using the PALM MicroLaser systems (Zeiss, P.A.L.M. Microlaser Technologies GmbH, Bernried, Germany) and collected in an adhesive cap (Zeiss, P.A.L.M. Microlaser Technologies GmbH, Bernried, Germany). Microdissected cells were resuspended in a guanidine isothiocyanate-containing buffer (RLT buffer from RNeasy MikroKit, Qiagen, Santa Clarita, CA, USA) with 10 µl/ml β-mercaptoethanol to ensure isolation of intact RNA. Approximately an area of 6 x 106 µm2 were pooled from a specific layer of interest in the same animal and used for RNA extraction.
Following microdissection, total RNA-extraction was performed with the RNeasy Micro Kit (RNeasy MicroKit Qiagen, Santa Clarita, CA, USA) according to the manufacturer’s instruction. A standard quality control of the total RNA was performed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

Following fragmentation, labeled cRNA of each sample was hybridized to Affymetrix GeneChip® Mouse Genome 430 2.0 Arrays covering over 34.000 genes and stained according to the manufacturer's instructions.
The hybridization was performed for 16 hours at 60 rpm and 45°C in the GeneChip® Hybridization Oven 640 (Affymetrix). Washing and staining of the arrays were done on the Gene Chip® Fluidics Station 400 (Affymetrix) according to the manufacturers recommendation. The antibody signal amplification, washing and staining protocol (Affymetrix) was used to stain the arrays with streptavidin R-phycoerythrin (SAPE). To amplify staining, SAPE solution was added twice with a biotinylated anti-streptavidin antibody (Vector Laboratories, CA) staining step in between

Total RNA (175ng) was used to generate biotin-labeled cRNA (10 µg) by means of Message Amp aRNA Premium Amplification Kit (Ambion, Austin, TX). Quality control of cRNA was performed using a bioanalyzer (Agilent 2001 Biosizing, Agilent Technologies).

Lung samples were derived from SP-C/c-raf mice in the C57BL/6 background for at least five generations (aged 5 – 10 months); dysplastic and unaltered lung tissue were always isolated from the same dysplasia-bearing transgenic mouse (aged 5 – 7 months). Endogenous normal lung tissue was studied of non-transgenic mice (aged 7 – 10 months). The non-transgenic littermates (wild-type) served as control for transgenic effects.
Mice were sacrificed and the lung tissues were immediately frozen on dry ice and stored at -80°C until further analysis.

Growth protocol: Human prostate cancer cells M12 were maintained in serum-free RMPI-1640 containing L-glutamine (10ng/ml), epidermal growth factor (0.1μM), dexamethazone, ITS (5μg/ml each of insulin, transferring and selenium), 0.05mg/ml gentamicin, and 2.5 ug/ml amphotericin B.

The raw Affymetrix expression values were normalized and analyzed for differential expression using the Limma package of the R program. T-tests were performed to establish p-values for differential expression.

RNA Purification: RNA was extracted from shSCR-M12 (scrambled control) or shEGR3-M12 cells using the RNeasy Plus kit (Qiagen) and resuspended in water. RNA integrity was assessed by electrophoresis on formaldehyde gels and the RNA was quantified using a Beckman Du800 spectrophotometer. The excellent quality of the RNA was confirmed using an Agilent Bioanalyzer 2100. One μg RNA was converted to cDNA using the Quanta qScript cDNA Super-mix (5 min at 25C; 30 min at 42oC; 5 min at 85oC) in a thermocycler.

The University of California Genomics High Throughput Facility carried out the in vitro transcription and the hybridization according to their standard protocol (http://ghtf.biochem.uci.edu)

human prostate cancer cells; clone 2-2
human prostate cancer cells

Splenic B-cells were collected from 1-week-old CBA (used as controls), Xid/CBA (obtained from Charles River Laboratories, Sweden), and BtkKO/CBA mice (created by back-crossing BtkKO/SW129 mice on CBA background strain for nine generations). In the spleens of 1-week-old mice, all B-cells are of T1 origin [26]. CD19+ (PE-conjugated rat anti-mouse-CD19 antibodies) B-cells were sorted in a FACS Vantage Diva Cell sorter, Beckton–Dickinson. The purity of the cells was >92%. Total RNA from T1 B-cells was extracted with RNeasy Mini kit (Qiagen, Valencia, CA, USA). The Affymetrix small sample protocol consisting of two rounds of amplification was used to obtain a larger amount of cRNA. Hundred ng cRNA was hybridised to MOE430 2.0 GeneChips®. The cRNA synthesis and hybridisations were performed in the BEA core facility at Department of Biosciences, Karolinska Institutet, Novum, Huddinge, Sweden.

As recommended by Affymetrix.  The cRNA synthesis and hybridisations

Monocytes were plated in 6-well tissue culture plates (Nunclon, Denmark) at 1-2 x10^6 cells per well and incubated in complete IMDM medium containing 5% (v/v) human serum and 1% (v/v) penicillin/streptomycin, in a humidified incubator at 37 °C and 5% CO2.

Array data were extracted at the probe level with no background correction using Illumina's BeadStudio software. These raw data were quantile normalized. Statistical analysis and differential gene expression were carried out using the limma package in R 2.12.2/Bioconductor. Resulting p-values were corrected for multiple testing using the Benjamini-Hochberg false discovery rate.

Total RNA was extracted from monocytes using an RNeasy Mini Kit (Qiagen) as per the manufacturer's specifications. Extracted RNA was run and quantified on a Bioanalyser (Agilent) for quality control and used subsequently in the microarray assay.

Total RNA samples were amplified and biotinylated using the Illumina TotalPrep RNA amplification Kit (Ambion, Austin, TX).

three mice per group were used; the spleen from an individual mice was extracted and homogenized in TriFast; 5 µg total RNA were labeledand hybridized to MOE430A 2.0 GeneChips

The arrays were scanned using the Affymetrix Model 3000 scanner by the University of Iowa DNA Core Facility according to the protocols recommended by the manufacturer.

The RMA method was used to adjust the background of perfect match (PM) probes, apply a quantile normalization of the corrected PM values and calculate final expression measures using the Tukey median polish algorithm.

For each experiment a fresh batch of cells was used, which was stored in liquid nitrogen. Cells were propagated for one passage and then seeded at the density of 3×105 cells/cm2. After 48h of growth, when cultures achieved about 80% confluency, cells were treated with either 1 uM Rosi or the same volume of vehicle (DMSO) for 2, 24, and 72h. RNA was isolated for each time point using the RNeasy kit (QIAGEN Inc., Valencia, CA). Replicate experiments were performed independently on a fresh batch of cells.

The resulting biotinylated cRNA was fragmented and hybridized to the GeneChip® Mouse Genome 430 2.0 Array (Affymetrix, Inc.). The arrays were washed and stained using the Affymetrix Model 450 Fluidics Station by the University of Iowa DNA Core Facility according to the protocols recommended by the manufacturer.

RNA quality was assessed using the Agilent Model 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). For each microarray five micrograms of total RNA was processed using the Affymetrix GeneChip® one-cycle target labeling kit (Affymetrix, Inc., Santa Clara, CA) according to the protocol recommended by the manufacturer.

Murine marrow-derived U-33 cells (previously referred as UAMS-33) represent a clonal cell line spontaneously immortalized in long term bone marrow cultures. To study the effect of PPARg2 on marrow mesenchymal stem cell differentiation, U-33 cells were stably transfected with either a PPARg2 expression construct (U-33/g2 cells) or an empty vector control (U-33/c cells). Several independent clones were retrieved after transfection and carefully analyzed for their phenotype. Clone 28.6 (representing U-33/g2 cells) and clone gammac2 (representing U-33/c cells) were used in the presented experiments.  Cells were maintained in alphaMEM supplemented with heat-inactivated 10% FBS (Hyclone, Logan, UT), 0.5 mg/ml G418 for positive selection of transfected cells, 100 U/ml penicillin, 100 ug/ml streptomycin, and 0.25 ug/ml amphotericin (Sigma) at 37oC in a humidified atmosphere containing 5% CO2. Media and additives were purchased from Life Technologies (Gaithersburg, MD).

U-33 cells stably transfected with an empty vector control (U-33/c cells);72 hrs;Rosiglitazone present

Samples were snap frozen in liquid nitrogen at the time of collection

N/A - samples were biopsies collected at the time of endoscopy from the normal oesophagus, Barrett's oesophagus and gastric cardia

Softwares/Tools used for the data processing were Affymetrix GeneChip Command Console Software (AGCC), and Partek Genomic Suite 6.5. For the creation of the summarized log-signal, the Robust Multichip Average (RMA) with Quantile normalisation and Median Polish for Probe set summarisation were used

Biopsies were homogenised in Trizol using the Precellys. A standard Trizol extraction method was used.

Samples were hybridized to Affymetrix Human GeneChip 1.0ST arrays using Affymetrix Hybridization Kit following manufacturer's instructions for the 49/64 format array. Wash and stain of arrays was carried out on geneChip Fluidics 450 Workstation using protocol FS450_0007

WT Expression Kit (Ambion) was used to obtain ss cDNA which was then labelled and fragmented using Affymetrix WT Terminal Labelling Kit according to manufacturing instructions

Background and Aims:  Although the zinc finger transcription factor GATA4 has been implicated in regulating jejunal gene expression, the contribution of GATA4 in controlling jejunal physiology has not been addressed. Methods: We generated mice in which the Gata4 gene was specifically deleted in the small intestinal epithelium.  Measurements of plasma cholesterol and phospholipids, intestinal absorption of dietary fat and cholesterol, and gene expression were performed on these animals. Results: Mice lacking GATA4 in the intestine displayed a dramatic block in their ability to absorb cholesterol and dietary fat. Comparison of the global gene expression profiles of control jejunum, control ileum, and GATA4 null jejunum by gene array analysis demonstrated that GATA4 null jejunum lost expression of 53% of the jejunal-specific gene set and gained expression of 47% of the set of genes unique to the ileum. These alterations in gene expression included a decrease in mRNAs encoding lipid and cholesterol transporters as well as an increase in mRNAs encoding proteins involved in bile acid absorption. Conclusion: Our data demonstrate that GATA4 is essential for jejunal function including fat and cholesterol absorption and confirm that GATA4 plays a pivotal role in determining jejunal versus ileal identity.

Gata4Loxp/-VillinCre adult male jejunum (6-8wk). GATA4 conditional knockout (mutant) sample.

Primary data analysis was done with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Data were normalized using a rank based normalization algorithm (rank mean) in MatLab.

Total RNA was extracted from rectal suction biopsies of CF patients and non-CF individuals using the RNAeasy mini kit (Qiagen, Hilden, D). Quality of total RNA was monitored by gel electorphoresis.

The Human GeneChip HG-U133A was hybridized and analyzed in an Affymetrix workstation (fluidic-station and scanner). Primary data were obtained with the Affymetrix microarray suite version 5.0.

Labeled cRNA was prepared following the basic Affymetrix protocol with minor modifications. In short, double stranded cDNA was synthesized using a customary oligodT-T7 cDNA synthesis primer (Affymetrix, Santa Clara, CA, USA). The labeled antisense cRNA was generated using T7-RNA-polymerase (Enzo, Farmingdale, NY, USA) and biotin-labeled NTPs (Enzo).  For fragmentation labeled cRNA was heated to 94° C for 35 min in the presence of 150 mM magnesium (Mg2+).

experimental design: Collect rectal mucosal epithelia by suction biopsy from CF-patients, homocygous for the CFTR D508 mutation and from non CF-individuals; monitor activity of mucosal epithelia by ICM; analysis of gene expression profiles.

GeneChips were scanned using the Affymetrix (HP) GeneArray Scanner G2500A.

Trizol extraction, Qiagen RNEasy clean-up with on-column DNAse treatment

Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Samples prepared with Arcturus RiboAmp protocol from 2 ug of total RNA

Gene expression data comparing ABCA1 over-expression in LDL receptor +/- genetic background

Transfection conditions for each clear cell ovarian cancer cell line were optimized for maximum efficiency in preliminary experiments using Dy547-labeled miRIDIAN hairpin inhibitor and mimic transfection controls (Dharmacon). OVSAYO cells were transfected in 6-well plates (3.0 x 105 cells/well) using 3 μl Invitrogen Lipofectamine 2000 and 3 μg total hairpin inhibitor (66 nM). Knockdown of hsa-mir-30 family miRNAs was achieved using a mix of 2 μg hsa-mir-30a inhibitor (44 nM) and 1 μg hsa-mir-30d inhibitor (22 nM). Control groups were cells treated with transfection reagent alone (mock transfection), and cells transfected with miRIDIAN hairpin inhibitor negative control #1 or mimic negative control #2, which are based on C. elegans miRNAs that have minimal sequence identity to human miRNAs (Dharmacon).

OVSAYO cells were cultured in RPMI 1640 (Invitrogen), with 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin solution (Invitrogen).

The image data were compiled into a project using  Beadstudio software gene expression module version 3.2.7.  No normalization was used. The data was exported as txt files using the build-in function of export to GeneSpring GX format. The option of sample probe profile was chosen. Data were subsequently quantile normalized for the analysis.

Cells were harvested 48 hours after transfection. Total RNA was extracted using the mirVana miRNA Isolation Kit (ABI). RNA quality were inspected on a 2100 Bioanalyzer (Agilent).

hsa-mir-30a/30d inhibitor (mir-30a knockdown in OVSAYO), biological rep1

MDA-MB-231_TR6196: transfected with a vector containing a shRNAs against CD146

Preparation of cRNA, hybridizations, washes and detection were done as recommended by the supplier.
www.affymetrix.com

Total RNA was isolated from 1 to 2 x 106 cells using an RNA extraction kit (Macherey-Nagel GmBH & Co, Düren, Germany)

MDA-MB-231 transfected with a vector containing a shRNAs against CD146

MDA-MB-231_TR6194: transfected with a vector containing a shRNAs against CD146

MDA-MB-231_TR30003: transfected with a vector containing a non-effective shRNA cassette against GFP

MDA-MB-231 transfected with a vector containing a non-effective shRNA cassette against GFP

MDA-MB-231_TR20003: transfected with the original vector plasmid

PIO was incorporated in the diet at 84 ppm yellding approximately 18 mg/kg body weight/day

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling (target intensity = 100 ) for quality control. gcRMA ( justgcRMA function in bioconductor in R v.2.7.1 ) was run on all chips simultaneously to generate probe set signal intensities.

Nictoine (5 uM; Sigma®, Saint Louis, MO) or cigarette smoke extract (5 uM nicotine-equivalent) was added to the culture media, and after 2 hours, cells were irradiated with one dose of 6 Gy ionizing radiation (cesium-137 source), or cisplatin (1 uM; Sigma®) was added to the culture medium. All treatments were performed concurrently using a total of nine 6-well cuture plates. After another 2 or 24 hours, cells were harvested by scraping into the culture medium, spun down, washed in 10 ml phosphate-buffered saline, and collected as cell-pellets after another round of centrifugation at room temperature. The total 54 cell-pellets were stored frozen at -80 ºC until RNA extraction.

3x10e5 NCI-H460 cells, at passage number 9 after procurement from ATCC® (Manassas, VA) and maintained in RPMI-1640 medium (Life Technologies®, Grand Island, NY) with 10% fetal bovine serum (Atlanta Biologicals®, Lawrenceville, GA) at 37 ºC under 5% carbon dioxide, were seeded per well of 6-well tissue culture dishes. After 24 hours, the culture medium was replaced with that without serum and cells were grown for another 24 hours.

Arrays were scanned on an Affymetrix® GeneChip™ Scanner 3000 instrument using protocols provided by Affymetrix®. This work was performed as a commercial service by a shared genomic facility of the University at Buffalo, Buffalo, NY.

Raw data for all 54 arrays (in .CEL files) was processed together using Affymetrix® Power Tools (version 1.15.0) on Mac OS X 10.6.8. Briefly, background signals were adjusted using the 'rma' method. Array data was then quantile normalized and median polish summarized. All arrays appeared to have yielded data of good quality as assessed using criteria suggested by Affymetrix®.

Total RNA was extracted from -80 ºC-frozen cell-pellets using the Total RNA Purification kit (catalog# 37500, Norgen-Biotek®, Thorold, ON, Canada) following the kit manufacturer's guidelines. The kit uses silicon carbide spin-columns. On-column DNase I treatment was performed to reduce contaminating genomic DNA. RNA eluted from the columns was treated on-column with DNase I again as per the manufacturer's guidelines provided with the RNase-Free DNase I kit (Norgen-Biotek®). Absorbance at 260 nm and electrophoresis on Bioanalyzer™ 2100 (Agilent®, Austin, TX) was used to estimate RNA concentration and quality.

Hybridization and washes were performed on an Affymetrix® GeneChip™ Fluidics Station 450 instrument using protocols provided by Affymetrix®. This work was performed as a commercial service by a shared genomic facility of the University at Buffalo, Buffalo, NY.

The WT Expression kit from Ambion® (Austin, TX) was used to generate sense-strand complementary DNA (cDNA) from 100 ng total RNA. The cDNA was fragmented and labeled with biotin as per protocols provided with the GeneChip™ WT Terminal Labeling and Hybridization kit (Affymetrix®). This work was performed as a commercial service by a shared genomic facility of the University at Buffalo, Buffalo, NY.

NCI-H460;human lung large cell carcinoma cells;cisplatin and nicotine;2 hours

In order to investigate the physiological as well as pathological role of MnSOD in the heart and muscle, we generated conditional MnSOD knockout mice using the Cre-loxP system.
We used MCK-Cre transgenic mice for the selective expression of Cre protein in muscle tissues as shown previously. Crossbreeding of homozygous MnSOD flox mice (flox/flox, f/f) with MCK-Cre transgenic mice gave rise to heart/muscle-specific MnSOD-deficient mice (del/del, d/d).
Keywords = Mn-SOD
Keywords = manganese superoxide dismutase
Keywords = knockout
Keywords = heart failure
Keywords = heart
Keywords = muscle

NCI-H460;human lung large cell carcinoma cells;control (none);24 hours

NCI-H460;human lung large cell carcinoma cells;nicotine;24 hours

HIV seropositive, CD4 cells decrease over time, sampled at time point 1
Keywords = HIV, Human, PBMC, in vivo

Total RNA was extracted from the shaved dorsal skin using Trizol (Invitrogen) followed by RNeasy kit (Qiagen).

5 µg of total RNA was processed to produce biotinylated cRNA targets.

HIV seropositive, samples used to test HIV infection status

GeneChips were scanned using the Affymetrix GCS3000 gene chip scanner with GCOS 1.4.

The data were analysed using Bioconductor packages 'affy' and 'limma' under R-2.7.0. Background correction, normalization and probe summarization was performed with RMA (function just.rma()).

Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

57B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

58B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

55B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

56B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; not assessable

59B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

Sample_ID:t21 // Patient:J-275 // Histology:Intestinal // Metastasis:+ // p53_mut:++ // E-cadherin_mut:+ // beta-Catenin_mut:-
Keywords = Gastric cancer

Sample_ID:t20 // Patient:J-274 // Histology:Intestinal // Metastasis:+ // p53_mut:- // E-cadherin_mut:+ // beta-Catenin_mut:-

C57BL/6 mice were bred with mice heterozygous for Nf1.  Their male pups were euthanized at P10 and  brains quickly dissected and flash-frozen.  Their livers were also removed and frozen for the purpose of genotyping.  Hippocampi from two wild-type mice were pooled and RNA extracted for expression profiling.
Lot batch =

C57BL/6 mice were bred with mice heterozygous for Nf1.  Their male pups were euthanized at P20 and  brains quickly dissected and flash-frozen.  Their livers were also removed and frozen for the purpose of genotyping.  Hippocampi from two NF+/- mice were pooled and RNA extracted for expression profiling.
Lot batch =

C57BL/6 mice were bred with mice heterozygous for Nf1.  Their male pups were euthanized at P10 and  brains quickly dissected and flash-frozen.  Their livers were also removed and frozen for the purpose of genotyping.  Hippocampi from two NF+/- mice were pooled and RNA extracted for expression profiling.
Lot batch =

C57BL/6 mice were bred with mice heterozygous for Nf1.  Their male pups were euthanized at P15 and  brains quickly dissected and flash-frozen.  Their livers were also removed and frozen for the purpose of genotyping.  Hippocampi from two wild-type mice were pooled and RNA extracted for expression profiling.
Lot batch =

C57BL/6 mice were bred with mice heterozygous for Nf1.  Their male pups were euthanized at P15 and  brains quickly dissected and flash-frozen.  Their livers were also removed and frozen for the purpose of genotyping.  Hippocampi from two NF+/- mice were pooled and RNA extracted for expression profiling.
Lot batch =

C57BL/6 mice were bred with mice heterozygous for Nf1.  Their male pups were euthanized at P28 and  brains quickly dissected and flash-frozen.  Their livers were also removed and frozen for the purpose of genotyping.  Hippocampi from two NF+/- mice were pooled and RNA extracted for expression profiling.
Lot batch =

C57BL/6 mice were bred with mice heterozygous for Nf1.  Their male pups were euthanized at P20 and  brains quickly dissected and flash-frozen.  Their livers were also removed and frozen for the purpose of genotyping.  Hippocampi from two wild-type mice were pooled and RNA extracted for expression profiling.
Lot batch =

Pairs of normal and tumor tissue samples were obtained at the time of surgery from resected pancreas of 36 pancreatic cancer patients. The tissue samples were snap-frozen in liquid nitrogen immediately upon surgical removal and maintained at −85°C. For histological evaluation, sections were stained with haematoxylin and eosin. The resected cancer specimens were not microdissected.

Affymetrix GeneChip Operating Software (GCOS) Version 1.4 was used for low-level scanning data processing. The data was subsequently normalized using the RMA algorithm using the Bioconductor 1.9 package (http://www.bioconductor.org/) running under R version 1.9.1.

Total RNA was extracted from the frozen tissue samples in two steps: RNA isolation using the TriReagent (Sigma) protocol, followed by RNA clean-up performed as described in the RNeasy (Qiagen) protocol. Briefly, tissues were homogenized in TriReagent (1 mL of TriReagent per 50-100mg of tissue). Then, RNA was precipitated from the aqueous phase with addition of isopropanol at half the volume of the original TriReagent volume and centrifugated at 12000 × g for 10 min. RNA was cleaned using an RNeasy column according to the manufacturer’s instructions (RNeasy Mini Kit, Qiagen) and eluted in 100 µL of RNase-free water. RNA sample quantitation was performed by means of spectrophotometry (Genequant, Pharmacia), while RNA quality (integrity) control was done with microfluidics technology (2100 Bioanalyser, Agilent Technologies).

The fragmented cRNA was hybridized to the oligonucleotide microarray, which was washed and stained with streptavidin-phycoerythrin.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

For neural differentiations, NPCs were dissociated with Accutase and plated in neural differentiation media (DMEM/F12-Glutamax, 1XN2, 1X B27-RA, 20 ng/ml BDNF, 20 ng/ml GDNF (Peprotech), 1 mm dibutyrl-cyclicAMP (Sigma), 200 nm ascorbic acid (Sigma) onto PORN/Laminin-coated plates. 200,000 cells/well of a 6-well plate. hiPSC derived-neurons were differentiated for 6 weeks.

Data in the sample data tables are rma background corrected, quantile normalized, log2 transformed and mean probeset summarized. Further processed data on the Series record were performed by Partek Genomics Suite.

Cells were lysed in RNA BEE (Tel-test, Inc). RNA was chloroform extracted, pelleted with isopropanol, washed with 70% ethanol and resuspended in water. RNA was treated with RQ1 RNAse-free DNAse (Promega) for 30 minutes at 37C and then the reaction was inactivated by incubation with EGTA Stop buffer at 65C for 10 minutes.

GeneChip WT Sense Target Labeling and Control Reagents (900652) and GeneChip WT cDNA Synthesis and Amplification Kits (900672 and 900673)

Differentiation of ES cells into Neural progenitors was performed as previously described in Ying et al 2003. Independent samples 1 and 2 (both conditional and Sox3 null) are from an independent differentiation series to that of samples 3 and 4 (both conditional and Sox3 null).

R1 ES cells (Both Conditional and Sox3 null) were mantained on gelatine coated plates in standard ES media before differentiation.

Samples scaned using the Affymetrics GeneChip scanner 3000 7Gplus at the Adelaide Microarray Centre

Performed by the Adelaide Microarray Centre using the Partek Genomics Suite

RNA extractions at day 4 of N2B27 differentiation were performed using a QIAGEN Rneasy mini kit

Samples hybridised using a GeneChip 450 fluidics station at the Adelaide Microarray Centre

Samples labeled using a GeneChip 450 fluidics station at the Adelaide Microarray Centre

Sox3 positive;R1;Embryonic stem cells differentiated into neural progenitor cells

Raw data values were imported into GENESPRING 7.2 software (Agilent Technologies, Palo Alto, CA) and processed using GC-RMA, followed by normalization. A three-step normalization procedure was applied to raw expression values (Genespring 2004).  First, values less than 0.01 were set to 0.01 (data transformation). Second, per chip normalization was performed by dividing each measurement by the 50.0th percentile of all measurements in that sample. Third, each gene was divided by the median of its measurements in all samples (per gene normalization).

Total RNA was extracted from whole blood samples using the PaxGene Blood RNA System according the manufacturer’s specifications.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hrs at 45C on the Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using wash protocol EukGE-WS2v5.

Biotinylated cRNA were prepared from 3 micrograms of total RNA according to the standard Affymetrix protocol

Gene expression in blood of children with autism spectrum disorder (ASD) was studied. Transcriptional profiles were compared with age and gender matched, typically developing children from the general population (GP) or IQ matched children with mental retardation or developmental delay (MR/DD).

Cardiac malformations due to aberrant development of the atrioventricular (AV) valves are among the most common forms of congenital heart disease. At localized swellings of extracellular matrix known as the endocardial cushions, the endothelial lining of the heart undergoes an epithelial to mesenchymal transition (EMT) to form mesenchymal progenitors of the AV valves. Further growth and differentiation of these mesenchymal precursors results in formation of portions of the atrial and ventricular septae, and generation of thin, pliable valves. The transcription factor Gata4 is expressed in the endothelium and mesenchyme of the AV valves. Using a Tie2-Cre transgene, we selectively inactivated Gata4 within endothelial-derived cells. Mutant endothelium failed to undergo EMT, resulting in hypocellular cushions. Mutant cushions had decreased levels of Erbb3, an EGF-family receptor essential for EMT in the atrioventricular cushions. In Gata4 mutant embryos, Erbb3 downregulation was associated with impaired activation of Erk, which is also required for EMT. Expression of a Gata4 mutant protein defective in interaction with Friend of Gata (FOG) cofactors rescued the EMT defect, but resulted in decreased proliferation of mesenchyme and hypoplastic cushions that failed to septate the ventricular inlet. We demonstrate two novel functions of Gata4 in development of the AV valves. First, Gata4 functions as an upstream regulator of an Erbb3-Erk pathway necessary for EMT, and second, Gata4 acts to promote cushion mesenchyme growth and remodeling.

Mouse were kept and breeding was done at Freimann Life Scinece Center, University of Notre Dame, IN.

The acquisition if array image was undertaken by using Affymetrix GeneChip Command Console 1.1 (AGCC).

The data were analyzed using DNA-Chip Analyzer (D-Chip) with the .CEL files obtained from AGCC. We used a PM/MM difference model for estimating gene expression level and quantile approach for data normalization.
Thresholds for selecting significant genes were set at a relative difference ³1.5-fold, absolute difference ³100 signal intensity units and p<0.05. Genes that met all three criteria simultaneously were considered as significant change.

Total RNA from brain, liver and speleen was isolated using 'Roche MagNa Pure Compact automated System' according to the manufacturer's instructions.

Affymetrix mouse 430 2.0 array hybridization were performed by 'UCLA Clinical Microarray Core, UCLA, Los Angeles, CA, USA, according to manufacturer's instrcutions

Biotinylated cRNA were prepared using 'MessageAmpTM Premier Amplification Kit (Invitrogen)' according to the manufactureres instrcutions.

Gene expression data from brain of Npc1+/+ mouse1 of age 20 days

Gene expression data from brain of Npc1+/+ mouse1 of age 25 days

European-American (EA);Female;Systemic lupus erythematosus (SLE) patient;Peripheral blood;CD8-PE;CD8 positive T cells

We depleted c-Myc endogenous expression by transfecting lentivirus-delivered c-Myc shRNA into BASCs, After several generations of puromycin selection, stable c-Myc knock down cell lines were established and the degree of c-Myc reduction in both mRNA and protein level was confirmed

BASCs were isolated from the lungs of 4-6 week old ICR mice. In brief, Mice were sacrificed, and their lungs were removed and cut into small pieces. Tissue dissociation was performed, then passing the lungs through a 70 μM filter to obtain a single cell suspension. After washing with PBS. cells were stained with Biotin-conjugated anti-CD31 and anti-CD45, APC-conjugated streptavidin, PE-conjugated anti-Scal, and FITC-conjugated anti-CD34. Cells were washed and sorted for CD31neg, CD45neg, CD34pos and ScaIpos cells on an Aria Flow Cytometry machine. Sorted BASCs were cultured onto irradiated MEF (mouse embryonic fibroblast) cells with BASC media.

The data were analyzed with Partek Genomics Suite 6.4 using Affymetrix default analysis settings and GC-RMA as normalization method

The targets for Affymetrix DNA microarray analysis were prepared according to the manufacturer’s instructions. Biotin-labeled cRNA, produced by in vitro transcription, was fragmented and hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 Arrays at 45°C for 16 hr and then washed and stained using the GeneChip Fluidics.

Gene expression data from mouse bronchoalveolar stem cells
BASC-CMYC-depletion-2

BASC-CMYC-depletion-1

BASC-CMYC-C-2

BASC-CMYC-C-1

mRNA extracted from lung fibroblasts derived from open lung biopsies of a patient (FASSc3) with fibrosing alveolitis associated with systemic sclerosis. Lung fibroblasts were grown to confluence in DMEM with 10% fetal calf serum. At confluence, lung fibroblasts were serum-deprived overnight, and exposed to 4 ng/ml of activated TGF-ß1 (R&D Systems) in serum-free culture-medium with the addition of 0.1% BSA for 4 hours. At the end of treatment period total RNA was harvested, quantified, and integrity was verified by denaturing gel electrophoresis.

lung fibroblasts from a patient (FASSc3) with fibrosing alveolitis associated with systemic sclerosis

mRNA extracted from lung fibroblasts derived from open lung biopsies of a patient (FASSc2) with fibrosing alveolitis associated with systemic sclerosis. Lung fibroblasts were grown to confluence in DMEM with 10% fetal calf serum. At confluence, lung fibroblasts were serum-deprived overnight, and exposed to 4 ng/ml of activated TGF-ß1 (R&D Systems) in serum-free culture-medium with the addition of 0.1% BSA for 4 hours. At the end of treatment period total RNA was harvested, quantified, and integrity was verified by denaturing gel electrophoresis.

lung fibroblasts from a patient (FASSc2) with fibrosing alveolitis associated with systemic sclerosis

mRNA extracted from lung fibroblasts derived from open lung biopsies of a patient (FASSc3) with fibrosing alveolitis associated with systemic sclerosis. Lung fibroblasts were grown to confluence in DMEM with 10% fetal calf serum. At confluence, lung fibroblasts were serum-deprived overnight, and exposed to serum-free culture-medium with the addition of 0.1% BSA for 4 hours. At the end of treatment period total RNA was harvested, quantified, and integrity was verified by denaturing gel electrophoresis.

Each rescue ES clone was grown in +Dox (1ug/ml) media; Dox withdrawal was performed for 5days

rtTA-expressing ES cells Aniv15 were used for derivation of rescue clones and were maintained on primary mouse embryonic fibroblasts with DMEM media supplemented with 15% FBS, 100 mM MEM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 1 mM l-glutamine and 103 U ml-1 of LIF (Chemicon) and doxycycline (1ug/ml)

Data was VST transformed, RSN normalized in R using LUMI package

total RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.

Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were performed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, performs quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin) in CORRECTED column.

Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.

Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

infected with lentivirus and selected with 0.5 ug/ml puromycin for a week.

Gata4loxP/+VillinCre adult male jejunum (6-8 wk). Control sample.

LPS mice were spontaneously breathing room air and received 2 microliter/gm LPS (2.5 ng/microliter) in the oropharynx with a pipette.  They were sacrificed 4 hrs later, whole lung removed, homogenized and total RNA isolated.  Labeled cRNA was prepared and hybridized to an Affymetrix GeneChip 430A microarray using Affymetrix protocol.  Microarray was scanned with the GeneChip Scanner and image analysis was performed with Affymetrix MAS 5.0 software.  Background adjustment and quantile normalization of microarray data was performed using RMAExpress.

MV+LPS mice received 2 microliter/gm LPS (2.5 ng/microliter) in the oropharynx with a pipette, 30 minutes later they were anesthetized, intubated and ventilated at a tidal volume of 10 microliter/gm body wt, PEEP = 0 and FiO2 = 0.21  They were sacrificed 4 hrs later, whole lung removed, homogenized and total RNA isolated.  Labeled cRNA was prepared and hybridized to an Affymetrix GeneChip 430A microarray using Affymetrix protocol.  Microarray was scanned with the GeneChip Scanner and image analysis was performed with Affymetrix MAS 5.0 software.  Background adjustment and quantile normalization of microarray data was performed using RMAExpress.

ON-TARGETplus SMARTpool siRNA targeting human PDE1C were employed to deplete the transcript levels of PDE1C. In addition, these cultures were transfected in parallel with ON-TARGETplus non-targeting siRNA pool. Cells were seeded at 40-50% confluency and incubated for 48 hours before commencing siRNA transfections. Cells were transfected twice; first at day1 and secondly at day 6. At the end of day 10, cells were collected.

short-term cell cultures were prepared from approximately 10mg of adult GBM biopsy tissue and maintained in Hams F10 nutrient mix containing 10% foetal calf serum in a 37C non-CO2 incubator

scanned with the GeneChip Scanner 3000 7G according to manufacturers’ standard protocols

Raw microarray data from Affymetrix CEL files for each of the biological replicates of siNT and siPD in IN1472 and IN1760 were initially normalised using the MAS5 (Affymetrix Microarray Suite, version 5.0) algorithm. The raw intensity values were further assessed by the Robust Multi-array Analysis (RMA) as implemented in R/Bioconductor [Irizarry et al, 2003]. The RMA intensity in log2 scale was generated for each probe set and the perfect-match (PM) intensities per probe set were background-corrected, quantile-normalised and signal intensities for each probe set were summarised using median signal intensity to fit linear model (GeneSpring GX 12). Array background, Q values, and mean intensities were within acceptable ranges for all arrays

Total RNA was extracted using RNeasy Mini Kit  according to the manufacturers’ instructions.

Hybridised on to the Human Genome U133 Plus 2.0 oligonucleotide array. The arrays were washed and stained using the GeneChip Fluidics Station 450

1 µg total RNA was reverse transcribed using the MessageAmp™ II-Biotin Enhanced Kit according to the manufacturer's instructions

Gata4LoxP/+VillinCre adult male jejunum (6-8 wk). Control sample.

Synovial fibroblasts were isolated by collagenase digestion and caltured up to 6 passages in 10% fetal calf serum (FCS) in DMEM (Dulbecco's Modified Minimal Essential Medium). Cells were serum depriviated (0.5% FCS) for overnignt and then treated or left untreated. Triplicate-quadraplicate synovial fibroblast cell cultures were treated either with 5 ng/ml TNFalfa, 200 ng/ml lipopolysaccharide, 120 ug recombinant mouse TSG-6/ml, 24 ug hyaluronan (HA)/ml, or 120 ug TSG-6 plus 24 ug/ml HA for 12 hours in serum depriviated DMEM.

Female (wild-type) and TSG-6-KO (tumor-necrosis factor-alfa-stimulated protein-6: Tnfaip6-deficient) BALB/c mice were immunized intraperitonelly with the emulsion of cartilage PG (100 µg protein) and 2 mg dimethyldioctadecyl-ammonium bromide (DDA) adjuvant. Arthtitic mice were sacrificed, synovial tissue dissected and cells released by pronase/collagenase combined digestion.

Affymetrix GeneChip arrays were scanned according to standard Affymetrix protocols on an ‘Affymetrix GeneChip Scanner 3000 7G’.  Each array was analyzed for the following quality metrics:  3’/5’ signal ratio of house-keeping genes, signal intensity of species-specific house-keeping genes, signal intensities of Poly-A controls, signal intensities of hybridization controls, relative logarithmic probe cell intensity- and relative logarithmic expression signal values.

Data was analyzed in GeneSpring GX 10.0 (Agilent Technologies, Santa Clara, CA).  Robust Multi-array Average (RMA) (Irizarry, 2003) summarization algorithm (with Quantile Normalization and Median Polish probe summarization procedure) and baseline transformation (baseline to median of all 42 samples) was run on data using logarithmic scale. All 42 samples passed quality control based on hybridization controls, 3'/5' ratios for internal controls, Pearson correlation and Principal Component Analysis (PCA). Probe sets were filtered by expression values based on percentiles. For pairwise comparisons, Student-Newman-Keuls (SNK) Post Hoc test was done on oneway ANOVA result to identify statistically significant (p-value cutoff 0.05), differentially expressed transcripts. Statistical test p-values were corrected for False Discovery Rate (FDR) by Benjamini-Hochberg (BH) procedure. Differentially expressed transcripts were annotated with GeneSpring GX 10.0.

Cells were washed with RNAse-free PBS, RNA isolated with TriZol reagent, and qulatiy measured by Agilent 2100 Bioanalyzer

Following fragmentation, 1.5 ug of labeled cRNA were hybridized according to standard Affymetrix protocols on Affymetrix GeneChip ‘Mouse Genome 430 2.0’ arrays using ‘GeneChip Fluidics Station 450’.

Biotinylated cRNA were prepared according to standard Affymetrix recommended protocols from 2 to 5 ug total RNA (Affymetrix Expression Analysis Technical Manual, P/N 702232 Rev.2).

Treatment type: compound
Agent: N-nitrosodiethylamine
Treatment dose: 10 ug/g of body weight
Treatment time: 3 months

Creator: GenePix Pro 5.1.0.11
Scanner: GenePix 4000A [54243]
ScanPower: 100;; 100
LaserPower: 2.58;; 1.42
Temperature: 41.24

mAdb Data Processing Protocol (v. 2)
Calculation Method: After background correction, ratios were median centered based on signals greater than 100 in both channels and linear transformed to obtain the log and linear values given in the data table.

CsCl Gradient Extraction Protocol
Extraction method: CsCl gradient centrifugation
Other: Total RNA was isolated from snap-frozen liver tissue using the CsCl gradient centrifugation method.

NCI cDNA Microarray Hybridization
Other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42°C for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 µl COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100°C for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42°C just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42°C in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), for 1 minute in 0.05X SSC, and spin for 3 minutes at 650 rpm to dry. (Refer to "NCI Microarray Manual")

Cy5 Labeling Protocol
Other: The Cy3 and Cy5 dyes (Amersham Biosciences) were also dissolved in 20 ìl of water. For the coupling reaction, 2 ìl of dye was added to each sample, and the mix was left in a dark box for an hour. Labeled cDNA was purified again with a MinElute kit (Qiagen ), and Cy3- and Cy5-labeled target and reference samples were combined.

B6129;male;12 weeks;liver;adult;B6129;male;12 weeks;liver;adult;Alb-Cre +/-

Gene expression data from early passage CCM3-knockdown endothelial cells.

Treatment time: 5 months

LaserPower: 2.53;; 1.3
Temperature: 36.78

Cy3 Labeling Protocol

B6129;male;12 weeks;liver;adult;129SV/C57BL6;male;20 weeks;liver;adult;genotype/variation gene knock out;Alb-Cre +/-; Met Fl/Fl

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

Total RNA extraction was performed from homogenized testes using Qiagen RNAeasy minikit according to the manufacturer's instructions.

According to Affymetrix standard procedure, 10 micrograms of fragmented cRNA were hybridized to an array for 16-18 hours at 45°C with constant rotation at 60 rpm. After hybridization, the array was washed and stained using an Affymetrix Fluidics Station.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

Mice were fasted 24 hours, sacrificed, and whole livers were removed.

Mice were fed a standard diet, or weaned onto a high-fat Western diet (42% fat)

RMA (Robust Multi-array Analysis) was used for normalizing and summarizing probe-level intensity measurements from Affymetrix Gene Chips (Affymetrix Expression Console). Starting with the probe-level data from a set of Gene Chips, the perfect-match (PM) values were background-corrected, normalized and finally summarized resulting in a set of expression measures.

Gene expression data from 12 week old SIRT3KO mouse liver tissue fed a high-fat diet
12-KO3

MDA-MB-231cells were exposed to regimens on a 10-day cycle:  a 3-day treatment with 30 nM paclitaxel and followed by a 7-day exposure to control medium.  Paclitaxel resistant MDA-MB-231 cells (MDA-PR) were established within 8 cycles of such treatment (80 days).  When these MDA-PR cells were then treated with the combination of  30 nM paclitaxel ( 3 days on and 7 days off) and 1 µM Targretin (10 days on) in a new 10-day cycle for 3 months, MDA-PR cells became re-sensitized to paclitaxel again.

The human breast cancer cell line MDA-MB-231 was obtained from American Type Culture Collection (Manassas, VA), and MDA-MB-231cells were routinely cultured in RPMI 1640 supplemented with 10% fetal bovine serum and 2 mM glutamine in 5% CO2.

After washing and staining on Affymetrix Fluidics Station 450, the arrays were scanned with the Affymetrix GeneArray 2500 Scanner.

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 250.

The labeled target was subsequently hybridized to a human Affymetrix U133A microarray in an Affymetrix Hybridization Oven 640

Gene expression data from paclitaxel resistant MDA-MB-231 Cells and paclitaxel sensitive cells with bexarotene treatment

MDA cells resistant to paclitaxel were treated with 30 nM Paclitaxel + 1 µM Targretin

MDA cells resistant to paclitaxel were treated with 30 nM Paclitaxel

control wild-type prostate epithelial cell line maintained in RPMI-1640 medium supplemented with 5% fetal bovine serum
Keywords = prostate
Keywords = epithelial

PTEN mutant and control animals were injected a total of five times with polyinosinic-polycytidylic acid (Poly I:C), with single injections of 250 micrograms/mouse/day given every other day. Injections were performed on days 21, 23, 25, 27, 29. Mice were analyzed 30 days after the final Poly I:C injection.

Animals were maintained under specific pathogen free conditions in vivarium with a 12 hour light/12 hour dark cycle. Animals had food and water ad libitum.

Affymetrix GeneChip Scanner 3000 with GCOS GeneChip Operating software Version 1.2.0.037

Normalized against other samples in series by log regression on signal obtained with control spots (first 64 samples). For this sample VALUE=RAW_SIGNAL* 100/(2.0635*LN(RAW_SIGNAL)+56.98)

Total RNA was extracted by Trizol Reagent (Invitrogen) according to manufacturer's protocol. Quality and quantity of the total RNA was assessed using a Bioanalyzer (Agilent).

Hybridization to Affymetrix mouse Genome 430 2.0 arrays using GeneChipFluidics Station450. 20 micrograms of fragmented cRNA was used for each chip hybridization. Hyridization and wash protocols were as described in Affymetrix Technical Manual, "GENE EXPRESSION MONITORING, GeneChip®
Expression Analysis" 701021 Rev. 5. Hybridization buffer was 100 mM MES(2-(N-Morpholino)ethanesulfonic acid sodium salt), 1M [Na+], 20 mM EDTA, 0.01% Tween-20. Hybridization was performed at 45 celsius for 16 hours.

Biotin-labeled cRNA was prepared from 6 micrograms of total RNA using the Affymetrix One-cycle protocol. (Affymetrix Cat. #900493). Quantity and quality of unfragmented cRNA and fragmented cRNA was assessed using a Bioanalyzer (Agilent).

The study examines the effect of conditional PTEN deletion in the small intestine. Deletion of the PTEN exon 5 (encoding the phosphatase motif) was accomplished using the interferon-inducible Mx1-Cre, induced by five injections of polyinosinic-polycytidylic acid. The experiment compared the gene expression profiles of polyp regions from three PTEN mutant animals with intestines from two control animals. Genes were considered up-regulated or down-regulated if all of the following conditions were met: 1) There was at least a two-fold change in the average values measured between controls and mutants; 2) There was no overlap between the range of mutant and control data; and 3) The control mean was outside the 95% confidence interval of the PTEN-mutant mean.

Mixed genetic background, predominantly (>87.5%) C56BL/6 with some CD1. Genotype: Mx1-Cre negative: PTENfx/+. Sex: Female;eight and a half weeks (at tissue isolation). Tissue: Small Intestine (jejunum/ileum region).

The data were analyzed with Bioconductor using normexp background correction and quantiles as normalization method.

TRIzol extraction of total RNA followed by purification in Qiagen Rneasy columns

Following fragmentation, cRNA were hybridized for GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared using GeneChip 3’ IVT Express Kit according to manufacturer's protocol

Gene expression data from white adipose tissue from 6-8 week old C57BL/6 Rap1 knockout mouse

tissue was disected, imaged by digital microscopy and randomly sorted into one of three sample vials

Samples were stored in RNAlater RNA stabilization reagent (Qiagen, Canada) and then isolated using the RNeasy Micro kit (Qiagen, Canada).

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse MOE430v2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

one cycle amplification as per Affymetrix protocol from 1ug of total RNA

Hoxb7-Cre:EGFP mice ( Zhao, et al. (2004) Dev Biol 276:403-415) were crossed with mice containing loxP sites flanking exon 3 of the ß-catenin allele (ß-catdelta3/delta3) (Harada,et al. (2002) Cancer Res 62:1971-1977) to generate ß-catenin gain-of-function mutant mice specifc to the uteric bud, termed ß-catGOF-UB .Eighteen ß-catGOF-UB mutant kidneys and 9 WT kidneys were micro-dissected at E12.5. Mutant kidneys were divided into three random pools (n=3) consisting of 6 kidneys each.
Expression data for mouse ß-catGOF-UB mutant kidneys embryonic day E12.5

ß-catenin gain-of-function mutant (ß-catGOF-UB);kidney (uteric bud);embryo;12.5 days

LaserPower: 2.47;; 1.28
Temperature: 33.32

For differentiation RA was treated, For SNF5 level change we generated stable cell line for kd and transfected SNF5 for oe.

The data were normalized using quantile normalization with R package lumi

RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment and Quality control experiment performed

The RNA from murine liver was directly labeled with Cy dyes using oligo dT primers, for complete details see http://mgm.duke.edu/genome/dna_micro/core/protocols/ for detailed labeling and hybridization protocols

Sample is C57/Bl6 C3KO murine liver RNA extract after mock infection with 200ul if PBS at 6 hpi.

C57/BL6 C3KO murine Liver RNA- 6 hours post-injection with 200ul PBS (Mock).;Murine Universal RNA (Stratagene, La Jolla, CA) which is a mixture of RNA from 10 control cell lines approximating the expression profile of the majority of murine genes was used.

Sample is C57/Bl6 C3KO liver RNA extract after infected with 1st generation LacZ adenovirus (1.5x10E11 particles per mouse) at 6 hpi.

C57/BL6 C3KO murine Liver RNA- 6 hours post-injection with a 1st generation (E1-E3-CMVLacZ) vector.;Murine Universal RNA (Stratagene, La Jolla, CA) which is a mixture of RNA from 10 control cell lines approximating the expression profile of the majority of murine genes was used.

Simple annotation: Cell-line, Drug treatment
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56612.gif

Sample is C3KO murine liver RNA extract after infected with 1st generation LacZ adenovirus (1.5x10E11 particles per mouse) at 6 hpi.

F1 (C57BL6 X 129/SvEv);AGTR1A-KO mice;kidney;male;ANG II +NS diet

The probe arrays were scanned using the Affymetrix GeneChip Scanner 7G.

Total RNA was isolated from muscle tissue using the TRIReagent method (Molecular Research Center, Inc.) following the manufacturer’s protocol. Concentrations were determined using a NanoDrop 1000 spectrophotometer. Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual.

15 micrograms of fragmented cRNA were hybridized to U133 Plus 2.0 chips for 16 hours at 45 °C, 60 rpm. The chips were washed and stained in the Affymetrix Fluidics Station 450, using instructions and reagents provided by Affymetrix.

In vitro transcription (IVT) was performed using the GeneChip Expression Amplification Reagents kit following the standard Affymetrix protocols.

Hela cells were nucleofacted with respective siRNAs and RNA was isolated after 72 hours

GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 running GCOS software.

The data were analyzed with RMA (Bioconductor) using Affymetrix default analysis settings and quantile normalisation as normalization method.

Subsequent labelling and hybrisation to HG_U133 Plus 2.0 arrays (Affymetrix, Santa Clara, CA) using the FL-Ovation cDNA Biotin Module v2.

40ng of RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN, San Carlos, CA).

Raw intensities values of all samples were normalized by RMA normalization (Robust Multichip Analysis) (background correction and quantile normalization) using Partek version 6.4 (Partek Inc., St. Louis, MO). To visualize the clustering of the samples, PCA (Principal Component Analysis) was used. The normalized datafile was transposed and imported into OmniViz version 6.0.1 (Biowisdom, Ltd., Cambridge, UK) for further analysis.
samples  A06 and A18 were excluded after signal processing due to outlying global signal intensities

Cells were subsequently disrupted (Qiashredder kit; Qiagen), and RNA was isolated (RNeasy minikit; Qiagen) with an additional DNAse digestion step (RNase-free DNase set; Qiagen), all according to the manufacturer’s protocol, diluted in nuclease free water, and frozen at –80 C before use. Before freezing, RNA purity and quantity was assessed with the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies).

Biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 plus 2.0 GeneChip© microarray containing 54,675 probe sets (Affymetrix Co).otinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

isolated RNA was biotinylated into cRNA using the One-Cycle Target Labeling and Control Reagents Kit (Affymetric Co) according to the manufacturer’s protocol. Before hybridisation RNA quality and integrity was assessed using the Agilent 2100 BioAnalyzer (Agilent). Biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 plus 2.0 GeneChip© microarray containing 54,675 probe sets (Affymetrix Co).otinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

PBMCs;acutely admitted, severely psychotic schizophrenia patient;male

The mice were treated with trastuzumab (20 mg/kg), pertuzumab (20 mg/kg) and trastuzumab + pertuzumab (20 mg/kg each)

Adult female nu/nu mice were implanted subcutaneously with SKOV3 tumor fragments (previously established from the cell line) or primary ovarian tumor fragments in the flanks and allowed to grow to 4–6 mm in diameter (over a period of approximately 1 month).

The data were normalised using quantile normalisation with the BioConductor package, Lumi in R

Total RNA was prepared from 10-50 mg of frozen tissue after 4 days of treatment, preincubated with RNAlater-ICE (Ambion, Austin, TX) using the miRNeasy Mini kit (Qiagen) and TissueRuptor (Qiagen) following the manufacturers’ instructions

Thereafter, a bare metal stent (Express2, 2.5 x 16 mm stent, Boston Scientific Corporation, MA, USA) was implanted (1 min, 10 bar) into one of the three LIMA pieces and a paclitaxel-eluting stent (TAXUS Express2 2.5 x 16 mm stent, Boston Scientific Corporation, MA, USA) was implanted into another. The third part was left as unstented control. Forty-eight hours post stent implantation, the stents were removed and the LIMA samples snap frozen in liquid nitrogen.

As part of elective Coronary Artery Bypass Graft Surgery procedures performed at Lund University Hospital, Sweden, tissues containing parts of the LIMA from four coronary artery bypass graft (CABG) patients (68-73 year old males with stable angina and 3-vessel coronary atheroslerosis, two had hypertension, none were diabetic) were collected  and stored in DMEM low glucose at 4C. Each LIMA (n=4) was dissected free of surrounding tissues, cut into three equal parts and incubated under tissue culture conditions in serum-free DMEM. All LIMA vessel segments were approximately 2 mm in diameter. The vessel segments were incubated for 24 h to induce quiescence.

The data were analyzed with Expression Console ver.1 using Affymetrix default analysis settings followed by MAS5 as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

Tissues were homogenized in TRIzol and RNA purified as described in Amisten et al 2008 (PMID 17920662).

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Hu133Plus2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

Human LIMA artery from patient 5, treatment: paclitaxel-eluting stent

Human LIMA artery from patient 4, treatment: bare metal cardiovascular stent

Human LIMA artery from patient 4, treatment: paclitaxel-eluting stent

Human LIMA artery from patient 5, treatment: bare metal cardiovascular stent

Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)

The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.

Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).

MLL_00259;PBMC;Multilineage dysplasia, acute myeloid leukemia, biallelic

Mice were sacrificed by a rising concentration of CO2 and livers were immediately removed for preparation of RNA. Total RNA was isolated from mouse liver with a phenol-guanidine isothiocyanate reagent, TRIzol (Invitrogen) and further purified with RNeasy Mini Kit (Qiagen Ltd) in accordance with the manufacturer’s instructions. RNA was pooled from three animals of each genotype for each experiment, and the experiments were carried out twice. Results from the two experiments were exactly the same. The A260/280 ratio of total RNA used was typically ³ 1.9. The quality of RNA was assessed by using the Agilent 2100 Bioanalyzer.
The probe labelling and hybridisation procedures were conducted by following the Affymetrix Technical Manual (Affymetrix, Santa Clara, CA). cDNA was synthesized from the total RNA by using Superscript ds-cDNA Synthesis Kit (Invitrogen Ltd, Paisley, U.K.) with a T7-(dT)24 primer incorporating a T7 RNA polymerase promoter. The cRNA was prepared and biotin-labelled by in vitro transcription by using BioArray High Yield RNA Transcript Labelling Kit (ENZO Biochemical). Labelled cRNA was fragmented by incubation at 940C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100mM potassium acetate, and 30 mM magnesium acetate. The samples were tested with hybridization to GeneChip Test3 arrays and analysed by Agilent Bioanalyzer. Fragmented cRNA (15 mg) was hybridized 16h at 450C to an MG_U74Av2 array (Affymetrix). After hybridization, the gene chips were washed and stained with streptavidin-phycoerythrin by using a fluidics station (Affymetrix). The chips were scanned in an Agilent G2500A scanner. Affymetrix oligonucleotide microarrays utilize multiple perfect-match and mismatch oligonucleotides to determine expression levels, so Affymetrix GCOS software was used to scan, determine the presence and the average difference value, and assess signal intensity of each probe set. Chip fluorescence was normalized by scaling total chip fluorescence intensity to a common value of 100 prior to comparison, and a normalisation value was set at 1. Data and statistical analyses were performed with Genespring Ver 6.1 (Silicon Genetics, Redwood City, CA) bioinformatics algorithms.

arrays were scanned with the GenePix 4000B microarray scanner and analyzed using GenePix Pro 4.1 software (Axon Instruments)

raw data processing was performed using ArrayMagic (Buness et al., 2005) and VSN normalization method; after removal of bad quality spots, two hybridizations of this sample were merged; generalized log2 ratios from 30498 cDNA clones were given in the data table.

2µg total RNA was amplified one round based on T7 RNA Polymerase (Ambion Message Amplification Kit Reagents, 6h IVT)

ch1 and ch2 together are solved in 50 µl 1x DIG-Easy hybridization buffer (Roche Diagnostics, Mannheim, Germany), containing 10x Denhardt’s solution and 2 ng/µl Cot1-DNA (Invitrogen); sample was denaturated at 65°C for 2min, hybridzation of arrays were performed in Corning chambers 14h at 37°C; slides were washed twice in 1xSSC+0.1SDS and once in 0.1xSSC+ 0.1SDS before air pressure drying and scanning.

direct fluorescent labelling of 2 µg amplified RNA, anneling of 0.5µg Random Primer and reverse-transcribed into cDNA with Superscript III reverse transcriptase for 1h at 42°C in the presence of 0.4 mM dGTP, 0.4 mM dATP, 0.4 mM dTTP, 0.24 mM dCTP, 0.125 mM Cy5-dCTP. After hydrolysis of RNA in 0.2 M NaOH, Cy5-labeled probes were purified with Microcon YM-30 column.

sparse HUVECs stimulated 100 ng /ml COMP-Angiopoietin-1 after starvation overnight

Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

Total RNAs were extracted using RNAzol. 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).

10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

Sparse HUVECs were stimulated with COMP-Ang1 or 1 hour after overnight starvation

HUVECs stimulated 100 ng /ml COMP-Angiopoietin-1 after starvation overnight

Confluent HUVECs were stimulated with COMP-Ang1 for 1 hour after starvation overnight

The array probe summaries were calculated in BeadStudio and quantile normalised. Using limma (R-package), a linear model fit was applied and the top differentially expressed genes were tabulated for each contrast using the method of Benjamini and Hochberg to correct the p-values.
Non-normalized signal intensity values are shown in the non-normalized matrix (linked as a supplementary file on the Series record); whereas in the data table below, quantile normalized values are depicted. No error model was applied in any case.

Total RNA was extracted using the TRIzol reagent (Invitrogen) and  an RNeasy kit (Qiagen).

Biotinylated cRNA were prepared with using the Illumina TotalPrep-96 RNA Amplification kit (Ambion, UK), according to the manufacturers instructions.

Sparse HUVECs were stimulated with COMP-Ang1 after overnight starvation

sparse HUVECs stimulated with Angiopoietin for 1 hour after overnight starvation

The hybridization slides were washed, stabilized, dried, and immediately scanned by Agilent Technologies Microarray Scanner (Agilent Technologies, Wilmington, DE).

During the initial analysis at UNC Microarray Database, all genes were retrieved, appropriately annotated, and filtered. Eventually, only genes with an absolute value of a Log2 Red/Green Lowess Normalized Ratio of at least 1 (doubled in intensity) for all 4 arrays were selected.

Total cellular RNA was purified from HeLa cells using RNeasy ® Mini Kit (Qiagen, Valencia, CA) according to manufacturers instructions.

The labeled cRNA samples were then fragmented in fragmentation buffer at 60°C for 30 min before the microarray hybridization. Each sample was hybridized to a whole separate Human Genome (4×44K) microarray (Agilent Technologies, Wilmington, DE) overnight at 65°C in a hybridization oven.

RNA samples representing four separate experiments from cells overexpressing tNASP and four experiments from cells treated with NASP siRNA, along with appropriate controls, were submitted for analysis.

MRI-no-lytic-lesion sample

Recombinant lentivirus were produced by co-transfecting human embryonic kidney 293T cells with miR-517a or empty vector (ViraPower™ Lentiviral Packaging Mix, Invitrogen, Carlsbad, CA) using Lipofectamine 2000. Supernatant containing lentivirus was collected 48h after transfection. Huh-7 cells were transduced with the lentivirus. GFP+ cells were sorted by fluorescence-activated cell sorting (FACS) analysis (Becton Dickinson Instrument, San Jose, CA).

Cells were cultured in DMEM medium with 10% FBS at 5% CO2, 37oC.

Human hepatocellular carcinoma cell line infected with GFP protein (control) 2

Signal intensities were normalized using RMA algorithm implemented in GenePattern ExpressionFileCreator module (http://www.broadinstitute.org/genepattern).

Human hepatocellular carcinoma cell line infected with GFP protein (control) 1

Granulosa cells collected by puncture of antral follicles; cells processed immediately, no further treatment

21-day mice were injected with 5IU PMSG for 44-46 hours or 44-46 hours PMSG followed by 6 hr 5IU hCG

GCRMA (Genespring 10.0.2, default parameters, baseline transformed to median of all samples)

Human hepatocellular carcinoma cell line infected with MIR517A and GFP protein 3

Human hepatocellular carcinoma cell line infected with MIR517A and GFP protein 2

Human hepatocellular carcinoma cell line infected with MIR517A and GFP protein 1

C57BL/6J;129S5/SvEvBrd;wild type;granulosa cell;44-46hr PMSG, 6hr hCG

Cells were FACS-purified from hindlimb muscle of uninjured or injured mice as indicated  and were NOT cultured after isolation

The data were analyzed with the Affymertix Expression Console software using Affymetrix default RMA analysis settings

Trizol extraction of total RNA followed by Qiagen Rneasy Plus cleanup was performed according to the manufacturer's instructions

Fragmented biotin-labeled single stranded DNA was hybridized to Affymetrix Mouse Gene 1.0  Array according to the standard Affymetrix protocol. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated single stranded cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA

Gene expression data from TSC1 KO, YFP+ muscle stem cells isolated from a noninjured animal

mixed C57BL6;TSC1flox/flox;Pax7CreER/+;Rosa26REYFP/+;3-5 months old;noninjured;hindlimb muscle;QSC;control

FACS purified YFP+ muscle stem cells, harvest immediately after isolation

Absence or presence of 4 mg/ml doxycycline for LITAF over-expression. Nucleofection (AMAXA) with Silencer Select Negative Control No. 1 (AM4611, Invitrogen) or a LITAF-specific siRNA (s18252, Invitrogen) for silencing. RNA was extracted 48h after the treatment.

Cell lines were grown at 37ºC and 5% CO2 in RPMI 1640 supplemented with 10% fetal bovine serum, 100 units/mL of penicillin and 100 mg/mL of streptomycin.

Data were normalized with Bioconductor software using the RMA algorithm.

The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133 Plus 2.0 chip according to the protocols provided by the manufacturer.

The cDNA was prepared from 2 microg total RNA using the One-Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthesizing the cRNA using the IVT labeling kit (Affymetrix). The synthesized cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).

VAL;diffuse large B-cell lymphoma (DLBCL) cells;LITAF-specific siRNA

HeLa cells were cotransfected (Lipofectamine; Invitrogen) with 5 μg of shRNA expression plasmid and 20 ng of pBabe-puromycin plasmid. BRCA1 shRNA (gccacaggaccccaagaaugag) was targeted to the 3’- untranslated region of the BRCA1 mRNA. The control shRNA was targeted against a mutant GFP construct  (gggccauggcacguacggcaag). Puromycin selection (2 μg/ml) was applied 24 h after transfection, and cells were harvested at 72 h post transfection.

HeLa cell line was maintained in DMEM media supplemented with 10% Bovine Serum, 100 I.U./ml Penicillin, 100 μg/ml Streptomycin in a humidified incubator at 37 C and 5% CO2.

The data were analyzed with Expression Console software (version 1.1.2) using Affymetrix default analysis settings and MAS5 algorithm.

Total RNA was prepared with Tri Reagent (Molecular Research) and further purified over RNeasy columns (Qiagen); mRNA was prepared using Dynabeads mRNA direct kit (Invitrogen)

Following fragmentation, 15 ug of cRNA was hybridized for 16 hours at 45ºC on Human Genome U133 Plus 2.0 GeneChips.  GeneChips were washed and stained in the Affymetrix Fluidics Station 460.

Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2007, Affymetrix).

Total RNA
Gene expression data of HeLa cells with depleted BRCA1

R/Bioconductor was used to apply the Robust Multi-Array Average (RMA) methodology to generate expression values for the combined samples.

Five (5) ug of fragmented, biotin-labeled cDNA was hybridized to Affymetrix Mouse Genome 430 2.0 Gene Chips for 18 hours, then washed/stained according to manufacturer's recommendations using the Affymetrix 450 fluidics station.

Primary cultures of amniocytes were collected from fetuses between 16-22 weeks of pregnancy, following routine diagnostic cytogenetic analysis of singleton pregnancies. The cells were grown in a commercial medium optimized for amniocyte culture at 37˚C in 5% CO2. Only culture flasks showing normal cell morphology were used for RNA extraction. Informed consent was given by the parents and the study design was approved by the research and ethics committee of the hospital.

After washing and drying under a nitrogen gun blowing, the microarrays were scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3 and 625 nm for Cy5. The scanned images were analyzed by Feature Extraction software (Agilent Technologies, USA), image analysis and normalization software was used to quantify the signal and background intensities for each feature.

The data were substantially normalized by the rank-consistency-filtering LOWESS method. Finally, the data were presented as log2.

Total RNA was extracted by Trizol® Reagent (Invitrogen, USA), followed by use of an RNeasy Mini Kit (Qiagen, Germany). The purified RNA was quantified by OD260nm using by a ND-1000 spectrophotometer (Nanodrop Technology, USA) and its quality was assessed by a Bioanalyzer 2100 (Agilent Technology, USA).

Cy-labeled cRNA (2 ug) was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60oC for 30 minutes. Correspondingly fragmented labeled cRNA was then pooled and hybridized to a Human 1A (version 2) oligo microarray (Agilent Technologies, USA) at 60°C for 17 h.

To serve as reference for microarray comparison, a human reference RNA pooled from 10 cell lines (Stratagene, USA) was used. Total RNA (0.5 ug) was amplified by a low RNA input fluor linear amp kit (Agilent Technologies, USA) and labeled at Cy3 (CyDye, PerkinElmer, USA) during in vitro transcription.

46, XY;Stratagene® QPCR Human Reference Total RNA Cell Line Derivations;Adenocarcinoma, mammary gland;Hepatoblastoma, liver;Adenocarcinoma, cervix;Embryonal carcinoma, testis;Glioblastoma, brain;Melanoma, skin;Liposarcoma;Histiocytic lymphoma; macrophage; histocyte;Lymphoblastic leukemia, T lymphoblast;Plasmacytoma; myeloma; B lymphocyte

MCF-7 sham-transfected, adapted for long-term growth in absence of E2

Fed male mice age 7-9 weeks were given 2100 mg/kg trichloroethylene in corn oil (10 ml/kg) by gavage or corn oil as vehicle

Feature Extraction Agilent .  Data was filtered by only accepting those genes with 70% or more values present.
sample batch normalization: Samples were run by batch with the same sample used for batch normalization by COMBAT.

Total RNA was extracted from liver using Qiagen mini kit per manufacturer's instruction.  Reference samples were pooled RNA from several organs from C57Bl/6J male mouse.

Aglient Hybridization kit catalog # 5190-0404 was followed per manufacturer's instruction

Low RNA Input Fluuorescent Linear Amp Kit (Agilent 5184-3253) per manufacturer's instruction.

Whole skin punch biopsies were homogenized in RLT with Beta-2-mercaptoethanol, RNA was extracted using RNeasy-Micro kit (QIAGEN, Valencia, CA).

anti-TNFa siRNA treatment in a mouse model of IBD: effects of various chemical modifications on clinical parameters and the inflammatory axis.

GeneChips were scanned using the Affymetrix GeneChip@ Scanner 3000.

Gene expression data was pre-processed and normalized using Partek Genomics Suite. The data was quantile normalized, and the summarization was obtained via RMA.

Total RNA was prepared using a RNEasy RNA extraction kit (Qiagen). Purity and integrity of the purified RNA was assessed on the Agilent Bioanalyzer 2100. Concentration was determined with a Nanodrop ND-1000 Spectrophotometer.

Hybridization of the samples to Affymetrix GeneChip® Mouse Gene 1.0 ST Arrays were performed according to the manufacturer’s instructions (http://www.affymetrix.com).

25 ng total RNA per sample was used for Whole Transcriptome Amplification (Sigma) according to manufacturer´s recommendations. 10 microgram cDNA was  fragmented, and biotinylated using Affymetrix' 10K v2 Assay Kit according to manufacturer's recommendations (http://www.affymetrix.com).

The U of U/miligramsg stands for Unit of MPO activity. One unit of MPO activity was defined as the amount that degraded 1.0 umol of peroxide per min at 25 C.

TNFa-OMe-P siRNA-C;09/06/22;09/06/30;6.1;159;2.607;0.477;colon;5% DSS

TNFa-OMe-P siRNA-C;09/06/22;09/06/29;7.1;151;2.127;0.082;colon;5% DSS

TNFa-OMe-P siRNA-C;09/06/19;09/06/30;6;167;2.78;0.056;colon;5% DSS

U133A arrays were scanned using an Affymetrix GeneChip Scanner 3000.

The expression intensity of each gene was determined by scaling to a trimmed-mean of 500 using the Affymetrix Microarray Analysis Suite (MAS) 5.0 software. The scaled expression intensities of all human genes on a U133A array were logarithmically transformed to the base 2, and normalized using quantile normalization.

Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA) and purified with RNeasy Mini Kit (Qiagen, Valencia, CA).

A cocktail was prepared by combining the specific amounts of fragmented cRNA, probe array controls, bovine serum albumin, and herring sperm DNA according to the protocol of the manufacturer. The cRNA cocktail was hybridized to oligonucleotide probes on the U133A array for 16 hours at 45˚C according to the Affymetrix protocol. Immediately following hybridization, the hybridized probe array underwent an automated washing and staining in an Affymetrix GeneChip Fluidics Station 450 using the protocol EukGE-WS2v5.

Biotin-labeled complementary RNA (cRNA) hybridization targets were prepared from 5 ug total RNA by in vitro transcription from cDNA templates according to the Affymetrix protocol. The cRNA was purified and chemically fragmented before hybridization.

Cells were cultured 2 days on MEF under the following conditions. (2) Serum: GMEM containing 2 mM L-glutamine (cat#11710-035; Invitrogen) with 1xMEM non-essential amino acids (cat#11140-050; Invitrogen), 1 mM sodium pyruvate (cat#11360-070; Invitrogen), 100uM 2-mercaptoethanol (cat#21985-023; Invitrogen), 1x10^3 units/ml LIF (cat#ESG1107;  Chemicon), and 20% FBS (Stem Cell Science).  (3) Serum without LIF: The same as the Serum medium except for removal of LIF.  (4) Serum+MEK inhibitor: The same as Serum excepto for addition of 0.4 uM MEK inihibitor PD0325901)

mESCs and mESC-like cells are culured on MEF in the following medium. 2i: N2B27 medium with 2i (PD0325901, 0.4 uM: Stemgent, San Diego, CA; CHIR99021, 3 uM: Stemgent) and LIF (1000 u/ml) .

The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix)

CEL data were generated by GeneChip Operating Software and then subjected to the dCHIP software.  Data were normalized together with the default settings.  The Model-Based Expression Indices (MBEI) were calculated using the PM/MM difference mode with log-2 transformation of signal intensity and truncation of low values to zero.

Total RNA was isolated with Qianeg RNeasy Micro according to manufacture's instruction.

Hybridization was performed according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic Target Hybridization)

Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic One-Cycle Target Labeling Assay)

C57BL/6;male;ESC-like cells;Prdm14 Knockout, pPyCAG-AGP14 transgene;Serum (day2)

Mice of each genotype were randomly assigned to fourteen day infusions of isoproterenol (120 µg/g/day) or no treatment

Twenty WT FVB, WT C57, and B2KO mice were given intraperitoneal injections of avertin (100μl/10g body weight) and sacrificed by cervical dislocation.  Half of the mice in each group had undergone fourteen day isoproterenol infusions.  RNA was extracted from the mouse hearts using Quiagen RNeasy® Midi kit.  Samples were homogenized in buffer containing guanidine isothiocyanate and beta mercaptoethanol.  Ethanol was then added to the lysate.  The sample was then applied to the RNeasy column.  RNA was eluted from the column using 80 ul of RNase-free water.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip 430-2 Mouse Gene array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

SMhu107

The scanned images of microarray chips were analyzed using the Affymetrix GenChip Operating Software (GCOS) with the default settings except that the target signal was set to 100.

RNA was extracted from biopsy samples using TRIzol Reagent (Invitrogen, USA) and purified by the RNeasy Mini Kit (Qiagen, UK).

The cDNA was synthesized, in vitro transcribed and labeled using standard Affymetrix protocols.

SMhu109

SMhu110

SMhu103

SMhu104

SMhu106

SMhu111

SMhu112

Induced with tetracycline (2ug/ml) over 24 hours prior to RNA isolation

RPMI +10% FBS + 1% PenStrep (2008), RPMI +10% FBS + 1% PenStrep + 100ug/ml Zeocin (2008-Ets1)

The data were analyzed with R version 2.9.2. Background correction and normalization was performed using the robust multi-array average (RMA) algorithm.

Total RNA was isolated using Trizol reagent (Invitrogen), DNase treated with Turbo DNA-free (Ambion), and cleaned up using RNeasy columns (Qiagen)

Following fragmentation, 5.5 ug of cDNA were hybridized on GeneChip Human Gene 1.0ST Array (Lot# 4067343). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cDNA were prepared according to the standard Affymetrix WT Kit from 300ng total RNA

in vivo Treatment: Formaldehyde, Vehicle for Chemical: Water, Amount of Vehicle: 40, Route of Exposure: Instillation (nasal), Units of Amount of Vehicle: ul per nostril, Dose or Concentration: 400, Units of Dose or Concentration: mM

Sample Type: cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs
nasal epithelium, formaldehyde instilation exposure, 400 mM formaldehyde, single exposure, 6 h time point

Rat230_2;15;ul;1.811;0.9;1.97;1:5;8.3;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;372;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;2.572;1.326;1.9;1:5;8.4;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;369;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;3.054;1.504;1.99;1:5;8.3;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;365;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 8, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 2, Units of Dose or Concentration: ppm

Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 8, Units of Harvest Time Point: days
nasal epithelium, formaldehyde inhalation exposure, 2 ppm, 6 hours per day, 5 days per week, 8 day time point

Rat230_2;15;ul;2.226;1.154;1.91;1:5;7.9;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;223;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

in vivo Treatment: Formaldehyde, Treatment Duration: 6, Units of Duration: hrs, Treatment Time: 6, Units of Treatment Time: hrs, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 2, Units of Dose or Concentration: ppm

Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 6, Units of Harvest Time Point: hrs
nasal epithelium, formaldehyde inhalation exposure, 2 ppm, 6 h time point

Rat230_2;15;ul;2.442;1.248;1.93;1:5;8.3;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;205;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 5, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 2, Units of Dose or Concentration: ppm

Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 5, Units of Harvest Time Point: days
nasal epithelium, formaldehyde inhalation exposure, 2 ppm, 6 hours per day, 5 days per week, 5 day time point

Rat230_2;15;ul;1.681;0.848;1.97;1:5;8.1;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;219;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 19, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 6, Units of Dose or Concentration: ppm

Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 19, Units of Harvest Time Point: days
nasal epithelium, formaldehyde inhalation exposure, 6 ppm, 6 hours per day, 5 days per week, 19 day time point

Rat230_2;15;ul;1.386;0.669;2.01;1:5;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;308;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;2.236;1.154;1.91;1:5;8.3;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;374;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;0.848;0.434;1.97;1:5;8.2;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;207;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.72;0.901;1.88;1:5;8.6;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;206;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Mice at postnatal day 22-25 were sacrificed, the brain extracted and sliced on a vibratome (Leica). Slices were incubated in ACSF with pronase E (1mg/mL; Sigma) for 1 hour and desired regions were microdissected. Three Pasteur pipettes with decreasing tip size were used for tritration in a 1.5 ml Eppendorf tube. Tritrated samples were diluted 20 times with ACSF with FBS (1%) and plated on a 10cm petri dish with Sylgard substriatum. Glass pipette of tip size around 50 um was used to aspirate fluorescent cells under a fluorescent stereomicroscope (Leica). Aspirated cells were transferred to a new dish with fresh ACSF and aspirated again to purify the sample. This wash was repeated twice more (total of 3 washes). After the last wash, the sample was transfered to a 200 ul PCR tube with 50 ul of XB (extraction and lysis buffer from PicoPure RNA Isolation Kit; Arcturus).

Mecp2 heterozygous null female mice were mated to male mice.  Either male or female carried one of the fluorescent alleles (G42, YFPH or TH). Male offsprings which are hemizygous to Mecp2 null allele and hemizygous to one of the fluorescent alleles were used for experiments. Littermates which are wild type for X chromosome and hemyzygous to one of the fluorescent alleles were used for controls. Mice were weaned around P30. Normal 12 hour-12 hour light dark cycle were used. Normally only up to 4 mice were put in a cage.

TH cells from LC, wild type control, young time point, biological replicate 1

GeneChips were scanned with the Affymetrix GeneArray Scanner G3000.

The data were processed with fRMA (McCall MN, Bolstad BM, Irizarry RA (2010) Frozen robust multiarray analysis (fRMA). Biostatistics 11:242-253) algorithm in the Bioconductor with default settings.

PicoPure RNA Isolation Kit (Arcturus) was used to extract total RNA according to the manufacturer's instructions.

Following fragmentation, 15 or 20 ug of cRNA were hybridized for 18 hr at 45C on GeneChip Mouse Genome 430 v2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared using two rounds of T7 in vitro transcription based aRNA amplification (Affymetrix Small Sample Target Labeling Assay Version II) from about 0.3 to 1 ng of total RNA.

Gene expression data from TH GFP labeled neurons from the locus coeruleus (LC), wild type control
TH_LCY_WT_1

C57BL6/J;No;Aug-11;95;male;LC (locus coeruleus);P23;Y/X;TH/-;brain;tyrosine hydroxylase (TH)-positive locus coeruleus (LC) neurons

Leukemic bone marrow samples were used for RNA extraction without further treatment.

Ficoll-enriched, cryopreserved diagnostic bone marrow samples were obtained from patients with newly diagnosed B-precursor acute lymphoblastic leukemia.

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 150.

Total RNA was extracted using the Allprep DNA/RNA minikit (Qiagen, Valencia, CA) and quality was verified by Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

Biotinylated cRNA (20ng) was fragmented,10 ug of cRNA were hybridized for 16hr at 45C on GeneChip Human Genome U133 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Total RNA (50 ng) was used as template in a single-amplification protocol (RiboAmp OA, Mountain View, CA) according to manufacturer's instructions.

bone marrow;B-precursor acute lymphoblastic leukemia, Non-Down syndrome

bone marrow;B-precursor acute lymphoblastic leukemia, Down syndrome

Crohn's Disease subject (33 year old caucasian female, SAK_1316622123)

Subject Age : 33
Subject Race : CAUCASIAN

Crohn's Disease subject (31 year old caucasian male, SAK_1315951533)

Subject Age : 31
Subject Gender : MALE

During autopsy dissection, parts of the frontal cortex, temporal cortex and hippocampus were cut out from each brain, and preserved at –80°C until RNA preparation.

We examined postmortem human brains donated for the Hisayama study.

GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000 7G.

CEL files were imported into Affymetrix Expression Console Software, and CHP files were generated.

Total RNA was isolated using a combination of Isogen (Nippon Gene) and the RNeasy Mini Kit (Qiagen), according to the manufacturers’ instructions.

Following fragmentation, 5.5 µg of cDNA were hybridized for 17 hr at 45℃ on Affymetrix Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

The Ambion WT Expression Kit and the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix) were used to generate amplified and biotinylated sense-strand DNA targets from expressed transcripts (100 ng of total RNA).

Cells were grown in 100 mm dishes in 10% FBS/DMEM to approximately 70-80 % confluence, and were washed once in serum-free DMEM, and then incubated for 16 h in DMEM containing 0.5 % (v/v) FBS.  The cells were then stimulated with 10% (v/v) FBS for 90 min then actinomycin D was added to a final concentration of 5 mg/ml for 120 minutes and were extracted for RNA.

The fibroblasts were maintained at 37oC (5% CO2) in Dulbecco Minimal Essential Medium supplemented with 10% FBS, 2 mM L-glutamine, 100U/ml penicillin and 100 mg/ml streptomycin.

Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450.  Arrays were then scanned with an Affymetrix Scanner 3000.  Data was obtained using the Genechip® Operating Software (Version 1.2.0.037).

quantile normalization of CEL file, PDNN (PerfectMatch) estimation, log2 transformation

The cell monolayer was rinsed twice in cold PBS, 5 ml each. Each plate of cells was then lysed in 0.6 ml of Buffer RLT (RNeasy Mini Kit, Qiagen) and total cellular RNA was prepared following the RNeasy protocol.

15ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol.

Gene expression analysis was conducted using Mouse Genome 2.0 array (Affymetrix, Santa Clara, CA).  Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol.  For each array, 15ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.  Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450.  Arrays were then scanned with an Affymetrix Scanner 3000.  Data was obtained using the Genechip® Operating Software (Version 1.2.0.037).

Fibroblast TTP WT cell line prepared from littermate E14.5 mouse embryos, derived from parental TTP +/- male and TTP +/- female strain 129/B6;  Embryo age:  E14.5, Tissue:  Whole embryo excluding head and organs

RNA prepared from fibroblast cell lines treated with 10% serum for 90 min followed by 0.5 µg/ml actinomycin D for 120 minutes

Cells were grown in 100 mm dishes in 10% FBS/DMEM to approximately 70-80 % confluence, and were washed once in serum-free DMEM, and then incubated for 16 h in DMEM containing 0.5 % (v/v) FBS.  The cells were then stimulated with 10% (v/v) FBS for 90 min then actinomycin D was added to a final concentration of 5 mg/ml for 90 minutes and were extracted for RNA.

RNA prepared from fibroblast cell lines treated with 10% serum for 90 min followed by 0.5 µg/ml actinomycin D for 90 minutes

Cells were grown in 100 mm dishes in 10% FBS/DMEM to approximately 70-80 % confluence, and were washed once in serum-free DMEM, and then incubated for 16 h in DMEM containing 0.5 % (v/v) FBS.  The cells were then stimulated with 10% (v/v) FBS for 90 min then actinomycin D was added to a final concentration of 5 mg/ml for 60 minutes and were extracted for RNA.

RNA prepared from fibroblast cell lines treated with 10% serum for 90 min followed by 0.5 µg/ml actinomycin D for 60 minutes

Cells were grown in 100 mm dishes in 10% FBS/DMEM to approximately 70-80 % confluence, and were washed once in serum-free DMEM, and then incubated for 16 h in DMEM containing 0.5 % (v/v) FBS.  The cells were then stimulated with 10% (v/v) FBS for 90 min then actinomycin D was added to a final concentration of 5 mg/ml for 30 minutes and were extracted for RNA.

RNA prepared from fibroblast cell lines treated with 10% serum for 90 min followed by 0.5 µg/ml actinomycin D for 30 minutes

Cells were grown in 100 mm dishes in 10% FBS/DMEM to approximately 70-80 % confluence, and were washed once in serum-free DMEM, and then incubated for 16 h in DMEM containing 0.5 % (v/v) FBS.  The cells were then stimulated with 10% (v/v) FBS for 90 min and were extracted for RNA.

RNA prepared from fibroblast cell lines treated with 10% serum for 90 min

Fibroblast TTP KO cell line prepared from littermate E14.5 mouse embryos, derived from parental TTP +/- male and TTP +/- female strain 129/B6;  Embryo age:  E14.5, Tissue:  Whole embryo excluding head and organs

We used the bone marrow transplantation mouse model of CML as an assay system, in which bone marrow cells from donor mice pre-treated with 5-fluorouracil (5-FU) and transduced with BCR-ABL result in development of CML in recipient mice. We transduced bone marrow cells from C57BL/6 (B6) mice or Hif1a-/- mice with retrovirus containing BCR-ABL/GFP under conditions for induction of CML, followed by transplantation of the transduced cells into B6 recipient mice. 14 days after BMT, bone marrow cells were isolated and subsequently sorted by FACS for LSCs (GFP+Lin-c-Kit+Sca-1+) .

The arrays are scanned with a GeneChip Scanner 3000. Images are acquired and CEL files generated, which are then used for analysis.

Average signal intensities for each probe set within arrays were calculated by and exported from Affymetrix’s Expression Console (Version 1.1) software using the RMA method, which incorporates convolution background correction and a summarization based on a multi-array model fit robustly using the median polish algorithm. These values were read into R/maanova and quantile-normalized. For this experiment, three pairwise comparisons will be used to statistically resolve gene expression differences between strain groups using the R/maanova analysis package (Wu et al. 2003). Specifically, differentially expressed genes will be detected by using Fs, a modified F-statistic incorporating shrinkage estimates of variance components from within the R/maanova package (Cui et al. 2005, Wu et.al 2003). Statistical significance levels of the pairwise comparison will be calculated by permutation analysis (1000 permutations) and adjusted for multiple testing using the false discovery rate (FDR), q-value, method (Storey, 2002). Differentially expressed genes are declared at an FDR q-value threshold of 0.05.

Total RNA is isolated by following the protocol for the RNeasy Micro Kit, and quality is assessed using a 2100 Bioanalyzer instrument and RNA 6000 Pico LabChip assay (Agilent Technologies, Palo Alto, CA). Utilizing the GeneChip Whole Transcript Sense Target Labeling Assay kit (Affymetrix, Santa Clara, CA.), between 100-300ng of total RNA undergoes reverse transcription with random hexamers tagged with T7 sequence. The double-stranded cDNA that is generated is then amplified by T7 RNA polymerase to produce cRNA. Second cycle first strand cDNA synthesis then takes place, incorporating dUTP which is later used as sites where fragmentation occurs by utilizing an uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1 enzyme mix.

Approximately 2.0µg of fragmented and biotin-labeled cDNA is then hybridized onto a Mouse Gene ST 1.0 Array (Affymetrix, Santa Clara, CA.) for 16 hours at 45°C. Post-hybridization staining and washing are performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).

The fragmented cDNA is then labeled by terminal transferase attaching a biotin molecule using Affymetrix proprietary DNA labeling Reagent.

DNA microarray analysis was carried out to compare gene expression between BCR-ABL-expressing WT LSCs and BCR-ABL-expressing Hif1a-/- LSCs.
Gene expression data from BCR-ABL-expressing WT LSCs.

D425 cells with inducible shRNA targetting or control cells were plated 24 hours before induction of with doxycycline. RNA was harvested at 0 to 96 hours.

Cells were cultured in MEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.

Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco

Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix)

Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.

10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

NB193
Medulloblastoma cell line D425 control at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.

Triceps muscle was isolated and directly homogenized in TriFast solution.

Array scanning was performed according to the manufacturer's instruction (Affymetrix).

Data were processed using RMA (Affymetrix Expression Console software).

RNA was isolated from the triceps muscles using peqGOLD TriFast (PeqLab Biotechnologie GmbH) according to the supplied protocol.  The cRNA synthesis and microarray hybridizaton was done according to standard protocols applied in the Laboratory of Functional Genome Research Charité - Core Facility. A total of 8 high-density oligonucleotide mouse GENE 1.0 ST arrays (Affymetrix) were used in this study. Samples from each animal (4 Nf1, and 4 wild-type) were applied individually to each array.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on MouseGene1.0ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Slides were scanned with the Agilent Bundle Microarray Scanner System (Agilent Technologies) and data were processed using the Feature Extraction 10.7.3.1 software (Agilent Technologies).

Among the 45,015 spots present in each array, only those with none flag for quality control (i.e., low intensity, saturation, controls, etc.) were selected for analysis. For analysis of replicate spots, the average intensity after background correction was calculated, normalization was performed using locally weighted linear regression (LOWESS) with α=0.2 within slides using the R software version 2.11.1 (R Development Core Team, 2010) and Linear Models for Microarray (LIMMA) from Bioconductor.

Total RNA was isolated using TRIzol (Sigma) according to the manufacturer's instructions.
RNA concentration was determined by spectrophotometry (NanoDrop, Thermo Scientific, US), and integrity was assessed using the 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).

brain (frontal cortex);schizophrenia;44 yr;white;295.3;9 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

Left and right kidneys were removed, snap frozen in liquid nitrogen and stored at -80C. Before RNA isolation, both kidneys were ground together in liquid nitrogen using a frozen mortar and pestle.

Mice were housed in standard conditions (12h light-dark, ad libitum standard diet and water).

Arrays were scanned using a GeneArray Scanner at an excitation wavelength of 488nm. Light emissions at 570nm are proportional to the bound target at each oligonucleotides position on the array. Performed at The Functional Genomics Platform of the McGill University and Génome Québec Innovation Centre.

The data were analyzed with Genespring GX (Agilent) using RMA normalization method and statistical analysis was done using unpaired Students' t-test and asymptotic p-value computation.

RNeasy midi RNA extraction kit was used according to manufacturer protocol.

Standard protocols were performed at The Functional Genomics Platform of the McGill University and Génome Québec Innovation Centre.

Target RNA was reverse transcribed into cDNA, and in-vitro transcription was performed to generate biotin-labeled cRNA for subsequent hybridization. Hybridized target cRNA was stained with streptavidin phycoerythrin. Performed at The Functional Genomics Platform of the McGill University and Génome Québec Innovation Centre.

Approximately 1x10^6 cells were infected with control adenovirus expressing GFP for 16 hours, then total RNA was isolated using RNEasy kit (Qiagen).

Approximately 1 µg of total RNA was processed to produce biotinylated cRNA targets.

Approximately 1x10^6 cells were infected with adenovirus expressing c-Myb and GFP for 16 hours, then total RNA was isolated using RNEasy kit (Qiagen).

Labeling and probe preparation was performed exactly as recommended by Affymetrix.

Trizol reagent was used to isolate total RNA from whole d17.5 fetal mouse hearts.

Labeling and probe preparation was performed exactly as recommended by Affymetrix, using the Superscript Choice System for RT/PCR (Gibco/BRL Life Technologies) for cDNA synthesis and the RNA Transcript Labeling Kit (ENZO) for cRNA preparation.

T6 fetal heart (treated on gd14.5 via oral gavage, collected on gd17.5)

Approximately 1x10^6 cells were infected with adenovirus expressing 3Mutc Myb and GFP for 16 hours, then total RNA was isolated using RNEasy kit (Qiagen).

Affymetrix HG-U133A GeneChips were scanned with the Agilent GeneArray Scanner

The raw data (CEL files) were read into R statistical package and normalised using the robust multi-chip average (RMA) method (Irizarray et al, 'Exploration, normalization and summaries of high density oligonucleotide array probe level data', Biostatistics, 2003).

Total RNA was isolated from human postmortem brain tissue using Trizol (Invitrogen, USA) or Tri reagent (Sigma, UK) total RNA isolation kits according to the manufacturer's instructions.

Following fragmentation, 15 micrograms of cRNA were hybridised to Affymetrix Human Genome 133A GeneChips for 16 hours at 45oC with constant rotation at 60rpm. Chips were washed and stained according to manufacturer's instructions using the Affymetrix GeneChip Fluidics Station 400.

Double-stranded cDNA was synthesised from 5 micrograms of total RNA using Superscript II double-stranded cDNA synthesis kit (Invitrogen, USA), purified, then in-vitro transcribed and labelled using BioArray HighYield RNA transcript Labeling Kit (Enzo Life Sciences, USA)

Bipolar disorder;30;Male;22;8;6.1;31;Right;60000;Yes;No;No;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 3

Bipolar disorder;48;Male;27;21;6.1;13;Right;200;No;No;No;Yes;0 (no use) to 5 (heavy use)): 3;0 (no use) to 6 (heavy use)): 2

Bipolar disorder;50;Female;25;25;6.3;62;Left;0;No;Yes;No;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 0

Bipolar disorder;50;Male;17;23;6.2;19;Left;60000;No;Yes;No;Yes;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 1

Bipolar disorder;48;Female;16;32;5.8;22;Left;32000;No;Yes;No;No;0 (no use) to 5 (heavy use)): 3;0 (no use) to 6 (heavy use)): 5

Bipolar disorder;61;Female;18;43;6.5;60;Left;40000;Yes;No;Yes (5 treatments);Yes;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 1

Healthy control;49;Female;N/A;N/A;6.72;45;Left;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 0

Healthy control;45;Male;N/A;N/A;6.81;18;Left;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 0

Bipolar disorder;31;Male;21;10;6.3;28;Right;30000;No;No;No;Yes;0 (no use) to 5 (heavy use)): 5;0 (no use) to 6 (heavy use)): 6

All-trans retinoic acid (atRA) (Cat. #R2625, Sigma, MD) and cycloheximide (chx) (Cat. #C7698, Sigma, MD) were dissolved in 100% ethanol (EtOH). The cells were pretreated with 1 µg/ml chx for 30 min before 7.5hr treatment with RA (1 µM) or vehicle (EtOH, 0.1%).

F9 Wt and RARaKO cells were propagated in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 5% calf serum and 5% fetal calf serum and maintained at 95% humidity in 37°C incubators equilibrated with 10% CO2. Prior to plating the tissue culture dishes were coated with 0.3% gelatin. For the microarray analysis 2 million cells were plated on 10 cm tissue culture dishes  were plated 16 hr prior to drug treatment.

The data were analyzed with GenespringGX version 7.0 using Affymetrix default analysis settings. The data sets were summarized using the GC-RMA algorithm, followed by a three-step normalization process consisting of: A) data transformation, converting values less than 0.01 to 0.01, B) chip normalization to the 50th percentile of total intensity and C) per gene normalization to median intensity. Genes were filtered by expression level to exclude genes with a raw signal below 100.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix MG-430.2 expression array. The chips were washed and stained in the Affymetrix Fluidics stations FS450.

Arrays were washed on Affymetrix’s GeneChip Fluidics Station 450 using a primary streptavidin phycoerythrin (SAPE) stain, subsequent biotinylated antibody stain, and secondary SAPE stain. Arrays were scanned on Affymetrix’s GeneChip Scanner 3000 7G with AutoLoader. Scanned images obtained by the Affymetrix GeneChip Operating Software (GCOS) v1.2 were used to extract raw signal intensity values per probe set on the array.

Two hundred microliters (containing 10 micrograms of fragmented cRNA) of each cocktail was separately hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array for 16h at 45 degree Celsius in the Hybridization Oven 640.

Isolated total RNA was double round amplified, cleaned, and biotin-labeled using Affymetrix’s GeneChip Two-Cycle Target Labeling kit (Santa Clara, CA) with a T7 promoter and Ambion’s MEGAscript T7 High Yield Transcription kit (Austin, TX) as per manufacturer’s protocol. Amplified and labeled cRNA was quantified on a spectrophotometer and run on a 1% TAE gel to check for an evenly distributed range of transcript sizes. Twenty micrograms of cRNA was fragmented to approximately 35-200bp by alkaline treatment (200 mM Tris-acetate, pH 8.2, 500 mM KOAc, 150 mM MgOAc) and run on a 1% TAE gell to verify fragmentation. Separate hybridization cocktails were made using 15 micrograms of fragmented cRNA from each sample as per Affymetrix’s protocol.

Data were Scanned with the HiScan Reader of Illumina and image acquisition was performed with a BeadStudio version 3.4.0.30825

Images were processed using the Affymetrix Microarray Suite 5.0, cel files were normalized with RMA and further analyzed using Bioconductir software based on R language

25 ng/ul fragmented and labeled DNA target was hybridized according to standard protocols

100 ng Total RNA Labeling protocol, whole transcript sense target labeling assay

Mice were killed by an overdose of diethylether at the mean age of 30 days (p29-p31) or 42 days (p41-p43). Afterwards, the eyes were enucleated, the retinas were prepared and immediately snap-frozen in liquid nitrogen. The retinas of 12 homozygous Egr-1 knock-out mice (hm) and 12 wildtype mice (wt) of the same strain were prepared for both time points (48 animals in total).

Animals were housed in standard cages with their littermates under a 12 hours light/dark cycle with unrestricted access to water and food pellets. Illumination was provided by standard fluorescent lamps and was approximately 200 lux.

Scanning and analysis were carried out using the Affymetrix Microarray Suite Software (version 5.0)

Signal intensities were analyzed using ArrayAssist 4.0 (Stratagene, La Jolla, CA). Transformation algorithm: GC-RMA.

Three single retinas from different mice were pooled to obtain 4 samples per group (wt30, wt42, hm30, hm42), and RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. The quality of total RNA was monitored by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) following the manufacturer's instructions.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5 ug total RNA (see manufacturer´s website: Expression Analysis Technical Manual, One-Cycle Target Labeling Assay, Affymetrix).

RNA sample consists of three separate retinal samples that were pooled

H157 cells grown in RPMI w/ 10% FCS transfected 3 consecutive days annd GITC lysed 96 hours after first transfection.  RNA isolated by column (Promega).  Then cRNA made and labeled, hybridized to Affy U133A array

Affymetrix GeneChip Microarray Suite 5.0 software was used for washing, scanning, and basic analysis. Sample quality was assessed by examination of 3’ to 5’ intensity ratios of certain genes.

Following fragmentation, 10 microg of cRNA was hybridizd onto arrays for 16 hours at 45oC in the GeneChip Hybridization Oven 640

Biotinylated cRNA were prepared using BioArray High Yield RNA Transcript Kit

Gene expression data from H157 cells  transfected with non-targetting scrambeled control siRNA oligomers

NSCLC cell line H157. Transfected with scrambeled control non-targetting oligomer siRNA - #2

NSCLC cell line H157. Transfected with scrambeled control non-targetting oligomer siRNA - #1

Gene expression data from H157 cells  transfected siRNA oligomers targeting DJ-1

NSCLC cell line H157. Transfected with siRNA oligomers targeting DJ-1 - #2

NSCLC cell line H157. Transfected with siRNA oligomers targeting DJ-1 - #1

Gene expression data from H157 cells Mock transfected with transfection reagent alone.

NSCLC cell line H157. Transfected with Oligofectamine (Invitrogen) without RNA

For transfection assays, cells were plated in antibiotic-free media and transfected with Lipofectamine 2000 (Invitrogen, Carlasbad, CA) according to the manufacturer's instructions.  Antagomirs were transfected at 100nM concentrations.

MCF7-FR cells were growing in phenol red-free medium with 10% charcoal-stripped fetal bovine serum (FBS) and 10E-7 mol/L fulvestrant

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using R default settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

MCF7 fulvestrant-resistant cell line transfected by antisense hsa-miR-221

MCF7 fulvestrant-resistant cell line transfected by antisense hsa-miR-222

Neonatal (P0) whole brain mRNA from 40,XX female In(X)/C3H x C57BL/6J

pancreas from 3 week old BDC2.5/NOD.scid mouse.  RNA was extracted by GITC method. Targets were produced using standard Affymetrix procedures from about 10ug of total RNA.  RNA was isolated twice from 6 animals each and pooled.
Pancreas
Keywords = BDC2.5/NOD.scid, pancreas

Neonatal (P0) whole brain mRNA from 39,Xp (XpO) In(X)/C3H x C57BL/6J

pancreas from 3 week old NOD.scid mouse.  RNA was extracted by GITC method. Targets were produced using standard Affymetrix procedures from about 10ug of total RNA.  RNA was isolated twice from 6 animals each and pooled.
Pancreas
Keywords = NOD.scid, pancreas

Neonatal (P0) whole brain mRNA from 40,XX females In(X)/C3H x C57BL/6J

pancreas from 3 week old NOD mouse.  RNA was extracted by GITC method. Targets were produced using standard Affymetrix procedures from about 10ug of total RNA.  RNA was isolated twice from 6 animals each and pooled.
Pancreas
Keywords = NOD, pancreas

Array normalization, expression value calculation and clustering analysis were performed using DNA-Chip Analyzer. The Invariant Set Normalization method was used to normalize arrays at probe cell level to make them comparable, and the model-based method was used for probe-selection and computing expression values.

Cells immortalized through SV40 driven largeT antigen expression.

PGC-1alpha -/- differentiated brown fat cells treated 4h cAMP (rep1)

Topic administration of TPA or acetone on the dorsal shaved skin of mice before extraction of skin.
WT mouse skin treated once with TPA (phorbol ester 12-O-tetradecanoylphorbol-13 acetate, 6.8 nmol in 200 μl acetone) and collected 24 hr later

WT mouse skin treated once with TPA and collected 24 hr later, replicate 2

Upon microarray hybridization, the raw data was normalized with RMA using RMAexpress software (v.1.0.5).

Total cellular RNA was extracted from three independent exponential cultures of the appropriate cell lines using the RNAeasy kit (Qiagen)

Total RNA was quantified using 6000 Nano Chips (Agilent Technologies, Santa Clara, CA) and used (2.3 μg/sample) to generated labeled cRNA probes according to the manufacturer’s instructions (Affymetrix).

WT mouse skin treated once with TPA and collected 24 hr later, replicate 3

WT mouse skin treated once with acetone and collected 24 hr later

WT mouse skin treated once with acetone and collected 24 hr later, replicate 3

WT mouse skin treated once with TPA and collected 24 hr later, replicate 1

WT mouse skin treated daily with TPA (phorbol ester 12-O-tetradecanoylphorbol-13 acetate, 6.8 nmol in 200 μl acetone) during 4 days and collected 24 hr later

WT mouse skin treated daily with TPA during 4 days and collected 24 hr later, replicate 3

WT mouse skin treated daily with TPA during 4 days and collected 24 hr later

WT mouse skin treated daily with TPA during 4 days and collected 24 hr later, replicate 1

WT mouse skin treated daily with TPA during 4 days and collected 24 hr later, replicate 2

Labeling, hybridization, and scanning done using Agilent reagents, hardware, and protocols

lung;;Sporadic IIP;;Usual Interstitial Pneumonia;Stratagene;;740000

Stratagene;;740000;lung;;Sporadic IIP;;Usual Interstitial Pneumonia

Lung, Sporadic Idiopathic Interstitial Pneumonia (S-IIP), Usual Interstitial Pneumonia (UIP)

All cells were cultured on Matrigel (BD Biosciences) in mTESR media (Stem Cell Technologies)

Arrays were scanned by the Genomics Resource Lab at Fred Hutchinson Cancer Center with an Illumina BeadArray Reader.

Raw expression files were loaded into Bioconductor. The Bioconductor package 'lumi' was used to read in the GenomeStudio Probe Level from unnormalized data, and quantile normalize the data.

RNA was extracted with Trizol reagent. Quality control was performed with Agilent 2100 Bioanalyzers and NanoDrop DN-1000 spectrophotometer.

cRNA samples were hybridized onto Human HT-12 v4 Expression BeadChip (Illumina) according to manufacture's protocols.

All RNA samples were amplified and labelled using Illumina's TotalPrep RNA Amplification Kit according to manufacturer's protocol.

hESC H1 cells were targeted with AAV-based vectors to knock out B2M gene, clone 2
Sample name: B2MKOc2

To deplete Rybp, ES cells (#10, #15) were treated with 4-hydoxytamoxifen (OHT) at a concentration of 800nM for 24 hours.

ES cells (#10, #15) were cultured in DMEM with 20 % fetal bovine serum, MEM nonessential amino acids (Invitrogen), sodium pyruvate (Invitrogen), L-glutamine (Invitrogen), 2-mercaptoethanol (Sigma), and ESGRO (Chemicon) either on irradiated MEF as feeder layers or directly on gelatin-coated surfaces.

GeneChip Scaner 3000 was used . The core software was used GCOS for image processing.

The summarized probe set data were generated using Expression console. RMA-sketch was used as the processing algorithm.

Heat the Hybridization Cocktail at 99C for 5 minutes. Cool to 45C for 5 minutes. Inject the appropriate amount of the specific sample into the Affymetrix Mouse Genome 430 2.0 array through one of the septa. Place array in 45C hybridization oven, at 60 rpm, and incubate for 16 hours.

The ds-cDNA derived from total RNA was incubated at 37C for 16hr with both IVT Labeling NTP mix and IVT Labeling Enzyme Mix to synthesize Biotin-Labeled cRNA.

10(+) 4d
Gene expression data from clone#10 (4 days after tamoxifen treatment: Rybp-KO)

15(-) 12d
Gene expression data from clone#15 (without tamoxifen treatment; Wild-type control)

Analysis of target genes induced by the Amyloid Precursor Protein Intracellular Domain

Analysis of target genes induced by the Amyloid Precursor Protein Intracellular Domain (AICD)

Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0. GeneChips were washed and stained using Standard protocol.

Affymetrix standard methods were applied using the high throughput protocal for PM arrays

Twenty ml of peripheral blood from patients and normal volunteers was collected in EDTA tubes and centrifuged at 150 x g for 10 minutes and platelet rich plasma (PRP) was carefully aspirated and re centrifuged at 150 x g for 5 minutes to remove remaining red and white cells. PRP was centrifuged again at 1500 x g for 10 min to pellet the platelets. The cell pellet was lysed twice with erythrocyte lysis buffer to remove traces of contaminating red blood cells. The pellet was than washed with phosphate buffered saline and checked for purity in a Cell-Dyn coulter counter (Abbott Diagnostics, Abbott Park, IL).

Hybridized chips were scanned using Affymetrix genechip scanner 3000

Affymetrix GCOS version 1.4 was used to calculate the signal intensity and the percent present calls on the hybridized Affymetrix chip. To select genes differentially expressed between patients and normals, the signal intensity values obtained for probe sets in the microarrays were transformed using an adaptive variance-stabilizing, quantile-normalizing transformation (Munson, P.J., GeneLogic Workshop of Low Level Analysis of Affymetrix GeneChip Data, 2001, software available at http://abs.cit.nih.gov/geneexpression.html.) The transform, termed S10 is scaled to match the logarithm transform, base 10.

Total Platelet RNA was extracted using RNAqueous micro RNA isolation kit (Ambion, Austin, TX) following the manufacturer’s directions. Platelets were lysed in lysis buffer containing guanidinium thiocyanate and the cell lysate was mixed with ethanol and applied to a silica based filter that selectively binds RNA. Genomic DNA was removed by DNase treatment. The concentration of the isolated RNA was determined using the Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE). Quality and integrity of the total RNA isolated was assessed on the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA).Total Platelet RNA was extracted using RNAqueous micro RNA isolation kit (Ambion, Austin, TX) following the manufacturer’s directions. Platelets were lysed in lysis buffer containing guanidinium thiocyanate and the cell lysate was mixed with ethanol and applied to a silica based filter that selectively binds RNA. Genomic DNA was removed by DNase treatment. The concentration of the isolated RNA was determined using the Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE). Quality and integrity of the total RNA isolated was assessed on the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA).

Twenty μg of biotin-labeled RNA was fragmented to ~200 bp size by incubating in fragmentation buffer containing 200 mM Tris-acetate pH 8.2, 500 mM potassium acetate and 500 mM magnesium acetate for 35 minutes at 94ºC prior to hybridization. Fragmented RNA was assessed for relative length on Agilent 2100 bioanalyzer and hybridized to Affymetrix HG-U133 plus 2.0 chips for 16 hours, washed, stained on an Affymetrix fluidics station.

T7 based RNA amplification was carried out on 10 ng of the isolated platelet total RNA (corresponding to ~ 4-5 ml of collected blood) using Riboamp OA two-round amplification kit as suggested by the manufacturer (Arcturus, Mountain View, CA). Briefly, total RNA was incubated with oligo dT/T7 primers and reverse transcribed into double stranded cDNA. In vitro transcription of the purified cDNA was performed using T7 RNA polymerase at 42ºC for 6 hours. The amplified RNA was purified and subjected to a second round of amplification and biotin labeling using Affymetrix’s IVT labeling kit following the manufacturer’s directions. The yield and integrity of the biotin labeled cRNA were determined using the Nanodrop ND-1000 spectrophotometer and the Agilent 2100 bioanalyzer.

The Biopsies were mechanically homogenized (Rotor/Stator homogeniser, PowerGen).

Scanning was done using a GeneArray Scanner at the McGill University and Genome Quebec Innovation Centre (www.genomequebec.mcgill.ca) and was performed in parallel for control and EBS samples

The scanned images were analyzed using the Microarray Analysis Suite 5.0 (MAS5, Affymetrix) and the raw image fils obtained (.CEL) were used for statistical analyses. Affy and Limma packages in Bioconductor (www.bioconductor.org) using R2.12.0 were used to perform quality tests, RMA normalization and Smyth's moderated t-test.

RNA was extracted using the RNEasy Fibrous Tissue Midi Kit (Qiagen) according to the manufacturer's instructions.

Hybridation was done at the McGill University and Genome Quebec Innovation Centre (www.genomequebec.mcgill.ca) and was performed in parallele for control and EBS samples.

Probe labelling was done at the McGill University and Genome Quebec Innovation Centre (www.genomequebec.mcgill.ca) and was performed in parallel for control and EBS samples.

Gene expression data from allergic asthmatic subject, without any stimulation. BAL was done at the same time of the day for each subject and only if he (she) did not experience inflammatory or allergen response.

allergic asthmatic;Keratinocytes;skin biopsies with no stimulation

Gene expression data from non EBS patients subject, without any stimulation.

healthy (non EBS);Keratinocytes;skin biopsies with no stimulation

Gene expression intensities were calculated using GeneChip Command Console Software (AGCC, v.3.2.4). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software (v.1.2.1) and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.

Whole kidney tissue total RNA  was extracted by Qiagen RNAeazy kit

The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix Human GeneChip 1.0 ST microarrays.  The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.

Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Human HuGene-1_0-st-v1 GeneChips (Affymetrix, Inc).  DNase treatment was included as part of isolation to remove possible contaminating DNA.  Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling.  300 ng of total RNA was used for labeling with theAmbion WT Expression Kit (cat#4411974)  and Affymetrix kit (Cat # 900652).After hybridization,  the probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).

C57BL/6;female;MMA wild type;kidney;high protein diet for 2 months

C57BL/6;female;Mut -/- ;TgINS-Alb-Mut (MMA mutant);kidney;high protein diet for 2 months

C57BL/6;female;MMA heterozygote;kidney;high protein diet for 2 months

plaque type psoriasis;epidermis;33;female;> 10 y;phototherapy;post-UV

Hybridized arrays were scanned with the GeneChip Scanner 3000 7G.

Cell intensity values and probe detection calls were computed using the Affymetrix GeneChip Operating Software (GCOS). Further data processing was performed in the R computing environment (http://www.r-project.org/) version 2.8.0 with BioConductor packages (http://www.bioconductor.org/). Robust Multi-Array Average (RMA) normalization was applied. Data were then filtered based on Affymetrix detection call and probeset intensity, so that only probesets that had a present call and intensity value >100 in at least one of the arrays were retained. Statistical analysis was performed with limma. P-values were adjusted for multiple testing using Benjamini and Hochberg’s method to control the false discovery rate. Genes with adjusted P values below 0.05 were considered differentially expressed.

Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions, treated with DnaseI (Ambion) and purified with the RNeasy Mini kit (Qiagen). RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was quantified with a NanoDrop 1000 spectrophotometer (Thermo Scientific).

Labeled cRNA was hybridized on Affymetrix GeneChip Mouse Genome 430A 2.0 Arrays, containing 22,690 probesets corresponding to approximately 14,000 well-characterized mouse genes. Hybridized arrays were stained and washed (GeneChip Fluidics Station 450).

A 10μg-amount of each total RNA sample was labeled according to the standard one-cycle amplification and labeling protocol (Affymetrix, Santa Clara, CA).

Vemurafenib was dissolved in dimethyl sulfoxide (DMSO) as a 10 mM stock solution. Final drug concentration (1000 nM) was obtained with further serial dilutions in culture medium. Negative controls were represented by cells treated only with DMSO at a concentration of 1:2500 v/v, which is the highest possible DMSO concentration present in cultures of cells treated with the drug (in particular, with 1000 nM drug, the highest drug concentration). After 48 hours to 72 hours, cultures were harvested and lysed.

7.5x105 primary leukemic cells MACS-purified from the peripheral blood of  HCL patients were seeded in flat-bottom 24-well plates  in complete medium (RPMI 1640 medium supplemented with 10% FBS, 1% Penicillin/Streptomycin and 1% Glutamine) and were then treated with Vemurafenib 1000 nM, or vehicle (DMSO) as control, for 48 hours or 72 hours

GeneChips were scanned using the GeneChip scanner 3000 with G7 update.

The data were analyzed by means of the GeneSpring Version 7.3.1 software (Agilent Technologies) with RMA pre-processing of the raw expression data (CEL files).

Lysates  (600 μl of Buffer RLT Plus supplemented with β-mercaptoethanol) were  stored at -80°C until total RNA extraction. Total RNA was isolated using AllPrep DNA/RNA Mini Kit (Qiagen) according to the manufacturer's protocol.

Fragmented cRNA was hybridized to HG-U133Plus_2.0 microarrays according to the 3' IVT Express Kit for sample preparation and microarray hybridization (Affymetrix, Santa Clara, CA, USA; catalogue no. 901229). The microarrays were then washed and stained according to the manufacturer's recommendation.

High-quality total RNA (50-100 ng) was converted into biotinylated cRNA, purified and fragmented employing the 3' IVT Express Kit for sample preparation and microarray hybridization (Affymetrix, Santa Clara, CA, USA; catalogue no. 901229).

Gene expression data from  primary HCL cell of  patient A treated with Vemurafenib 1000 nM for 72h
ET13

peripheral blood;primary leukemic cells;patient A;Vemurafenib 1000 nM for 72h

ET14

Gene expression data from  primary HCL cell of  patient A treated with Vemurafenib 1000 nM for 48h
ET11

peripheral blood;primary leukemic cells;patient A;Vemurafenib 1000 nM for 48h

Gene expression data from  primary HCL cell of  patient A treated with DMSO for 72h
ET12

Gene expression data from  primary HCL cell of  patient A treated with DMSO for 48h
ET9

ET10

RNA was extracted with QIAGEN Rneasy Columns as per manufacturer's instructions.

Gene expression data from  primary HCL cell of  patient B treated with DMSO for 48h
ET23

Gene expression data from  primary HCL cell of  patient B treated with Vemurafenib 1000 nM for 48h
ET24

peripheral blood;primary leukemic cells;patient B;Vemurafenib 1000 nM for 48h

Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=0 and B=0 (Non-acute rejection).

Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=0 and B=1 (Non-acute rejection).

Differentiation of NB4 cells was induced at 1 x 100,000 cells/mL by administration of 1 µM ATRA (Sigma) for 0, 48 or 72 hours.

The NB4 cell line (purchased from DSMZ GmbH) was cultured in RPMI 1640 Medium (Sigma) supplemented with (10% v/v) fetal bovine serum (FBS) (Sigma), 2 mM glutamine (Sigma), 100 U/mL penicillin and 100 µg/mL streptomycin solution (Sigma).

Affymetrix CEL files were imported into GeneSpring GX11 Software (Agilent). The RMA16 algorithm was used for probe summarization and then median normalization was performed.

10 ug of ss cDNA was fragmented and labeled with biotin, and hybridized for 16 hr at 45C on the GeneChip 1.0 ST Human Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated ss cDNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA using the WT Expression kit (Ambion).

3KD3
Gene expression data from 72 hour ATRA-differentiated TG2 knockout NB4.

3N2
Gene expression data from 72 hour ATRA-differentiated wild-type NB4.

3N3

3KD1

3KD2

GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health.

RNA extraction was performed by the CEEH Genomics Core Laboratory followed by the manufacturer’s protocols using the GeneChip platform by Affymetrix.

The standard hybridization protocol was used as recommended by Affymetrix.

RNA was processed for hybridization to Affymetrix Mouse Gene 1.0 ST Arrays through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

C57BL/6;male;postnatal day 9;right hippocampus;mild stress + saline vehicle

Gene expression data from HEK293 cells transfected with BAHD1  siRNA

Two-week spontaneous differentiation in KO medium without feeder cells and bFGF

Prior to differentiation - on foreskin-derived feeder cells with complete KO medium with bFGF

Extraction with Trizol and purification with phenol / chloroform using PLG tubes

Effect of wt versus mutant hsa-miR-122 overexpression on spontaneous hESC differentiation.

hESC transduced with mutant miR-122-expressing lentiviral vector

4-month-old WT and Csbm/m mice were fed either a standard AIN-93G diet (SD; carbohydrate:protein:fat ratio of 64:19:17 percent of kcal) ad libitum or at 40% CR, or a SD supplemented with 100 mg/kgchow resveratrol ad libitum, or a high-fat diet ad libitum consisting of AIN-93G with 60% of calories from fat, primarily hydrogenated coconut oil (HFD; carbohydrate:protein:fat ratio of 16:23:61). At one year of age, they were sacrificed and cerebellums were harvested.

Animal rooms were maintained at ~20°C and a 12-hour light/dark cycle.

Csbm/m Mouse_cerebellum_Standard diet supplemented with resveratrol_Ad Lib_Replicate-3

Sample name: CSB_Resv_3

C57BL/6;Csbm/m;male;cerebellum;1 year;a SD supplemented with 100 mg/kgchow resveratrol ad libitum

Csbm/m mouse, cerebellum, standard diet supplemented with resveratrol ad lib

Simple annotation: Diseased tissue, Vascular injury
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67340.gif; format: GIF

Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67341.gif; format: GIF

Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67342.gif; format: GIF

Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67343.gif; format: GIF

Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67344.gif; format: GIF

Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67345.gif; format: GIF

Preprocessing was carried out using GCRMA (through gcrma package from R/Bioconductor). Since samples were processed using two different kits, Combat was used to eliminate the batch effect. However, the presence of genes with small variance precluded successful estimation of the parameters in the sophisticated model used by Combat in this dataset. To circumvent this issue, genes with SD<0.2 were eliminated prior to Combat adjustment of the batch effect.

Total RNA was extracted using miRNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol with on-column DNase digestion

RNA was hybridized to HGU133 Plus 2.0 chips to measure relative gene expression.

Centrifugation of whole blood. Separation of mononuclear cells. Separation of moncoytes by plastic attachment .

GeneChip arrays were washed and scanned using a GeneArray Scanner, and scanned images were quantified according to Affymetrix standard procedures

Raw expression values were preprocessed using the RMA method , a three-step process which integrates background correction, normalization and summarization of probe values. These normalized values were the basis for all the analysis.
Previous to any analysis data were submitted to non-specific filtering to remove low signal genes and low variability genes (those genes whose standard deviation between all samples did not exceed a minimum threshold).

Total RNA was isolated from monocytes using Trizol (Invitrogen Corp), was further purified by using RNeasy kit (Qiagen Inc, Valencia, USA), and was quantified by spectrometry at 260 nm; purity was assessed by the ratio of absorbances at 260-280 nm. RNA integrity was assessed after agarose gel electrophoresis.

Human male subjects with familial combined hyperlipidemia  after treatment with atorvastatin (ATV), peripheral blood monocytes

Monocyte human familial combined hyperlipidemia after treatment with atorvastatin (ATV) sample

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_6-sp1

JMP Genomics
Background correction: RMA; Transformation: log2; Normalization: median scaling; Summary method: median

CD8 T cells isolated from spleen; transduced with shRNA targeting: Alk; Sample name: 6-sp1
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_5-sp3

CD8 T cells isolated from spleen; transduced with shRNA targeting: Arhgap5; Sample name: 5-sp3

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_5-sp2

CD8 T cells isolated from spleen; transduced with shRNA targeting: Arhgap5; Sample name: 5-sp2

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_5-sp1

CD8 T cells isolated from spleen; transduced with shRNA targeting: Arhgap5; Sample name: 5-sp1

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_4-sp3

CD8 T cells isolated from spleen; transduced with shRNA targeting: Ptpn2; Sample name: 4-sp3

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_4-sp2

CD8 T cells isolated from spleen; transduced with shRNA targeting: Ptpn2; Sample name: 4-sp2

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_4-sp1

CD8 T cells isolated from spleen; transduced with shRNA targeting: Ptpn2; Sample name: 4-sp1

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_3-sp3

CD8 T cells isolated from spleen; transduced with shRNA targeting: Egr2; Sample name: 3-sp3

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_3-sp2

CD8 T cells isolated from spleen; transduced with shRNA targeting: Egr2; Sample name: 3-sp2

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_3-sp1

CD8 T cells isolated from spleen; transduced with shRNA targeting: Egr2; Sample name: 3-sp1

DAOY cells were transduced with the indicated lentiviral shRNA and stable cell lines were generated by selection in puromycin (1 µg/ml). 2 x 105 cells of each stable cell line were plated onto 60 mm dishes in triplicates and harvested 4 days later.

Cells were grown in DMEM/10% fetal bovine serum in the presence of antibiotics and 1 µg/ml puromycin.

Following hybridization, arrays were stained on GeneChip Fluidics Workstation 450 and scanned on GeneArray Scanner 3000 according to manufacturer’s technical manual (Affymetrix).

Total RNA was isolated using affinity resin (Qiagen RNEasy Mini Kit, Qiagen AG). RNA integrity and purity were assessed wit the RNA 6000 Nano LabCHip system on the Bionalyzer 2100 (Agilent Technologies)

The labeled cRNA was purified on an affinity resin (RNeasy, Qiagen AG), quantified and fragmented into strands of approximately 50-200 nucleotides in length. Hybridization was carried out at 45ºC for approximately 18 hours.

cDNA was transcribed in vitro in the presence of biotinylated ribonucleotides (Bioarray High Yield T7 DNA transcription kit, ENZO Life Sciences)

Gene expression data from DAOY cells stably expressing Mel18 shRNA

Gene expression data from DAOY cells stably expressing Bmi1 shRNA

Immature (19/20 days of age) Alpk:APfCD-1 mice were treated with arachis oil (AO) vehicle or 0.4mg/kg 17beta-estradiol (E2), via a single subcutaneous injection, and sacrificed at 1hr, 2hr, 4hr, 8hr, 24hr, 48hr, 72hr post dose.
Keywords = estrogen
Keywords = gene expression
Keywords = phenotypic anchoring
Keywords = uterus

SOCS3 null, replicate 1
Keywords = embryonic stem cells
Keywords = endoderm
Keywords = SHP2
Keywords = SOCS3
Keywords = leukemia inhibitory factor
Keywords = ERK1/2

SOCS3 null, replicate 2

wildtype replicate 1

wildtype replicate 2

30 µl of PBS or PBS containing bleomycin (0.075U/mouse) instilled intratracheally for 5 days

Arrays were scanned with a GCS300 Scanner (Affymetrix) for images and intensities.

Data extraction was processed by Affymetrix MoGene 1.0ST v1 Array. The raw probe signal intensities were quantile normalized over all samples, summarized with the robust multi-array average (RMA) algorithm and log2 transformed with a median polish, using the Affymetrix Power Tools. We considered a transcript cluster (gene-level) to be reliably expressed in a sample if the Affymetrix implemented DABG (detection above ground) p-value was less than 0.05. We used local-pooled-error (LPE) estimates and robust statistical tests for evaluating significance of each gene's differential expression in a comparison.

Total RNA extraction was performed using Qiagen Rneasy micro kit according to the manufacturer's protocol.

Following fragmentation, 80 µl of hybridization cocktail containing 2.75 ug of fragmented cRNA placed on chip - Hybridized for overnight. The whole hybridization was performed according to Gene Chip Hybridization, Wash and Stain Kit.

First strand cDNA synthesis, 2nd strand cDNA, IVT, 2nd cycle cDNA synthesis, hydrolysis of cRNA, clean up of the 2nd cycle cDNA, fragmentation of cDNA, and labeling of fragmented single strand cDNA.

C57/129S;Fra-1+/+; wild type;female;2 months;30 µl of PBS for 5 days;lung

C57/129S;Fra-1+/+; wild type;female;2 months;30 µl of PBS containing bleomycin (0.075U/mouse) for 5 days;lung

Mice were infected intratracheally (i.t.) with 4 x 10^6 CFUs of P. aeruginosa strain PAO1 under light anesthesia.

Mice were 8-12 weeks of age at the beginning of the experiments, matched for age and sex, and kept under specific pathogen-free (SPF) conditions.

Scanning of microarrays was performed with 5µm resolution and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.10.1, Agilent Technologies). The extracted MAGE-ML files were further analyzed with the Rosetta Resolver, Build 7.2.2.0 SP1.31 (Rosetta Biosoftware, Seattle, USA). The values are the 'gProcessedSignal' from the Agilent Technologies Feature Extraction and represent signal intensities left after multiplicatively detrended background subtraction. No inter-array normalization was done.

Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier.

After precipitation, purification and quantification, 1.25µg labeled samples were hybridized according to the supplier's protocol (Agilent Technologies).

RNA was labeled with the single-color Quick amp Labeling Kit (Agilent Technologies) according to manufacturer’s instructions.

C57BL/6;AhR-deficient knockout (AhR-/-);lung;intratracheally infected with P. aeruginosa (PAO1)

C57BL/6;wild type;lung;intratracheally infected with P. aeruginosa (PAO1)

total RNA from biosource CC#12S
Treatment, type=dissect, description=dissection from cerebellar tissue

TIG3 diploid fibroblasts were were grown in DMEM media supplemented with 10% (v/v) fetal calf serum. For siRNA experiments cells were transfected with siRNA oligonucleotides specific for BMI-1 and harvested for preparation of RNA after 44 hours.

The Identification of gene expression changes in human embryonic fibroblast cells depleted of BMI-1. Sample B

Genechip array scan Images were scanned using an Affymetrix GeneArray Scanner, using default parameters. The resulting images were analysed using Microarray Suite version 5 (MASv5), Affymetrix cat# 690018.

Total RNA was extracted using the RNeasy mini/midi Kit (RNeasy Mini/Midi Kit, Qiagen). For each siRNA transfection, an RNA pool was obtained by mixing equal quantities of total RNA from each of the six independent RNA extractions.

Hybridization procedures and parameters: Hybridization mix for target dilution (100 mM MES, 1 M [Na +], 20 mM EDTA, 0.01% Tween 20) was prepared as indicated by Affymetrix, including pre-mixed biotin-labeled control oligo B2 and bioB, bioC, bioD and cre controls (Affymetrix cat# 900299) at a final concentration of 50 pM, 1.5 pM, 5 pM, 25 pM and 100 pM respectively. Targets were diluted in hybridization buffer at a concentration of 150µg/ml and denatured at 99°C prior to introduction into the GeneChip cartridge. Three copies of the complete GeneChip HG-U133 set (HG-U133A, HG-U133B) were then hybridized with each biotin-labeled target. Hybridizations were performed for 14-16 hours at 45°C in a rotisserie oven. GeneChip cartridges were washed and stained in the Affymetrix fluidics station following the EukGE-WS2 standard protocol (including Antibody Amplification): 1. Wash 10 cycles of 2 mixes/cycle with Wash Buffer A (6X SSPE, 0.01% Tween 20) at 25°C 2. Wash 4 cycles of 15 mixes/cycle with Wash Buffer B (100 mM MES, 0.1 M [Na+], 0.01% Tween 20) at 50°C 3. Stain the probe array for 10 minutes in SAPE solution (10 µg/mL SAPE in 100 mM MES, 1 M [Na +], 0.05% Tween 20, 2 mg/mL BSA) at 25°C 4. Wash 10 cycles of 4 mixes/cycle with Wash Buffer A at 25°C 5. Stain the probe array for 10 minutes in antibody solution (Normal Goat IgG 0.1 mg/mL, 6. Biotinylated antibody 3 µg/mL, 100 mM MES, 1 M [Na +], 0.05% Tween 20, 2 mg/mL BSA) at 25°C 7. Stain the probe array for 10 minutes in SAPE solution at 25°C 8. Final Wash 15 cycles of 4 mixes/cycle with Wash Buffer A at 30°C

Biotin-labelled cRNA targets were synthesized starting from 5µg of total RNA. Double stranded cDNA synthesis was performed with GIBCO SuperScript Custom cDNA Synthesis Kit, and biotin-labelled antisense RNA was transcribed in vitro using Ambion’s In Vitro Transcription System, including Bio-11-UTP and Bio-11-CTP (NEN Life Sciences, PerkinElmer Inc, Boston, Massachusetts, USA) in the reaction. All steps of the labelling protocol were performed as suggested by Affymetrix (GeneChip® Expression Analysis Technical Manual ). The size and the accuracy of quantitation of targets were checked by agarose gel electrophoresis of 2µg aliquots, prior to and after fragmentation. After fragmentation, targets were diluted in hybridisation buffer at a concentration of 150µg/ml.

TIG3 diploid lung embryonic fibroblasts were transfected with siRNA oligos specific for the Polycomb protein BMI-1. After 44 hours expression analysis was performed.

The data were analyzed with Microarray Suite version 5.0 (MAS5) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. The data were also analyzed with Robust Multiarray Analysis (RMA) and GC Robust Multiarray Analysis (GCRMA) using GeneSpring GX 7.3 (Agilent Technologies). The RMA and GCRMA data are available as supplementary files to the Series record.

Following fragmentation, 15 ug of cRNA were hybridized for 16-18 hr at 45C on GeneChip Human Genome U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Extensor carpi radialis brevis muscle from cerebral palsy patient

The data were analyzed with was performed by using customized R language-based script using the Bioconductor packages for quality control analysis, data normalization, hierarchical clusters and identification of differentially expressed transcripts.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human GeneChip U133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 11 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

9ml blood were collected and erythrocyte lysis using Qiagen Erythrocyte lysis buffer was performed immediately. White blood cells were washed in icecold PBS two times. Cells were then lysed using Trizol (Invitrogen).Phase lock gel tubes (Eppendorf) were used to extract the RNA containing phase. Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

Approximately 3 µg of total RNA was processed to produce biotinylated cRNA targets.

proband a, before exhaustive exercise, white blood cells, male, healthy, no medicamentation

proband g, before exhaustive exercise, white blood cells, male, healthy, no medicamentation

proband g, past exhaustive exercise, white blood cells, male, healthy, no medicamentation

proband g, before moderate exercise, white blood cells, male, healthy, no medicamentation

proband f, before exhaustive exercise, white blood cells, male, healthy, no medicamentation

proband f, past exhaustive exercise, white blood cells, male, healthy, no medicamentation

proband f, before moderate exercise, white blood cells, male, healthy, no medicamentation

proband f, past moderate exercise, white blood cells, male, healthy, no medicamentation

proband g, past moderate exercise, white blood cells, male, healthy, no medicamentation

proband a, before moderate exercise, white blood cells, male, healthy, no medicamentation

Total RNA was prepared using TRIzol reagent from the pancreas one 56 day old male mouse.  The genotype was gastrin+/-, CFTR+/+ on 95% black6, 5% 129Sv background.  Mice were fed Peptamen from age 10 days to prevent intestinal obstruction.

mouse left lungs were collected from 8-week-old Gata5 KO and wt mice.

Raw data were processed by Affymetrix Expression Console Build v1.3.0.187 using RMA and MAS5 Algorithm. Average intensity data at probe level were background subtracted, log2 transformed, and Quantile normalized.

Trizol extraction of total RNA and RNeasy kit cleanup were performed according to the manufacturer's instructions

Following fragmentation, 35 ug of cRNA were hybridized for 16 hr at 45C in a hybridization oven. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 ug total RNA (GeneChip Expression Analysis Technical Manual Rev5, Affymetrix).

Peripheral blood mononuclear cells (PBMC) were separated from granulocytes and red blood cells by density-gradient centrifugation.  Red cells were removed from granulocytes by hypotonic lysis, and PBMC and granulocytes were then immediately placed in TRIzol® reagent (Invitrogen, Carlsbad, CA) and stored at -80C.

CHP files were generated by Affymetrix expression console software using  the 3' exp array -RMA program.

Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was further purified using RNeasy MiniElute Cleanup kit including a DNase digest according to the manufacturer's instructions (QIAGEN, Valencia, CA).

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on Affymetrix Human U133 Plus 2.0 GeneChips following manufacturer's directions. GeneChips were washed and stained in an Affymetrix 450 Fluidics Station.

All signal intensity quantification was performed using an Illumina BeadStation 500GX Genetic Analysis Systems scanner, using the standard Illumina scanning protocol.

A single intensity (expression) value for each Illumina probe on the array was obtained using Illumina BeadStudio software with standard settings and no background correction.  Two types of processed data were used for analysis: 1. Data was Z-transformed based on probes which were Present for at least one sample (the Illumina Detection Pvalue was < 0.01).  Specifically, for each sample, define m to be the mean of the expression values for that sample taken over all probes present in at least 1 sample, and define s to be the corresponding standard deviation. Then for all  the probes on the array, for that sample the Z-transformed expression value corresponding to an expression value e is (e-m)/s. 2. For use in calculating correlations of gene expression levels with the values of clinical variables; the expression values for all the probes for each sample were scaled to have median 256 and then log (base 2) transformed. For the data matrices, the ID_REF is the Illumina probe identifier, and the Detection Pval is the Illumina call for whether the measured expression level is Present (above background).  Detection Pvalues near 0 indicate Present.  In our analysis we considered expression values with a Detection Pvalue below 0.01 to be Present. Z-transformed data (item 1) provided as a supplementary file on GSE26952. Data median scaled (to median = 256) and then log base 2 transformed (item 2) included in Sample table.

Tissue samples were obtained and prepared as described in the Methods section of the paper cited in the overall design section of this GEO submission. Total RNA was extracted from epidermis by using the QIAshredder spin column and RNeasy RNA isolation kits (Qiagen, Hilden, Germany). The quality of total RNA samples was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Total RNA was extracted from epidermis by using the QIAshredder spin column and RNeasy RNA isolation kits (Qiagen, Hilden, Germany).
The quality of total RNA samples was assessed using
an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

cRNA was hybridized to Illumina Sentrix HumanRef-8 Expression BeadChips, and signal was detected with streptavidin-Cy3, using the standard Illumina hybridization protocol.

Nonatopic Control;m;40s;African American;disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 0;YES, subject has history of AR (allergic rhinitis), asthma or both: no;normal (120-300 cells/ml): 160;normal (0-48.5 kIU/L): 2.9;detects IgE that reacts specifically with suspected or known allergens: negative;Skin culture positive or negative for S. Aureus: neg

Nonatopic Control;m;20s;Caucasian;disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 0;YES, subject has history of AR (allergic rhinitis), asthma or both: no;normal (120-300 cells/ml): 130;normal (0-48.5 kIU/L): 34.7;detects IgE that reacts specifically with suspected or known allergens: positive;Skin culture positive or negative for S. Aureus: neg

Nonatopic Control;f;20s;Caucasian;disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 0;YES, subject has history of AR (allergic rhinitis), asthma or both: YES;normal (120-300 cells/ml): 50;normal (0-48.5 kIU/L): 2.5;detects IgE that reacts specifically with suspected or known allergens: negative;Skin culture positive or negative for S. Aureus: neg

Nonatopic Control;m;40s;Caucasian;disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 0;YES, subject has history of AR (allergic rhinitis), asthma or both: no;normal (120-300 cells/ml): 140;normal (0-48.5 kIU/L): 2;detects IgE that reacts specifically with suspected or known allergens: negative;Skin culture positive or negative for S. Aureus: neg

The cells were grown at a density of 1 million cells/ ml in RPMI 1640 with 15% FBS, 1% penicillin-streptomycin, 2mM L-glutamine at 37°C in a humidified 5% CO2 chamber.

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix print default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

RNA was extracted using the Rneasy Mini-Kit (Qiagen) as per the manufacturer's instructions

Following fragmentation, 15 ug of cRNA were hybridized for 16-18 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the Ambion MessageAmp Premier RNA Amplification Kit protocol from 500 ng total RNA (MessageAmp Premier RNA Amplification Kit Instruction Manual, 2008, Ambion).

Gene expression data under ER stress from lymphoblastoid cells of individual GM11832 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM11831 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM11839 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM11832 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM11840 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM11839 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM11881 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM11840 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM11882 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM11881 treated with DMSO 8 hours.

Mice treated with 2.5ug/kg LPS intratracheally, samples at 24hr.  Mice given simvastatin 20mg/kg for 48 hr prior to sample collection (2 doses of simvastatin).
Sample_age: 7-8 weeks old
Sample_hybridization: total RNA was converted to first-strand cDNA using a hybrid reverse transcription primer consisting of oligo-dT and T7 RNA polymerase promoter sequences. The single-stranded cDNA was then converted to double-stranded cDNA. Complementary DNA corresponding to 5-10 µg of total RNA was used in a cRNA amplification step using T7 RNA polymerase and two biotinylated nucleotide precursors. The resulting biotinylated cRNA was fragmented to a size of approximately 50 bp, and approximately 20-30 µg of the biotinylated cRNA was hybridized to the Mouse430 2.0 GeneChip (Affymetrix, Santa Clara, CA). The bound cRNA was visualized by binding of streptavidin/phycoerythrin conjugates to the hybridized GeneChip, followed by laser scanning of bound phycoerythrin.
Sample_RNA_Isolation: Tissues (~50 mg) were taken frozen and directly solubilized in chaotropic solubilization buffer using a Brinkman Polytron tissue disruptor. Larger tissue fragments (>100mg) were pulverized into frozen powder with a mortar and pestle, pre-chilled to liquid nitrogen temperature, and then the frozen powder was solubilized with the Polytron. RNA was purified using Trizol LS (Life Technologies) and an additional RNA purification step was conducted using the RNAeasy purification kit (Qiagen Inc., Valencia, CA). Approximately 10 µg of purified, total RNA was used for analyses.
Sample_sex: male
Sample_strain: C57BL6
Keywords = Murine, endothelial cell barrier function, inflammation, Simvastatin, LPS

Adenoviral expression of Cre-recombinase was used to delete the RB and/or p53 genes, and retrovirus was used to achieve MYC overexpression.

Mammary epithelial cells were isolated from 8-week-old female mice and sub-cultured in DMEM/F12 media supplemented with 5% horse serum, 20ng/mL EGF, 10μg/ml insulin, 1ng/ml cholera toxin, 100μg/ml hydrocortisone, 100 U/ml penicillin/streptomycin and 2mM L-glutamine at 37oC in 5% CO2.

Arrays were scanned on an Affymetrix GeneChip Scanner 3000, using Command Console Software.

Raw intensity files from the Affymetrix Mouse Gene 1.0 ST GeneChip arrays were processed using Affymetrix Expression Console version 1.1.  Gene-level expression measurements were computed using the iterPLIER algorithm on the core probesets and exported with annotation release 32, dated June 23rd, 2011.

RNA was harvested from proliferating cell populations using the RNeasy Blood and Tissue kit (Qiagen, Inc., Valencia, CA) according to the manufacturer's suggested protocols, and quantified on a Nanodrop ND-100 spectrophotometer. RNA quality was assessed by analysis on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

Arrays were hybridized with fragmented and biotin-labeled target (2.5 µg) in 110 µl of hybridization cocktail. Target denaturation was performed at 99oc for 2 min. and then 45oc for 5 min., followed by hybridization for 18 hrs. Arrays then were washed and stained using GeneChip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).

Labeling was performed by the WT-Ovation Pico RNA amplification system (NuGen Technologies, Inc.)

The GeneChips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned using the GeneChip® Scanner 3000 7G System (Affymetrix).

The data were analyzed with Expression Console v1.1 software using the default RMA summarization method.

cRNAs were hybridized for 16 hours at 45oC on GeneChip® Human Gene 1.0 ST arrays using the GeneChip® Hybridization Oven 640 (Affymetrix).

Biotinylated cRNAs were prepared by IGBMC Microarray and Sequencing Platform according to the standard Affymetrix protocol from 1 ug total RNA.

Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_2

JLI_3

Macroscopically intact carotid tissue adjacent to the atheroma plaque

JLI_1

RMA normalized with GenePattern module ExpressionFileCreator, non-log transformed.  Affy probeset annotation used in processed data.

Ovation Biotin—RNA Amplification and Labeling System (NuGen Inc., San Carlos, CA)

Mouse embryonic fibroblast derived from MyoD-/-/Myf5-/- animals transduced with ER-MyoD RRR in differentiation media for 24hrs

C57BL/6x129Sv/B6 hybrid;Prkaca+/-;9 months;caudal vertebral bone

Rats 1h after injection with dose kainate.
Treatment, type=time_course, description=KA animals are treated with kainate., measurement=1.0 h

Total RNA was isolated with the guanidinium thiocyanate method, extracted with acid phenol and precipitated from 2-propanol.

Using a poly-dT primer incorporating a T7 promoter, double-stranded cDNA was synthesized from 10 micrograms total RNA using a cDNA synthesis kit (SuperScript double-stranded cDNA synthesis kit; Invitrogen, Carlsbad, CA).  Double-stranded cDNA was purified by phenol/chloroform extraction using a Phase-Lock Gel (PLG Heavy Brinkmann Instruments, Westbury, NY) followed by ethanol precipitation.  Biotin-labeled cRNA was generated from the double-stranded cDNA template though in-vitro transcription with T7 polymerase, and a nucleotide mix containing biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY).  The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).

Mouse embryonic fibroblast derived from MyoD-/-/Myf5-/- animals transduced with ER-MyoD RRR in differentiation media for 12hrs

Each mouse was anesthetized under halothane, its cecum exteriorized by laparotomy and manipulated (sham).  The cecum was then replaced and the belly closed in two layers.  Six hours later the spleen was harvested and the mouse euthanized.  The spleen was disaggregated over nylon mesh and CD4+ splenocytes were enriched by immunomagnetic selection (Miltenyi) according to manufacturer's instructions, lysed and RNA isolated.

GeneChips were scanned using the Affymetrix GeneChip Scanner G3000.

Total RNA was extracted according to the manufacturer's instructions (RNeasy, Qiagen)

Following fragmentation, cRNA was hybridized on the GeneChip Mouse Transcriptome 430 2.0 (Affymetrix) according to the manufacturer's instructions. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA was prepared using a two round amplification strategy for small (<1 microgram) samples  according to the manufacturer's instructions (Affymetrix)

Gene expression data from CD4+ splenocytes from a sham-manipulated mouse 6h after the induction of sham laparotomy.

negatively selected CD4+ splenocytes from an individual mouse treated with sham laparotomy

Mouse embryonic fibroblast derived from MyoD-/-/Myf5-/- animals transduced with ER-MyoD wt in differentiation media for 24hrs

MCF-7 cells were treated with DMSO vehicle, tRA, or tRA/H for 12 hours

MCF-7 human breast cancer cells were maintained in a 1:1 ratio of DMEM and Ham’s F-12 media (Gibco), 10% FBS (Invitrogen) and 1% penicillin/streptomycin.

Raw data was generated with Affymetrix GeneChip Operating Software on a Human Genome U133 plus 2.0 Affymetrix platform.  Briefly, gene chips were scanned with the Affymetrix GeneChip Scanner 3000 7G for data generation and Affymetrix AGCC software and Expression Console was used for data processing.

Background correction and normalization was performed and gene expression level was summarized over probes using the RMA method. A filtering method based on the percentage of samples with expression value above noise level was applied to filter out probe-sets with little or no expression. Generalized linear models were used to detect differentially expressed genes between DMSO-, tRA- or tRA/H-treated MCF-7 cells.  In order to improve the estimates of variability and statistical tests for differential expression, a variance shrinkage method was employed. The differentially expressed genes were claimed based on the p-values by controlling the average number of false positives at 1 over all the tested probe sets. Fold changes of at least 1.5 were used to further reduce the list of significant probe-sets after controlling the number of false positives.

RNA was extracted with Trizol reagent (Invitrogen) and chloroform (Sigma).  RNA integrity and quantity were determined by the Agilent Bioanalyzer 2100 by the MicroArray Shared Resource (MASR) for the OSU Comprehensive Cancer Center (OSUCCC).

15ug of labeled and fragmented cRNA was hybridized at 45 C for 16 hours at 60rpm. GeneChips were washed and stained on the Affymetrix Fluidics Station 450 according to Affymetrix protocol.

Biotinylated-cRNA was generated from 2 ug of RNA according to the manufacturer’s protocol in the Affymetrix GeneChip® Expression Analysis Technical Manual.

S100a10 bacTRAP/p11 KO mice were administered either a fluoxetine (0.167 mg/ml)/1% saccharine solution (FLX) or 1% saccharine alone (VEH) for 15-18 days and then sacrificed for TRAP profiling.

S100a10 cells, p11 KO, cortex, TRAP RNA, VEH treated, biological rep3

GCRMA normalization within biological replicate groups was performed in GeneSpring GX 7.3.1.

TRAP affinity purification of ribosomes from BAC transgenic mice (see accompanying manuscript), followed by Trizol-LS extraction, DNase treatment, and RNeasy Minelute Cleanup.

Affymetrix two cycle amplification kit, starting with 15 ng of total RNA.

backcrossed 3-5 generations on C57BL/6 from FVB;TRAP;S100a10;ES691/p11 KO;cortex;vehicle

S100a10 cells, p11 KO, cortex, TRAP RNA, FLX treated, biological rep3

backcrossed 3-5 generations on C57BL/6 from FVB;TRAP;S100a10;ES691/p11 KO;cortex;fluoxetine

Mouse embryonic fibroblast derived from MyoD-/-/Myf5-/- animals transduced with retrovirus without ER-MyoD insert in differentiation media for 24hrs

flow-cytometry: B220+, CD5–, CD19+, CD25–, CD69–, B7-1–, B7-2–, IgD+, sIgM+; clinical-signs: none

S100a10 cells, p11 KO, cortex, TRAP RNA, VEH treated, biological rep1

S100a10 cells, p11 KO, cortex, TRAP RNA, FLX treated, biological rep2

flow-cytometry: B220+, CD5+, CD9+, CD19+, CD23lo, CD25–, CD69–, sIgM+, B7-1+, B7-2+; clinical-signs: end-stage

ASC were seeded at 28,000 cells/cm2 in 6-well plates and transfected with MYC siRNA for 72 hours to reach confluence. Differentiation was initiated with adipogenic cocktail and maintained for an additional 72 hours.

Cells were maintained in Dulbecco’s Modified Eagle’s Medium supplemented with 10% fetal bovine serum, L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin at 5% CO2 in a 37°C humidified chamber.

Arrays were scanned on an Affymetrix GeneTitan array scanner to generate CEL files with corresponding intensity values.

Affymetrix CEL files were normalized by RMA using the BioConductor (release 2.13) package affy

Total RNA was extracted with the Qiagen RNeasy mini kit (Qiagen, Valencia, CA) and quantitated on a NanoDrop spectrophotometer (NanoDrop Tech, Wilmington, DE).

15ug of labeled cRNA for three biological replicates (n=3) was hybridized to an Affymetrix Human Genome U133 Plus PM Array for 16 h at 45°C and subsequently washed on a GeneChip Fluidics Station 450.

5ug of RNA was used to generate cDNA with the one-cycle cDNA synthesis kit (Affymetrix Corp., Santa Clara, CA). cRNA generated from the cDNA was biotin labeled with the GeneChip IVT labeling kit (Affymetric Corp.).

47, XX, +21;Stratagene® QPCR Human Reference Total RNA Cell Line Derivations;Adenocarcinoma, mammary gland;Hepatoblastoma, liver;Adenocarcinoma, cervix;Embryonal carcinoma, testis;Glioblastoma, brain;Melanoma, skin;Liposarcoma;Histiocytic lymphoma; macrophage; histocyte;Lymphoblastic leukemia, T lymphoblast;Plasmacytoma; myeloma; B lymphocyte

Each mouse was anesthetized under halothane, its cecum exteriorized by laparotomy and ligated and punctured (septic).  The cecum was then replaced and the belly closed in two layers.  Six hours later the spleen was harvested and the mouse euthanized.  The spleen was disaggregated over nylon mesh and CD4+ splenocytes were enriched by immunomagnetic selection (Miltenyi) according to manufacturer's instructions, lysed and RNA isolated.

negatively selected CD4+ splenocytes from an individual mouse treated with cecal ligation and puncture

47, XY, +21;Stratagene® QPCR Human Reference Total RNA Cell Line Derivations;Adenocarcinoma, mammary gland;Hepatoblastoma, liver;Adenocarcinoma, cervix;Embryonal carcinoma, testis;Glioblastoma, brain;Melanoma, skin;Liposarcoma;Histiocytic lymphoma; macrophage; histocyte;Lymphoblastic leukemia, T lymphoblast;Plasmacytoma; myeloma; B lymphocyte

Affymetrix Microarray Suite version 5.0 was used to generate .CEL files. The .CEL files was processed by Robust Multi-Array Analysis (RMA) in R/Bioconductor to generate expression values represented by RMA

For each individual sample, about 10-50mg flash frozen liver tissue piece was transfeered to -80oC cold RNALater-ICE (Ambion) and placed at -20oC overnight. Tissue was processed according to manufacture's protocol. Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

Approximately 15 ?g of total RNA was processed to produce biotinylated cRNA targets.

Scd1 wild type mice, liver, total RNA processed to biotin-labeled cRNA

Mus musculus (backcrossed to C57BL/6J mice for 5+ generations);Scd1 wild type mouse, chow diet, liver

Data was processed by means of  Genome Studio v2011.1 from illumina, Inc. The background noise was substrated and quantile normalization was applied.

Total RNA was extracted using Qiagen mini kit. Quality control and measurement were performed using NanoDrop and Agilent Bioanalyser.

Biotinylated cRNA were prepared using Ambion Totalprep RNA Amplification kit for Illumina arrays

Control hippocampus 3
Treatment, type=compound_based_treatment, description=Male Wistar rats receive control solution (N=7 in each group) through a gastric tube twice daily for 90 days.

Control hippocampus 2

Ulcerative Colitis (41 year old caucasian female, SAK_1318969188)

PBMCs from Ulcerative Colitis subject
Subject Disease : Ulcerative Colitis
Subject Age : 41

Ulcerative Colitis (41 year old caucasian female, SAK_1285223952)

Control brainstem 2

Control brainstem 1

Control brainstem 4

Control brainstem 3

Control brainstem 6

Control brainstem 5

Ulcerative Colitis (27 year old caucasian female, SAK_1286520426)

Subject Age : 27

Control brainstem 7

Wild type ES cells (E14) and Bmpr1a-/- cell lines (C1-6, Fr124 and Fr88) were grown in ES cell culture conditions and in differentiation conditions (N2B27)

Embryonic stem cells (ESCs) were grown in standard ESC conditions

The data was normalised using the RMA normalisation algorithm in Expression Console 1.2. The array QC was performed using Expression Console first and then Bioconductor.
RMA was used as the standard method for probe summarization (i.e. calculating a transcript signal value from multiple independent probes as on Affy arrays) and normalisation of Affymetrix expression array data.  Quality control of Affymetrix expression microarrays involves identifying outlier arrays, rather than setting defined cut-offs for the various quality control metrics that are generated from the various controls and the probe summarization/normalisation. Note that the signal values are all log base 2; this is standard practice for RMA analyzed data. The data was first QC'ed using the Affymetrix Expression console.

Cells were pelleted and total RNA was extracted using the Quiagen RNAeasy Kit and then prepared for analysis with the Ambion WT expression kit (Invitrogen).

The hybridisation protocols were performed on GeneChip Fluidics Station 450.

Biotinylated cRNA were prepared using the Affymetrix GeneChip® WT Terminal Labeling Kit (Ambion, Invitrogen).

Transgenic strains and MPTP Exposure experiment: all experiments were carried out in accordance with the Animal Care and Use Committee of the Hebrew University of Jerusalem (approval # MD-80.03-3), and the Safety Regulations of the Hebrew University. Na\357ere employed in 4 different experiments. These included the parent strain FVB/N, TgS (transgenic mice expressing the human AChE-S variant) and TgR (transgenic mice expressing human AChE-R) mice, whose brain regions before and after exposure were used for microarray and qRT-PCR analyses. Mice were kept on a 12h dark/12h light diurnal schedule. MPTP-HCl (Sigma, Rehovot, Israel) was dissolved in saline and injected in four doses of 20mg/Kg at 2h intervals for a cumulative dose of 80 mg/Kg. We injected 6 mice from each of the three strains with saline and 6 mice with MPTP, a total of 36 mice (Protocol 1). 4 days after injection, mice were decapitated following Isoflurane (Rhodia, Bristol, UK) anaesthesia, and CPu and PFC were dissected on ice and immediately stored at -80 C for subsequent tests. Brain sections: For histology, left hemispheres were dissected on ice and immediately transferred to 4% PBS-Paraformaldehyde (pH 7.4) for at least 72 hours prior to sectioning. Paraffin-embedded blocks were prepared, and coronal sections of 7um thickness were made on SuperFrost\256enzel-Glaser, Germany). Striatal sections were made in the rostral to caudal direction, starting at Bregma +1.1 coordinates.

The probe sets were summarized with Affymetrix Power Tools (APT) through Expression Console (EC) using RMA.

RNA was extracted from frozen CPu and PFC using the RNeasy lipid tissue kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions, with DNAse treatment.

Microarray procedures followed manufacturer’s instructions. Each array was hybridized with pooled RNA from 3-4 mice, except for one of the TgS MPTP injected groups, containing tissue from only two mice.

Gene expression data from the Pre-Frontal contex of naïve AChE-R mice

Mice containing the Ott1flox and Ott1null alleles were generated as previously reported [Raffel, 2007 #218]. Tg-Sox2-cre animals were obtained from Jackson labs (Bar Harbor, ME). Genotyping was performed by PCR analysis of murine or embryonic tissue [Raffel, 2007 #218]. Timed matings were determined by presence of a vaginal plug at E0.5.

Each cDNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis. The data is transferred to a file-system from which it can be downloaded via a password-protected URL.

The raw CEL files were preprocessed with the RMA algorithm.
(Irizarry R.A. et al. Exploration, normalization and summaries of high density oligonucleotide array probe level data. Biostatistics 4, 249-64 (2003)).

RNA was extracted from 3 hearts each from  either Ott1null/nullSox2-cre or Ott1null/wtSox2-cre E18.5 embryos using the RNeasy Micro kit (Qiagen, Valencia, CA) and treated with RNAse-free DNAse (Qiagen, Valencia, CA). 50 ng of purified total RNA was linearly amplified using the Ovation RNA amplification system V2 (Nugen, San Carlos, CA).

cDNA was then hybridized to Affymetrix Mouse expression array 430A2.0 chips by the Dana Farber Microarray Core Facility (Boston, MA).

Amplified RNA was biotinylated with the FL-Ovation Biotin Module V2 (Nugen, San Carlos, CA) per the supplied protocol.

Cardiac tissue from an embryonic OTT1 null/wt mouse was harvested. Gene expression was measured by Affymetrix 430A v2 chip.

Cardiac tissue from an embryonic OTT1 knockout mouse was harvested. Gene expression was measured by Affymetrix 430A v2 chip.

Gene expression data spleen marginal zone B in IRF8 conditional KO

spleen marginal zone B cells;IRF8 KO;C57BL/6J-lrf8-/- x CD19-Cre

Gene expression data spleen follicular B in WT

VSV-G pseudotyped pCL20c -MSCV-shRNAmir-PGK-mCherry carrying Control- or Nfix-shRNA was spinloaded in Retronectin (TaKaRA Bio USA, Madison, WI) coated 96 well plates. 15,000 freshly  isolated LSK cells from C57BL/6J mice cells resuspended in 200 ml of SFEM media was subsequently added per well.  Cells were incubated for 24 hours on virus and subsequently washed followed by six days of further culture.

Isolated whole bone marrow Lineage- Sca-1 + c-Kit+ (LSK) cells were cultured in SFEM media (StemCell Technologies, Vancouver, British Columbia, Canada) supplemented with 2 mM glutamine, 30 U/mL penicillin/streptomycin, 10 ng/mL rmScf, 20 ng/mL rmTpo, 20 ng/mL rmIgf-2 (all from Peprotech, Rocky Hill, NJ), 10 ng/mL rhFGF-1 (R&D Systems, Minneapolis, MN) and 10 mg/ml heparin (Sigma, St Louis, MO) at 37°C and 5% CO2.

The data were analyzed with Partek Genomics Suite 6.6 by the RMA method.

Total RNA was isolated from 15,000 sorted mCherry+/LSK cells seven days post transduction using the Qiagen RNeasy Micro Kit (Qiagen, Santa Clarita, CA). RNA was amplified using the NuGEN Ovation Pico WTA V2 system and then labeled with the NuGEN Encore Biotin Module (NuGen, San Carlos, CA).

Labeled targets were hybridized on the HT_MG-430_PM plate array and processed using the GeneTitan system.

RNA was amplified using the NuGEN Ovation Pico WTA V2 system and then labeled with the NuGEN Encore Biotin Module.

Abca1 +/- ES cell line was grown on irradiated MEF feeders using standard culture conditions.  Feeders were then depleted and ES cells plated on gelatin for ~2 days.  RNA was isolated using Trizol/RNeasy, then hybridized to AffyMetrix mouse U74Av2 chip according to manufacturer's protocol.  Data were normalized by AffyMetrix MAS5.0 using defaults.
Keywords = embryonic stem cholesterol transport

ES cell line was grown on irradiated MEF feeders using standard culture conditions.  Feeders were then depleted and ES cells plated on gelatin for ~2 days.  RNA was isolated using Trizol/RNeasy, then hybridized to AffyMetrix mouse U74Av2 chip according to manufacturer's protocol.  Data were normalized by AffyMetrix MAS5.0 using defaults.

Feeder-independent ES cell line was grown using standard culture conditions.  RNA was isolated using RNeasy, then hybridized to AffyMetrix mouse U74Av2 chip according to manufacturer's protocol.  Data were normalized by AffyMetrix MAS5.0 using defaults.

E14 +/+ wildtype ES cell line (control for Cdk4 +/- ES cell line)

the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100

10 um lumbar spinal cord frozen sections were fixed, washed and stained with toluidine blue. They were then washed and dehydrated through graded ethanol concentrations (70%, 90%, 100%) and xylene.
From each animal 1000 motor neurons (MN) were isolated using a PixCell II laser-capture microdissection system (Arcturus Bioscience)
PicoPure RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions

15µg of cRNA molecules were heat fragmented and applied to the Mouse Genome 430A GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

Biotinylation of antisense RNA carried out according to Affymetrix protocol

normal;IA, IB, II, IIIA, IIIB, or IV=IB;40;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

HL-60 cells were treated for 24h with the different substances in 5ml tissue flasks

HL-60 cells were cultivated in RPMI medium with 10 % FCS, 1 % penecillin and 1 % streptavidin at 37°C and 5 % CO2

GeneChips were scanned using the Agilent GeneArray Scanner 2500A.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on human GeneChip U133 2A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

normal;IA, IB, II, IIIA, IIIB, or IV=IB;63;female, male:female;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

Animal were treated with saline or PE  injected subcutaneously by continuous osmotic pump (100 mg/kg/day) for five days

9 week old mice were used to test the effects of Gata4 S105 on response to 5 days of pseudophedrine cardiac stress

GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 7G

RNA was extracted from snap‐frozen hearts of 9 week-old mice using a Qiagen fibrous tissue RNeasy kit.

Following fragmentation, cRNA were hybridized to theAffymetrix Mouse ST 1.0 genes  GeneChip which was then washed and stained in the Affymetrix Fluidics Station.

Biotinylated cRNA were prepared according to the standard Ambion WT labeling kit.

Whole Human Genome oligo DNA microarray with 41000 distinct probes was scanned using an Agilent DNA microarray scanner (G2505B, Agilent Technologies). Images were quantified using Agilent Feature Extraction Software (version A.7.5.1).

LOWESS normalized, background subtracted VALUE data obtained from ratio of processed Red signal/processed Green signal using Agilent Feature Extraction Software (version A.7.5.1).

Total RNA was extracted using the RNeasy kit (Qiagen, Valencia, CA), followed by treatment with DNase I. Double-stranded cDNA was synthesized from 500 ng of total RNA using MMLV-RT and poly dT primer incorporating the T7 promoter.

Cy5-sample cRNA and Cy3-sample cRNA were generated and hybridized to a Whole Human Genome oligo DNA microarray kit (Agilent Technologies) with 41000 distinct probes.

Male mice were established in weight-matched groups fed either regular chow diet and high fat diet (20% carbohydrate, 60% fat, 20% protein : D12492: Research Diets Inc., New Brunswick, NJ) for 12 weeks.

Mice were maintained in temperature-controlled (24±2C) facility with a 12h light/dark cycle, and fed regular chow diet (Lab Diets, IN, USA) ad libitum with tap water.

The microarray images were scanned with the Agilent microarray scanner.

All analysis of microarray data was carried out in R software. The expression data was preprocessed with affy package from bioconductor.

Total RNA was extracted using the mirVana miRNA isolation kit (Ambion, Austin, TX, USA) according to the manufacturer's instruction

The resultant labeled cDNA was hybridized to Affymetrix Mouse Gene 1.0 ST arrays.

Extracted RNA was amplified and labeled according to the Affymetrix (Santa Clara, CA) GeneChip Whole Transcript Sense Target Labeling protocol

Total RNA was extracted from the entire brain of NF-I-A-deficient and wild-type control mice (n=3 each) using TRIzol (Invitrogen) according to the manufacturer’s instructions. Further purification of RNA was performed with the RNeasy Mini Kit (Qiagen). Total RNA concentration was determined using a spectrophotometer at 260 nm and 280 nm wavelength. To check RNA integrity, total RNA was separated in a 1% agarose gel containing formaldehyde, and the intensity ratio of 28S and 18S ribosomal RNA bands was assessed after ethidium bromide staining.

Procedures for cDNA synthesis, labeling and hybridization were carried out according to the manufacturer's protocol (Affymetrix). All experiments were performed using Affymetrix mouse genome Genechip U74A version 2. Briefly, 15mg of total RNA were used for first strand cDNA synthesis with an HPLC-purified T7-(dT)24 primer. Synthesis of biotin-labeled cRNA was carried out using the ENZO RNA transcript labeling kit (Affymetrix). For hybridization, 15 µg of fragmented cRNA were incubated with the chip in 200 µl of hybridization solution in Hybridization Oven 640 (Affymetrix) at 45oC for 16 hours. Genechips were washed and stained with streptavidin-phycoerythrin using the microfluidic workstation™ (Affymetrix) and scanned with a laser scanner (Agilent Technologies).

Normal volunteer;  RNA extracted from muscle biopsy, which was flash-frozen in isopentane cooled in liquid nitrogen immediately after excision

The bladder tissues were treated with liquid nitrogen, embedded with OCT medium, and then cut into frozen sections. A quick H&E staining was performed before processing LCM. The dissected cells were collected for RNA extraction.

The transgenic mice and normal mice were sacrificed at 8-month-old age, when the H-rastransgenic and p53 knockout mice had developed high-grade invasive carcinomas in the bladders.

Data was processed by importing CEL files into Partek Genomics Suite Software and RMA normalization was performed.  A 1-way ANOVA was then used to generate fold changes.

Total RNA was extracted using RNeasy Micro Kit (Qiagen) according to the instructions.

Prepare hybridization cocktail using the GeneChip Hybridization Wash and Stain Kit and hybridize arrays according to the manufacturer's instructions.

100 ng of each sample was labeled using the Affymetrix IVT expression Kit accoring to the manufacturer's protocol. Normal aRNA yield is about 60 ug.

Left ventricular gene expression profiles from 12-, 16- and 20-months old spontaneously hypertensive rats (SHRs) were compared with left ventricular profiles seen in age-matched Wistar-Kyoto (WKY) rats by screening Affymetrix U34A arrays (there are 4 samples in each timepoint except 3 samples of 20-months old WKYs).
Keywords = SHR

Cells were cultured in DMEM medium supplemented with 10% FCS, 1% penstrep and appropriate concentration of selective antibiotics

Arrays were scanned in the Affymetrix GeneChip Scanner 3000 wit G7 update

RNA was extracted using the RNeasy mini kit (QIAGEN), treated with DNase I, followed by cleaning-up on spin columns (RNeasy mini kit. Qiagen)

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on Human Gene 1.0 ST. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Affymetrix Hybridization, Wash and Stain Kit..

Amplified cDNA was prepared according to the Ambion WT Expression Kit protocol starting from 200 ng total RNA. Amplified cDNA was fragmented with UDG and APE1 and finally labelled using the Affymetrix WT terminal labelling kit

Gene expression data from cell line T-REx293-NPAP1, not induced, technical replicate 3

Gene expression data from cell line T-REx293-NPAP1, not induced, technical replicate 2

Gene expression data from cell line T-REx293-NPAP1, not induced, technical replicate 1

RNA samples were labeled and hybridized by standard protocol to Affymetrix GeneChip Human Genome  U133+ Array Set HG-U133A array

K562 (Iscoves + 10% FCS) and TF-1 (RPMI + 10%FCS + rhGM-CSF.  Cells were cultured at 37oC, 5% CO2 and split every 3 to 4 days

0.5 mg/kg/ml Isoproterenol treatment, 1 hour time point,  biological rep 4

Chips were pre-processed using robust multichip analysis. Normalized data were fit to a linear model with dose and time contrasts using the GLM procedure of SAS 9.1 (SAS Institute, Carey NC)

Extraction of total RNA was performed from the heart tissues using RNAeasy Mini kit (Qiagen) according to the manufacturer's protocol

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

CHIPEXP_NAME: 230_2_050531tpj_36h
LIMS_SITE: Nutley_3
CHIP_TYPE: RAT230_2
TREATMENT: Isoproterenol
TREAT_TOX_MECHANISM1: Heart_Cardiotoxic
TISSUE_OR_CELL_TYPE: Heart
DOSE_AMOUNT: 0.5
SAMPLING_TIME: 1
PROJECT: ISO_TG
STUDY_NO: 9143

0.5 mg/kg/ml Isoproterenol treatment for 1 hour,  biological rep 4

0.5 mg/kg/ml Isoproterenol treatment, 1 hour time point,  biological rep 5

CHIPEXP_NAME: 230_2_050531tpj_37h

0.5 mg/kg/ml Isoproterenol treatment for 1 hour,  biological rep 5

CHIPEXP_NAME: 230_2_050531tpj_7h
TREATMENT: Vehicle_Control
TREAT_TOX_MECHANISM1: Liver_Non_Toxic
DOSE_AMOUNT: 0
SAMPLING_TIME: 3

CHIPEXP_NAME: 230_2_050531tpj_8h

CHIPEXP_NAME: 230_2_050531tpj_9h

0.5 mg/kg/ml Isoproterenol treatment, 3 hour time point,  biological rep 1

CHIPEXP_NAME: 230_2_050531tpj_38h

0.5 mg/kg/ml Isoproterenol treatment, 3 hour time point,  biological rep 2

CHIPEXP_NAME: 230_2_050531tpj_39h

0.5 mg/kg/ml Isoproterenol treatment, 3 hour time point,  biological rep 3

CHIPEXP_NAME: 230_2_050531tpj_40h

0.5 mg/kg/ml Isoproterenol treatment, 3 hour time point,  biological rep 4

CHIPEXP_NAME: 230_2_050531tpj_41h

CHIPEXP_NAME: 230_2_050531tpj_16h
SAMPLING_TIME: 24

The animals were maintained under a 12-hour light-dark cycle. Conditional DGCR8 knockout mice were crossed to the cone-specific Cre recombinase driver line D4-cre resulting in C-DGCR8 KO mice. To visualize cones, C-DGCR8 KO line mice were crossed to the floxed tdTomato reporter line Ai9. D4-cre or D4-cre/Ai9 animals served as wild type controls.

Scanning was performed using the Affymetrix GCC Scan Control V. 3.0.0.1214 on GeneChip Scanner 3000 with autoloader.

Arrays were normalized and probeset-level expression values were calculated with R/Bioconductor's (v2.15) 'affy' package using the rma() function.

Cones were isolated by FACS from wild type and C-DGCR8 KO mice at different time points (P30, P40, P50, P60, and P90). RNA extraction was performed with Trizol or Arcturus PicoPure RNA Isolation Kit (Applied Biosystems) according to the manufacturer's instructions. Quantitative and qualitative analysis was performed using 2100 Bioanalyzer.

10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

The sense-strand cDNA obtained was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling kit.

C57BL/6;wild type (D4-cre/Ai9 tdTomato);retina;cone photoreceptors;postnatal day 30

C57BL/6;wild type (D4-cre/Ai9 tdTomato);retina;cone photoreceptors;postnatal day 40

GeneChips were scanned using the GeneChip Scanner 3000 with Autoloader

The data were analyzed using  BRB-Array Tools versions: 3.8.1 (as described in the manuscript) and 4.2.1 (the processed matrix GEO data).  Cell files were imported into the BRBArray Tools package, and converted to normalized intensity values using the Almost RMA (aRMA) algorithm.  A total of 199 cel files were imported into the project, including expression data obtained from patients with other psychiatric disorders.  Normalized intensity values reflect the a-RMA parameters employed across the entire sample dataset.   Analyses were performed on the sub-set of samples relevent to the study hypothesis.  Cel files and processed matrix data for those samples are uploaded here.

Total RNA was extracted from leukocytes using the QIAamp RNA Blood Mini Kit (Qiagen), with an off-collumn Dnase (Qiagen) treatment followed by  purification using an RNeasy MinElute column (Qiagen). All procedures were performed according to the manufacturer's instructions (Qiagen).

Following fragmentation, 10 ug of cRNA was hybridized to an Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400, using standard procedures.

Each cRNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, GCS3000, and the positions and intensities of the fluorescent emissions were captured.

The data were analyzed with RMA (Gene Pattern's ExpressionFileCreator version 8). Parameters: method RMA quantile normalization yes background correct yes compute present absent calls no normalization method none value to scale to clm file annotate probes yes The data were analyzed with RMA (Gene Pattern's ExpressionFileCreator version 8). Parameters: method RMA quantile normalization yes background correct yes compute present absent calls no normalization method none value to scale to clm file annotate probes yes.

The fragmented cRNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution was then removed. The chips were transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

The double-stranded cDNA was used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) waas purified from the IVT reaction mixture using magnetic particles. The cRNA was quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. The purified cRNA was fragmented in order to facilitate the subsequent hybridization step.    Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

skeletal muscle;mixed background (C57Bl/6 and 129);wild type;6 months

AML with normal karyotype, molecular analyses performed for BCOR mutations

Male Rsk2-KO and WT mice with a C57Bl/6J genetic background were killed by cervical dislocation.
Brains were rapidly dissected and the hippocampus isolated using a standard dissection procedure. Tissue samples were immediately frozen in liquid nitogen and kept at - 80 °C until use.

Microarrays were scanned using Affymetrix GeneChip Scanner 3000 (Affymetrix Inc. Santa Clara, CA 95051, USA).

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

gene expression data from pools of 2 hippocampi of Rsk2-KO males

Placental biopsies were obtained during Caesarean section from normotensive patients. A mixture of 3 placentas from normal subjects were used for a template control.

Placental tissue from normal pregnancy;A mixture of placental tissue from normal pregnancy

Swiss;adult mouse intestine, kidney, and liver plus fetus tissue;C57BL/6J;wildtype;12 weeks;colon epithelium

T cells from 5C.C7 RAG2-/- CD45.1 and 5C.C7 RAG2-/- CD45.1 CTLA-4-/- mice were activated by immunization with MCC peptide and LPS and after 4 days sorted for RNA extraction.

T cells from 5C.C7 RAG2-/- CD45.1 and 5C.C7 RAG2-/- CD45.1 CTLA-4-/- were transferred into B10.A recipient mice.

The data were analyzed with Partek and Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

Quality check and Robust Multichip Normalization using R/Bioconductor affy package

Following fragmentation,  cRNA were hybridized for 16 hr at 45C on Affymetrix human gut microbiota community GeneChip, then washed and stained in the Affymetrix Fluidics Station 400.

MAT1A knockout at 15 month age, tumoral tissue, biological replicate 4

The data were acquired with GCOS 1.4 instrument and processed using RMA normalization method.

2-4 mg of liver. The tissue received was pulverized in mortar with presence of liquid nitrogen. Total RNA was then extracted using Qiagen’s RNeasy Mini kit recovering each sample in 35μl of water.

Following fragmentation, 15 μg of cRNA was hybridized on Affymetrix GeneChip® Mouse Genome 430A 2.0 Array. GeneChips were washed and stained in the Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2μg of total RNA (Expression Analysis Technical Manual, Affymetrix).

MAT1A_T4
Gene expression data from MAT1A knockout at 15 month, when the tissue has been histopathologically determined to be hepatocellular carcinoma.

C57B6SJL;MAT1A knockout;15 months;liver, tumoral tissue;hepatocellular carcinoma

Mouse liver tumoral tissue, MAT1A knockout, hepatocellular carcinoma, 15 months

MAT1A knockout at 15 month age, tumoral tissue, biological replicate 5

MAT1A_T5

GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health (http://depts.washington.edu/ceeh/ServiceCores/FC1/FC1.html).

RMA normalization log2 using the Affymetrix Expression Console,  version 1.1

E14.5 brains were removed, and neocortexes were immediately dissected.

For microarray hybridization, RNA was processed for hybridization to Affymetrix Mouse Gene ST Array through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

Murine BMDM were prepared from C57BL/6 mice or NOD2 deficient mice on C57BL/6 background. Mature BMDM were plated in 6 well plates at 1x10^6 cells/well

Raw affinity data was normalized using a Robust Multichip Analysis (RMA) method at probe level

Cells lysates were made and RNA was isolated  using Rneasy Mini Kit, Qiagen

Samples were hybridized using Affymetrix hybridization kit materials

infected with Neisseria gonorrrhoeae, strain MS11, MOI 10:1 for 3 hrs

BMDM;C57BL/6;wild-type;infected with Neisseria gonorrrhoeae, strain MS11, MOI 10:1 for 3 hrs

biotin-14-CTP (Invitrogen, CarlsBad, CA, USA) and biotin-16-UTP (Roche)

GCOS with the default settings exept that the target signal was set to 100

At least 1000 normal ductal cells were microdissected from cryosections using the VeritasTM Laser Capture Microdissection System (Arcturus Bioscience, Inc., USA) according to standard protocols. Caps with captured cells were directly placed in 100 ul lysis buffer (Qiagen, Hilden, Germany). Total cellular RNA was isolated (RNeasy® Micro Kit, Qiagen) according to manufacturer´s recommendations and subsequently quantified on a Nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

The biotinylated cRNA preparation was fragmented, assessed by gel electrophoresis, and placed in hybridization cocktail containing biotinylated hybridization controls (GeneChipTM Eukaryotic Hybridization Control Kit, Affymetrix). Sample was first hybridized to Test3 Arrays for 16 hours, washed, stained using antibody-mediated signal amplification and scanned. After passing this quality control stage, the sample was hybridized onto the large Human Genome U133 Plus 2.0 Array.

Fifty nanograms of total RNA were reverse transcribed and amplified by Microarray Target Amplification Kit (Roche diagnostics, Basel, Switzerland). In brief, total RNA (50 ng) was converted into cDNA using a modified oligo (dT) primer (TAS-T7 Oligo (dT)24). A unique Target Amplification Sequence (TAS) with no homology to any known sequences in public databases generated the 3´ anchor on the cDNA for subsequent PCR amplification. In order to include a 5´ anchor sequence on the cDNA, the TAS-(dN)10 primer was used for the initiation of the second strand cDNA synthesis. After purification using the Microarray Target Purification Kit (Roche), PCR was performed using the TAS primer and Expand PCR Enzyme Mix which is optimized for long (>1kb) and unbiased PCR products. In order to ensure that messages were not amplified to saturation, the optimal number of PCR cycles was estimated by preliminary PCR and agarose electrophoresis of PCR products from cycles 21, 24, 27, 30 and 33. After purification with the Microarray Target Purification Kit (Roche), the PCR products were labeled with biotin-14-CTP (Invitrogen, CarlsBad, CA, USA) and biotin-16-UTP (Roche) by in vitro transcription using Microarray RNA Target Synthesis Kit T7 (Roche). The labelled cRNA was purified using the Microarray Target Purification Kit (Roche), quantified by spectrophotometer and checked by agarose electrophoresis. The entire amplification and labelling process was monitored by GeneChip® Eukaryotic Poly-A RNA Control Kit (Affymetrix, Santa Clara, CA, USA) with exogenous positive controls which were spiked into the total RNA before cDNA synthesis and finally detected on Human Genome U133 Plus 2.0 Arrays (Affymetrix).

Amplified total RNA from microdissected normal lobular cells from mastectomy specimen from postmenopausal patient with invasive lobular carcinoma (ILC)

normal tissue from mastectomy specimen from postmenopausal patient with invasive lobular carcinoma (ILC)

Amplified total RNA from microdissected tumor cells from mastectomy specimen from postmenopausal patient with invasive lobular carcinoma (ILC)

tumor tissue from mastectomy specimen from postmenopausal patient with invasive lobular carcinoma (ILC)

Stratagene;;740000;lung;;Familial IIP;;Usual Interstitial Pneumonia

Lung, Familial Idiopathic Interstitial Pneumonia (F-IIP), Usual Interstitial Pneumonia (UIP)

lung;;Familial IIP;;Usual Interstitial Pneumonia;Stratagene;;740000

Amplified total RNA from microdissected normal ductal cells from mastectomy specimen from postmenopausal patient with invasive lobular carcinoma (ILC)

The data were analyzed using Bioconductor (R-project)  packages. Specifically, gene expression data were normalized using RMA background correction, quantile normalization and Tukey biweight summary method. Data were filtered on variance and differentially expressed genes were identified using LIMMA library.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hrs at 45C on Affymetrix Mouse430.2 Mouse Genome GeneChip. Subsequently, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to standard Affymetrix protocol for One-Cycle Target Labeling Assay from 5 ug of total RNA.

Gene expression data from cochleas of nicotinic cholinergic receptor alpha9 subunit knockout mice at P60.
The mice are a hybrid strain. They are 129S6 (old nomenclature: 129Sv/Ev) x CBA/CaJ. They have been backcrossed to the CBA/CaJ line at least 7 generations.
P60_a9knockout_rep3

Infection of wd-NHBE cells were conducted in serum-free growth media provided by manufacturer (MatTek).  Wd-NHBE cells, cultured at the air-liquid interface, were washed two times with Dulbecco’s phosphate buffered saline (DPBS) to remove mucus accumulation.  Virus stocks were diluted in DPBS and cells were infected at a multiplicity of infection (MOI) of 3.0 for 1 h at 37°C, 5% CO2.  Cells were washed twice with DPBS to remove unbound virus.  Basal medium was removed and replaced with complete medium.  Over the time course of infection, the basal media was removed and apical layer washed twice with DPBS supplemented with 0.2% BSA (Sigma) and stored at -80 degrees celcius until use.

well-differentiated cells (wd-NHBE) were purchased from MatTek Corporation (EpiAirway PC-12, Ashland, MA). Cells were maintained by incubating the 12-well formatted transwell inserts at the air-liquid interface at 37°C under 5% CO2.  The basal surface was submerged in AIR 100 (MatTek) complete growth media, made up of DMEM , epidermal growth factors, 5 µg/ml gentamicin, 0.25 µg/ml amphotericin B, and phenol red, and was replaced every 24 h until used for experiments.

Prior to statistical analyses, raw data were processed by Plier Workflow normalization method using Gene Console software (Affymetrix, version 1.3.1).

Following fragmentation, 12.5ug of aRNA were hybridized for 16 hr at 45C on GeneChip Human (HG_U133 plus 2.0) Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450/250.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Gene Chip 3' IVT Expression Kit User Manual, 2008, Affymetrix).

Gene expression data from well-differentiated primary human lung bronchial epithelial cells un-infected

Un-infected control;cultured primary human lung epithelial cells

Well-differentiated human lung epithelial cells, un-infected for 36h

Gene expression data from well-differentiated primary human lung bronchial epithelial cells infected with H1N1

2009 pandemic H1N1 Influenza virus;cultured primary human lung epithelial cells

Well-differentiated human lung epithelial cells, infected with KY/180 (pdmH1N1) for 36h

Cells were treated with 500nM PLX4032 for 16 days period with media containing inhibitor being changed every 3 days

Cells were grown RPMI media supplimented with 5% FCS, 2mM L –Glutamine and 2x Penstrep .

Affymetrix Scanner: GCS3000; AGCC (Command Console Software  AGCC_3_1_1.)

Geneexpression Console v.1.1, Affymetrix (Expression Console  EC_1_1_2) using Affymetrix default analysis settings for generation of CEL-files.
Data Pre-Processing and Filtering (Partek Software, v.6.6): RMA  (background correction, quantile normalization across all chips in the experiment, log2 transformation, median polish summarization); Anova

Affymetrix Human Gene 1.0 ST Array (Cat No. 901085); GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix Genechip®  fluidics station 450: protocol FS450_0007 for Cartridge Arrays

The Ambion® WT Expression Kit; For Affymetrix® GeneChip® Whole Transcript (WT) Expression Arrays, 09/2009 Rev C (Cat No. 4411973 ), Affymetrix WT Terminal Labeling Kit 30rxn (Cat No. 900671)

no special treatment to the cells before harvest, collected the cells when the confluence 85-90%

the transformed cell lines are already stable prostate cancer cell lines, so growing transformed cells in DMEM medium with 10% FBS, while control PEC cells were cultured in prostate epithelial primary culture medium, change to normal DMEM medium with 10% FBS one night before harvest.

Arrays were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.

RMA summarization, PM BG correction, and quantile normalization were performed in Affymetrix Expression Console 1.1

Arrays were hybridized with fragmented and biotin-labeled target (2.5 µg) in 110 µl of hybridization cocktail. Target denaturation was performed a 99C for 2 min. and then 45C for 5 min., followed by hybridization for 18 hrs. Arrays then were washed and stained using Genechip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).

FVB;transformed by v-src gene;Primary prostate epithelial cell culture, oncogene-transduced

Cells were cultured in RPMI 1640 medium with Glutamax (Invitrogen, Carlsbad, CA), supplemented with 10% heat-inactivated FCS, 100 IU/mL penicillin and 100 g/mL streptomycin (all PAA Laboratories, Pasching, Austria) and kept in humidified incubators at 37° C and 5% CO2

RNA was extrated usingTrizol according to the manufacturer's instructions.

REH E/R positive leukemia;treated with specific E/R targeting shRNA

AT2 E/R positive leukemia;treated with specific E/R targeting shRNA

Study of change in gene expression in mouse kidney after feeding control or low phosphate diet to normal or Hyp mice for 5 days.  RNA from 3 mice is pooled for each sample.
Keywords = low phosphate diet
Keywords = Hyp
Keywords = Phex
Keywords = X-linked hypophosphatemia

Keywords = hyp
Keywords = phex
Keywords = x-linked hypophosphatemia

Gene expression data from the Pre-Frontal cortex of naïve AChE-R mice

Gene expression data from the Pre-Frontal cortex of naïve AChE-S mice

Gene expression data from the Pre-Frontal cortex of naïve FVB/N mice

Gene expression data from the Caudate-Putamen of naive AChE-R mice

Gene expression data from the Caudate-Putamen of MPTP-exposed AChE-R mice

The data were processed using Affymetrix Expression Console to generate MAS5 data.

Total RNA was extracted from mouse mammary tumors using the Qiagen RNeasy Midi Kit.

The resulting biotin-labeled RNA samples were then hybridized with Affymetrix Mouse 430A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).

The data were log2 transformed and normalized using quantile normalization with BRB array tool (developed by Biomertric Research Branch of Division of Cancer Treatment and Diagnosis of National Cancer Institute)

total RNA was extracted with ambion mirVara miRNA isolation kit.

Biotinylated cRNA were prepared with illumina TotalPrep RNA Amplification Kit

PGC-1a null (PGC-1a-/- ) and wild-type (PGC-1a+/+) mice were obtained by breeding heterozygous (PGC-1a+/-) founder mice as described (Leone et al., 2005).

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56940
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.55; Parameter Scan Time = 20:00:32; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 12048; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.55; Parameter Scan Time = 20:00:32; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 185653; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.55; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56925
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.33; Parameter Scan Time = 19:07:03; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 11996; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.33; Parameter Scan Time = 19:07:03; Parameter PMT Volts = 650; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 185601; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.55; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56923
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.64; Parameter Scan Time = 20:38:09; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 12086; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.64; Parameter Scan Time = 20:38:09; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 185691; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.55; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56908
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.24; Parameter Scan Time = 19:39:39; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 11067; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.45; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.24; Parameter Scan Time = 19:39:39; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 184672; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56905
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.30; Parameter Scan Time = 19:51:49; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 11079; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.45; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.30; Parameter Scan Time = 19:51:49; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 184684; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.53; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56921
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.36; Parameter Scan Time = 19:21:52; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 12009; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.36; Parameter Scan Time = 19:21:52; Parameter PMT Volts = 670; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 185614; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56904
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.48; Parameter Scan Time = 18:09:59; Parameter PMT Volts = 550; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 10977; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.45; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.48; Parameter Scan Time = 18:09:59; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 184582; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-09/55569
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.90; Parameter Scan Time = 17:57:56; Parameter PMT Volts = 550; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 6502; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.90; Parameter Scan Time = 17:57:56; Parameter PMT Volts = 660; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 180043; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.52; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-09/55567
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.84; Parameter Scan Time = 19:34:42; Parameter PMT Volts = 550; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 6599; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.84; Parameter Scan Time = 19:34:42; Parameter PMT Volts = 660; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 180140; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-09/55568
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.63; Parameter Scan Time = 18:58:06; Parameter PMT Volts = 550; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 6563; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.63; Parameter Scan Time = 18:58:06; Parameter PMT Volts = 660; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 180104; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

The BeadStation 500 G system was then used to scan the beadchips.

Raw expression values were log2 transformed and median normalized.

The cerebellum was dissected for RNA extraction by using TissueLyser and RNeasy Lipid Tissue Kit (Qiagen).

After 17-h hybridization at 55°C, beadchips were washed according to recommended protocols from Illumina. FluoroLink Cy3-labeled Streptavidin (Amersham Biosciences) was used to detect expression signals.

Messenger RNA molecules were amplified using the MessageAmp II Kit (Ambion) according to the manufacturer's instructions. First strand cDNA was synthesized using  1ug of total RNA and oligo(dT) primers. In vitro transcription was carried out at 37°C for 14 h during which biotinylated UTPs (75 mM Biotin-16-UTP, Ambion) were used for RNA labeling.

This BeadChip targets approximately 25,600 well-annotated RefSeq transcripts, over 19,100 unique genes, and enables the interrogation of eight samples in parallel.

RNA interference (RNAi) with the CIITA-BX648577 fusion transcript was performed using lentiviral transduction of a vector (pGIPZ-sh.FLJ27352, clone V2LHS_212659, Thermo Scientific Open Biosystems, Huntsville, AL, USA) expressing a small hairpin RNA (shRNA: TGCTGTTGACAGTGAGCGCGACAGCCACCTCACTATCAAATAGTGAAGCCACAGATGTATTTGATAGTGAGGTGGCTGTCTTGCCTACTGCCTCGGA) that, after processing to mature siRNA, interferes with BX648577 exon 2 sequence as part of the CIITA-BX648577 fusion transcript.

The data were analyzed using DCHIP, http://biosun1.harvard.edu/complab/dchip/

Following fragmentation, cRNA were hybridized O/N at 45C on Affymetrix GeneChip HG 2.0 Plus Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol (1-cycle)

Pleural effusion cells
Gene expression data of transduced KM-H2 cells

Pathohistological and clinical examination of Patient UC09 (29 year-old female) yielded to diagnosis of ulcerative colitis.
Target Labeling and Hybridization procedure:
100-250 ng mRNA was isolated from total RNA for each patient using the Oligotex kit (Qiagen) according to the manufacturer’s instructions.  Prior to hybridization, 20ng of Arabidopsis thaliana DNA template was labeled with a-33P dCTP (10 microCi/microL; Amersham) during a random priming labeling reaction (pd(N)6, Amersham) (Feinberg and Vogelstein, 1983).  Reversed transcribed cDNA from patient targets were prepared in a final volume of 30microL as described in detail previously, with the exception that the labeling reaction was carried out at 42°C for 50 min (Eickhoff et al. 2000).  RNA was hydrolyzed under alkaline conditions by the addition of 3.5 microL of 3M NaOH and incubation for 20 min at 68°C. The samples were neutralized with the addition of 10 microL of 1M Tris-HCl (pH 7.4) and 10.5 microL of 1M HCl.  Unincorporated radioactive nucleotides were removed from both control and patient targets by filtration through Microspin G-50 columns according to the product manual (Amersham).
Prior to each hybridization reaction, unused filters were initially washed in 1 X SSC; 0.1% SDS at room temperature for 10 min (X 2) followed by three washes in 0.1 X SSC; 0.1% SDS for 20 min at 80°C.  These washes eliminated the potential problem for unbound or loosely bound probe cDNA from interfering with the hybridization reaction.  Each cDNA filter was pre-wetted with deionized water and placed in a hybridization bottle (3.5 X 25 cm).  The water was completely poured off and the filter was pre-hybridized for 2 hrs at 50°C in a 10 mL of hybridization solution containing 7% SDS, 50% formamide, 5 X SCC, 2% blocking reagent (Roche Diagnostics), 50mM sodium phosphate (pH 7.0) and denatured herring sperm DNA (50microg/microL).  The labeled target was added to the filters in 5 mL of the same preheated solution and hybridization of the filters was performed overnight (24 hrs) at 42°C.  Following overnight hybridization, membranes were removed from the bottles and washed in 1 X SSC/0.1% SDS buffer for 10 min at room temperature followed by two washes for 30 min in 0.2 X SSC/0.1% SDS at 65°C.  Excess moisture was removed by briefly placing the membranes on filter paper (Whatman) and the damp filters were wrapped in commercial grade plastic wrap.  Filters were exposed ~24 hrs to imaging plates (BAS-MS 2325, Fujifilm, Japan) and scanning was carried out at a resolution of 50microns on a FLA-3000G imaging system (Fujifilm, Japan). After hybridization, filters were individually stripped in a boiling solution of 0.5% SDS for 5 min, taken off the heat and agitated for an additional 3 hrs at room temperature and stored damp wrapped in plastic wrap at –20ºC for 7-8 weeks (half-life of 33P is 25.4 days). Prior to re-use, filters were re-scanned as above to ensure that residual radioactivity was negligible
Spot quantitation:
An exposure time of ~24 h was sufficient to yield signals from cDNA clones, yet keeping the data overflow to a mimimum.  Images were quantified using VisualGrid® software V3.4 (http://www.gpc-biotech.com). Each grid was manually adjusted to the image such that the linear correlation coefficient between duplicate spots was greater than 0.984. ID (Location) 95A01 - 96P24 contained spotting buffer only and were flaged as empty / set to zero.
References:
Eickhoff, H. et al. Tissue gene expression analysis using arrayed normalized cDNA libraries. Genome Res 10, 1230-40. (2000).
Feinberg, A.P. & Vogelstein, B. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem 132, 6-13. (1983).

Pathohistological and clinical examination of Patient UC10 (43 year-old male) yielded to diagnosis of ulcerative colitis.

human prostate cancer cells; clone 3-2

Pathohistological and clinical examination of Patient UC05 (29 year-old male) yielded to diagnosis of ulcerative colitis.

Pathohistological and clinical examination of Patient UC06 (38 year-old female) yielded to diagnosis of ulcerative colitis.

Pathohistological and clinical examination of Patient UC07 (33 year-old male) yielded to diagnosis of ulcerative colitis.

Pathohistological and clinical examination of Patient UC08 (51 year-old male) yielded to diagnosis of ulcerative colitis.

type: chronic
blast count: 1

Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction) using the R/Bioconductor package affy.

TRIzol (Invitrogen) followed by RNeasy column cleanup (Qiagen) using the manufacturers protocols

Affymetrix Eukaryotic Target Hybridization protocol (GeneChip Expression Analysis Technical Manual)

Affymetrix GeneChip IVT Labeling Kit, according to manufactuer's protocol (GeneChip Expression Analysis Technical Manual)

RNA isolated from lung tissue of Nrf2 knock-out mouse, smoke treated

lung tissue;CD-1_Nrf2 -/-;13 weeks + 5 month + 1 day;2R4F whole mainstream smoke 750 µg/ml, treatment over 5 month + 1 day recovery, 2x1h exposure per day

Center code: 5
imatinib analysis: 1

This dataset is a time series and is intended to be used as a control for the non-infarcted left ventricle samples (same region of heart on a mouse with myocardial infarction) and the infarcted left ventricle samples (region between the LAD artery and the apex on a mouse with myocardial infarction).  For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html
Keywords = acute myocardial infarction, AMI, cardiac

Region of the left ventricle above the LAD artery of a sham operated mouse

Keywords = acute myocardial infarction
Keywords = AMI
Keywords = cardiac

This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv].  Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction.  Lv2 samples are from the same region in a sham operated mouse.  Nilv samples are taken from the region above the infartion and the lv samples mimic that region in a sham mouse.  The lv and lv2 samples can be compared as both are from normal functioning hearts.  For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html

Region of the left ventricle [lv] above the LAD artery of a sham operated mouse

The human EOC cell lines OVCAR-3 and OV-90 were purchased from American Type Culture Collection (ATCC, Manassas, VA). OVCAR-3 and OV-90 cells were transfected with the eukaryotic expression vector pcDNA3.1 containing the full-length cDNA for CD157 or no insert (mock).

Slides were washed with the Agilent wash procedure and scanned with the dual-laser microarray scanner Agilent G2505B (Agilent Technologies).

Images were then analysed using Feature Extraction software (Agilent Technologies) version 10.7. Raw data elaboration was carried out with Bioconductor (Gentleman et al., 2004), using R statistical language. The limma package was used to identify differentially expressed genes, applying a cut-off on the p-value, adjusted for multiple testing by the Benjamini-Hochberg approach (<0.01), followed by filtering on expression level (logFC >1 or < -1 in at least one cell line, excluding transcripts with opposite sign). This criterion allowed the identification of transcripts with concordant modulation and took into account intrinsic biological differences of distinct cell lines that might be reflected in the amplitude of fold changes.

Total RNAs extracted from 70-80% confluent cultures using TRIZOL® reagent (Invitrogen). For each sample and reference pair, equal amounts of mRNA were amplified by means of the Amino Allyl MessageAmp II aRNA Kit (Ambion Inc., Austin, TX) to obtain amino allyl antisense RNA following the method developed by Eberwine and co-workers (Van Gelder et al, 1990). One round of amplification was performed and both dsDNA and aaRNA underwent a purification step using columns provided with the kit.

Hybridization with dye-swap duplication was performed to compare sample versus reference. The same quantity of differentially labelled sample and reference was put together, fragmented and hybridized to oligonucleotide glass arrays with sequences representing >41K human unique genes and transcripts. All steps were performed using the Gene Expression Hybridization kit (Agilent Technologies) following the 60-mer oligo microarray processing protocol (Agilent Technologies).

Labelling was performed using NHS ester Cy3 or Cy5 dyes (GE HealthCare, Buckinghamshire, UK) able to react with the modified RNA.

OVCAR3;eukaryotic expression vector pcDNA3.1 containing the full-length cDNA for CD157;eukaryotic expression vector pcDNA3.1 containing no insert;OVCAR3

Expression values were determined using Affymetrix Microarray Suite 5.0. GeneSpring GX version 11.0 was used to analyze the data using MAS5.0 normalization with all probes with absent flags removed from the data. The data was baseline transformed to the median of all samples. The condition average signal for each probe was filtered by significance using an unpaired t-test with unequal variance (Welch correction, P<0.05) using multiple testing correction (Benjamini-Hochberg), followed by a two-fold change cut-off.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133 Plus 2.0 Arrays.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA using two-cycle amplification (Expression Analysis Technical Manual, 2001, Affymetrix).

tibial muscular dystrophy (TMD);extensor digitorum longus;65;male

Total RNA was obtained using the TRIzol (Invitrogen) according to the manufacturer’s instructions.

Lentivirus containing hairpin RNA were made using 293T cells transfected with 1µg hairpin plasmid, 1µg packaging plasmid (pCMV-dR8.2) at 8:1 ratio with envelope plasmid (pCMV-VSV-G) and 10µL TransIT-LT1 (Mirus). Cells incubated 24hr. Fresh media added for 24 hours. Supernatant was saved from 1250 xg 5' spin. Cells were infected with 1:5 diluted virus supernatant and polybene added to 10 µg/mL. After 24 hours virus was removed and cells incubated in fresh media containing puromycin (HEK293 @ 2 µg/mL; HEK001 @ 0.5 µ/mL). Drug selection continued ~2 weeks. NCSTN knockdown confirmed by quantitative real-time PCR.

Both lines grown at 37C and 5% CO2. HEK293 were cultured in DMEM supplemented with 10% FBS, 200mM glutamine and 1% pen/strep. HEK001 cells were cultured in Keratinocyte-SFM media supplemented with 200mM glutamine, EGF and bovine pituitary extract (Life Technologies, Cat #17005042).

Arrays were scanned on an Illumina iScan (v3.2.45) device following the standard Illumina scanning protocol.

Image-derived data were processed with Illumina GenomeStudio (v2010).
Started with background subtracked, non-normalized data. Removed any probe without at least one significant detection p-value in one sample. Shifted each array so that minimum average value was 2.0. Transformed by log2 and normalized with quantile normalization (normaliseIllumina, Bioconductor beadarray v2.12.0, R 3.0.2).

miRNeasy mini kit (Qiagen, 217004) following manufacturer's instructions.

Biotinylated cRNAs were hybridized with standard Illumina hybridization protocol, and detected by staining with Cy3 strepavidin.

Starting with 100ng total RNA, biotinylated cRNA were prepared with Ambion MessageAmp TotalPrep Amplification kit for Illumina arrays

Mice were supplemented with the oxidized (Q10) or reduced form (QH2) of CoQ10, or a respective control diet for 6 or 14 months. Based on mean food intake and mean body weight, mice consumed 500 mg/ kg BW/ d QH2 or Q10. After supplementation period (6 or 14 months), mice were sacrificed, corresponding to an age of  7 or 15 months in total.

SAMP1 mice were reared in the Division of Laboratory Animal Research, Research Center for Human and Environmental Sciences, Shinshu University, under specific pathogen-free (SPF) conditions at 24 + 2 °C and a 12-h light-dark cycle. Water and food intake were available ad libitum. At the beginning of the long-term controlled study, 4-week-old female SAMP1 mice were purchased from Japan SLC (Hamamatsu, Japan) and housed 3 to 6 per cage (20 cm wide, 30 cm long, 10 cm deep). Grouping of the animals remained unchanged throughout the study. Body weights, food intake and degree of senescence were calculated monthly while mice were inspected daily.

Microarrays were scanned with a GeneChip® Scanner 3000 7G (Affymetrix).

Expression data was normalized with Affymetrix GeneChip Operating Software (GCOS) 1.4 using mean value (global normalization).

Triazol (Qiazol, Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

15 µg of fragmented cRNA was hybridized to a Mouse Genome 430 2.0 Array for 16 hr at 45 °C at 60 rpm. Arrays were washed on GeneChip®  Fluidics station 450 (Affymetrix) and stained with streptavidin-phycoerythrin

Biotinylated cRNA was prepared according to the standard Affymetrix protocol (IVT Labeling Kit, Affymetrix).

breast cancer derived cell line treated with fresh medium for 24 hours

Female mice used were 129/SvImJ wildtype (Jackson Lab), 10-16 weeks
of age.  14 days after ovariectomy, mice were injected
subcutaneously with progesterone dissolved in sesame oil (Sigma;
0.2mg/0.1mL/mouse), followed by sacrifice and removal of uterine
horns at 6 hours after injection.  8 uterine horns from 4 mice were
pooled to form one sample.  Total RNA preparation, cRNA labeling and
hybridization were performed according to recommendations by
Affymetrix.

horns at 9 hours after injection.  8 uterine horns from 4 mice were

horns at 1 hour after injection.  8 uterine horns from 4 mice were

horns at 3 hours after injection.  8 uterine horns from 4 mice were

Female mice used were SvJ/129, 10-16 weeks of age, with both copies
of the Hoxa-10 gene (GenBank # NM_008263) disrupted.  These mice
were littermates of Hoxa-10+/+ mice used in parallel experiments.
14 days after ovariectomy, mice were injected with sesame oil
(Sigma; 0.1mL/mouse), followed by sacrifice and removal of uterine

of age.  14 days after ovariectomy, the mice were sacrifice and
uterine horns were removed.  8 uterine horns from 4 mice were pooled
to form one sample.  Total RNA preparation, cRNA labeling and

horns at 6 hour after injection.  8 uterine horns from 4 mice were

OVCAR3;eukaryotic expression vector pcDNA3.1 containing no insert;eukaryotic expression vector pcDNA3.1 containing the full-length cDNA for CD157;OVCAR3

Cells were lysed directly in the culture dish and the lysates were used for extraction.  Total RNA was extracted by Qiagen RNEasy kit according to the manufacturer's instructions.

Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

empty retroviral vector-infected immortalized mouse embryonic fibroblasts

21-day-old felmale C57BL/6 mice from Harlan (Indianapolis, IN) were ovariectomized on day 26 and fed with phytoestrogen-free diet two days later (AIN-93G purified rodent diet, Dyets, In., Bethlehem, PA). Experimental treatments began on day 30. Animals were fed with a diet containing 1500 ppm genistein (Indofine Chemicals, Somerville, NJ) ad libitum by adding genistein to the AIN-93G diet. RNA were extracted at day 6 after experiment started. Total 6 animals were treated. RNA samples were pooled from 3 animals, resulting two independent biological replicates.

Whole tissues corresponding to the proximal and distal small intestine and to the colon were dissected from each rat, washed with ice-cold saline solution and immediately frozen in liquid nitrogen. Rats were either control or treated with Amoxicillin (100mg/kg/day). Small intestine was divided in two identical length considered as the proximal and distal part. In each intestinal part 1 cm of tissue was taken in the middle of this part to perform the RNA extraction and then the GeneArray analysis.
Keywords = gastrointestinal tract, microarray, antibiotic, suckling rats, amoxicillin

Cerebellum_transgenic nuclear exclusion signal Htt exon1 142Q A61_8 months_replicate 3

MAS 5 global scaling at defalut values; normalization factor=1, target value=500

A61 NES 142Q TG3	F6/23	A61	NES Htt exon 1 142Q	Mouse	8 months	Cerebellum	Male

Cerebellum_transgenic nuclear exclusion signal Htt exon1 142Q A39_4 months_replicate 3

A39 NES 142Q TG3	F7/4	A39	NES Htt exon 1 142Q	Mouse	4 months	Cerebellum	Male

Cerebellum_transgenic nuclear exclusion signal Htt exon1 142Q A39_4 months_replicate 4

A39 NES 142Q TG4	F7/5	A39	NES Htt exon 1 142Q	Mouse	4 months	Cerebellum	Male

Sorted GFP-positive Dot1l flox/flox MLL-AF9 leukemia cells were transduced with retroviral Cre-YFP or YFP control vector. GFP/YFP positive cells were sorted on days 3, 5, and 7.

Leukemias were generated by injecting 100 000 MLL-AF9-GFP transduced Dot1l flox/flox 4 days after transduction into B6129 recipients. Bulk leukemia cells were isolated from leukemic mice.

RMA background correction and quantile normalization was done with the GenePattern ExpressionFileCreator module (http://www.broad.mit.edu/cancer/software/genepattern/), which uses the Bioconductor implementation of RMA (http://www.bioconductor.org/). This function computes the Robust Multichip Average expression measure described in Irizarry et al. Biostatistics (2003).

Total RNA was extracted using Trizol. RNA was prepared using the Nugen Ovation Pico WTA system.

5 μg of labeled cDNA was hybridized to the Affymetrix 430 2.0 microarray using standard conditions.

Amplified cDNA was labeled using the Nugene Encore TM Biotin Module.

No specific treatment was used in cells cultures. Growing cells were used in the media described above.

Cells were cultured in DMEM-F12 (Life Technologies) supplemented with 15% Foetal Bovine Serum (HyClone), 1% Non-essential aminoacids solution (Life Technologies), 1% penicillin-streptomycin solution (Life Technologies), in a humidified incubator at 37oC and 5% CO2. For storage, cells were frozen in medium containing 90% FBS and 10% DMSO (LGC Biotecnologia). Protocols are also described in Bueno et al, 2011 Stem Cell Reviews and Reports.

Data were analyzed with Expression Console (Affymetrix) and normalized by RMA method.

Total RNA isolation was performed with NucleoSpin RNA II kit (Macherey-Nagel), following manufacturer’s recommendations. RNA quality and concentration were assessed using Nanodrop 1000 and agarose gel electrophoresis. Only RNA samples with absorbance ratio 260/280 > 1.8, preserved rRNA ratio (28S/18S) and no signs of degradation were used.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip®Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 and hybridized for 16 hr in the Affymetrix Hybridization Oven 640.

gene expression data from dental pulp stem cells extracted from deciduos tooth

Non-syndromic cleft lip/palate (NSCL/P);decidous teeth dental pulp;male

We used Agilent GeneSpring GX v.11.0 for the analysis of the data. We used Robust Multichip Average (RMA) algorithm as the initial method for chip summarization.

Trizol, according to manufacturer’s manual, followed by purification with Quigen RNA easy kit.

"male subject, 18-45 yrs, peripheral blood mononuclear cells 6 h after intravenous endotoxin challenge"

Expression Console were used to generate chp files (program-version = 1.1.2800.19935, algorithm-version = 1.0, algorithm-name = rma-gene-default).

Flow sorting of KLS cells and MEP cells.
Trizol RS extraction of total RNA was performed according to the manufacturer's instructions.

All  patients received IM at 600mg daily by mouth for 8-12 weeks.

The data matrix was generated using a two-color Agilent microarray with tumor or biopsy samples in channel 1 and human reference RNA in channel 2.

Total RNA extracted using Trizol following manufacturer's instructions

Labeled sample and reference were combined and hybridized on 44K Whole Human Genome Oliho Microarray (Agilent) at 60 degrees for 17hrs.

50ng of RNA from tissue samples and universal human reference RNA were amplified using Ovation Aminoallyl RNA amplification and labeling system.  Sample aminoallyl cDNA was labeled with AlexaFluor 647 dye (Invitrogen) and reference aminoallyl cDNA was labeled with AlexaFluor 555 (Invitrogen) dye.

Ovation Aminoallyl RNA amplification and labeling system (NuGEN)

n/a;exon 11;GIST Tumor;Universal Human Reference RNA (Stratagene)

0.682539683;exon 11;GIST Tumor;Universal Human Reference RNA (Stratagene)

0.333333333;exon 11;GIST Tumor;Universal Human Reference RNA (Stratagene)

n/a;unknown;GIST Tumor;Universal Human Reference RNA (Stratagene)

n/a;wildtype;GIST Tumor;Universal Human Reference RNA (Stratagene)

0;wildtype;GIST Tumor;Universal Human Reference RNA (Stratagene)

The arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.

The data were analyzed with JMP Genomics (SAS Institute), using the RMA algorithm.  RMA was run separately for biceps and quadriceps.

Total RNA from biceps biopsies was extracted using the RNeasy Fibrous Mini Kit (Qiagen) according to the manufacturer's instructions.  Quadriceps biopsies were homogenized in Trizol reagent (Invitrogen) using the Geno/Grinder (Zymo Research) and total RNA was isolated following phase separation and precipitation.

Following fragmentation, 2.2 ug of  labeled cDNA were hybridized for 16 hr at 45C to U133 Plus2.0 GeneChips in an Affymetrix Model 640 hybridization oven. GeneChips were washed and stained on an Affymetrix FS450 Fluidics station.

Biotinylated cDNA was prepared using the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)

One well of a 6-well dish of E14 cells was treated with purified esiRNA (0.33 ng/ul) and Lipofectamine 2000 (Invitrogen) for 72 hr to knockdown expression of Tip60 (Htatip).

Arrays were scanned using the Agilent microarray scanner (Agilent) and raw signal intensities were extracted with Feature Extraction v8.9 software (Agilent).

Raw log-intensities are normalized using quantile normalization method that is proposed by Bolstad et al (2003). No background subtraction was performed, and the median feature pixel intensity was used as the raw signal before normalization.

RNA was isolated using Trizol reagent combined with PureLink Micro-to-Midi columns (Invitrogen).

Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays (Agilent). Hybridizations were performed for 14 hrs, according to the manufacturers protocol (Agilent).

Total RNA quality was assessed using a Pico Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol (Agilent).

Sample preparation, labeling, and array hybridizations were performed according to standard protocols from the UCSF Shared Microarray Core Facilities and Agilent Technologies (http://www.arrays.ucsf.edu and http://www.agilent.com).

To mimic the defect found in TBD-BMSCs, TERC expression was reduced in N-BMSCs in two different ways.  Initially, TERC short hairpin (sh) RNA lentiviral particles were used to generate cells with stably-reduced expression of TERC.  However, these cells were unable to grow.  Thus, transient knockdown of TERC was performed using siTERC-RNA (SilencerTM Select, pre-designed and validated, AM 16706, Ambion) and a negative control siRNA [(siNC), SilencerTM negative control No. 2 siRNA, AM4637, Ambion].  Constructs were transfected into N-BMSCs using Lipofectamine RNAiMAX (#13778-075, Life Technologies), according to the manufacturer’s instructions.

Cell lines were cultured and maintained in growth medium (alpha-MEM, 2 mM glutamine, 100 U/ml penicillin, 100ug/ml streptomycin sulfate, 20% lot-selected fetal bovine, non-heat inactivated serum, 10-8 M dexamethasone and 10-4 M ascorbic acid-2-phosphate)

According to the Affymetrix standard protocol. (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array)

Genes that were under/over-represented by >2-fold were analyzed using GeneSpring software.  Signal intensity values were normalized using RMA (Robust Multi-array Analysis) summarization and baseline transformation to median of all samples was performed.  Entities were filtered based on their signal intensity values.  Hierarchical clustering was performed on filtered signal intensity (>20.0), non-averaged, fold change >2.  A fold change analysis (>10-fold) was performed to generate a list of top genes under/over represented between the groups.

Gene expression data from N-BMSCs were transfected with negative control (siNC) construct.

Gene expression data from non-clonal BMSC cultures from normal donors.

BM single-cell suspensions from bone fragments and aspirates were used to establish non-clonal BMSC cultures from normal donors (N-BMSCs)

Total RNA was extracted from lymphoblastoid cells of AU046708 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;AU046708 is a male with autism and full mutation of FMR1.

Total RNA was extracted from lymphoblastoid cells of AU046706 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;AU046706 is a male with autism and full mutation of FMR1.

Total RNA was extracted from lymphoblastoid cells of AU046707 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;AU046707 is a male with autism and full mutation of FMR1.

Mouse embryonic fibroblast derived from MyoD-/-/Myf5-/- animals transduced with ER-MyoD wt in differentiation media for 0hr

Gene expression data from skeletal muscle of two months old mouse

C57BL/10J, Gender: Male, Age: 2 months, Tissue: Gastrocnemius Muscle Treated with Phosphate-Buffered Saline, Deficient in Dystrophin

C57BL/10J, Gender: Male, Age: 2 months, Tissue: Gastrocnemius Muscle Treated with AAV carrying Galgt2, Deficient in Dystrophin

C57BL/10J x C57BL/6J, Gender: Male, Age: 2 months, Tissue: Gastrocnemius Muscle, Deficient in Dystrophin, Galgt2 Transgenic

C57BL/6J, Gender: Male, Age: 2 months, Tissue: Gastrocnemius Muscle. Galgt2 Transgenic

spinal cord, ventral spinal cord: EP134/L - hSOD1(Chan)/e14-wildtype hSOD1_le2

wildtype SOD1 - biological replicate 4/pool of 5 positive embryos

spinal cord, ventral spinal cord: EP133/L - hSOD1(Chan)/e14-wildtype hSOD1_le2

wildtype SOD1 - biological replicate 3/pool of 5 positive embryos

spinal cord, ventral spinal cord: EP132/L - hSOD1(Chan)/e14-wildtype hSOD1_le2

wildtype SOD1 - biological replicate 2/pool of 5 positive embryos

The mice were divided into 10 groups of 6 mice each, housed in groups of 3 per cage and fed one of the following diets for 20 weeks : AIN93G (control), AIN93G containing 0.05% quercetin (0.05% quercetin, (Funakoshi, Tokyo, Japan)), a high fat, high cholesterol and high sucrose Western-style diet (39.9% of energy from fat (20% unsalted butter, 1% soy oil, 0.15% cholesterol) and 34.0% of energy from sucrose) (Oriental Yeast) or this Western diet supplemented with 0.05% quercetin.

Five-week-old male C57BL/6J mice were obtained from the Institute for Animal Reproduction, Charles River Japan Inc. (Ibaraki, Japan). The mice were housed under conditions of 24± 1°C, 55 ± 5% humidity, and 12 hour light/dark photocycles (dark period from 0800 to 2000) with free access to water and a standard nonpurified diet (NMF, Oriental Yeast Co., Tokyo, Japan) for a week prior to the experiment.

After hybridization, the gene chips were washed and stained using a GeneChip Fluidics Station 450 (Affymetrix) and then scanned (GeneChip Scanner; Affymetrix) with the GeneChip Operation Software Ver. 1.4 (Affymetrix).

Data analysis was performed with a GeneChip Operating Software (Ver. 1.4) using Affymetrix default analysis settings and global scaling as normalization method..

The mice were killed under anesthesia with pentobarbital, and blood and liver tissue were immediately collected. Total RNA was extracted from liver tissues using an RNeasy Midi Kit (Qiagen KK, Tokyo, Japan) according to the manufacturer’s instructions.

Fragmented cRNA were hybridized to an array (Mouse Genome 430 2.0 array, Affymetrix) at 45°C for 16 h.

Double-stranded cDNA was synthesized from the total RNA of each mouse using the One-Cycle cDNA Synthesis Kit (Affymetrix Japan KK, Tokyo, Japan) with a T7-(dT)24 primer. Biotin-labeled cRNA was then synthesized using an IVT Labeling Kit (Affymetrix). The biotin-labeled cRNA was further purified and fragmented using the Sample Cleanup Module (Affymetrix).

Gene expression data from liver after 20 week feeding of control AIN93G diet

Sendai virus (SeV), strain 52, was obtained from American Type Culture Collection and stored at -70°C. Cultures were inoculated with SeV or an equivalent amount of UV-inactivated SeV (SeV-UV) in the apical compartment for 1 h at 37 °C, then removed by washing.  RNA was collected 24 hours after inoculation.

Primary-culture mouse tracheal epithelial cells (mTECs) were established on Transwell membranes using air-liquid interface (ALI) conditions as described previously (Tyner et al, 2006).

Chips were scanned, and hybridization data were acquired using Affymetrix MicroArray Suite (MAS) 5.0 software.

Microarray normalization and statistical analysis were carried out using packages from the Bioconductor project (Gentleman RC et al, 2004, ver 2.0), executed in the R programming environment. Data was normalized using the empirical Bayes version of the GCRMA algorithm as implemented in the GCRMA package (Wu Z et al, 2004). Differential expression was assessed by using linear models and empirical Bayes moderated F statistics as implemented in the LIMMA package (Smyth GK, 2004). Differences in gene expression were considered significant if the P values were <0.05 after adjustment for multiple testing (Benjamini & Hochberg, 1995), and thus, false discovery rate was controlled to be <5%. Visualization and plotting were performed using Spotfire DecisionSite for Functional Genomics (Spotfire, Somerville, MA).

Total RNA was isolated from mTEC cultures using the Micro RNA Isolation kit (Stratagene) and converted to Poly(A)+ RNA.

Samples were hybridized in duplicate to gene chip U74Av2 (Affymetrix, Santa Clara, CA) according to the manufacturer’s protocol.

Poly(A)+ RNA was amplified using RiboAmp (Arcturus, Mountain View, CA), and then labelled with biotin using the BioArray High Yield RNA Transcript Labeling Kit (Enzo, Farmingdale, NY)

UV-inactivated Sendai virus infected mouse tracheal epithelial cells.

WM-266 cells were seeded in 6-well plates 24 hours prior to siRNA transfection. 200 pmol of siRNA oligos were transfected with Oligofectamine (Invitrogen, Carlsbad, CA) in serum-free medium. 72 hours later,  cells were harvested for RNA extraction.

WM-266 cells were grown in MEM medium with Glutamax supplemented with 10% FCS, 0,1mM sodium pyruvate, 0,1mM non-essential amino acids.

WM-266 cells that underwent transfection without addition of oligonucleotides - Replica 2

The data were analyzed with GeneChip operating system (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

Total RNA was extracted using TRIzol Reagent (Gibco), followed by clean up on RNeasy mini/midi columns (RNeasy Mini/Midi Kit, Qiagen). For each sample, an RNA pool was obtained by mixing equal quantities of total RNA from each of the three independent RNA extractions.

Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip GeneChip HG-U133 Plus v.2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station. Two copies of the GeneChip HG-U133 Plus v.2 were  hybridized with each biotin-labeled target.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA  The size and the accuracy of quantitation of targets were checked by agarose gel electrophoresis of 2ug aliquots, prior to and after fragmentation. After fragmentation, targets were diluted in hybridisation buffer at a concentration of 150ug/ml.

WM-266 cells that underwent the transfection procedure without the addition of any oligonucleotides.
NO_B

Lens was cryosectioned, stained with Cressyl Violet, and dehydrated. Laser capture microdissection (Arcturus PixCell2e) was used to remove epithelial cells from each section.

7G GeneChip Scanner, single scan, 570 nm filter, software GCOS1.4

Global scaling in GCOS1.4 using all probsets and TGT value of 500

GeneChip Hybridization Oven at 45ºC with rotation, washing on GeneChip Fulidics Station_450 using EukGE-Ws2v4_450 washing/staining protocol with Antibody Amplification Staining Protocol

Two cycle amplification using Ambion MessageAmp II aRNA amplification kit and MessageAmp II-biotin enhanced amplification kits

Each data set was taken from one lens only.  All lens data sets were from one litter of animals.

WM-266 cells that underwent transfection without addition of oligonucleotides - Replica 1

NO_A

WM-266 cells transfected with on-target plus siCONTROL siRNA (Dharmacon) for control.
siCTR_B

Either 1) Naïve cells treated with DMSO for 4 hours 2) Naïve cells treated with 0.8 uM INCB18424 for 4 hours or 3) Persistent cells treated with 0.8 uM INCB18424 for 4 hours

Please see AffymetrixExpression Analysis Technical Manual, with Specific Protocols for Use with the Hybridization, Wash, and Stain Kit (http://www.affymetrix.com/estore/browse/products.jsp?categoryIdClicked=&productId=131415#1_3)

Partek GS (v.6.5): GCRMA Background Correction : Quantile Normalization : Log2 transform : Median Polish

Total RNA extracted using Trizol according to manufacturer's guidelines

Please see Affymetrix Expression Analysis Technical Manual, with Specific Protocols for Use with the Hybridization, Wash, and Stain Kit (http://www.affymetrix.com/estore/browse/products.jsp?categoryIdClicked=&productId=131415#1_3)

Please see Affymetrix 3' IVT Express Kit Documentaion (http://www.affymetrix.com/estore/browse/products.jsp?categoryIdClicked=&productId=131415#1_3)

BaF3;MPLW515L3;normal condition (Naïve);0.8 uM INCB18424 for 4 hrs;acute

BaF3;MPLW515L3;0.8 uM INCB18424 for 4 wks (Persistent);0.8 uM INCB18424 for 4 hrs;persistent

BaF3 cell line transduced MPLW515L3 mutant grown in 0.8 uM INCB18424 for 4 wks

The data output was analyzed using GeneSpring GX 10.0 commercial software (Agilent Technologies Inc., Palo Alto, CA, USA).  p-values were calculated using an unpaired t-test.  Expression values with a p-value ≤0.05 and a fold difference of ≥1.5-fold relative to wild-type baseline expression levels were considered significant.
Affymetrix Gene Expression, MOE 430A chips   Filter by expression    Raw data    Filter by percentile    Upper cutoff = 100.0    Lower cutoff = 20.0    At least 1 out of 6 samples have values within range   T-test unpaired   p-value computation: Asymptotic   Multiple testing correction: No correction   p-value cutoff = 0.05   Fold change cutoff = 1.5   Clustering: Hierarchical    Interpretation: A. All Samples                 B. Genotype    Cluster on: Entities and Conditions

Whole whisker pads were dissected from E12.5 embryos.
Total RNA was isolated using the RNeasy® Mini Kit (Qiagen).

15 ug of cRNA were hybridized to Affymetrix GeneChip® MOE430A microarrays.

Mouse embryonic fibroblast derived from MyoD-/-/Myf5-/- animals transduced with ER-MyoD RRR in differentiation media for 6hrs

Hematopoietic stem and progenitors cells were isolated from rTA and MSI2-inducible mice using high-speed multiparameter flow cytometry.

Affymetrix GCS 3000 7G scanner using Affymetrix standard protoco

Signal normalization was performed by RMA method. RMA expression measure was computed using Bioconductor Affy package in R language (Bioconductor 2.5; R version 2.11.0)

Hematopoietic stem and progenitor cells (LineageLow, Sca1+, Kit+; LSK)

Mouse embryonic fibroblast derived from MyoD-/-/Myf5-/- animals transduced with retrovirus without ER-MyoD insert in differentiation media for 6hrs

Slides were scanned using the Affymetrix 7G scanner, and CEL files generated using the GeneChip Operating System (GCOS)

All CEL files were imported into ArrayAssist and the Robust Multi-Array Averge (RMA) algorithm was applied.

Laser capture microdissection was used to isolate epithelial cells from snap-frozen surgical specimens. Total RNA was then isolated using the Stratagene Absolutely RNA MicroPrep kit.

Biotin-labeled cDNA was hybridized to Affymetrix GeneChip U133A Plus 2.0 arrays according to manufacturer's instructions.

Reverse-transcription, linear amplification and biotin labeling was performed using the NuGEN Biotin Ovation kit (from 10ng of input total RNA).

To investigate the role of Serum Response Factor (SRF) in the heart, we utilized the Cre-loxP system to generate SRF-null neonatal mouse cardiomyocytes.

Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 53 hours, replica 2

1 ug/ml doxycyline;53 h;A673;doxycyclin  inducible EWS-FLI1 knockdown;Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown construct

Early passages of cells were cultured in a humidified atmosphere containing 5% of CO2 in Dulbecco's modified Eagle's medium (DMEM) (Cellgro, Herndon, VA), supplemented with 10% Fetal Bovine Serum (ATCC, Manassas, VA), 1% penicillin (Cellgro), and kept in a humidified incubator (Kendro Lab, New Town, CT) at 37°C.

The arrays were scanned using a Genepix 4000B microarray scanner. Images were analyzed using Codelink expression II analysis suite, and visually inspected for defects and quality control parameters as recommended by the manufacturer.

Total RNA was extracted from fibroblasts of UIP histology lung tissue or normal histology lung tissue using TRIzol reagent (GIBCO-BRL, Gaithersburg, MD) according to the manufacturer protocol for RNA extraction and purification. RNA was stored at - 80°C until use.

Fragmented cRNA was hybridized to Codelink Uniset I slides. After hybridization, arrays were washed and stained with streptavidin-AlexaFluor 647.

The extracted total RNA was used as a template to generate double-stranded cDNA and biotin-labeled cRNA, as recommended by the manufacturer of the arrays.

8396 genes that had an Entrez gene ID demonstrate minimal changes in gene expression between fibroblasts from UIP histology lung tissue and normal histology lung tissue. Among them, 236 genes were substantially changed (TNoM=0 and t-test p-value <0.05).

U2OS;osteosarcoma cells;nonspecific siRNA (SiNS);dexamethasone (Dex) for 0h

Wild type and mcad-/- mice where injected with vehicle or lps and subsequently fasted for 12 hrs , liver was isolated and RNA was extracted

The data where normalised using gcRMA normalisation protocols using MADMAX analysis pipeline pmid: 21778530

TRI -reagent was used to isolate RNA, and Qiagen Rneasy columns where used to purify the RNA

wild type;Male;BL6/SV129 mixed;50-60 days of age;12 hrs fasted;vehicle;liver

Loss of stearoyl–CoA desaturase-1 function protects mice against adiposity

mixed 129 and C57BL/6J; Age: 6 weeks old; Gender: female; Diet: chow; Non-fasted; Genetic modification: Scd1 -/-.

C57BL/6J; Age: 6 weeks old; Gender: female; Diet: chow; Non-fasted; Genetic modification: None (Scd1 +/+; wide type control).

mixed 129 and C57BL/6J; Age: 6 weeks old; Gender: female; Diet: chow, non-fasted; Genetic modification: Scd1 -/-.

The chips were washed using Fluidics protocol midiEuk2v3_450 on an Affymetrix GeneChip Fluidics Station 450 and scanned on an Affymetrix Genechip Scanner.

Microarray experiments were performed using whole-mouse-genome oligoarrays (Mouse430a; Affymetrix), and array data were analyzed using MAYDAY 2.12 software. Array data were subjected to robust multiarray average normalization. For determination of differential expression, we calculated fold changes and tested for significance by Significance Analysis of Microarrays (SAM) using 100 permutations with a false discovery rate (Storey) adjusted p<0.05. Data with >1.5 × differential expression (log2 0.5849) were included in the analysis.

Total RNA was isolated using Rneasy (Quiagen). RNA integrity and quantity was analyzed using a DU640 (Beckman-Coulter).

10 microgram of labeled aRNA was fragmented, and 6.5 microgram of the fragmented aRNA was hybridized to the Affymetrix Mouse 430A_2 chips.  Hybridization conditions were 16hrs at 45C.

100ng of totalRNA was labeled using Ambion's MessageAmp Premier RNA Amplification Kit (PN:4383452)

CEL files were pre-processed and normalized using the RMA algorithm through the Affy package of R/Bioconductor.

Tissues were homogenized with an RNase-free pestle alternating freeze/thaw cycles and subsequently passed through a QIAshredder column (Qiagen). RNA fraction was extracted using mirVana (Ambion) kit.

Arrays were washed and hybridized using Affymetrix Fluidics Station 450.

RNA was reverse-transcribed and biotin-labeled using Affymetrix one-cycle cDNA synthesis and IVT labeling kits (Affymetrix).

T166;Mouse tumorgraft, cohort 0;Male;56;Clear-cell renal cell carcinoma;mutant;wild type;mutant

Gene expression profiling of mouse tumorgraft, cohort 0 of patient T166

Cells were transfected (using Oligofectamine; Invitrogen) with 25nM siRNA targetting AP-2gamma or non-silencing control siRNA or no siRNA (transfection reagent only).

MCF-7 cells were cultured in DMEM, 10% FCS; plus insulin (10ug/ml).

AP-2 gamma targetting siRNA 1: AAUGAGAUGGCAGCUAGGAAG Technical Replicate 2

Arrays were scanned using an Affymetrix GeneArray 3000 scanner.  Array images were assessed by eye to confirm scanner alignment, the absence of significant bubbles or scratches, and a low background.

The data were pre-processed using the “affy” package in BioConductor: “mas5” background correction, “quantiles” normalisation (Bolstad et al. 2003), “pmonly” correction and “medianpolish” summarisation. The resulting log2 scale transformed data were imported into the Genespring package (Genespring GX 7.3, Agilent Technologies) and filtered to retain the 2500 probe sets with the highest variance across all the arrays. Welch’s t-test was then applied in conjunction with a False Discovery Rate (FDR) multiple test correction to identify the most significantly regulated genes (p<0.01).

Total RNA was extracted using Trizol (Sigma) following the standard protocol but including a Qiagen RNAeasy Mini column (with RNAse free DNAse step) for clean up and elution.

15 ug of cRNA was hybridized for 16 hr at 45C to Human Genome U133 Plus 2.0 oligonucleotide arrays (as described at http://www.affymetrix.com/products/arrays/specific/hgu133plus.affx).  Arrays were washed and stained using the Affymetrix Fluidics Station 450.

Total RNA (8ug) from each sample was used to prepare biotinylated target RNA, using the One Cycle Target Labelling kit (Invitrogen) according to the manufacturer’s recommendations (http://www.affymetrix.com/support/technical/manual/expression_manual.affx)

AP-2 gamma targetting siRNA 1: AAUGAGAUGGCAGCUAGGAAG Technical Replicate 1

AP-2 gamma targetting siRNA 2: GCGGCCCAGCAACUGUGUAAA Technical Replicate 1

AP-2 gamma targetting siRNA 1: AAUGAGAUGGCAGCUAGGAAG Technical Replicate 3

AP-2 gamma targetting siRNA 2: GCGGCCCAGCAACUGUGUAAA Technical Replicate 3

AP-2 gamma targetting siRNA 2: GCGGCCCAGCAACUGUGUAAA Technical Replicate 2

BM-GMMs were lifted off the plate and replated in a 12-well tissue culture plate. After cells were re-attached, E0771 tumor cells were added to the well using cell culture insert. After 18hr of GM-BMM, E0771 co-culture, tumor cell inserts were tossed away. Treated GM-BMMs were lysed for total RNA isolation.

Bone marrow cells were collected from naive C57BL/6 and E-FABP knockout mice of 6~8 week old. GM-BMMs were derived using GM-CSF(20ng/ml) in RPMI1640 with 5%FBS for 7 days in 100mm plates before tumor treatment. Fresh media with GM-CSF were added every 2 days to replace about half the old media.

GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000.

The data were analyzed using R package Affy (version 1.36.1), affycoretools (version 1.34.0), limma (version 3.14.4) and gcrma (version 2.30.0).  The QC of the data was assessed using AffyQCReport (version 1.36.0). RMA function with default setting was used to globally normalize the data. Probes with absent call values in any of the samples using mas5calls function were treated as non-expressed probes and excluded from the downstream analysis. The probe annotation is done using mouse4302.db package (version 2.9.0) from BioConductor.

Total RNA was extracted from tumor-stimulated GM-BMMs of WT and E-FABP-/- mice using RNeasy Mini Kit (Qiagen), following the manufacturer's protocol.

The IVT products were column-purified, fragmented and hybridized at 45º C for 16 h. Subsequent to hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.

Microarray analysis was conducted according to the manufacture's instructions for Affymetrix 3' IVT Express Kit.  RNA quality was assessed by Agilent Bioanalyzer. Reverse transcription to second strand cDNA was generated from 100 ng of high quality total RNA. Subsequently, the products were column-purified (Affymetrix) and then in vitro transcribed to generate biotin-labeled cRNA.

C57BL/6;mouse bone marrow;E-FABP knockout;1x10^6 cells in a 12-well plate co-cultured overnight with 1x10^6 E0771 tumor cells in an sterile insert

Murine prostates were isolated from transgenic mice (probasin driven AKT) v. littermate wild-type controls treated with either RAD001 (MTOR inhibition) or placebo. 10 micrograms of total RNA was used to synthesize biotin-labeled cRNA using our standard protocol
Keywords = Prostate AKT RAD001 MTOR

Animals were housed under a 12 h light/12 h dark cycle and ad-lib access to food and water. Animals were sacrificed by cervical dislocation.

GeneChips were scanned using the Affymetrix GeneChip 3000 7G scanner

Retinal tissue was dissected free of retinal pigment epithelium (RPE) and placed in guanidine HCL.  The samples  were subsequently disrupted and homogenized using a rotor–stator  (Polytron PT2100).  Total RNA used for microarray studies was purified  from a caesium chloride gradient produced by high-speed  ultra-centrifugation.

Following fragmentation, cRNA was hybridized on the GeneChip Array and the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2007, Affymetrix).

Biotinylated cRNA was prepared from the total RNA according to the Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2007, Affymetrix)

DRG collected from ipsilateral limb 14 days after chronic constriction injury

GeneChip Fluidics station 400
(Affymetrix Inc.) was used to wash and stain the arrays. The standard protocol suggested by the manufacturer was used to detect the hybridized biotinylated cRNA. The chips were then scanned with a specific scanner (Affymetrix Inc.) to generate digitized image data (DAT) files.

DAT files were analyzed by GCOS (Affymetrix, USA) to generate background-normalized image data (CEL files).
Probe set intensities were obtained by means of GCRMA, a robust
multiarray analysis method.
The full data set was normalized according to the
quantiles method.

Total RNA (ttlRNA) was extracted and
purified from stably transfected H1299 cell lines with the Concert
Cytoplasmic RNA Purification Reagent (Invitrogen, Carlsbad, CA), as suggested by the manufacturer. ttlRNAs were then quantified and inspected
with a Bioanalyzer (Agilent Technologies).

Affymetrix HGU133plus2 array chips were hybridized with biotinylated cRNA
(20 μg/chip, 16 hr, 45°C using the hybridization buffer and control provided
by the manufacturer (Affymetrix Inc.).

cRNAs were generated and hybridized on HGU133plus2 Affymetrix DNA chips according to the Affymetrix protocol, ttlRNA (8 μg) was used to prepare double-stranded cDNA with the one-cycle cDNA synthesis kit (Affymetrix, USA). The cDNA was then used as a template to synthesize a biotinylated cRNA (16 hr, 37°C) with the IVT kit (Affymetrix, USA). In vitro transcription products were purified with the IVT cleanup module and approximately 35 μg of cRNA were treated with the fragmentation buffer (35' at 94°C).

Human lung carcinoma H1299 cells (p53 null, no p63 expression) Tet-on

Lot batch = Replicate 2

Lot batch = Replicate 3

Cells were plated on collagen-coated six-well plates and filled with maintenance medium. Upon arrival of the cells, the medium was discarded and was replaced by Hepatocyte Culture Medium (HCM) with additives. The additives included Gentamicin sulphate/Amphotercin-B, Bovine serum albumin (Fatty acid free), Transferrin, Ascorbic acid, Insulin, Epidermal growth factor, Hydrocortisone hemisuccinate.  The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (50 uM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.

Human hepatocytes and Hepatocyte Culture Medium Bulletkit were purchased from Lonza Bioscience (Verviers, Belgium). Primary hepatocytes were isolated from surgical liver biopsies obtained from six individual donors who underwent surgery after informed consent was obtained for surgery with subsequent use of samples in experiments. Lonza utilizes the hospital's Institutional Review Board (IRB) to obtain approval before obtaining these tissues. Hepatocytes were isolated with two-step collagenase perfusion method and the viability of the cells was over 80%.

Arrays were scanned on an Affymetrix 3000 7G scanner, as described n the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

Expression estimates were calculated using GCRMA, applying the Emperical Bayes (EB) estimate for background adjustment.

Total RNA was prepared from human primary hepatocytes using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns.

Hybridisation of 500ng cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.

Primary hepatocytes isolated from Donor 6 treated with DMSO for 6h

Primary hepatocytes isolated from Donor 6 treated with Wy14643 for 24h

Primary hepatocytes isolated from Donor 6 treated with DMSO for 24h

The arrays were washed and stained according to the manufacturer's recommendations and scanned in a GeneChip scanner 3000 (Affymetrix, Santa Clara, CA, USA).

CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing GCRMA (Wu et al., Journal of American Statistical Association, 99(468), 909-917, 2004). Scatter plots were performed using in-house developed functions in Matlab.

RNA was extracted from ESCs and sorted PGCLCs using the RNeasy Mini Kit (Qiagen, Hilden, Germany)

African-American (AA);Female;Systemic lupus erythematosus (SLE) patient;Peripheral blood;CD4-FITC;CD4 positive T cells

Colitis was induced with 3% DSS, 36,000-50,000 M.W. (MP Biomedicals, Lot No. 3865K) in the drinking water for 3 days.

All the mouse protocols were approved by the Animal Experimentation Committee of the University of Tokushima. The mice were housed in a room maintained at 22℃ (71.6 F), with a 12:12 h light-dark cycle starting from 8:00 AM under SPF conditions.

Slides were scanned immediately after washing and drying on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%, NoXDR setting).

The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014868_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

The colons of the untreated or DSS-treated mice were snap frozen in Liquid nitrogen, and total RNA was extracted using the conventional acid guanidinium thiocyanate phenol-chloroform (AGPC) procedure and cleaned up using the RNeasy MinElute Cleanup Kit according to manufactuer's instructions (QIAGEN Valencia, CA).

1.65ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent Fragmentation buffer and 2x Agilent Blocking Agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent GE Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17.5 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then air-dried immediately.

Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng RNA using the Low Input Quick Amp Labeling Kit (One-Color) (Agilent) according to the manufacturer's instructions, followed by RNeasy mini column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

Gene expression of mouse (WT) colon after 3days treatment of 3% DSS

When scaled to a target intensity of 100 (using Affymetrix MAS 5.0 array analysis software), scaling factors for all arrays were within acceptable limits (0.607-0.982), as were background, Q values and mean intensities.

Embryo dissections: All procedures involving animals have been approved previously by the Animal Care and Use Committee Tel Aviv University. ADNP heterozygous mice were housed in a 12-h light and 12-h dark cycle facility and free access to rodent chow and water was available. Mice were checked for plug every three hours. Plug day was assigned as day 0 (E0). A definitive determination of the developmental stage of each embryo at the time of harvesting was also based on anatomical analysis. E9 whole embryos were separated from the extra embryonic tissue (yolk sac and amnion), immersed in ice-cold magnesium- and calcium-free phosphate-buffered saline, snap-frozen in liquid nitrogen, and stored at -80°C until analysis. The extra embryonic tissue was stored separately and used for genotyping. Genotyping: Genomic DNA was extracted from embryonic yolk sacs. Lysis buffer (100 mM Tris HCl pH 8.5, 5mM EDTA, 0.2% SDS, 200 mM NaCl, proteinase K 0.35 mg/ml) was added to each sample (0.5ml) followed by a 16hr incubation period at 37°C with gentle shaking. Isopropanol (0.5 ml) was then added and samples were mixed. Precipitated DNA was then transferred to a new tube containing 1ml ethanol, subjected to centrifugation at 20,000g and the resulting DNA pellet was air-dried and dissolved in 50 microLl 10 mM Tris-HCl, pH 8, 1 mM EDTA (TE) buffer. The resulting DNA was then subjected to polymerase chain reaction (PCR) amplification to check for the existence of ADNP and/or neomycin resistance gene in the embryonic genome. The PCR mixtures contained 0.5μg genomic DNA, 0.25 μM of each primer (sense and antisense), 1.5 mM MgCl2 and 3 units Taq polymerase in a final volume of 50 μl. (Buffers and enzyme were obtained from Life Technology Gibco BRL, Paisley, Scotland). PCR was performed using the following cycle parameters: 94 °C for 4 min, followed by 30 cycles, each including 94 °C for 30 s, specific annealing temperature for 40 s and elongation at 72 °C for 40 s. Reactions were terminated at 72 °C for 10 min. Control reactions containing water instead of DNA template for each primer used (PCR-) were included. RNA extraction: Two embryos from the same genotype and gestational time were pooled and RNA was isolated using Qiagene RNeasy mini kit (Quiagene, Hilden, Germany). Because of the small amounts of RNA extracted from one embryo at age E9 (~1.5μg) a two embryo pool comprised of littermates possessing the same genotype was used. For comparative experiments all embryos were at approximately the same age. Gene array: All experiments were performed using Affymetrix MOE430A oligonucleotide arrays, as described at http://www.affymetrix.com/products/arrays/specific/mouse430a_2.affx. Total RNA from each sample was used to prepare biotinylated target RNA, with minor modifications from the manufacturer's recommendations (http://www.affymetrix.com/support/technical/manual/expression_manual.affx). Briefly, 3-5 µg of mRNA was used to generate first-strand cDNA by using a T7-linked oligo(dT) primer. After second-strand synthesis, in vitro transcription was performed with biotinylated UTP and CTP (Enzo Diagnostics), resulting in approximately 100-fold amplification of RNA. A complete description of procedures is available at: http://bioinf.picr.man.ac.uk/mbcf/downloads/GeneChip_Target_Prep_Protocol_CRUK_v_2.pdf. The target cDNA generated from each sample was processed according to manufacturer's recommendation using an Affymetrix GeneChip Instrument System (http://www.affymetrix.com/support/technical/manual/expression_manual.affx). Briefly, spike controls were added to 10 µg fragmented cDNA before overnight hybridization. Arrays were then washed and stained with streptavidin-phycoerythrin, before being scanned on an Affymetrix Gene Chip scanner. A complete description of these procedures is available at http://bioinf.picr.man.ac.uk/mbcf/downloads/GeneChip_Hyb_Wash_Scan_Protocol_v_2_web.pdf Additionally, quality and amount of starting RNA was confirmed using an agarose gel. After scanning, array images were assessed by eye to confirm scanner alignment and the absence of significant bubbles or scratches on the chip surface. 3'/5' ratios for GAPDH and beta-actin were confirmed to be within acceptable limits (0.8-0.88), and BioB spike controls were found to be present on all the arrays, with BioC, BioD and CreX also present in increasing intensity.

C57BL/6, Genotype: ADNP gene knockout Gender: mixed Age:E9 Tissue: whole embryonic body;Activity-dependent neuroprotective protein: a novel gene essential for brain formation.;83-90.;12888219 [PubMed - indexed for MEDLINE]

MDA-MB-231 cells were transfected with siRNA of either  MTDH-WT or MTDH-isoform (200 pmols) for 24 h.

MDA-MB-231 cells were grown in DMEM  supplemented with 10 % Foetal Bovine Serum, 2mM glutamine and Pen-Strep

Probe level data were quantile normalized using 'normalize.quantiles' function available in preprocessCore package (v. 1.26.1) of R (v. 3.1.0) and log2 transformed.

MDA-MB-231;Breast adenocarcinoma, estrogen receptor-negative;Control

JoMa1 cells were grown as described (Maurer et al. Differentiation, 2007 (PMID 17381545)).

Scanning of chips was performed using a GeneArray scanner (Agilent).

Cells were harvested when they reached 80% confluency, and lysed using Trizol. RNA was purified using the QIAGEN RNeasy Mini Kit.

Hybridization to Mouse 430 2.0 arrays was performed according to the manufacturer's recommendations (Affymetrix).

Biotin labelling was performed according to the manufacturer's recommendations (Affymetrix).

JoMa1 cells transfected with MYCN (JoMa1-MYCN) are tumorigenic in immunocompromised mice. Expression profiles of four independent tumors induced by JoMa1-MYCN were obtained.

Primary splenocytes were harvested by digestion with Collagenase B and DNAse1

Data were processed using RMA Quantile Normalization with DNASTAR Arraystar software.

RNA was prepared using the RNAqueous-Micro kit (Invitrogen).
WT and Notch2f/f CD11c-cre DC Sorts: WT and Notch2 KO Splenic CD11b+ DCs were sorted as MHCII+ CD11c+ CD11b+ CD24-, WT and Notch2 KO Splenic DEC205+ DCs were sorted to as MHCII+ CD11c+ CD11b- CD24+ DEC205+

Ambion WT Expression kit, Genechip WT Terminal Labeling and Controls Kit

Cells expressing IkBa dominant negative cultured in absence of dox, TNF stimulation for 6 h

Cells expressing IkBa dominant negative cultured in absence of dox, TNF stimulation for 3 h

Cells expressing IkBa dominant negative cultured in absence of dox, TNF stimulation for 1 h

The animals were sacrificed 48 hours after treatment and organs were frozen for later analysis. Tissue samples of the left lateral lobe of the liver were snap frozen in liquid nitrogen, transferred to dry ice and stored at approximately -80?C

treated with Roziglitazone, 1000 mg/kg in Methylcellulose soln per orally, extracted 48h after treatment, biol. rep4

The data were analyzed with RMA. R was used with the affy package. Expresso with the following settings (bgcorrect.method=rma, normalize.method = quantiles.robust, pmcorrect.method=pmonly, summary.method=liwong) was used to normalize

Frozen liver samples were homogenized in 2 ml TRIzol® reagent (Invitrogen ; Life Technologies, Scotland)  using an Ultra Turrax T25 basic homogenizer (IKA Labortechnik; IKA-Werke, Staufen, Germany). Chloroform (400 ?l) was added and homogenized samples were shaken vigorously by hand for 15 seconds. Phase separation was achieved by centrifugation for 15 min at 10,000 × g at 4°C. Total RNA from the aqueous phase was purified using the RNeasy 96 Qiagen vacuum system following the “Clean-up” procedure.

Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Rat 230 version 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Gene expression data from rat liver 48 hours after treatment with compound.

treated with Roziglitazone, 1000 mg/kg in Methylcellulose soln per orally, extracted 48h after treatment, biol. rep3

treated with Roziglitazone, 1000 mg/kg in Methylcellulose soln per orally, extracted 48h after treatment, biol. rep2

treated with Roziglitazone, 1000 mg/kg in Methylcellulose soln per orally, extracted 48h after treatment, biol. rep1

Rat liver, treated with NMF, 1000 mg/kg in saline i.p., extrated 48 hours after treatment, biological rep5

Rat liver, treated with NMF, 1000 mg/kg in saline i.p., extrated 48 hours after treatment, biological rep4

Rat liver, treated with NMF, 1000 mg/kg in saline i.p., extrated 48 hours after treatment, biological rep3

Rat liver, treated with NMF, 1000 mg/kg in saline i.p., extrated 48 hours after treatment, biological rep2

Mice were anesthetized with pentobarbiturate (Dolethal, Vetoquinol, Spain) and transcardially perfused with 4% paraformaldehyde in 0.1 M phosphate-buffered saline (PBS), pH7.5. The inner ear was dissected out.

Igf1+/+ and Igf1-/- mice were studied at different time points (E18.5, P15 and P90) to follow their progression from embryonic stage to adult mice.

The data were analyzed with mmBGX (Turro et al, 2010) to quantify false positives and uncertainty of the measurements. mmBGX is a full hierarchical Bayesian method, where alternative matching of the probes are also considered and estimated of alternative splicing expression are provided. Gene expression estimated with mmBGX are posterior summaries for transcript that is associated with a measure of uncertainty (PROB) used to detect diﬀerential expression. The three biological replicates where combined into one summarised value using a hierarchical bayesian model.

Affymetrix GeneChip Mouse Gene 1.0 ST arrays were hybridized to 11 mg of labeled, amplified cDNA, washed, stained and scanned according to the protocol described in WT Sense Target Labeling Assay Manual

100ng of total RNA were amplified and labeled using the Whole Transcript (WT) Sense Target Labeling Protocol

transcripts expression data from Igf1 -/- mouse vestibular organ at P15

transcripts expression data from Igf1 +/+ mouse vestibular organ at E18.5

vestibular organ;hybrid Mf1 with 129/sv background;E18.5;Igf1 +/+

Rat liver, untreated (control), extrated 48 hours after treatment (no treatment in this case), biological rep1

treated with Roziglitazone, 1000 mg/kg in Methylcellulose soln per orally, extracted 48h after treatment, biol. rep5

SNI surgery was performed where the tibial and common peroneal branches of the sciatic nerve were tightly ligated with a silk suture and transected distally, while the sural nerve was left intact (Decosterd and Woolf, 2000). In sham-operated controls, the sciatic nerve was exposed but not ligated. Operation performed under isofluorane.

Standard laboratory rodent housing, with free access to water and food and were exposed to a 12:12 hour on/off light cycle. Pups left with mothers following surgery.

The Bioconductor affy library was used to import CEL file data and the gcrma library was used to normalize the raw data.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

Sprague-Dawley;spinal cord (ipsilateral dorsal horn);Adult (8-12wks);7 day post sciatic nerve SNI injury

Sprague-Dawley;spinal cord (ipsilateral dorsal horn);Adult (8-12wks);sham

A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factors can be identified. This entry corresponds to the RNA isolated from uninduced INS-1 cell line #3b containing MODY5 mutant A263insGG of hepatocyte nuclear factor-1b (HNF1b).
Keywords = A263insGG
Keywords = MODY5

Approximately 1x10^6 cells were infected with adenovirus expressing v-Myb and GFP for 16 hours, then total RNA was isolated using RNEasy kit (Qiagen).

Mice were anesthetized with CO2 and sacrificed by decapitation. The dissected cerebella were homogenized using Lysing Matrix D tubes and FastPrep® FP120 Instrument with Proteinase K digestion (20 mg/ml, >30U/mg) according to the manufacturer’s instructions.

Cstb-/- and wild type mice were grown under standard conditions in animal facilities. Cerebella from P5 pups were dissected and meninges removed in HHGN (1x HBSS, 2.5 mM HEPES, 35 mM glucose, 4 mM NaCO3). Intact cerebella were trypsinated in 10 mg/ml trypsin, 200 U/ml DNase in HHGN for 20 min at RT and triturated in 200 U/ml DNase in BME (Basal Medium Eagle). Cells were cultured in BME, 10% calf serum, 25 mM HCl. After 16-20 h from plating, 10 μM AraC (cytosine 1-β-d-arabinofuranoside) was added to prevent glial proliferation. Cells were harvested at DIV2.

The quality control of each microarray was inspected using the Affymetrix GeneChip® Operating Software (GCOS) v1.4.

The raw data were imported to GeneSpring GX software and expression signal values were generated using the RMA (Robust Multiarray Average) algorithm (Irizarry et al., 2003) for background adjustment, quantile-normalization and summarization. Filtering of the probe sets was based on the expression with lower and upper cutoff 20 and 100 percentile, and on the fold-change (FC) with cutoff 1.3. In overall statistics of differentially expressed genes, t-test unpaired equal variance with corrected p-value ≤ 0.05 (cerebella) and p-value ≤ 0.01 (CGCs), with Benjamini and Hochberg multiple testing correction was used.

Total RNA was extracted using the ABI Prism 6100 Nucleic Acid PrepStation and PerfectPure RNA Cultured Cell kit according to the manufacturer’s instructions from cerebella and CGCs, respectively.

The sample preparation and hybridzation of each cRNAs on Affymetrix GeneChip® Mouse Genome 430 2.0 arrays based on manufacturer's instruction.

CGC_WT4.CEL
Gene expression data from wild type mouse cerebellar granule cells.

CGC_WT5.CEL

CGC_KO2.CEL
Gene expression data from pre-symptomatic Cstb-/- mouse cerebellar granule cells.

129SvJ;cystatin B (CSTB)-deficient (Cstb-/-);female;P5+2 DIV;cerebellar granule cells

A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and induced cells, target genes of introduced transcription factor can be identified. This entry corresponds to the RNA isolated from tet-induced INS-1 cell line #2 containing hepatocyte nuclear factor-6 (HNF6; onecut1).
Keywords = HNF6
Keywords = onecut1

P30 WT3.CEL
Gene expression data from wild type mouse cerebellum.

CGC_KO1.CEL

129SvJ;cystatin B (CSTB)-deficient (Cstb-/-);male;P5+2 DIV;cerebellar granule cells

P30 WT1.CEL

P30 WT2.CEL

P30 KO2.CEL
Gene expression data from symptomatic Cstb-/- mouse cerebellum.

129SvJ;cystatin B (CSTB)-deficient (Cstb-/-);male;postnatal day 30 (P30);cerebellum

P30 KO3.CEL

Hybridization intensities were quantified and normalized across all arrays using the RMA algorithm with GC adjust available as an array processing tool on Partek® Genomics Suite™ 6.5 software (St. Louis, MS).

A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

Affymetrix Power Tools were used to process and quantile normalize fluorescent hybridization signals using Robust Multichip Averaging. Transcript values were log2 normalized.

cDNA was amplified with NuGen WT Ovation Pico kit and hybridized to Affymetrix GeneChip Mouse Gene 1.0 ST microarrays at the University of Pennsylvania’s Microarray facility.

Microarrays were washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain

We used the RMA normalization protocol as implemented by the following website:  http://www.webarraydb.org/webarray/index.html

Embryo was harvested at the designated time point.  Total RNA was extracted with the Qiagen RNeasy Plus Mini Kit according to manufacturer's protocol from the secondary palate.

strain: C57B6
genotype: Tgfbr2fl/fl;Wnt1-Cre
tissue: Secondary palate
age: E14.5
gender: Not determined

C57B6;Tgfbr2fl/fl;Wnt1-Cre;Secondary palate;E14.5;Not determined

Primary erythroid cells were infected with lentiviruses harboring short hairpin RNAs (shRNAs) targeting individual HDAC transcripts.

Cryopreserved human bone marrow CD34+ cells were obtained from Cambrex (Poietics, Cambrex).  Umbilical cord blood was harvested at Brigham and Women’s Hospital under an IRB approved protocol.  Mononuclear cells were purified by Ficoll Hypaque sedimentation, and CD34+ cells were selected using magnetic beads coupled to a CD34 monoclonal antibody (Miltenyi Biotec).  Erythroid differentiation was induced in vitro in two steps.(1)  For the first seven days, cells were cultured in Serum Free Expansion Medium (SFEM, Stem Cell Technologies) supplemented with 100 U/mL penicillin/streptomycin, 2 mM glutamine, 100 ng/mL stem cell factor (SCF), 10 ng/mL interleukin-3 (IL-3),  40 ug/mL lipids, and 0.5 IU/mL erythropoietin (Epo).  After 7 days, cells were cultured in the same medium supplemented with 3 IU/mL Epo.

Raw expression values were normalized using Robust Multiarray Averaging (RMA).

RNA was purified from mononuclear cells using Trizol (Invitrogen). Linear amplification of 20 ng of total RNA was performed using the Ovation Biotin RNA Amplification and Labeling System (Nugen).

Primary human erythroid progenitor cells expressing HDAC2 B10 shRNA biological replicate 1

Primary human erythroid progenitor cells expressing HDAC2 B10 shRNA

Primary human erythroid progenitor cells expressing HDAC1 G10 shRNA biological replicate 3

Primary human erythroid progenitor cells expressing HDAC1 G10 shRNA

Primary human erythroid progenitor cells expressing HDAC1 G10 shRNA biological replicate 2

Primary human erythroid progenitor cells expressing HDAC1 G10 shRNA biological replicate 1

Primary human erythroid progenitor cells expressing HDAC1 A3 shRNA biological replicate 3

Primary human erythroid progenitor cells expressing HDAC1 A3 shRNA

Primary human erythroid progenitor cells expressing HDAC1 A3 shRNA biological replicate 1

Primary human erythroid progenitor cells expressing a luciferase control shRNA biological replicate 3

Luciferase Control shRNA;Primary human erythroid progenitor cells

Primary human erythroid progenitor cells expressing a luciferase control shRNA

Primary human erythroid progenitor cells expressing a luciferase control shRNA biological replicate 2

Primary human erythroid progenitor cells expressing HDAC2 B10 shRNA biological replicate 3

Primary human erythroid progenitor cells expressing HDAC2 B10 shRNA biological replicate 2

Probe arrays were scanned using Affymetrix GeneChip Scanner 3000

Biotin-modified mRNA labeling were carried out using Affymetrix manufacturer’s protocol

54;Carcinoma of breast, squamous cell;G3;IIB;T2;N1a;NA;NA;85;0;0

MCF-7 cells expressing endogenous ERalpha were plated in 100mm dish in 5% CD-stripped calf serum.  Cells were infected with adenovirus carrying either estrogen receptor beta (AdERb) or no insert (Ad) at multiplicity of infection (moi) of 5 or 50.  Cells were infected with adenovirus for a period of 48hr before treatment with ligand (vehicle control (veh), 10nM 17beta-estradiol (E2), or 10nM trans-hydroxytamoxifen (TOT)) for a additional period of 24hr before harvest.  Total RNA was extracted using 1mL of TRIzol (Invitrogen) per 100mm dish.

Approximately 8 micrograms of total RNA was processed to produce biotinylated cRNA targets.

The data were acquired with GCOS instrument and processed using RMA normalization method.

Following fragmentation, cRNA was hybridized on Affymetrix Mouse430_2.na21 platform. GeneChips were washed and stained in the Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, Affymetrix).

GNMT_3ko1
Gene expression data from GNMT knockout at 3 month, when the tissue has been histopathologically determined to be non-alcoholic steatohepatitis.

C57B6SJL;GNMT knockout;3 months;liver;non-alcoholic steatohepatitis

Mouse liver, GNMT knockout, non-alcoholic steatohepatitis, 3 months

GNMT_3ko2

GNMT_3WT4
Gene expression data from the wild type used for GNMT knockout at 3 month.

GNMT_3WT5

GNMT_3ko5

GNMT_8WT1
Gene expression data from the wild type used for GNMT knockout at 8 month.

GNMT_3ko3

GNMT_3ko4

GNMT_8WT2

GNMT_8WT3

Standard Illumina scanning protocol, with Illumina iScan System.

The data were normalised using quantile normalisation with BeadStudio 3.0

RNA was extracted with Ambion mirVana, in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

GeneChips were scanned using an Affymetrix GeneChip scanner 3000.

The resulting image data was captured and converted to digital output using GeneChip Operating Software v.1.4.0.036. The absolute results (*.chp) from the different experiments (probe arrays of the same type) that were scaled to the same target signal using the All Probe Sets scaling option (scaling factor, 500) may be directly compared (Parameter: Alpha1=0.05, Alpha2=0.065, Tau=0.015). Gene expression was quantified by robust multi-array analysis (RMA) using the Genomic Suite software from Partek.

Super RNApure (Geneisis Biotech Inc, Taiwan) was used to extract total RNA from the frozen liver samples.

Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

The data were analyzed with RMA (log2) normalized data using the just.rma function in the affy package in Biocinductor

Gene expression data of gastrocnemius muscle mRNA from young (10 week old) wild-type mice

Gastrocnemius muscle mRNA from young (10 week old) wild-type mice

HIV-1 positive male, 18-60 years old, weight loss of 5-15% in preceding 6 months, stable anti-retroviral therapy. CD4+ T-cells >50/ml, HIV copies =< 10,000/ml, free testosterone <50pg/ml.

NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 1 h. U0126 (20 uM) was added 30 min before stimulation.

Cells were cultured overnight in DMEM 10% FBS (pen/strep).  Media was changed with cells receiving either control media, 1 micromolar rosiglitazone, 10 micromolar carboplatin or combination of carboplatin and rosiglitazone.

Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

Samples were scraped into trizol and transfered to phaselock tubes.  RNA was extracted according to manufactures directions.

The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The cRNA is purified from the fragmentation reaction using phenol/chloroform extraction and ethanol precipitation.
The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C.
The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out.
The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.
The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen).

Trasnsformed Lymphocytes Bipolar Disorder Affected Twin Pair 1 (DCBD1.1)(TP5)

Expression profiles were generated by hybridizing 5 µg of total RNA to Affymetrix Human Genome U133 plus 2.0 Gene Chips (HG U133plus 2.0) according to the Affymetrix Eukaryote One-cycle protocol. Briefly, 5 µg of total RNA were used to generate biotinylated cRNA, which was fragmented and hybridized to a chip for 16 hours at 45ºC in an Affymetrix Hybridization Oven 640. Arrays were then washed and stained on an Affymetrix Fluidics Station 450 and subsequently scanned on an Affymetrix GeneChip Scanner 3000 to obtain fluorescence intensities.

Relative expression values were generated for each transcript using the Affymetrix MAS5.0 algorithm in GeneChip® Operating Software (GCOS) Version 1.2, with the average intensity of all transcripts on each array scaled to 150 so that the same target signal across all arrays could be compared

LCLs were established by Epstein-Barr virus (EBV) transformation of lymphocytes (as described Neitzel H. A routine method for the establishment of permanent growing lymphoblastoid cell lines. Hum Genet. 1986; 73(4):320-6) To limit any cell culture effects on gene transcription levels cell lines were all grown under tightly controlled growth conditions in the same batch of RPMI 1640 medium with 10% foetal bovine serum (FBS) and antibiotics prior to RNA extraction. When cells were in log phase growth they were pelleted and washed with phosphate-buffered saline (PBS) and total RNA was extracted using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value. All samples had an RIN of 9.9 or 10, which designates very high quality RNA according to the grading (on an ascending quality scale of 1-10) of Agilent 2100 RIN Software

TP5;DCBD1.1;BD1 with psychotic features;19;55;58;Female;lithium & citalopram (22.5 years)

Trasnsformed Lymphocytes Bipolar Disorder Affected (Affected pateint of MZ twin pair 1)

During section, the distal colon was rinsed with 70% ethanol at 4°C, subsequently scraped with sterilized glass slides and fixed in RNAlater® (Ambion®, Cambridgeshire, U.K.) according to the manufacturer’s protocol.

Rats were fed either 10 g quercetin/kg diet or the control diet(RM3 [E] FG SQC rat breeder diet obtained from SDS Special Diets Services, Witham, England) for 11 weeks.

Affymetrix® GeneChip® arrays were scanned with the GeneChip® Scanner 3000 7G (Affymetrix® Inc., Santa Clara, California, U.S.A.).

Data were processed with MAS 5.0 and a scaling factor of 200 was applied.

RNA extraction was performed with the TRIzol Reagent (Life Technologies, Paisley, U.K.), as described by the manufacturer.
Total RNA was purified with the NucleoSpin® RNA II kit (Machery-Nagel, Düren, Germany), including a DNAse incubation step to digest possible traces of DNA. Subsequent analysis on the Agilent 2100 bioanalyser (Agilent Technologies, Palo Alto, California, U.S.A.) indicated high quality total RNA (28S/18S ribosomal RNA ratios ~2.0) that was suitable for hybridization

Hybridisation on Affymetrix® GeneChip® arrays was processed according to the GeneChip® One-Cycle Eukaryotic Target Labeling Assay.

For RNA labeling, GeneChip® One-Cycle Eukaryotic Target Labeling Assay for expression analysis was performed, as described in the Affymetrix® GeneChip® Expression Analysis Technical Manual

Trasnsformed Lymphocytes Bipolar Disorder Affected Twin Pair 2 (DCBD2.1)(TP7)

DCBD2.1;TP7;BD1 with psychotic features;19;20;24;Male;lithium & olanzapine (64 weeks)

Trasnsformed Lymphocytes Bipolar Disorder Affected (Affected pateint of MZ twin pair 2)

MI operated rat 1 day post-operation
Heart left ventricle and septum excluding infarct zone
Keywords = MI
Keywords = 1 day

Eye dissociation was preformed with 25 units/ml papain for 30 minutes followed by mechanical dissociation. Dissociated cells were resuspended in HBSS.

alpha-Cre or Pax6 flox alpha-Cre female ICR mice were time mated with wildtype or Pax6 flox ICR males respectively. 12 days after vaginal plug detection pregnant dames were euthanized and embryos dissected out. Eye were taken out and dissociated.

according to the instruction manual, as described in the Affymetrix website

RMA normalization, summarization by mean (using Affymetrix expression console)

Essentially, the cells were cultured for 4-6 weeks in media containing mouse recombinant IL-3 (30 ng/ml) (Peprotech, Rocky Hill, NJ) and mouse recombinant SCF (unless otherwise indicated: 100 ng/ml) (Peprotech). The cells were maintained at 37 ˚C in a humidified incubator gassed with 95% air and 5% CO2. The purity of the cultures, as assessed by toluidine blue staining and FceRIa and KIT expression, was >99%.

Bone marrow-derived mast cells (BMMCs) were developed from bone marrow obtained from the femurs of C57BL/6 mice (The Jackson Laboratory, Bar Harbor, ME) as described (Kuehn, H. S., M. A. Beaven, H. T. Ma, M. S. Kim, D. D. Metcalfe, and A. M. Gilfillan. 2008. Synergistic activation of phospholipases Cγ and Cβ: a novel mechanism for PI3K-independent enhancement of FcεRI-induced mast cell mediator release. Cell Signal 20:625-636 (PMID 18207701)).

Mouse bone marrow-derived mast cells treated with IL3+SCF, rep 4

GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus according to standard Affymetrix protocols.

The data were analyzed with GCOS 1.4 and EC 1.1 using Affymetrix default settings except the trimmed mean target intensity of each array was arbitrarily set to 1250.

RNAs were extracted using an RNeasy 96 kit (Qiagen, Valencia, CA) with each sample treated with 27 units DNase I during the extraction process.

Hybridization and fluidics were performed according to standard Affymetrix protocols (http://www.affymetrix.com).

Affymetrix GeneChip targets were made by amplification of 50 ng RNA using the WT-Ovation RNA Amplification System (Nugen Inc., San Carlos, CA).

Gene expression data from mouse bone marrow-derived mast cells treated with IL3+SCF, rep 4 of 6.

C57BL/6;bone marrow-derived mast cells;interleukin 3 and stem cell factor

Mouse bone marrow-derived mast cells treated with IL3+SCF, rep 5

Gene expression data from mouse bone marrow-derived mast cells treated with IL3+SCF, rep 5 of 6.

Data extraction was processed by Affy GeneChip® Operating Software v1.3 (Affymetrix).  Global scaling was equal to 500.  Normalization factor was equal to 1.  Analysis of differentially expressed transcripts was accomplished using a pairwise comparative analysis (Affy Data Mining Tool v3.1; Affymetrix).  3 sets CKO V x 3 sets CKOWT V comparison (1.5 fold cutoff (FC), Signal strength values were log-transformed to generate a normal distribution followed by independent two sample t-test < 0.05, 6 out of 9 comparisons). Also, ABS |FC - FC SEM| >= 1.5

Versagene RNA tissue kit was used for extraction of total RNA according to the manufacturer's instructions.

Following fragmentation, 1 200 ul of hybridization cocktail containing 7 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip Fluidics Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manul- Affymetrix)

cDNA step using Invitrogen SuperScript Double-stranded cDNA Synthesis Kit cDNA cleanup by Affymetrix GeneChip Sample Cleanup Module, cRNA amplification by Ambion MEGAscript T7 Kit, Cleanup by Qiagen RNeasy Mini Kit. cDNA synthesis by Invitrogen SuperScript Double-stranded cDNA Synthesis Kit using a T7-Oligo(dT) promoter primer from Affymetrix, cRNA amplification using ENZO BioArray HighYield RNA Transcript Labeling Kit, Metal-induced hydrolysis by Affymetrix 5 X Fragmentation Buffer, External controls (spikes)- Control Oligo B2 (3 nM), Eukaryotic Hybridization control (Affymetrix) (Small Sample Labeling Protocol vII, Affymetrix).

Keap1(flox/-), gender- male, age- 9 weeks, n = 1, # of tissue = 1 tissue: Liver

PRKO and wild-type mice were ovariectomized at 6 wk of age. Two weeks later, ovariectomized mice were injected with either vehicle (sesame oil) or P4 (in sesame oil; Sigma-Aldrich Corp., St. Louis, MO; 1 mg/mouse in 100 μl). The injections were repeated every 12 h, and groups of mice were killed 4 h after the first injection (acute P4 treatment) or 4 h after the fourth injection (chronic P4 treatment). The mice were killed by cervical dislocation after placing them under anesthesia (Avertin, 2,2-tribromoethyl alcohol, Sigma-Aldrich Corp.). Uterine tissues were flash-frozen at the time of dissection and stored at −80 C.

Mice were maintained at the designated animal care facility at Baylor College of Medicine according to the institutional guidelines for the care and use of laboratory animals.

The microarrays were stained in an Affymetrix Fluidics station with streptavidin-phycoerythrin conjugates, followed by staining with an antistreptavidin antibody and streptavidin-phycoerythrin. The arrays were scanned at 3 μm with a GeneArray scanner (Affymetrix).

DNA-Chip Analyzer dChip (version 1.3) was used to adjust arrays to a common baseline using invariant set normalization and to estimate expression using the PM-only model. All 24 Genechips were normalized to the uterus_P4_WT_40hrs_rep1 sample and all were modeled together. Data quality was reviewed using present call rates from MAS5 (average, 54%; range, 50–58%), ratios of 3′ to 5′ glyceraldehyde 3-phosphate dehydrogenase probe sets from MAS5 (average, 0.94; range, 0.8 to 1.5), and array outlier rates (average, 0.43%; range, 0.024–2.7%; only two of 24 chips >1%) from dChip.

Total RNA was extracted from uterine tissues using the RNeasy total RNA isolation kit (Qiagen, Valencia, CA). RNA was pooled from the uteri of five mice per genotype and treatment. All RNA samples were analyzed with a Bioanalyser 2100 (Agilent Technologies, Palo Alto, CA) before microarray hybridization.

The fragmented, labeled cRNA (15 μg) was hybridized to murine genome U74Av2 mouse oligonucleotide arrays (Affymetrix, Santa Clara, CA).

RT by oligo(deoxythymidine), followed by in vitro transcription and biotin labeling of cRNA, were performed (Enzo Biochem, Farmingdale, NY).

Uterus isolated from wild-type ovariectomized mice treated with vehicle for 4h.

The arrays were processed on a GeneChip Fluidics Station 450 and scanned on an Affymetrix GeneChip Scanner (Santa Clara, CA).

The expression signals were normalized by using the R-Affy package from Bioconductor version 1.1 to remove background noise and non-biological variations among arrays. The background noise was removed from the PM probe intensities using the "RMA" method. Normalization was performed using the quantile normalization method (Bolstad et al., 2003).  To remove outlier probes and summarize probe intensities within one probe set into a single expression value, the "Tukey Biweight" method was applied to the background adjusted, normalized PM intensities. Expression values were obtained based on PM intensities and not PM-MM intensities, because PM and MM intensities were found to be highly correlated, which suggested that MM intensities were composed of background noise as well as probe-specific signals. Significant gene expression alterations were identified using the computer software Significance Analysis of Microarrays (Tusher et al., 2001).

Total RNA was isolated from skin samples and DNase treated using the RNeasy Fibrous Tissue Kit (Qiagen Inc., Valencia, CA). RNA was ethanol precipitated and quantified using a spectrophotometer. Approximately 2 mug of total RNA from each sample was used to generate double-stranded cDNA using a T7-oligo (dT) primer.

Biotinylated cRNA, produced through in vitro transcription, was fragmented and hybridized to an Affymetrix human U133A 2.0 microarray.

The inclusion criteria for the acne lesion group included (a) men and women aged 18-45 years with inflammatory acne on their back, (b) subjects without other skin disease in the biopsy area, (c) subjects who were willing to have skin biopsies performed from their back, and (d) subjects who have not been treated with isotretinoin for acne within the previous 6 months.

Uterus isolated from PRKO ovariectomized mice treated with vehicle for 4h.

Uterus isolated from wild-type ovariectomized mice treated with progesterone for 4h.

Uterus isolated from PRKO ovariectomized mice treated with progesterone for 4h.

The cells were similarly seeded at a concentration of 500,000 cells in 10ml of culture medium in 10-cm tissue culture plate and incubated at 37oC in a 5.0% CO2 incubator for 24 hours.

300ng of total RNA were used for the experiments and the arrays were washed and stained using the FS450_0007 fluidics protocol and scanned using an Affymetrix 3000 7G scanner. The scanned images were inspected for hybridization efficiency and CEL files generated from GCOS (GeneChip Operating Software) were imported into Expression Console (EC) 1.1 software for array QC.

The data was processed using Bioconductor packages in the R statistical software.  RMA normalization was applied and p-values were generated by comparing against the detection above background probes. Probe sets with DABG p-value >0.01 in all samples was removed.

Total RNA from the various U-87MG parkin expressing and vector control cells were extracted using the RNeasy Mini Kit (Qiagen, USA). The concentration and quality of the total RNA extracted was assessed by the NanoDrop ND-1000 machine (Thermo Scientific, USA) and the Bioanalyzer (Agilent, USA).

The targets were hybridized to the GeneChip® Human Gene 1.0 ST Array according to the manufacturer hybridization protocol which constituted 28,000 gene-level probe sets.

After the quality of the RNA was ascertained, the GeneChip® WT cDNA Synthesis and Amplification Kit (Affymetrix, USA) was used to generate the first and second cycle cDNA synthesis and the cRNA synthesis through in vitro transcription amplification. After the second cycle cDNA synthesis and cRNA hydrolysis step, the GeneChip® WT Terminal Labeling Kit was used for the fragmentation and terminal labeling of the cDNA to generate targets compatible with the GeneChip arrays.

Resistant lines were grown in PLX4720-free media x 24 hours prior to harvesting

The data were first quantified using the MAS5 algorithm. The Robust Multiarray Analysis (RMA) algorithm was used to normalize and quantify the data.

Total RNA was extracted cell lines using the Qiagen RNeasy Kit according to the manufacturer's protocol.

hybridization to Affymetrix HGU133 plus2 according to the standard Affymetrix protocol

AFGE1068-2.CEL
Gene expression data from parkin-expressing U-87MG

normal section from mouse liver was dissected from Txnip deficient mice at 27 months of age.  RNA was extracted using TRIzol. Targets were produced using standard Affymetrix procedures.
This sample is also known as 4TC_signal.

This sample is also known as 4TB_signal.

This sample is also known as 4TA_signal.

Commercial Affymetrix Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). GeneChip CEL files were subjected to RMA  normalization using  the  GeneSpring GX 7.1.
Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
GeneSpring 7.3 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. All the samples were then normalized to the median of the controls.

Total RNA was extracted from whole blood using the PaxGene system.
Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto,CA].

Create a hybridization cocktail for a single probe array that contains 0.05 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 99°C for 5 minutes, to 45°C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45°C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization Oven rotating at 60 rpm.
Fluidics:  Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol EukGE-WS2v5_450. Arrays were stained with phycoerythrin-conjugated streptavidin [Molecular Probes, Eugene, OR] and hybridization signals were amplified using antibody amplification with goat IgG [Sigma-Aldrich] and anti-streptavidin biotinylated antibody [Vector Laboratories, Burlingame, CA], as described in the Affymetrix GeneChip® Expression Analysis Manual.

120 ng of total RNA from 2 wild type [WT] and 4 beta-catenin knock-out [KO] pancreata at the 14.5 and 16.5 time points was amplified twice with the Arcturus RiboAmp kit [Arcturus Bioscience, Inc., Mountain View, CA] and cRNA was labeled with biotin-UTP, CTP using T7 RNA polymerase [Enzo Life Sciences, Inc., Farmingdale, NY].

phosgene exposed mouse lung
CG
32 mg
48
chip replicate B
Keywords = phosgene, lung, toxic industrial chemical, TIC

CG
32 mg
48
chip replicate A

CG
32 mg
24

CG
32 mg
24

Upon harvest, cells without cisplatin treatment (controls) were washed with PBS and then scraped from plates in the Trizol solution (GibcoBRL).

MEFs were cultured in DMEM (high glucose, Invitrogen) with 10% FCS (Invitrogen) and passaged upon confluency at the ratio 1:3.  Cells were kept in culture before reaching passage 5.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Gene expression data from Rb null MEFs without cisplatin treatment.

Rb null MEFs;Primary mouse embryonic fibroblasts (MEFs) generated from embryos at E13.5

Gene expression data from wildtype MEFs without cisplatin treatment.

wildtype MEFs;Primary mouse embryonic fibroblasts (MEFs) generated from embryos at E13.5

Cells were treated with 16 microM cisplatin for 24 hrs prior to harvest. Upon harvest, cells were washed with PBS and then scraped from plates in the Trizol solution (GibcoBRL).

Gene expression data from Rb null MEFs with cisplatin treatment (16microM, 24hrs).

The initial analysis of generated affymetrix data was performed with their MAS 5.0 software.The chip data were scaled to 500,then exported as text files to be loaded into the Genespring 6.0 program (Silicon Genetics,Redwood City,CA).The prescaled data were normalized by using the normalization steps”per chip to 50th percentile” and “per gene to median” as recommended by the manufacturer.

Oral Squamous cell Epithelium Tissue-Tumor;OSCC-17;Tongue;47;M;T4N3M0;TNM,Tumor-node-metastasis

Oral Squamous cell Epithelium Tissue-Tumor;OSCC-18;Floor of Mouth;52;M;T4N2M0;TNM,Tumor-node-metastasis

Gene expression data from wildtype MEFs with cisplatin treatment (16microM, 24hrs).

Oral Squamous cell Epithelium Tissue-Tumor;OSCC-13;Floor of Mouth;54;M;TNM,Tumor-node-metastasis

Oral Squamous cell Epithelium Tissue-Tumor;OSCC-14;Floor of Mouth;60;F;T4N2bM0;TNM,Tumor-node-metastasis

Oral Squamous cell Epithelium Tissue-Tumor;OSCC-15;Floor of Mouth;51;M;T2N0M0;TNM,Tumor-node-metastasis

Oral Squamous cell Epithelium Tissue-Tumor;OSCC-16;Mandible;50;F;T4N0M0;TNM,Tumor-node-metastasis

Treated twice daily for 3 weeks on 1 upper limb with 1% pimecrolimus cream and on the other upper limb with 0.1% betamethasone valerate cream in a double blind manner.

Following fragmentation, approximately 10 ug of cRNA were hybridized for 17 hr at 45C on Gene Chip HG U133 plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Gene expression data from human skin biopsy sample from atopic dermatitis patient treated with pimecrolimus
13_PC

Gene expression data from human skin biopsy sample from atopic dermatitis patient
13_Bsl

14_Bsl

Gene expression data from human skin biopsy sample from atopic dermatitis patient treated with betamethasone valerate
14_BM

12_Bsl

12_BM

13_BM

12_PC

15_BM

14_PC

HEK293-cells transiently transfected with EWS-FLI1 type I, 48h post transfection, first of two independent transfections

HEK293-cells transfected with EWS-FLI1 type I, G418 selected, clone F

B cells from 12-week old irf4-/- and irf4+/+ littermate mice were isolated by magnetic depletion of non-B cells from splenic mononuclear cells.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on  U133_Plus2 Gene Expression Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Normal testicular parenchyma from a 29 years old organ donor with no known history of cancer
Keywords = testis
Keywords = normal
Keywords = testicular neoplasm
Keywords = human

wild type HEK293-cells, second of two independent RNA isolations

Laser Capture Microdissection (LCM) to isolate tissue sections of the hippocampus area of Rasgrf1 knockout mice brains

RNA was extracted and prepared with MirVana miRNA Isolation Kit (Invitrogen) in accordance with the prescribed protocol provided with the kit.

Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit (Invitrogen).

The data were processed and scaled to a target intensity of 100 for all probe sets by MAS5 in Biocondutor affy package.

111;Clear-cell renal cell carcinoma (ccRCC) tumor;Female;72;Clear-cell renal cell carcinoma;T1NxMx;n/a;2;wild type;wild type;wild type

Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 111

111;Normal cortex;Female;72;Clear-cell renal cell carcinoma;wild type;wild type;wild type

83;Clear-cell renal cell carcinoma (ccRCC) tumor;Female;85;Clear-cell renal cell carcinoma;T1N0M0;I;2;wild type;loss;mutant

Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 83

83;Normal cortex;Female;85;Clear-cell renal cell carcinoma;wild type;wild type;wild type

75;Normal cortex;Female;48;Clear-cell renal cell carcinoma;wild type;wild type;wild type

42;Clear-cell renal cell carcinoma (ccRCC) tumor;Male;45;Clear-cell renal cell carcinoma;T2N0M0;II;2;wild type;mutant;mutant

Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 42

42;Normal cortex;Male;45;Clear-cell renal cell carcinoma;wild type;wild type;wild type

Naïve CD4 and CD8 T cells were sorted from wild-type and HIF1a-deficeint mice. For activation, wild-type and Tsc1-deficient naïve CD4 T cells were stimulated by plate-bound aCD3-CD28 for 4h.

Naïve CD4 and CD8 T cells were cultured with Click medium for aCD3-CD28 stimulation.

wild-type naïve CD4 T cells with CD3-CD28 stimulation for 4h KAI268

The data were analyzed with Partek Genomics Suite 6.5 using the RMA algorithmn

Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Affymetrix standard methods were applied after RNA isolation and amplification

wild-type naïve CD4 T cells with CD3-CD28 stimulation for 4h KAI265

Epidermal cell (eC) suspensions were prepared from tail skin of C57BL/6 and AhR-/- mice as described previously. EC were seeded 1.5x106 cells/ml in 6-well plates in serum free Melanocyte Growth Medium (Promocell, Heidelberg, Germany). Normal mouse melanocytes (NMM) were grown for 6-8 weeks, and passaged when confluent. All cells contained visible amounts of melanin at the end of the culture.

Total RNA was isolated with Trizol™ (Invitrogen) according to the manufacturers’ instructions. For microarray analysis mRNA was amplified prior to chip-hybridization using the MessageAmp™ Kit of Ambion (Woodward St. Austin, USA).

RNA was hybridized to MOE430A 2.0 gene chips (Affymetrix).   Standard Affymetrix protocol.

RNA was biotinylated (Enzo Bio Array™HighYield™ RNA transcript labeling kit (Affymetrix, High Wycombe, UK)) and purified.

Gene expression data from mouse embryonic fibroblasts isolated from 13.5 day C57BL/6 Rap1 knockout embryos, immortalized with SV40LgT, expressing Rap1-I312R

normal;IA, IB, II, IIIA, IIIB, or IV=IIIB;69;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

normal;IA, IB, II, IIIA, IIIB, or IV=IIIB;50;female, male:female;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

normal;IA, IB, II, IIIA, IIIB, or IV=IIIB;69;female, male:female;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

normal;IA, IB, II, IIIA, IIIB, or IV=IIIB;73;female, male:female;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=intestinal type

normal;IA, IB, II, IIIA, IIIB, or IV=IIIB;49;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

normal;IA, IB, II, IIIA, IIIB, or IV=IIIB;36;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

normal;IA, IB, II, IIIA, IIIB, or IV=IIIB;66;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=mixed type

normal;IA, IB, II, IIIA, IIIB, or IV=IV;60;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

biotin labeled with standard Affymetrix fluorescent stain cocktail

Cultures were maintained in α-MEM (Stem Cell Technologies; Vancouver, BC, Canada) with 10% FBS (Invitrogen) and 100 U/mL penicillin streptomycin (Invitrogen) at 37 oC and 5% CO2. Cells were passaged at confluence by 0.25% trypsin EDTA (Invitrogen).

B6; gender: mix; age: 0-2d; tissue: calvariae; passage #: 4; treatment: untreated; biological replicate: 2

B6; gender: mix; age: 0-2d; tissue: calvariae; passage #: 4; treatment: untreated; biological replicate: 3

brain (frontal cortex);bipolar disorder;42 yr;white;296.64;20 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);bipolar disorder;63 yr;white;296.89;43 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);bipolar disorder;29 yr;white;296.54;22 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);bipolar disorder;58 yr;white;296.54;27 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);bipolar disorder;54 yr;white;296.89;45 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

Freshly prepared 5A2dC (Sigma; Saint Louis, MO, USA) stock solution was diluted in growth medium to a concentration of 5 μM. A new preparation of the drug in growth medium was added every 24 hours for a total of 96-hour drug exposure. Cells were grown in normal medium following treatment for an additional 24 hours.

treated with 5-aza-2'-deoxycytidine for 96 hours plus 24 hours in normal medium; biological replicate 1

B6; gender: mix; age: 0-2d; tissue: calvariae; passage #: 4; treatment: 5-aza-2'-deoxycytidine; biological replicate: 1

treated with 5-aza-2'-deoxycytidine for 96 hours plus 24 hours in normal medium; biological replicate 2

B6; gender: mix; age: 0-2d; tissue: calvariae; passage #: 4; treatment: 5-aza-2'-deoxycytidine; biological replicate: 2

treated with 5-aza-2'-deoxycytidine for 96 hours plus 24 hours in normal medium; biological replicate 3

B6; gender: mix; age: 0-2d; tissue: calvariae; passage #: 4; treatment: 5-aza-2'-deoxycytidine; biological replicate: 3

B6; gender: mix; age: 0-2d; tissue: calvariae; passage #: 4; treatment: control; biological replicate: 1

Cells were treated with 100 nM AM580 (AM). Ligands or vehicle were added to the cell culture starting from the first day.

Monocytes were resuspended into six-well culture dishes at a density of 1.5x106 cells/ml and cultured in RPMI 1640 (Sigma) supplemented with 10% Fetal bovine serum (FBS) (Invitrogen), containing 800 U/ml GM-CSF (Peprotech) and 500 U/ml IL-4 (Peprotech).

cRNA was generated from 5 μg of total RNA by using the SuperScript Choice kit (Invitrogen) and the High Yield RNA transcription labeling kit.

Monocytes (98% CD14+) were obtained from Buffy coats by Ficoll gradient centrifugation and magnetic cell separation using anti-CD14-conjugated microbeads (VarioMACS; Miltenyi Biotec).

Peripheral blood was drawn and PBMC were isolated over Ficoll.  Samples were stored in Trizol at -80oC until extracted according to manufacturers directions.

SKI-DLCL cells, not treated and cultured for 24h. Total RNA was isolated using RNeasy kit

HepG2 cells stably transfected with empty vector treated with 100 nM T3 for 6h

HepG2 cells stably transfected with empty vector treated with vehicle for 6h.

The arrays were washed and dried according to the Agilent SSPE wash protocol and scanned using the Agilent Microarray Scanner. The data was extracted from the images using the Agilent Feature Extraction Software, v7.1.

The open source R software package (http://www.r-project.org) and tools from the BioConductor project (http://www.bioconductor.org) were used for processing and analysis of the microarray data.
The Agilent control features were removed. Features that were saturated on at least one array were also excluded from analysis. For each array the VSN (variance stabilizing normalization) function was applied to the mean foreground Cy5 and Cy3 intensities, resulting in a ’generalized log ratio’ value for each feature. This was followed by quantile normalization across the arrays.

A total lymphocyte reference RNA was created using the total peripheral lymphocyte fraction from 20 healthy donors (10 male, 10 female) varying evenly in age from 25 to 65 years. PBMCs from these donors were obtained from the Stanford Blood Center. Granulocytes and monocytes were depleted from the PBMCs using RosetteSep depletion cocktails (Stemcell Technologies, Canada). An aliquot of the purified lymphocytes was taken for antibody staining to determine purity. The cells were incubated with fluorescently conjugated monoclonal mouse anti-human antibodies to CD3, CD56, CD16, CD8, CD4, and CD19 for 30 mins, washed, analyzed by flow cytometry (FACS Calibur, BD Biosciences) and were determined to be >99% pure lymphocytes. The remainder of the purified lymphocytes were homogenized in 10mL TRIzol plus 50μg linear acrylamide and stored at -80°C. Total DNA-free RNA was isolated. 100μg total RNA from each of the 20 healthy donor total lymphocyte samples was pooled to create the total lymphocyte reference RNA.

750ng Cy3-labeled aRNA, 750ng Cy5-labeled total lymphocyte reference aRNA and 50μl Agilent control targets were pooled, and fragmented using the Agilent Fragmentation buffer for 30 mins at 60°C. Agilent hybridization buffer was added, and 490μl of target solution was hybridized onto Agilent Human 1A Oligo Microarrays (v2) using the SureHyb (Agilent) assembly and incubated at 60°C at 4rpm for 17 hours.

1μg total lymphocyte reference RNA was used as input for one round of aRNA amplification using the Amino Allyl MessageAmpTM II aRNA Amplification Kit (Ambion).
The aRNA sample was vacuum dried to completion and resuspended in coupling  buffer (Ambion, Inc).
aRNA was labeled with 20,000pmol Cy Dye Post Labeling Reactive Dyes (Amersham Biosciences Corp., NJ) at room temperature for 30 mins followed by addition of hydroxylamine to 0.18M to quench unreacted dye, for 15 mins at room temperature protected from light. Labeled aRNA was purified using the RNeasy MinElute Cleanup kit (Qiagen). The labeling resulted in 30-60 dye molecules/1000nt.

Gene expression profiles of pure sorted peripheral blood lymphocytes from melanoma patients and healthy controls.

A pool of two pure subsets of peripheral blood CD56dim natural killer cells (CD19- CD3- CD56dim Cd16+), stringently sorted by flow cytometry, from two age and gender matched healthy donors.;Pooled RNA from the total peripheral lymphocyte fraction from 20 healthy donors, used as a common reference.

For the initial normalization and data analysis steps, data were retrieved using Affymetrix GCOS software. The frequency of positive genes on each slide was 48–55%. After scaling of all probe sets to a value of 100, the amplification scale was reported to be between 1.1 and 2.5 for all slides. The signals yielded by the poly(A)-RNA, hybridization, and housekeeping controls (GAPDH 3′:5′ ratio <2) were indicative of the good quality of the amplification and hybridization procedures.
Statistical analyses of the microarray data were further performed using GeneSpring software (Agilent, Palo Alto, CA). For each slide, scaled data were normalized to the 50th percentile value for each chip and to the median value for each gene. The data were assessed by analysis of variance (ANOVA) with or without Benjamini-Hochberg corrections for multiple comparisons.

Total RNA was extracted from synovial biopsy tissue using the Nucleospin RNA II extraction kit (Macherey-Nagel, Düren, Germany), which included DNase treatment of the samples.

GeneChip Human Genome U133 Plus 2.0 arrays (spotted with 1,300,000 oligonucleotides informative for 47,000 transcripts and originating from 39,000 genes; Affymetrix UK) were hybridized overnight at 45°C in monoplicate cultures with 10 μg cRNA. The slides were then washed and stained using the EukGE-WS2v5 Fluidics protocol on the GeneChip Fluidics Station (Affymetrix UK).

Labeling of RNA (complementary RNA [cRNA] synthesis) was performed according to a standard Affymetrix procedure (One-Cycle Target Labeling kit; Affymetrix UK, High Wycombe, UK). Briefly, total RNA was first reverse transcribed into single-stranded complementary DNA (cDNA) using a T7-Oligo(dT) Promoter Primer kit (Affymetrix UK) and Superscript II reverse transcriptase. RNase H was then added together with Escherichia coli DNA polymerase I and E coli DNA ligase, followed by a short incubation with T4-DNA polymerase in order to achieve synthesis of the second-strand cDNA. The purified double-stranded cDNA served as the template for the in vitro transcription reaction, which was carried out overnight in the presence of T7-RNA polymerase and a biotinylated nucleotide analog/ribonucleotide mix. At the end of this procedure, the biotinylated cRNA was cleaned and fragmented by a 35-minute incubation at 95°C.

tissue: synovial biopsy tissue (15–20 synovial samples per patient) was obtained by needle arthroscopy of the affected knee of patients with systemic lupus erythematosus (SLE n = 4), patients with rheumatoid arthritis (RA n = 7), patients with osteoarthritis (OA n = 5), patients with seronegative arthritis (SA, n = 4) and patients with microcrystalline arthritis (MIC n = 5). For each patient, 4–6 synovial samples were snap-frozen in liquid nitrogen and stored at −80° for later RNA extraction. The same amount of tissue was also kept at −80° for future immunostaining experiments on frozen sections. The remaining material was stored in formaldehyde and paraffin-embedded for conventional optical evaluation and immunostaining of selected cell markers.
patients: all patients with SLE met the American College of Rheumatology (ACR; formerly, the American Rheumatism Association) revised classification criteria for SLE (5), all were female, and the mean age was 32 years (range 19–40 years). All SLE patients had active articular disease at the time of synovial tissue sampling, and none had received immunosuppressive therapy; some of the SLE patients were receiving nonsteroidal antiinflammatory drugs. All patients with RA met the ACR classification criteria for RA (6) and all had early (<1 year's duration) active disease at the time of tissue sampling. Among the patients with RA, 2 were female and 5 were male, and the mean age was 51 years (range 37–69 years). In these patients, the mean C-reactive protein (CRP) level was 25 mg/liter (range 9–96 mg/liter), and the mean Disease Activity Score in 28 joints (including the CRP) (7) was 5.08 (range 3.76–5.82). None of the RA patients had received any treatment, except with nonsteroidal antiinflammatory drugs. Among the patients with OA, 5 were female and 1 was male, and the mean age was 63.2 years (range 51–73 years). The diagnosis of seronegative arthritis was based on the presence of psoriasis or x-ray evidence of sacro-iliacal joint involvement). The diagnosis of microcrystalline arthritis was based on the identification of urate or calcium pyrophosphate crystals in the synovial fluid.

Synovial biopsies (n = 4 to 6), obtained by needle arthroscopy from the swollen knee of a patient with osteoarthritis

Hybridized chips were processed using affymetrix 450 Fluidic station, using GeneChip hyb, Wash and Stain kit according to the instructions and scan using affymetrix GeneChip scanner 3000

.CEL files were generated using GCOS software and data anlyzed using Partek software to identify 1.5 fold changed transcripts in Het, and KO compared to WT, as well as Het versus KO.

Affymetrix Mouse Gene 430.2  arrays were hybridized with fragmented and labelled cRNA for 18 h at 45C using Affymetrix hybridization oven

Biotin labelling according to Standard Affymetrix  protocol using 20ug of  cRNA

"male subject, 18-45 yrs, peripheral blood mononuclear cells 168 h after intravenous endotoxin challenge"

"male subject, 18-45 yrs, peripheral blood mononuclear cells prior to (baseline - 0 h) intravenous endotoxin challenge"

"male subject, 18-45 yrs, peripheral blood mononuclear cells 24 h after intravenous endotoxin challenge"

"male subject, 18-45 yrs, peripheral blood mononuclear cells 30 min after intravenous endotoxin challenge"

The arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix) and raw data was extracted from the scanned images and analyzed with the Affymetrix GeneChip Command Console Software (Affymetrix).

Array data were preprocessed using RMA  (apt-1.14.2 and HuGene-1_0-st-v1.r4.analysis-lib-files) and analyzed using the limma package (version 3.8.2, R version 2.11.1, and hugene10sttranscriptcluster.db_7.0.1). Note that arrays were scanned on several different dates (indicated by batch number in sample description), and when computing expression differences it is advisable to include a factor to correct for the batch effects, either directly of with a factor for cohort (as samples within each cohort were scanned on the same date).

A portion of each biopsy sample (ranging between 50-200mg) was snap frozen in liquid nitrogen immediately after procurement and stored at -80°C for RNA extraction. Total RNA was isolated from frozen muscle tissues using TRIzol reagent (Invitrogen).

Hybridization was performed using 5 micrograms of biotinylated target, which was incubated with the GeneChip Human Gene 1.0 ST array (Affymetrix) at 45°C for 16–20 hours. Following hybridization, non-specifically bound material was removed by washing and detection of specifically bound target was performed using the GeneChip Hybridization, Wash and Stain kit, and the GeneChip Fluidics Station 450 (Affymetrix)

Biotin-labeled target for the microarray experiment was prepared using 100 ng of total RNA and cDNA was synthesized using the GeneChip WT (Whole Transcript) Sense Target Labeling and Control Reagents kit as described by the manufacturer (Affymetrix). The sense cDNA was then fragmented by UDG (uracil DNA glycosylase) and APE 1 (apurinic/apyrimidic endonuclease 1) and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labelling kit (Affymetrix).

Gene expression data from Biceps, control, cohort 22, subject 22U

Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.

Total RNA was extracted from wild-type mouse small intestines at 18.5 dpc using the Macherey-Nagel Nucleospin kit.

The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The cRNA is purified from the fragmentation reaction using phenol/chloroform extraction and ethanol precipitation. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA.s that fall outside of an acceptable range will not be carried forward in the analysis. Should this occur, investigators would be notified and asked to provide a new RNA sample

Murine ESCs (cell lines: Eed KO J1, Eed KO E14, V6.5 WT (Open Biosystems), J1 wt) were expanded in 15% ESC FCS (PAA), non-essential amino acids solution and LIF-conditioned medium on Mitomycin C-inactivated MEFs. Eed KO ESCs were kindly provided by Dr. A. Wutz, Cambridge, UK. Differentiation in hanging drop cultures was done as described. Briefly, 1000 MEF-depleted ESCs were pipetted onto a lid of a petri plate in 30μl of differentiation medium (10% FCS, without LIF). After 2 days, EBs were collected and replated in suspension cultures. Cell number determination was done by counting single cell suspension of pooled and Trypsin-treated EBs under Trypan blue staining and microscopy. To assess CFC frequencies, 1000 undifferentiated ESCs were plated and cultured for 2 days under ESC expansion conditions before numbers of ES cell-type alkaline phosphatase (AP)-active colonies were determined by staining of fixed cultures with the 'leukocyte alkaline phosphatase'-kit (Sigma-Aldrich). To determine frequencies of EB formation, 1000 undifferentiated ESCs were plated under differentiation condition into semisolid methylcellulose cultures. EB numbers were counted at days 5-7 of differentiation. In addition, graded numbers of ESCs (7, 15, 31, 62, 125, 250 cells) were plated into hanging drops in differentiation medium. After 5-7 days, numbers of drops without EBs were scored. Based on drops without EBs, regression analysis was done using Excel software.

CEL files were processed using the Affymetrix Power Tools (APT) Software Package. Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).

Total RNA was extracted using RNeasy Mini kit (Qiagen, Hilden, Germany) with DNase digestion using the manufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.

Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.

Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 94°C for 35 minutes in Fragmentation buffer of the company.

The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA.s that fall outside of an acceptable range will not be carried forward in the analysis. Should this occur, investigators would be notified and asked to provide a new RNA sample

Brains from 3 mice were pooled into 1 sample and samples were run in triplicate (total of 9 mice per condition)

8-week old male mice were infected intranasally with 107 pfu of VSV-Indiana strain. At 5 days post-infection mice were perfused and whole brain was harvested for RNA extraction.

The data were processed using MAS5. Genepattern software filtered the MAS5 values for the genes that were significant. These data are on the Series record.

whole brain;C57BL/6J;wild type;8 weeks, 5 days;107 pfu of VSV-Indiana strain

Gene expression data from left lung samples from B6.129P2-Il10tmlCgn/J male mice exposed to 0.3 ppm O3  for 48 hours

B6.129P2-Il10tmlCgn/J;Il10-/-;6-8 weeks;Male;Left lung;Jackson Labs, Bar Harbor, ME;48 hours;ozone;0.3 ppm O3;10028-15-6

The sample is a part of an analysis of colonic gene expression in patients with ulcerative colitis

Ulcerative colitis patient, biopsy taken from the descending colon, no macroscopic signs of inflammation.

Neonatal (P0) whole brain mRNA from 40,XX female C57BL/6J x C3H/Paf

2e4 HeLa cells/well were seeded in a 96-well plate for 20 h prior to transfection with siRNAs LMG2 and LMG4. Cells were transfected in triplicates with 1 µl of siRNA (50 nM/well).

HeLa cells cultured at 37°C and 5% CO2 in RPMI 1640 medium supplemented with 10% fetal calf serum and 1% streptomycin/penicillin (Biochrome; Berlin; Germany).

The microarray chips were washed and scanned at 560 nm in a Affymetrix GeneChip Scanner according to the insturctions of the manufacturer (Affymetrix).

The data were analyzed by the Affymetrix GCOS software with default analysis settings. BioRetis database was used for the statistical analyses (www.bioretis.com).

RNA was isolated after 48 h post transfection using the RNeasy 96 BioRobot® 8000 (Qiagen). Knockdown rates were independently measured three times by quantitative PCR using the Quantitec SYBR Green RT-PCR Kit according to Qiagen protocol. Total RNA was treated with DNAse-I (Quiagen). Quality of RNA samples was assessed by micro fluidic technology using the Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany) and the RNA 6000 Nano Assay Kit (Agilent Technologies). RNA quantity and 260/280 ratios were measured in a NanoDrop 1000 (NanoDrop Technologies, Wilmington, USA). Only RNA samples which fulfilled the criteria of RNA quality required for microarray analysis (28S/18S RNA ratio >2.2; RIN value >7) were used for labelling.

Hybridisation to Affymetrix™ GeneChip Human Genome U133 Plus 2.0 microarrays was perforemd with Biotin labelled cRNAs according to the manufacturer (Affymetrix).

After extraction RNA was converted to cDNA, amplified to cRNA and labelled with Biotin according to the manufacturer instruction manual (Affymetrix).

HeLa, epithelial cells, adenocarcinoma (CCL-2; American Tissue Culture Collection ATCC, Manassas, VA, USA)

Total RNA was isolated from Qiagen QIAzol lysed cells using Qiagen RNeasy 96 Universal Tissue 8000 Kit.

Invitrogen SuperScript Double-Stranded cDNA Synthesis Kit with T7-Oligo(dT) primer followed by Ambion MessageAmp II-Biotin Enhanced In Vitro Transcription.

Marrow was taken from femurs, tibias, pelvic girdles and humerus after Halothane (Halocarbon Laboratories, River Edge, NJ) vapor terminal inhalation in accordance with the American Veterinary Medical Association (AVMA) Panel on Euthanasia.  All animal procedures were approved by The Scripps Research Institute (TSRI) Institutional Animal Care and Use Committee (IACUC).  Bone marrow single cell suspensions were labeled with FITC-conjugated anti-CD71 and PE-conjugated anti-TER-119 monoclonal antibodies (mAbs; Pharmingen, BD Biosciences, San Jose, CA) in ice-cold 2 mM EDTA: 0.5% BSA: PBS.  Fc-R saturation was achieved by pre-incubation with a purified anti-CD16/32 mAb.  >=92% cell viability was ensured using the Trypan blue exclusion assay.  Prior to sorting, cells were centrifuged and resuspended in 1 mM EDTA: 25 mM HEPES: 1% FCS: PBS containing 10 μg/ml propidium iodide (PI; Sigma-Aldrich, St. Louis, MO).  Pairs of Sod2+/+ and Sod2-/- samples were sorted in parallel using two FACSDiva sorters (BD Biosciences) simultaneously; sorting was operated at medium pressure (35 psi) using 80 μm nozzles.  Purity and quality of preparations were ensured by microscope examination of Wright-Giemsa-stained sorted cells cytospun onto slides and by flow cytometry analysis using a FACSCalibur cytometer running CellQuest Pro (BD Biosciences).

Heterozygous B6-Sod2tm1Cje mice were bred in timed matings to obtain Sod2-/- (KO) and Sod2+/+ (WT) littermates at E13.5-16.5 of development to serve as donors for fetal liver cell transplantation.  Embryos were harvested; fetal livers were dissected and mechanically dissociated into single cell suspensions in culture medium (RPMI, 7% FCS, glutamine, penicillin-streptomycin, 10e-5 M betamercapto-ethanol).  C57BL/6 mice congenic at the Ly5 locus (B6.SJL_PtprcaPep3b/BoyJ [Ly5.1], National Cancer Institute) were used as recipients in order to allow for differentiation of host (Ly5.1) versus donor (Ly5.2) hematopoietic cells.  11–15 week old Ly5.1 host animals were subjected to 10.50 cGy (1,050 rad) of gamma irradiation divided into two equal doses 4 h apart on the day of transplant.  10e6 fetal liver cells, prepared as above, were injected intravenously into irradiated Ly5.1 congenic recipients. Animals were maintained on chlorinated water for 21 d after irradiation.  All experiments were approved by the Animal Use Committee (Friedman et al. J. Exp. Med. 2001).

Arrays were scanned using a ScanArray 3000 running the GCOS v1.3.037 algorithm (Affymetrix), default settings and a target intensity of 250 for scaling according to the manufacturer’s protocol (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).  After scanning, array images were assessed by eye to confirm scanner alignment and the absence of significant bubbles or scratches on the chip surface.  3'/5' ratios for GAPDH and β-actin were confirmed to be within acceptable limits (all but one Sod2-/- sample GAPDH 3'/5' ratios were below 2.0; the off range sample was legitimately removed from analysis), and BioB spike controls were found to be present on all chips, with BioC, BioD and CreX also present in increasing intensity.  When scaled to a target intensity of 250, scaling factors for all arrays were within acceptable limits (4.089-7.955), as were background (48-67), Q values and mean intensities.

Arrays were scanned using GCOS v1.3.037 (Affymetrix), default settings and a target intensity of 250 for scaling.  The data was RMA-normalized and log base 2-transformed through import of .CEL files on GeneSifter Version 2.3.7.2007.05.25 (VizX Labs, Seattle, WA).

Total RNA was extracted using the RNeasy Mini kit according to the manufacturer’s suggested ‘spin’ protocol for isolation of total RNA from animal cells (Qiagen, Valencia, CA).  Briefly, we disrupted and lysed 5-10 million sorted cells in RLT Buffer, homogenized and sheared genomic DNA through centrifugation on QIAshredder spin columns; we performed on-column DNA digestion with the RNase-Free DNase Set (Qiagen) and eluted total RNA in RNase-free water (Sigma-Aldrich).  Quality and amount of starting total RNA were checked with an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA) and on formaldehyde-containing agarose gels.

The target cRNA generated from each sample was processed as per manufacturer's recommendation using an Affymetrix GeneChip Instrument System (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).  Briefly, spike controls were added to 10 µg fragmented cRNA before overnight hybridization on 430 2.0 arrays.  Our hybridization cocktail contained control oligo B2 and eukaryotic controls (Affymetrix), herring sperm DNA (Promega, Madison, WI), BSA (Invitrogen), hybridization buffer (Affymetrix recommended recipe) and water.  Cocktails were hybridized to GeneChip Mouse Genome 430 2.0 arrays (http://www.affymetrix.com/products/arrays/specific/mouse430_2.affx) at 45 °C for 16 hours.  After hybridization, arrays were washed and stained with streptavidin-phycoerythrin.

Total RNA from each sample was submitted to one-round cDNA synthesis to prepare biotinylated target RNA using standard Affymetrix protocol (http://www.affymetrix.com/support/technical/manual/expression_manual.affx) as previously described (Lockhart et al. Nat Biotechnol, 1996. 14(13): p. 1675-80).  Briefly, 5 µg of total RNA was used to generate first-strand cDNA by using a T7-linked oligo(dT) primer and a SuperScript II Reverse Transcriptase (Invitrogen).  Second-strand synthesis was performed using Escherichia coli DNA ligase and polymerase I (Invitrogen); Escherichia coli RNAse H (Invitrogen) removed the remaining total RNA.  The target was amplified and biotin-labeled through in vitro transcription (IVT) with biotinylated UTP and CTP ribonucleotides (Enzo Life Sciences, Farmingdale, NY), generating a biotinylated cRNA.  Quality and amount of cRNA were checked with an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).

human skeletal muscle from insulin sensitive individuals before insulin therapy

whole tissue section of breast cancer.
Clinical information: Sample.ID=1304;Tumor.type=D;Size=2;Grade=3;Nodes=0/14;ER=Pos;PR=Pos;HER2=Neg;Age=57;DFS=20;Status=recur
Keywords = breast cancer, tamoxifen, recurrence

Gene expression data from Biceps, control, cohort 12, subject 12V

Gene expression data from Deltoid, control, cohort 12, subject 12U

Gene expression data from Biceps, control, cohort 12, subject 12U

Gene expression data from Biceps, control, cohort 09, subject 09U

Gene expression data from Deltoid, control, cohort 09, subject 09U

in vitro Treatment: siLuc (Sense 5'-rCrGUrArCrGrCrGrGrArAUrArCUUrCrGrCTT-3’ Antisense 5’-UrCrGrArArGUrAUUrCrCrGrCrGUrArCrGTT-3’), Treatment Repeat: 1, Units of Treatment Repeat: dose, Treatment Duration: 50, Units of Duration: hrs, Treatment Time: -48, Units of Treatment Time: hrs, Vehicle for Chemical: Lipofectamine`, Amount of Vehicle: 0.44, Route of Exposure: Transfection, Units of Amount of Vehicle: microliter, Dose or Concentration: 3.3, Units of Dose or Concentration: nM
Treatment_2: in vitro Treatment: Heat, 43ºC, Treatment Repeat: 1, Units of Treatment Repeat: exposure, Treatment Duration: 1.5, Units of Duration: hrs, Treatment Time: 0, Units of Treatment Time: hrs, Route of Exposure: Convection, Dose or Concentration: 43, Units of Dose or Concentration: degrees Celcius

Growth Conditions: 37 C_5% CO2

TP082505-27_HG-U133A_2_IMFGN0023: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

Sample Type: Cells, Cell Line: HeLa, ATCC Number: CCL-2, Number of Cells Seeded: 2.20E+05, Cell Type: Cervical Carcinoma, Separation Type: Trypsin, Harvest Time Point: 2, Units of Harvest Time Point: hr

Clinical information: Sample.ID=607;Tumor.type=D;Size=1.2;Grade=2;Nodes=5/14;ER=Pos;PR=Pos;HER2=Neg;Age=76;DFS=114;Status=non-recur

Clinical information: Sample.ID=605;Tumor.type=D;Size=2.2;Grade=2;Nodes=6/18;ER=Pos;PR=Pos;HER2=Neg;Age=70;DFS=110;Status=non-recur

Clinical information: Sample.ID=547;Tumor.type=D/L;Size=1.5;Grade=2;Nodes=ND;ER=Pos;PR=Pos;HER2=Neg;Age=74;DFS=129;Status=recur

Clinical information: Sample.ID=518;Tumor.type=L;Size=5.5;Grade=2;Nodes=3/20;ER=Pos;PR=Pos;HER2=Neg;Age=68;DFS=156;Status=non-recur

Clinical information: Sample.ID=469;Tumor.type=D;Size=1;Grade=1;Nodes=0/19;ER=Pos;PR=Pos;HER2=Neg ;Age=66;DFS=161;Status=non-recur

Clinical information: Sample.ID=420;Tumor.type=D/L;Size=2;Grade=3;Nodes=ND;ER=Pos;PR=Pos;HER2=Neg;Age=72;DFS=58;Status=recur

Clinical information: Sample.ID=374;Tumor.type=D;Size=1;Grade=3;Nodes=0/15;ER=Pos (<10%);PR=Pos;HER2=Pos;Age=57;DFS=47;Status=recur

Clinical information: Sample.ID=356;Tumor.type=D;Size=1;Grade=2;Nodes=2/20;ER=Pos (<10%);PR=Neg;HER2=Pos;Age=58;DFS=24;Status=recur

Clinical information: Sample.ID=342;Tumor.type=D;Size=3;Grade=2;Nodes=9/21;ER=Pos;PR=Neg;HER2=Neg;Age=62;DFS=102;Status=recur

Clinical information: Sample.ID=319;Tumor.type=D;Size=4;Grade=2;Nodes=1/13;ER=Pos;PR=Pos;HER2=Neg;Age=67;DFS=44;Status=recur

Signal quantification and normalization were performed using RMA

Tothova Z, Kollipara R, Huntly BJ, Lee BH, Castrillon DH, Cullen DE, McDowell EP, Lazo-Kallanian S, Williams IR, Sears C, Armstrong SA, Passegue E, DePinho RA, Gilliland DG. (2006) FoxO are critical mediators of hematopoietic stem cell resistance to physiologic oxidative stress. Cell 2007

Bone marrow hematopoietic stem cells or myeloid progenitors from pooled Mx-Cre-; FoxO1/O3/O4LoxP/LoxP or Mx-Cre+; FoxO1/O3/O4LoxP/LoxP mice were sorted and RNA was prepared using the Qiagen RNeasy micro kit. Amplification and biotin labeling of fragmented amplified cDNA was carried out using the NuGen Ovation Biotin labeling system (NuGEN Technologies, Inc) in triplicate. Labeled probes were hybridized to Affymetrix Mouse Genome 430 2.0 (MOE430_2) GeneChip arrays.

Study the effect of the deficiency of FoxO1, FoxO3, and FoxO4 in murine bone marrow hematopoietic stem cells and myeloid progenitors on expression of genes involved in reactive oxygen species (ROS) metabolism.

Prospectively purified bone marrow hematopoietic stem cells (LSK, defined as Lineage- Sca-1+ c-Kit+) and myeloid progenitors (defined as Lineage- Sca-1- c-Kit+) from Mx-Cre-; FoxO1/O3/O4LoxP/LoxP and Mx-Cre+; FoxO1/O3/O4LoxP/LoxP mice 4 weeks after induction of excision with polyinosine-polycyticylic acid (pIpC, 300ug)

Swiss;adult mouse intestine, kidney, and liver plus fetus tissue;C57BL/6J;wildtype;12 weeks;colon

GeneChips were scanned using the Affymetric Gene-Array scanner 3000

The data were analyzed with Gene Chip Operating Software (GCOS v1.4) using Affymetrix default analysis settings

RNA extracted using Trizol, clean up using Qiagen Rneasy Cleanup kit

Fragmented and biotin-labeled 10 ug target in 200ul hybridization cocktail was used for each Affymetrix Mouse Genome 430 20. array

biotinylated cRNA was prepared from 2ug total RNA using Affymetrix One-Cycle Target Labeling Assays

Gene expression data from mouse heart tissue at 5-6mos of age, male mice, 6 hours fasted

Fibroblasts were grown in 15% FBS DMEM in a 37º incubator with 7% CO2.

Mouse Embryonic fibroblasts were isolated by standard tecnique by E13.5 embryos

Gene expression levels were estimated from GeneChip® probe intensities using RMA, quantile-normalization and background-correction algorithms.

Following fragmentation, 15 ug of cRNA was hybridized for 16 hours at 45ºC on Mouse Genome 430 2.0 GeneChips.  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

2nd Gen. FVB/N from 129Sv/Ev and Black Swiss mix;13.5 days;whole body;Fibroblasts;Pten+/+

Mouse Embryonic Stem cells were treated with either control siRNA containing random oligo pool or siRNA targetting the pCIP proteins. Two different siRNAs (siRNA1 and siRNA1) were used to silence pCIP.

Mouse Embryonic Stem cells were grown on adherant plates in vitro at 37C and 5% CO2.

The Data was analyzed using Partek Genomic Suit Version 6.6
The data was normalized to baseline and no filtering was applied.

RNA was isolated using Qiagen, Rneasy Mini Kit (74104) according to manufacturer's instuctions.

Xenograft tumors from DU145, KPL4, and NCI-H1650 were treated with 30 mg/kg of MEDI5117 or IgG isotype control IgG1 for a total of two doses.

Cancer cell lines were purchased from the American Type Culture Collection (Manassas, VA) and grew according to protocols of the vendor. Cell line authentication was conducted by STR-based DNA fingerprinting and multiplex PCR.  IMPACT tests were also performed on all cell lines.

All GeneChip® washing, staining, and scanning procedures were performed with Affymetrix standard equipment.

Data capture and initial array quality assessments were performed with the GeneChip Operating Software (GCOS) tool.

Total RNA was extracted from snap-frozen xenograft tumor samples using the ZR RNA MicroPrep kit (Zymo Research, Orange, CA)

Fifteen micrograms of each biotin-labeled cRNA was fragmented for hybridization on Affymetrix Human Genome U133 Plus 2.0 GeneChip® arrays.

Generating biotin-labeled amplified cRNA from 75 ng of total RNA was accomplished using the MessageAmpTM Premier RNA Amplification Kit (Ambion, Austin, TX).

HaCaT cells (Boukamp et al., 1988) were grown in DMEM (0.06 mM CaCl2) till 90-100% confluence, then media was changed to DMEM (1.8mM CaCl2) for 12 days to induce differentiation.

Total RNA was isolated using TRI REAGENT (Molecular Research Center, Inc.) and subjected to DNaseI treatment (New England Bio-Labs), followed by Qiagen Rneasy kit cleanup.

Following fragmentation, 5 µg of biotinylated sense strand cDNA were hybridized for 16 hr at 45C on Human gene 1.0ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station450.

Biotinylated sense strand cDNA were prepared according to Affymetrix protocol from 300 ngtotal RNA (GeneChip® Whole Transcript (WT) SenseTarget Labeling Assay Manual, 2007, Affymetrix).

Gene expression data from HaCaT cells at day 12 of calcium induced in-vitro differentiation

HaCaT cells at day 12 of calcium induced in-vitro differentiation;control

HaCaT cells at day 12 of in-vitro calcium induced differentiation

Purified T cells were cultured in RPMI 1640 medium for 5h at 37oC or 40oC and at 5% CO2

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as a normalization method.   The trimmed mean target intensity of each array was arbitrarily set to 100.  Statistical analysis was performed using two-way ANOVA and SAS software.

Total RNA from activated T cells were isolated using RNA easy Kit according to manufacturer's protocol. The RNA quantification and quality was performed using a Model 2100 bioanalyzer.

Following fragmentation, 20μg of cRNA were hybridized for 16h at 45C on whole mouse Affymetrix 430-2.0 Mouse Genome Array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA was prepared by transcribing  2.5 μg of Total RNA according to standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix)

5hr activation with plate bound anti-CD3
Gene expression data from HSF1+/+ T cells activated at 37oC for 5h with plate bound anti-CD3.

siRNA oligonucleotides (Dharmacon) were transfected with Lipofectamine2000 and LipofectamineRNAiMax (Invitrogen) into LNCaP cells.  Cell lysates were prepared 48h after siRNA transfection.

The data were normalised using quantile normalisation with Partek Software

RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.

RWPE1 cells were treated with medium containing 100 nM of 1,25(OH)2D or vehicle (0.1% ethanol) for 6, 24 or 48 hours (n=4 per treatment, 24 total samples).

RWPE1 cells were plated in T75 flasks (1x10^6 cells per flask) and grown until cells reached 60% confluence. For the 48 hours time point media was replaced at 24 hours.

Chip scanning was carried out by using standard Affymetrix protocols (Affymetrix, Santa Clara, CA) at the Ohio State University Comprehensive Cancer Center  (Columbus, OH).

Microarray data from CEL files for all 24 chips was normalized simultaneously and expression levels were generated using the gcRMA package in Bioconductor.

Total RNA was isolated from the cells using TriReagent (Molecular Research Center, Inc., Cincinnati, OH) in accordance with the manufacturer’s instructions. Isolated total RNA was further purified using the RNeasy kit (Qiagen, Valencia, CA). The quality of the isolated RNA was confirmed using agarose gel electrophoresis.

Chip hybridization was carried by using standard Affymetrix protocols (Affymetrix, Santa Clara, CA) at the Ohio State University Comprehensive Cancer Center (Columbus, OH).

The transcripts levels in each sample were measured by using the Affymetrix HU133 plus 2.0 GeneChip (Affymetrix, Santa Clara, CA;  54,210 probe sets covering over 47,000 transcripts and splice variants).  RNA labeling was carried out by using standard Affymetrix protocols (Affymetrix, Santa Clara, CA).

RWPE-1;Immortalized normal prostate epithelial cells.;100 nM 1,25(OH)2D;48 hours

RWPE-1;Immortalized normal prostate epithelial cells.;Vehicle (0.1% ethanol);48 hours

Gene Chips were scanned using the affymetrix GeneArray Scanner 3000.

The scanned image was converted into numerical values of the signal intensity (Signal) and into categorical expression level measurement (Absolute Call) using the Affymetrix GCOS V1.1.1 software with default parameters.

Gastrocnemius-soleus muscles were powdered in the liquid nitrogen and Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA were further subject a cleanup protocol using a Qiagen Rneasy minikit.

Following fragmentation,  labeled cRNA were hybridized at 45°C for approximately 16 hr to Gene Chip Mouse Genome 430 2.0 Expression Array (Affymetrix). The arrays were stained on Gene Chip Fluidics Workstation 450.

Biotinylated cRNA were prepared according to the manufacturer's instructions (One-Cycle Target Labeling kit, Affymetrix,Inc.)

Expression profiles generated from the gastrocnemicus and soleus muscles from integrin alpha7 transgenic mice

Gastrocnemius muscle from integrin alpha7 transgenic mouse;SJ6/C57BL6 background;integrin alpha7 transgenic;Female;5 week;gastrocnemius and soleus muscle;non-fasted

Gastrocnemius-soleus muscles, basal status, integrin alpha7 transgenic  mouse

The data were normalised using quantile normalisation in R. Data were log2transformed. Day effect was eliminated using standarization with saline samples.

Day: 1; Drug: Methamphetamine; Phase: Drug treatment; Replicate: 1

Day: 12; Drug: Methamphetamine; Phase: Drug treatment; Replicate: 1

257;6MP 50mg;5/16/64;F;CAUCASIAN;FALSE;FALSE;FALSE;unknown;FALSE;FALSE;6/2/05;7;0;0;0;0;0;0;0;TRUE;0;unknown;unknown;unknown;unknown;unknown;6/2/05;BOTH;BOTH;BOTH;unknown;unknown;9/14/05;DISEASE IN REMISSION;ex;2/1/05;0-4;None;UC;11-15-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

257;6MP 50mg;5/16/64;F;CAUCASIAN;FALSE;FALSE;FALSE;unknown;FALSE;FALSE;6/2/05;7;0;0;0;0;0;0;0;TRUE;0;unknown;unknown;unknown;unknown;unknown;6/2/05;BOTH;BOTH;BOTH;unknown;unknown;9/14/05;DISEASE IN REMISSION;ex;2/1/05;0-4;None;UC;11-15-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

258;Azathioprine 200mg Pentaza 1g TDS;10/26/64;M;CAUCASIAN;6/1/87;6/1/88;FALSE;FALSE;FALSE;YES;FALSE;FALSE;6/7/05;3;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;unknown;unknown;unknown;6/7/05;BOTH;BOTH;unknown;unknown;unknown;8/15/05;DISEASE IN REMISSION;never;unknown;None;UC;11-15-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

259;pentaza 2g D;9/20/78;F;CAUCASIAN;8/1/03;1/13/04;FALSE;FALSE;FALSE;NO;FALSE;FALSE;6/7/05;2;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;unknown;unknown;unknown;6/7/05;BOTH;BOTH;BOTH;BOTH;BOTH;8/15/05;DISEASE IN REMISSION;ex;1/1/03;5-14;none;UC;11-15-01;descending colon;Inflamed;total RNA from 10 human cell lines

254;Asacol 800mg TDS, Predfoam;7/25/59;F;ASIAN;1/1/00;11/1/00;FALSE;FALSE;FALSE;NO;FALSE;FALSE;5/31/05;3;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;unknown;unknown;unknown;5/31/05;BOTH;BOTH;unknown;unknown;unknown;8/15/05;DISEASE IN REMISSION;never;unknown;None;UC;11-15-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

255;Asacol 800mg BD;3/14/77;F;CAUCASIAN;1/1/93;1/1/93;FALSE;FALSE;FALSE;NO;FALSE;FALSE;5/31/05;0;0;0;0;0;0;0;0;TRUE;0;BOTH;BOTH;BOTH;BOTH;BOTH;5/31/05;BOTH;BOTH;BOTH;BOTH;BOTH;8/15/05;DISEASE IN REMISSION;ex;1/1/01;0-4;none;UC;11-15-01;ascending colon;Inflamed;total RNA from 10 human cell lines

255;Asacol 800mg BD;3/14/77;F;CAUCASIAN;1/1/93;1/1/93;FALSE;FALSE;FALSE;NO;FALSE;FALSE;5/31/05;0;0;0;0;0;0;0;0;TRUE;0;BOTH;BOTH;BOTH;BOTH;BOTH;5/31/05;BOTH;BOTH;BOTH;BOTH;BOTH;8/15/05;DISEASE IN REMISSION;ex;1/1/01;0-4;none;UC;11-15-01;descending colon;Inflamed;total RNA from 10 human cell lines

255;Asacol 800mg BD;3/14/77;F;CAUCASIAN;1/1/93;1/1/93;FALSE;FALSE;FALSE;NO;FALSE;FALSE;5/31/05;0;0;0;0;0;0;0;0;TRUE;0;BOTH;BOTH;BOTH;BOTH;BOTH;5/31/05;BOTH;BOTH;BOTH;BOTH;BOTH;8/15/05;DISEASE IN REMISSION;ex;1/1/01;0-4;none;UC;11-15-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

259;pentaza 2g D;9/20/78;F;CAUCASIAN;8/1/03;1/13/04;FALSE;FALSE;FALSE;NO;FALSE;FALSE;6/7/05;2;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;unknown;unknown;unknown;6/7/05;BOTH;BOTH;BOTH;BOTH;BOTH;8/15/05;DISEASE IN REMISSION;ex;1/1/03;5-14;none;UC;11-15-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

261;Asacol 800mg BD;1/7/57;M;CAUCASIAN;1/1/98;1/1/98;FALSE;FALSE;TRUE;NO;FALSE;FALSE;6/14/05;2;0;0;0;0;0;0;0;TRUE;2;BOTH;BOTH;unknown;unknown;unknown;6/14/05;BOTH;BOTH;BOTH;BOTH;BOTH;8/15/05;DISEASE IN REMISSION;never;unknown;none;UC;11-15-01;ascending colon;Inflamed;total RNA from 10 human cell lines

Cells were seeded onto 6-well plates and treated with DMSO (0.005%), 500 nM JQ1 (BPS Bioscience) or 500 nM MLN8237 (Axon Medchem) for 24 h.

Cells were cultured in RPMI medium supplemented with 10% FCS, penicillin (100 U/ml), streptomycin (100 µg/ml), 1% N2 and 2% B27.

Data were normalised using the RMA algorithm implemented in Partek Genomics Suite 6.6 (Partek, Inc.) using the default settings.

Total mRNA was isolated from cells using the QIAGEN miRNeasy Mini Kit.

Hybridisation to murine arrays (Mouse430_2 ) was performed according to the manufacturer's recommendations (Affymetrix).

11_MLN8237-2_(Mouse430_2)
Cell line from MYCN-driven murine neuroblastoma.

mNB-A1;mixed C57BL/6 x 129X1/SvJ;MYCN-driven neuroblastoma;MLN8237

GV oocyte;mixed 129/Sv and C57BL/6J;Ring1+/+Rnf2F/FZp3-cre (Rnf2 mutant)

Peripheral blood mononuclear cell isolation: Peripheral blood from sickle-cell patients, and healthy African-American volunteers, was collected into Vacutainer cell preparation tube (CPT) with sodium citrate and Ficoll (Becton Dickinson, Franklin Lakes, NJ). Purified peripheral blood mononuclear cell (PBMC) suspensions were resuspended in buffer RLT (700-1000 µL per 107 cells) and passed through Qiashredder columns (Qiagen, Valencia, CA) then stored at –70° C.

Affymetrix GCOS version 1.4 was used to calculate the signal intensity and the percent present calls on the hybridized Affymetrix chip. The signal intensity values obtained for probe sets in the microarrays were transformed using an adaptive variance-stabilizing, quantile-normalizing transformation termed “S10” (Munson, P.J., GeneLogic Workshop of Low Level Analysis of Affymetrix GeneChip Data, 2001, software available at http://abs.cit.nih.gov/geneexpression.html.).

Peripheral blood mononuclear cell RNA isolation: Total RNA was extracted from peripheral blood mononuclear cells using RNeasy Mini Kit (Qiagen).  Isolation of RNA from whole blood specimens: Blood Specimen (2.5ml) collected in PAXgene™ tubes from each subject was incubated at room temperature for 4h for RNA stabilization and then stored at − 80 °C. RNA was extracted from whole blood using the PAXgene™ Blood RNA System Kit following the manufacturer's guidelines. Briefly, samples were removed from -80°C and incubated at room temperature for 2 hours to ensure complete lysis. Following lysis, the tubes were centrifuged for 10 min at 5,000 × g the supernatant was discarded and 500 μL of RNase-free water added to the pellet. The tube was vortexed thoroughly to re-suspend the pellet, centrifuged for 10 min at 5000 × g and the entire supernatant was discarded. The pellet was re-suspended in 360 μL of buffer BR1 by vortexing and further purification of RNA was done following the manufacturer's protocol with on-column DNase digestion.  Depletion of Globin Transcripts: Globin mRNA was depleted from a portion of each total RNA sample isolated from PAXgene tubes using the GLOBINclear™-Human kit (Ambion, Austin, TX). In brief 4 µg of total RNA from human whole blood was mixed with a biotinylated Capture Oligo Mix in hybridization buffer. The mixture was incubated for 15 minutes to allow the biotinylated oligonucleotides to hybridize with the globin mRNA species. Streptavidin magnetic Beads were then added, to capture the globin mRNA and the magnetic beads were then pulled to the side of the tube with a magnet and the RNA, depleted of the globin mRNA, was transferred to a fresh tube. The RNA was further purified using a rapid magnetic bead-based purification method.

Twenty µg of biotin-labeled RNA was fragmented to ~200 bp size by incubating in fragmentation buffer containing 200 mM Tris-acetate pH 8.2, 500 mM potassium acetate and 500 mM magnesium acetate for 35 minutes at 94ºC prior to hybridization. Fragmented RNA was assessed for relative length on Agilent 2100 bioanalyzer, and hybridized to Affymetrix HG-U133 plus 2.0 chips for 16 hours, washed, and stained on an Affymetrix fluidics station.

The cRNA labeling and hybridizations were performed according to protocols from Affymetrix Inc. (Santa Clara, CA). Briefly, 2 µg of total RNA from PBMC (n=10, 5 controls and 5 SCD), whole blood (PAX) (n=10, 5 controls and 5 SCD) and Globin depleted (PAX-GR) (n=10, 5 controls and 5 SCD) samples was converted to double-stranded cDNA with a T7-(dT) 24 primer. The cDNA was in vitro transcribed to biotinylated complementary RNA (cRNA) by incorporating biotin-CTP and biotin-UTP using affymetrix IVT labeling kit.

Brain tissue was removed with a Post-Mortem Interval (PMI) of 9.03±2.2 hr for Control samples and 7.05±1.25 hr for the PD samples, subsequently sectioned and frozen.

Trizol lysis extraction of total RNA was performed on an M48 BioRobot with a Quiagen Megatrack Kit.

Following fragmentation, 10 ug of cRNA were hybridized for >16 hr at 45C on GeneChip Human Genome U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Gene expression data of substantia nigra from postmortem brain of PD patients

Gene expression data of substantia nigra from postmortem brain of normal controls

5_DMSO-5_(Mouse430_2)

8_JQ1-2_(Mouse430_2)

C57BL6;Transgenic ATF6-MER;male;40 weeks;left ventricle;tamoxifen

Transgenic ATF6-MER mouse;C57BL6;male;~30 weeks;heart LV;tamoxifen

Skeletal muscle gene expression profiling in Mitochondrial disorders
Keywords = mtdna
Keywords = mitochondrial disorders

Nrl-ko mice were mated with wt-Gfp mice in which Gfp expression is driven by Nrl promoter. Gfp+ photoreceptors were purified by FACS and RNA was extracted and amplified by Nugene kit.
This is wt-Gfp P6 replicate 4.

This is wt-Gfp P10 replicate 4.

This is wt-Gfp P2 replicate 1.

This is wt-Gfp P2 replicate 2.

This is wt-Gfp P2 replicate 3.

This is wt-Gfp P2 replicate 4.

This is wt-Gfp P6 replicate 1.

This is wt-Gfp P6 replicate 2.

This is wt-Gfp P6 replicate 3.

NOMO-1 cells were infected with control and ZFX shRNA lentiviruses at an MOI of 1. RNA was collected for microarrays 48 hours after selection.

Affymetrix Expression Console (1.1) was used for RMA normalization of all microarray data.

Biotinylated DNA probe was made according to the standard Affymetrix protocol

Used the Ambion WT labelling kit as per manufacturer's instructions using 200ng of starting total RNA

Mice injected i.p. 2x/week for 4 weeks with saline, sacrificed 2 days after last dose.

For RNA isolation, liver was homogenized in RNeasy RLT buffer using Polytron homogenizer, layered onto 5.7M CsCl2 and pelleted after overnight centrifugation at 35000 rpm, room temp.  The pellet was resuspended in RLT buffer and RNA was isolated on RNeasy midi columns following the manufacturer's instructions, and including an on-column DNase digestion step.

RAW macrophages treated with 100 ng/ml LPS for 18 hours.  RNA was isolated using Ultraspec RNA isolation system.  Hybridization and measurements were performed at the Univeristy of Pittsburgh Genomics and Proteomics Core Facilities.  3 replicates of untreated were compare to 3 replicates each of 100 ng/ml LPS stimulation for 18 hours and CstF-64 constituitive over-expression.
Keywords = RAW 264.7 macrophage

RAW macrophages constituitively over-expressing CstF-64.  RNA was isolated using Ultraspec RNA isolation system.  Hybridization and measurements were performed at the Univeristy of Pittsburgh Genomics and Proteomics Core Facilities.  3 replicates of untreated were compare to 3 replicates each of 100 ng/ml LPS stimulation for 18 hours and CstF-64 constituitive over-expression.

RAW macrophage Untreated Control.  RNA was isolated using Ultraspec RNA isolation system.  Hybridization and measurements were performed at the Univeristy of Pittsburgh Genomics and Proteomics Core Facilities.  3 replicates of untreated were compare to 3 replicates each of 100 ng/ml LPS stimulation for 18 hours and CstF-64 constituitive over-expression.

we treated the 36M2 cell line with carboplatin 100μM or vehicle-control for 24hrs and cells were harvested and processed for RNA isolation at 24, 30 and 36hrs after treatment.

Cells were grown in RPMI 1640 media with L-glutamine, 10% fetal bovine serum and 1% of penicillin/streptomycin.

Total RNA was isolated using the RNeasy Mini Kit (Qiagen Valencia, CA, USA) according to manufacturer’s instructions

cDNA synthesis and hybridization on oligonucleotide microarrays (U133 Plus 2.0 Array GeneChip, Affymetrix, Inc., Santa Clara, CA) containing approximately 54,700 transcripts were carried out using standard protocols.

Gene expression data from 36M2 trated with Vehicle-Control for 36hrs

After culturing the primary human B cells for a minimum of 36 hours, cells were transferred to retronectin-coated plates and incubated with virus for 6-8 hours in IMDM 5% FCS medium. Thereafter, cells were cultured with CD40L-L cells in 10% FCS medium for 72 hours after which YFP positive cells were sorted and RNA was isolated. For cell line transductions, cell lines were transferred to retronectin-coated plates and incubated with virus for 24 hours. Thereafter, medium was refreshed and cells were cultured for 24 hours after which YFP positive cells were sorted and RNA was isolated. For siRNA-mediated knockdown, cells were transiently transfected using the Lonza nucleofection system. 2 days after transfection, RNA was isolated.

Isolated human B cells were cultured on CD40L-L cells, IL-21(25 ng/ml, R&D systems, Abingdon, UK) and IL-2 (40U/ml, prospec, East Brunswick, NJ) in Iscove’s modifies Dulbecco’s medium (IMDM) containing 10% FCS, 100 units per ml of penicillin, and 100 μg per ml of glutamine (IMDM 10% FCS). DLBCL cell lines OCI-Ly1 and OCI-Ly7 were cultured in IMDM 10% FCS. OCI-Ly10 was cultured in IMDM 20% medium, supplemented with 35 μM β-mercaptoethanol.

Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol

Total RNA was isolated from primary B cells using the Rneasy micro kit (Qiagen, Valencia, CA),according to the manufacturer’s protocol or from DLBCL cell lines, using using Trizol (Invitrogen) according to manufacturer’s protocol,

RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 200 ng of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

OCI-Ly7;diffuse large B-cell lymphoma (DLBCL);LZRS-FOXP1-IRES-YFP;FOXP1 overexpression

total RNA extracted from cells obtained using biopsy in a patient having inflammatory bowel disease

total RNA extracted from cells obtained using biopsy in a patient having colorectal cancer

Gene expression data from N-BMSCs were transfected with siTERC-RNA (siTERC) construct

Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

Gene expression intensities were calculated using GeneChip® Command Console® Software (AGCC) and Expression Console™ Software. RMA normalziation was performed to generate the CHP files. Genesifter software and Pairwise comparisons were perfomed with Benjamini and Hochberg correction.

Embryos were dissected and peripheral blood was collected
RNA-Stat 60 extraction of total RNA was performed according to the manufacturer's instructions.

The hybridization cocktail containing the fragmented and Biotin labeled cDNAs was hybridized to The Affymetrix Mouse 430 2.0 GeneChip. The chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described by Affymetrix. The probe arrays were stained with streptavidin phycoerythrin solution (Molecular Probes, Carlsbad, CA) and enhanced by using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA).

Per RNA labeling, 5 micrograms  of total RNA was used in conjunction with the Affymetrix recommended protocol One-Cycle Target Labeling and Control Reagents(Catalog# 900493 ).

peripheral blood from 8-10 E12.5 embryos;Cbfb+/MYH11;Cbfb+/MYH11 x C57/Bl6

after transfection and selection, cells were grown to confluence and harvested

Affymetrix M10 scanner, using software Affymetrix Genechip Command Console v2.0.0.1029

All analysis performed in R. Data normalized using RMA from the limma package, and further normalization for Twist1-expression was carried out. For R script used for analysis, see supplemental data (Gajula et al., 2013)

Affymetrix Mouse Exon 1.0 arrays, according to manufacturer's instructions, washed with Fluidics 450

Affymetrix WT Labeling kit, according to manufacturer's instructions

14 days hindlimb suspended, 1 day reloaded
RNA was isolated from cryosections using RNeasy kit (Qiagen). 5 microgram total RNA was subjected to microarray analysis.

RNA was isolated from cryosections using RNeasy kit (Qiagen). 5 microgram total RNA was subjected to microarray analysis

background correction, VS, RSN using Bioconductor package lumi (Du et al., 2008)

Qiagen miRNeasy Mini kit and TissueRaptor following manufacturer's instructions

Illumina TotalPrep RNA Amplification Kit (Ambion) according to manufacturers’ standard procedure

The data were analysed using Expression Console 1.0 (Affymetrix) and Bioconductor package 'affy' under R-2.7.0. Background correction, normalization and probe summarization was performed with RMA (function just.rma()).

Scanned on an Agilent G2565BA scanner.
Images were quantified using Agilent Feature Extraction Software (version A.9.5).

gMedian and rMedian signal were used. Array values were normalized to equal median.

Total RNA extracted using Qiagen RNAeasy mini kit following manufacturer's instructions. In the co-culture condition, LM2 cells were labeled with GFP, and HMVEC-L cells were labeled with SNARF before co-culture. LM2 cells were isolated by FACS 48 hours after co-culture.

Sample RNA was hybridized on the two color Agilent human 4x4k arrays with reference RNA. Agilent Gene Expression Hybridization kit was used.

Labeled with Agilent Low RNA Input Amplification kit following manufacturer's instructions.

LM2 cancer cells were cultured alone or on top of a monolayer of human lung endothelial HMVEC-L cells

CML CD34+CD38- cells were selected using flow cytometry sorting and treated with IM, LBH and the combination of IM and LBH or cultured without exposure to drugs (controls) for 24 hours (n=3 each).

Microarray data analyses were performed using R (version 2.9) with genomic analysis packages from Bioconductor (version 2.4).
Expression data were normalized using the robust multiarray average (RMA) algorithm, with background adjustment, quantile normalization and median polish summarization.
Differentially expressed genes were identified by calculating empirical Bayes moderated t-statistic, and p-values were adjusted by FDR using the “LIMMA” package.
Gene Set Enrichment Analyses (GSEA) was performed using GSEA software version 2.04 [http://www.broadinstitute.org/gsea/] to detect enrichment of predetermined gene sets using t-scores and gene sets in C2 (curated gene sets) category from the Molecular Signature Database (MsigDB).

Total RNA from 5000 cells was extracted using the RNeasy kit (Qiagen), amplified and labeled using GeneChip Two-Cycle Target Labeling and Control Reagents (Affymetrix, Santa Clara, CA).

Standard Affymetrix protocol (15 µg cRNA from each sample was hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays)

sorted CML CD34+CD38- cells cultured without exposure to drugs (controls)

Female (age range 33-49), skin biopsy from upper nates taken 48 hours after nickel exposure

Discarded MPM surgical specimens (n=40), normal pleura specimens (n=5), and normal lung specimens (n=4) were freshly collected (and snap frozen) from patients who underwent surgery at Boston’s Brigham and Women’s Hospital (BWH) between October 1998 and August 2000.  All of these patients underwent extrapleural pneumonectomy with heated intra-pleural cisplatin chemotherapy delivered after the specimens were removed.  All normal specimens were obtained from patients who were never diagnosed with MPM.  Two human MPM cell lines (MS589 and MS428) were kindly provided by Jonathan A. Fletcher, M.D., Department of Pathology, BWH.  The JMN1B MPM cell line19,20 has been described previously.  The SV40-immortalized, non-tumorigenic mesothelial cell line (Met-5A)21 and the MPM cell line MSTO-211H22 were purchased from the American Type Culture Collection.  Normal tissues were obtained from additional consented patients undergoing treatment for diseases other than MPM.  All MPM samples used in these studies contained relatively pure tumor (greater than 50% tumor cells per high power field examined in a section adjacent to the tissue used).  The microscopic slides from the patients’ resection specimens were reviewed by one of the authors (J.G.), and the diagnosis and histologic subclassification of MPM confirmed in all cases.  Linked clinical and pathological data were obtained for all patients who contributed tumor specimens.  Specimens and data were rendered anonymous to protect patient confidentiality.  Studies utilizing human tissues were approved by and conducted in accordance with the policies of the Institutional Review Board at BWH.

7 days following CBDL or sham surgery, the animals were euthanized and the jejunum was harvested under sterile conditions.

The data were normalized by Affymetrix Expression Console using RMA method.

Trizol extraction of total RNA performed per manufacturer instructions.

10ug of cRNA were hybridized for 16 hours at 45degrees on Mouse Gene 1.0 ST Arrays.

Biotinylated cRNA was prepared per standard Affymetrix protocol from 1ug total RNA.

The data were normalised using quantile normalisation with Beadstudio

Total RNA was isolated from Peripheral Blood using the PAXgene RNA isolation kit (PreAnalytix, GmbH, Germany). Total RNA yield (ng) was determined spectrophotometrically using the NanoDrop ND-1000 (Wilmington). Total RNA profile was determined using the Bioanalyzer 2100 (Agilent).

Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification kit for Illumina arrays

The JAK2V617F-mutant AML cell line HEL was treated with 2 independent shRNA lentiviruses for JAK2 in a pLKO-puromycin selectable vector as well as 2 non-targeting shRNA controls (sh-Luciferase and GFP vector control).

The cDNA was fragmented, labeled and hybridized to Affymetrix HG_U133AAofAv2 microarrays (Affymetrix, Santa Clara, CA)

Linear amplification of 20 ng of total RNA was performed using the Ovation Biotin RNA Amplification and Labeling   System   (Nugen)

JAK2V617F-mutant AML cell line HEL;JAK2 knockdown (Jak2-10 shRNA)

immortalized human mammary epithelial cell line treated with fresh medium for 36hours

breast cancer derived cell line treated with fresh medium for 12 hours

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

The tumor tissue (100 mg) was homogenized in Ultraspec (Biotecx Labs, Houston, TX), and total RNA was extracted according to the manufacturer's protocol.

Following fragmentation, 10 ug of cRNA were hybridized on Murine Genome 430 2.0 Array GeneChip. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

Six PyV-mT St6gal1 null and wild-type tumor pairs were used, in four independent pools of three tumors each.

The data were analyzed with the Affymetrix GeneChip Operating Software 1.4 (GCOS 1.4) using Affymetrix default analysis settings and global scaling to a target intensity value of 500.

Tissue was processed and extracted using TRIzol reagent (Invitrogen) and total RNA was purified using RNeasy columns (Qiagen) according to manufacturer's protocols.

Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45C on the GeneChip Human Genome U133 Array Set HG-U133A. GeneChips were washed and stained on the Affymetrix Fluidics Station 450 using Fluidics Script EukGE-WS2v5

Biotinylated cRNA was generated according to the standard Affymetrix protocol from 5 ug of total RNA (GeneChip Expression Analysis Technical Manual; Affymetrix).

LCLs were established by Epstein-Barr virus transformation of lymphocytes as previously described.22  LCLs were grown for RNA isolation under tightly controlled growth conditions to minimize transcriptional variations due to minor differences in cell culture.  RNA was extracted when cells were in log phase growth using Qiagen RNeasy Midi Kits as per the manufacturer’s instructions.  RNA quality was accessed using an Agilent 2100 bioanalyzer and expressed as an RNA integrity number (RIN) value.  All samples had an RIN of 9.9 or 10, which designates very high quality RNA

Concordant for Epilepsy twin pair 3 (Affected patient of MZ twin pair CCE3)

25-day-old rats were treated with either solvent or acrylamide daily (30 mg/kg) via oral gavage. Tissues (cerebellum, right and left sciatic nerves, and spinal cord) were collected 21 days after treatment.

25-day-old male Wistar rats were housed two per cage and maintained in a 12 h light / 12 h dark cycle with food (Purina 5001) and water provided ad libitum.

Image analysis, scaling (TGT = 500), and probeset-level data analysis was performed using default parameters in GCOS v1.1.

The Qiagen RNeasy Lipid Tissue Midi-kit was used for total RNA extraction.

Affymetrix GeneChip Hybridization protocol, and GeneChip Fluidics Station 450 default protocol were used. GeneChip Rat Genome 230 2.0 arrays were used.

ACRL_SN__Treated_A
Gene expression data from acrylamide-treated rat pups.

ACRL_SN__Control_B
Gene expression data from saline-treated rat pups.

ACRL_SN__Control_A

ACRL_SC__Treated_B

ACRL_SC__Treated_A

ACRL_SC__Control_B

ACRL_SC__Control_A

Discordant twin pair 5 (Unaffected patient of MZ twin pair DCE5)

ACRL_CBM__Treated_A

TP22;CCE1.2;Childhood Absence Epilepsy + Febrile Seizures;-5;22;25;FEMALE;None

Concordant for Epilepsy twin pair 1 (Affected patient of MZ twin pair CCE1)

in vitro Treatment: V2O5, Treatment Time: 4, Units of Treatment Time: hour, Dose or Concentration: 10, Units of Dose or Concentration: ug/cm2

cells_ATCC 16Lu_human lung fibroblasts_JCB_10_4_37_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

JCB_10_4_37_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

cells_ATCC 16Lu_human lung fibroblasts_JCB_10_4_7_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

JCB_10_4_7_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

in vitro Treatment: V2O5, Treatment Time: 8, Units of Treatment Time: hour, Dose or Concentration: 10, Units of Dose or Concentration: ug/cm2

cells_ATCC 16Lu_human lung fibroblasts_JCB_10_8_23_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

JCB_10_8_23_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

cells_ATCC 16Lu_human lung fibroblasts_JCB_10_8_38_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

JCB_10_8_38_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

cells_ATCC 16Lu_human lung fibroblasts_JCB_10_8_8_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

JCB_10_8_8_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

Cells were transfected with double-stranded RNA oligonucleotides using the Lipofectamine RNAiMax reverse transfection method (Invitrogen, UK), according to manufacturer's protocols. Two different siRNAs against LRH-1 were used: ON-TARGETplus siRNA J-003430-07 (siLRH-1_#2) and J-003430-08 (siLRH-1_#3) from Dharmacon. siGENOME Non-targeting siRNA (Dharmacon, cat. no.:D-001210-01) (siControl) was used as negative control. All siRNA experiments used the double-stranded RNA oligonucleotides at a final concentration of 80 nM.

The BeadChiP image data were preprocessed using GenomeStudio (Illumina). The expression data were then log2 transformed and quantile-normalised using Partek Genomics Suite.

Total RNA was extracted using the RNeasy Kit from QIAGEN following manufacturer's instructions.

Labelled cRNA was hybridised to the Illumina HumanHT-12 V3.0 expression BeadChip according to the Illumina Whole-Genome Gene Expression Direct Hybridization Assay Guide.

Biotinylated cRNA were prepared with the Ambion Illumina® TotalPrep™-96 RNA Amplification Kit for Illumina arrays.

Peripheral blood mononuclear cells;healthy control;GTE6;90min;White;Male

Peripheral blood mononuclear cells;healthy control;GTE6;80min;White;Female

Peripheral blood mononuclear cells;healthy control;LT6;80min;White;Female

Peripheral blood mononuclear cells;TTF=65min;Race=White;Sex=Female

Peripheral blood mononuclear cells;healthy control;GTE6;85min;White;Female

Gene expression data from human colon biopsies; involved area UC active patient

Human colon biopsies from UC patient with active disease (involved mucosa)

Gene expression data from human colon biopsies; non-involved area UC active patient

Human colon biopsies from UC patient with active disease (non-involved mucosa)

This is wt-Gfp P10 replicate 2.

Peripheral blood mononuclear cells;healthy control;GTE6;90min;White;Female

Peripheral blood mononuclear cells;healthy control;LT6;100min;White;Male

PBMCs were isolated at day 0, day 180 (6months) and day 365 (12 months) from the following groups:i) placebo (control), n=6 arrays (6 diabetic males); ii) grape extract, n=6 arrays (6 diabetic males); iii) resveratrol-enriched grape extract, n=6 arrays (6 diabetic males)

Male patients' heparinised blood was processed within two hours after extraction and used to isolate PBMCs. Isolation was carried out under sterile conditions to avoid the activation of monocytes. Blood was diluted 1:1 with RPMI 1640 cell culture medium and processed by density gradient centrifugation with Histopaque-1077 (Sigma Aldrich) according to the manufacturer instructions. After washing the cells (x2) with phosphate buffer solution (PBS), the PBMCs were lysed using RLT Buffer (Qiagen) and stored at –80C for RNA extraction.

The data were analyzed with Robust Multichip Average (RMA), using CEL files obtained from Affymetrix Expression Console (version 1.1.2).

Total RNA was isolated using AllPrep DNA/RNA/Protein Mini Kit (Qiagen) according to the manufacturer's instructions. RNA was eluted in RNAse free water, aliquoted and stored at –80C.

Following fragmentation, 18 cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix Human Gene 1.0 ST. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA was prepared according to the One-Cycle target IVT labeling Affymetrix protocol from 4 μg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

male;placebo (A);day 0 (basal);Isolated peripheral blood mononuclear cells (PBMCs)

Isolated PBMCs from diabetic male patient_Placebo_basal expression level

siRNA was synthesized as duplex by Life Technology and transfected directly using Invitrogen RNAiMAX. All steps were conducted according to the included vendor protocol.

Cells were cultured in culture dishes pre-coated with 0.1% gelatin with commercial EGM2 media from Lonza

standard Affymetrix protocol, performed by Penn Genomic Analysis Core

standard Affymetrix protocol, conducted by Penn Bioinformatics Core and Dr. John Tobias
Expression level of genes in RISC-free or siYAP treated HUVEC

Whole blood from affecteds and controls according to protocols approved by the institutional review board.

GeneChips were scanned using the Affymetrix GCS 3000 G7 scanner.

The open source R/Bioconductor packages (Fred Hutchinson Cancer Research Center, Seattle, WA, USA) were employed to normalize the data by GC Robust Multi-array Average (GC-RMA) algorithm. High-level analyses were performed using MEV and PARTEK Genomics Suite (Partek® software, Partek Inc., St. Louis, MO, USA.). We used MATLAB (The Math Works, Inc., Natic, MA) and PARTEK Genomics Suite for the statistical analysis.

The Paxgene Blood RNA kit was used for total RNA isolation according to the manufacturer's instructions.

Following fragmentation, 15 ug of cRNA were hybridized according to the standardized protocol from Affymetrix on Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed in the Affymetrix automated fluidic station.

cDNA and biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA.

This is wt-Gfp E16 replicate 3.

This is wt-Gfp E16 replicate 2.

This is wt-Gfp P10 replicate 1.

This is wt-Gfp E16 replicate 4.

This is wt-Gfp 4 weeks replicate 3.

This is wt-Gfp E16 replicate 1.

This is wt-Gfp 4 weeks replicate 4.

human skeletal muscle from diabetic individuals before insulin therapy

skeletal muscle;insulin resistant;untreated;0.79;88;101;1652;86;43.1;46.1;3706.6

human skeletal muscle from diabetic individuals after insulin therapy

GeneChips were scanned using the Affymetrix GeneChip scanner 3000 running GCOS software.

Probe signals were quantile normalized and probeset signal intensity estimates generated using RMA.

Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer’s instructions, whereby 600 μl RLT buffer / 30 μg of tissue were first homogenized by pipetting or using a glass dounce homogenizer, before further disruption in a QIAshredder column (Qiagen).

The standard PICR hybridisation protocol was followed for hybridisation RNA labelled using the 1-cycle protocol to standard GeneChips with 11mciron featrue sizes (http://bioinformatics.picr.man.ac.uk/mbcf/downloads/_HYBRIDISATION_PROTOCOLS/PICR%20One%20Cycle%2011uM%20feature.pdf). This is derived from the Affymetrix Standard Eukaryote Sample Preparation Protocol (section 2, chapter 3) of the GeneChip Expression Analysis Technical Manual (version April 2004) (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA. A complete description of all procedures is available online at http://www.affymetrix.com/support/technical/manual/expression_manual.affx and at http://bioinformatics.picr.man.ac.uk/mbcf/One_Cycle_Target_Prep_Protocol_PICR_v1-0.pdf

Gene expression data from HtrA2 KO mouse cortex tissue at post-natal day 29

Pineal glands and retinas were collected during the day (ZT6) and night (ZT20). 6 pineal glands or retinas were pooled per sample. ZT20 samples were collected under dim red lighting conditions.

NeuroD1 conditional knockout (cKO) mice were generated by crossing NeuroD1flox/flox mice with NeuroD1+/flox::Crx-cre+/- mice to produce NeuroD1flox/flox/Crx-cre+/- (cKO) mice and  NeuroD1flox/flox::Crx-cre-/- (CON) mice. CON and cKO mice (both genders, 2 months of age) were bred and housed in LD 12:12 light cycles with food and water ad libitum.

Total mouse pineal and retina RNA was isolated using the RNeasy Micro RNA isolation kit (Qiagen).

GeneChip® One-Cycle Target Labeling from Affymetrix. Fluidics script EukGE_Ws2v5 was used with GeneChip® Fluidics Station 450.

Nugen Ovation RNA amplification system V2 and FL-Ovation cDNA Biotin Module V2.

CR_D3
Gene expression from the retina of a control mouse at ZT6.

CR_D2

CR_N2
Gene expression from the retina of a control mouse at ZT20.

CR_N1

TP_N1
Gene expression from the pineal gland of a NeuroD1 cKO mouse at ZT20.

C57BL/6J; NeuroD1flox::Crx-Cre+/-;NeuroD1 cKO;2 months;pineal gland;ZT20

2.5 million cells were resuspended in 10ml of fresh media in 10cm dishes.  The next day, DMSO, TNKS inhibitor, MEKi inhibitor or the combination of both was added for 4hrs and 16hrs

Micorarray Analysis Suite version 5.0 (MAS 5.0) background correction, scaled to 150

RNeasy Plus kit (qiagen) following the manufacturers instructions

Affymetrix GeneChip eukaryotic hybridization protocol (Affymetrix Inc.)

Nugen Ovation RNA Amplification System+ WB + FL cDNA Biotin Module V2 (NuGen Lts)

Gene expression data from SW480 cells treated with MEK+TNKS inhibitors for 16h

Gene expression data from SW480 cells treated with MEK inhibitor for 16h

Gene expression data from SW480 cells treated with TNKS inhibitor for 16h

Gene expression data from SW480 cells treated with MEK+TNKS inhibitors for 4h

Expression intensity for each probe set was calculated using the RMA method available in the rma package from Bioconductor.  Differential expression analysis was conducted using empirical Bayes moderated t statistics available in the limma package from Bioconductor.

For DNA microarray analysis, labeled RNA (n = 6) prepared from brown adipose tissues was hybridized to Affymetrix mouse genome 430 2.0 arrays.

gemcitabine resistant Calu3 were treated with vehicle in analogy to cultures treated with compounds

cells were cultured in RPMI 1640 supplemented with 10% FBS and 2 mM glutamine in 95% air, 5% CO2

GeneChips were scanned using the Affymetrix GeneArray scanner 2500.

Rneasy column (Qiagen) purification of total RNA was performed according to the manufacturer's instructions.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 701021 Revision 4, Affymetrix).

gemcitabine resistant Calu3 cells, treated for 10 cycles of 10 days each with vehicle (still gemcitabine resistant)

gemcitabine resistant Calu3 derivative generated from the parental Calu3 line by consecutive treatments with 50 nM gemcitabine over a period of 3 months

Calu3 human non-small lung cancer cells, gemcitabine resistant (Ligand)

parental Calu3 were maintained in regular growth medium and not subjected to treatment

epithelial, Organ: lung, Disease: adenocarcinoma (pleural effusion), Gender: male, Ethnicity: caucasian

The processed array was scanned using a GeneChip Scanner 3000 7G (Affymetrix).

Data was analyzed using ArrayAssist 5.0 software (Stratagene). Probe levels were calculated using the GCRMA algorithm.

Total RNA (5 µg) from Placenta (E10.5) was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany).

10 µg of fragmented cRNA were hybridized (16h) to the array. Staining and washing was conducted according to the Affymetrix protocol.

Double stranded cDNA was synthesized (GeneChip® Expression 3' Amplification One-Cycle Target Labeling and Control Reagents, 900493) and biotin labeled cRNA was in vitro transcribed (GeneChip® Expression 3' Amplification One-Cycle Target Labeling and Control Reagents, 900493). Cleanup of the cDNA and the fragmented cRNA was carried out with the GeneChip Sample Module (Affymetrix,900371). The integrity of the total RNA and of the subsequent preparation steps was validated using the Agilent 2100 bioanalyzer (Waldbronn, Germany).

The whole procedure was carried out according to the Affymetrix standard protocol (Eukaryotic Sample and Array Processing).

The placenta (E 10.5) of a congenic adra2B+/+ mouse embryo (maternal genotype Adra2b+/-) was rapidly dissected and flash frozen.

Tissue was dissected in an RNase free manner and stored in RNAlater (Ambion) at -20C for no more than 1 month. Homogenisation in QIAzol was conducted mechanically and the aqueous phase separated using a PLG column (Eppendorf). RNA was further purified using RNeasy minelute cleanup kit  (Qiagen). RNA quality was confirmed using nanodrop and bioanylizer 2100 (Agilent).

Protocol available at http://www.AMBION.com/catalog/CatNum.php?1753

Sample represents the supraoptic nucleus from 5 dehydrated animals (3 Days)

Additional details provided in accompanying manuscript, BC1TC_NOC

Additional details provided in accompanying manuscript, BC1 TC_TCR

The data were analyzed with R/Bioconductor version 2.10 using Affy package default analysis settings. The trimmed mean target intensity of each array was arbitrarily set to 100.

RNA Isolation was performed using the Tripure Isolation Reagent (Roche).Quality control was performed with Agilent Bioanalyser.

The biotinylated cRNA targets are were cleaned up, fragmented, and hybridized to GeneChip expression arrays according to standard Affymetrix protocols.GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA using GeneChip IVT Labeling Kit.

Mkn28;human gastric tubular adenocarcinoma;stomach (70 year-old female)

AML blasts from bone marrow;test;mutated;M5b;internal tandem duplication (ITD)/D835 mutation

Sample name: NASH1
GC1966new.CEL

Peripheral blood mononuclear cells (PBMCs) were separated from 50 ml Buffy Coat blood of healthy donors (DRK-Blutspendedienst, Frankfurt, Germany) by Ficoll-Hypaque density gradient centrifugation (Biochrom AG, Berlin, Germany). Human monocytes were isolated from PBMCs by magnetic-associated cell sorting (MACS) using paramagnetic microbeads conjugated to monoclonal anti-human CD14 antibodies (Miltenyi, Bergisch Gladbach, Germany).

Differentiation of monocytes into immature DCs(iDCs) was achieved by cultivating cells in RPMI 1640 medium (Invitrogen, Karlsruhe, Germany) supplemented with 100 mg/ml Refobacin (Merck, Darmstadt, Germany), 10% fetal calf serum (FCS, Sigma-Aldrich, Taufkirchen, Germany), 100 ng/ml recombinant human granulocyte-macrophage colony-stimulating factor (Leukine, Novartis, Basel, Switzerland) and 20 ng/ml interleukin-4 (R&D Systems, Wiesbaden, Germany). Cultures were fed with fresh medium and cytokines every other day. After culturing for 6 days at 37°C and 5% CO2, iDCs were collected, washed with Hanks buffer and 1x 106 cells were resuspended in 1 ml complete medium. If iDCs were stimulated with fungi, 1 x 106 Aspergillus fumigatus germ tubes were added for 6h.

Dendritic cells generated from blood of donor 1 + A. fumigatus germ tubes

The probe arrays were scanned by using a GeneChip Scanner 3000 (Affymetrix).

For evaluation and analysis of array data, software packages from the Bioconductor project (www.bioconductor.org; Gentleman et al., 2005) were run under R (www.r-project.org). Data were normalized using the function expresso from the affy-package, using variance stabilization normalization (VSN; Huber et al., 2002) and perfect match values only.

Total RNA was isolated using RNeasy Mini kit and QiaShredder spin columns (Qiagen, Hilden, Germany) according to the manufacturer‘s protocol. RNA was eluated with 35 µl RNase-free water and quality and concentration was determined with the 2100 Bioanalyzer (Agilent, Waldbronn, Germany).

Labeled RNA was fragmented and incubated for 16 h at 45°C with a HG-U133 Plus 2.0 human genome array (Affymetrix). The gene chips were automatically washed and stained with streptavidin-phycoerythrin on a fluidics station.

cRNA was prepared and biotin-labeled by in vitro transcription from 2 µg of total RNA according to the manufacturers protocol without modification (One-Cycle Labeling Kit, Affymetrix, Santa Clara, USA)

Immature dendritic cells cultivated together with Aspergillus fumigatus germ tubes for 6h

Dendritic cells generated from blood of donor 2 + A. fumigatus germ tubes

Transfected with 50nM Renilla Luciferase siRNA. 72h later, cells were cutured 4h without FCS

Data were normalized using RMA as implemented in the Affy package (version 1.28.0) of Bioconductor. Expression values are represented on a log2-scale.

Cell lysates were homogenized with the QiaShredder Column (Qiagen), and total cellular RNA was extracted with the Rneasy Mini kit (Qiagen) following manufacturer’s instructions.

Following fragmentation, 15 microgram of cRNA were hybridized for 17 hr at 45°C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 nanogram total RNA.

Transfected with 50nM Renilla Luciferase siRNA. 72h later, cells were cutured 4h without FCS and stimulated with 10ng/ml LIF 1h

Transfected with 50nM SIN3A siRNA. 72h later, cells were cutured 4h without FCS

Transfected with 50nM SIN3A siRNA. 72h later, cells were cutured 4h without FCS  and stimulated with 10ng/ml LIF 1h

MCF-7 human breast cancer cells were transfected with 20 nM of siGENOME ctrl (siGL3) or ERK5 (Thermo Scientific) using Dharmafect1 following the manufacturer’s instructions. After 72 h of transfection, cells were treated with 0.1% control ethanol vehicle or 10 nM E2 for 24h

Gene expression data from MCF-7 cells, siERK5 treatment 72h, 0.1%EtOH for 24h

Gene expression data from MDA-MB231 PIAS1 shRNA cells grown in SCM for 30 h.

RNA isolated from lung tissue of Nrf2 knock-out mouse, control group

lung tissue;CD-1_Nrf2 -/-;13 weeks + 1 day;fresh air, treatment over 1 day, 3x1h exposure per day

Gene expression data from MDA-MB231 control shRNA cells grown in SCM for 30 h.

lung tissue;CD-1_Nrf2 -/-;13 weeks + 1 day;2R4F whole mainstream smoke 125 µg/ml, treatment over 1 day, 3x1h exposure per day

Gene expression data from MDA-MB231 PIAS1 shRNA cells grown in DMEM for 30 h.

total RNA from biosource CC#4S

Mice were used as control or exposed to intratracheal 2% polidocanol 3 days prior to collection (injury).  Mice were culled by pentobarbitol overdose and exsanguinated.  Whole trachea was isolated, excess connective tissue removed, and immediately processed for RNA purification.

Mice were maintained on a reversed 12:12-h light-dark cycle with controlled temperature (21 ± 1°C) and humidity. Food and water were provided ad libitum.

Microarrays were scanned using the Agilent Technologies Scanner G2505B US45102871 (ChipScan software version A.7.0.1), scan region 61 X 21.6mm, scan resolution 5 micron single pass, extended dynamic range selected (XDR Hi 100%; XDR Lo 10%).

Data was extracted from the scanned image using the Agilent Feature Extraction Software version. 9.1.3.1 (protocol GE1-v5_91_0806). The VALUE column came from the gProcessedSignal column of the result table.

Total RNA was isolated using the Qiagen RNeasy kit. The integrity of the RNA was confirmed with analysis by the Agilent 2100 bioanalyser using the RNA 6000 LabChip kit

The Agilent Hybridisation Kit (catalogue number 5188-5242) was used in conjunction with Agilent Mouse Oligo Arrays (catalogue number G4122F). 2μg of the labelled sample RNA were used for hybridisation according to the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol The hybridisation was performed for 17 h at 65 ºC at 10 rpm. Slides were them washed for 1 min at 22 ºC in Wash Solution 1 (catalogue number 5188-5325) and 1 min at 22 ºC in Wash Solution 2, pre-warmed to 37 ºC (catalogue number 5188-5326). Slides were incubated for 30s in Agilent Stabilisation and Drying Solution (catalogue number 5185-5979).

600 ng RNA and 3 µl Agilent One-Color RNA Spike-In RNA were labelled with the Agilent Low RNA Input Linear Amplification Kit PLUS, One-Color according to Manufacture’s instructions as follows: 1.2 µl T7 Promoter Primer was added to 600 ng RNA and 3 µl spike in control and denatured at 65 ºC. First Strand Buffer, DTT, dNTP MMLV and RNaseOut was added. The cDNA was synthesised during the following incubation step (2h at 40 ºC). After 10 min denaturation at 65 ºC and the addition of Cy-labelled CTP, Transcription Buffer, DTT, NTP, PEG, RNaseOUT, Inorganic Phosphatase, and T7 RNA Polymerase the synthesis of the fluorescent labelled cRNA was performed during the second incubation step (2 h at 40 ºC). The labelled cRNA was purified with the Qiagen RNeasy Mini Kit according to Manufacturer’s protocol.

Total RNA was extracted from exponentially growing ES cells previously tryptinizied and collected.

ES cell lines were grown on 0.1% gelatinaized tissue culture dishes in DMEM in presence of  15% Serum and Leukemia inhibitory factor.

GeneChip arrays are scanned using default parameters. Affymetrix GeneChip Command Console software (AGCC) was used to acquire GeneChip images and generate .DAT and .CEL files.

Microarray data is analyzed using Affy (quantile-normalized with rma method) and Limma packages in R. For annotating affy IDs, mogene10sttranscriptcluster.db is used.

GeneChip Hybridization, Wash and Stain Kit (Affymetrix cat #900720) is used to prepare the Hybridization Cocktail. The kit contains mix for target  dilution, DMSO at a final concentration of 7% and pre-mixed biotin-labelled control oligo B2 and bioB, bioC, bioD and Cre controls (Affymetrix cat  #900299) at a final concentration of 50 pM, 1.5 pM, 5 pM, 25 pM and 100 pM, respectively. These control oligos serve as positive controls for  hybridization. Biotin-labeled sense targets were diluted in hybridization buffer at a concentration of 25 ng/ul and denatured at 99 °C for 5 minutes.  Hybridization cocktails were incubated at 45 °C for 5 minutes and centrifuged at maximum speed for 1 minute prior to loading into the GeneChip® array cartridge. Hybridizations were performed for 16 h at 45 °C in a rotisserie oven at 60 RPM. Upon hybridization, GeneChip cartridges were washed and stained with GeneChip Hybridization, Wash and Stain Kit in the Affymetrix Fluidics Station 450 following the FS450_0007 standard protocol. The cartridge is then loaded into the GeneChip Scanner 3000 7G.

Biotin-labeled cDNA targets were synthesized starting from 150 ng of totRNA. Double stranded cDNA synthesis and related cRNA amplification was performed with Ambion® WT Expression Kit (Ambion, Austin, TX). cRNA was reverse transcribed to cDNA fragmented and terminal labeled with Affymetrix GeneChip® WT Teminal Labeling Kit (Affymetrix, Santa Clara, CA). All steps of the protocol were performed according to manufacturer’s specifications. Efficacy of fragmentation procedure was checked on Agilent Bioanalyzer 2100.

Injury: Laminectomy of lumbar vertebra L2-L3, spinal cord transect at S2 and 1-2mm of spinal cord tissue removed. Wound closed suturing muscles, muscle fascia and skin separately. Sham opration: laminectomy with intact dura. Wound closed. Pain relieved with buprenorfin the first 48 hours.

Expression values were calculated using R and Bioconductor. RMA expression summaries were calculated based on PM intensity values that were normalised (linear quantile plus quantile projection) and background subtracted (global minimization) (Ryge et al, Plos One, 2008). The genes were filtered prior to analysis such that only probe sets annotated in the Ensembl database was included (using biomaRt bioconductor package), so the probe set was reduced from 31099 to 12919.

Spinal cords were snap frozen in liquid nitrogen, cryosectioned into 10 micro meter slices, which were mounted onto POL-membrane metal frame slides (Leica) and fluorescently identied motor neurons were laser microdissected into a collector tube. Total RNA was extrated using the Picopure RNA isolation kit (Arcturus), which were then subject to a two round amplification using the RiboAmp HS RNA amplification kit (Arcturus) according to manufactors instructions. A DNAse treatment was included in the isolation protocol.

Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45 °C on Affymetrix Rat Genome 230 2.0 Arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

Motor neurons retrogradely labelled with flourogold injected into the muscle and intra peritoneally 5-7 days prior to cell extraction.

Gene expression data from motor neurons of the sacral rat spinal cord 21 days post sham operation

100-200 motor neurons, sacral spinal cord, 21days post sham opration

uterus - Mid secretory endometrium from patient with  endometriosis

Gene expression data from the hippocampus of S1P3-knockout mouse

Gene expression data from the hippocampus of S1P2-knockout mouse

Pixel Size	1.56
Filter	570
Scan Temperature
Scanner ID	50103010
Number of Scans	1
Scanner Type	M10

Protocol	EukGE-WS2v4_450
Wash A1 Recovery Mixes	0
Wash A1 Temperature (C)	25
Number of Wash A1 Cycles	10
Mixes per Wash A1 Cycle	2
Wash B Recovery Mixes	0
Wash B Temperature (C)	50
Number of Wash B Cycles	4
Mixes per Wash B Cycle	15
Stain Temperature (C)	25
First Stain Time (seconds)	600
Wash A2 Recovery Mixes	0
Wash A2 Temperature (C)	25
Number of Wash A2 Cycles	10
Mixes per Wash A2 Cycle	4
Second Stain Time (seconds)	600
Third Stain Time (seconds)	600
Wash A3 Recovery Mixes	0
Wash A3 Temperature (C)	30
Number of Wash A3 Cycles	15
Mixes per Wash A3 Cycle	4
Holding Temperature (C)	25
Station	1
Module	3

3 female K5cre-caNrf2 (tg/tg) and 3 female K5cre-wt (tg/wt) mice of one litter were sacrificed at P2.5

Raw gene expression data generated by the GeneChip Operating Software (Affymetrix) were normalized for all probe sets on the array using the Robust Multichip Average (RMA) method.

back skin was cut out and snap frozen in N2, RNA was extracted using GSCN and phenol/chloroform

10 μg of cRNA/sample were hybridized for 16 h at 45°C. Washing and staining with streptavidin-conjugated phycoerythrin were done using a GeneChip Fluidics Station 400 (Affymetrix).

Biotinylated cRNA were prepared from 2 ug total RNA using Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents according to the manufacturer’s protocol.

ESCs (OG2 ESCs carrying an Oct4-EGFP reporter construct and V6.5 ESC line) were cultured on mitomycinC-inactivated DR4 mouse embryo fibroblasts (MEFs) expressing multiple antibiotic-resistances in high-glucose Dulbecco's modified Eagle's medium (DMEM) (all reagents obtained from PAA Laboratories) supplemented with 15% fetal calf serum (FCS), leukemia inhibitory factor (LIF)-conditioned medium, 1% nonessential amino acids (NEAA), penicillin (100 U/ml)/streptomycin (100 U/ml), L-glutamine (2 mM), sodium pyruvate (1 mM), and 2ME (0.1 mM; Sigma-Aldrich) at 37°C in a 5%CO2 incubator. Medium was changed daily and cultures were passaged every 1-2 days before reaching confluence. For differentiation of Pcgf6 KD ESCs, cells were dissociated by trypsin treatment, and cultured in high-glucose Iscove's modified Dulbecco's medium (IMDM) supplemented with 10% FCS (Gibco, Life Technologies), 1% nonessential amino acids (NEAA), penicillin (100 U/ml)/streptomycin (100 U/ml), L-glutamine (2 mM), sodium pyruvate (1 mM) and 2ME (0.1 mM; Sigma-Aldrich)) as hanging drops. EBs were harvested after 48h and transferred into suspension culture with fresh medium. The medium was changed every 2-3 days. For doxycycline treatment, cells were cultured in medium containing 1µg/ml dox (PAA). Representative pictures were taken by phase-contrast microscopy (EVOS) and ESC colony size was analyzed using ImageJ Software.

Subsequent to hybridization, the arrays were washed and stained with streptavidin-phycoerythrin, then scanned in an Affymetrix GeneChip® Scanner 3000 (Santa Clara, CA). All control parameters were confirmed to be within normal ranges before normalization and data reduction was initiated.

Raw data was processed by MAS.5 (Affymetrix) and analyzed using GeneSpring GX10

RNA was extracted from flash frozen patient tissue samples (anaplastic thyroid carcinoma, matched normal thyroid tissue, and unmatched normal thyroid tissue) using TRIzol (Invitrogen) and chloroform (Sigma). All tumor samples are from the primary tumor site. RNA extracts were purified on Spin Chroma column (BD bioscience K1332-2). The 18S/28S bands were verified on a 1% agarose gel. RNA samples were shipped to Advanced Genomic Technology Center Gene Expression Core at the Mayo Clinic in Rochester, MN for further analysis. RNA quality was assessed by Agilent Bioanalyzer (Santa Clara, CA). Reverse transcription to second strand cDNA was generated from 100 ng of good quality total RNA.

The IVT products were column-purified, fragmented, and hybridized onto Affymetrix U133 Plus 2.0 GeneChips® at 45º C for 16 h.

The RNA products were column-purified (Affymetrix) and then in vitro transcribed to generate biotin-labeled cRNA.

cells were grown in Dulbecco's modified Eagle's medium supplemented with 10% (v/v) foetal calf serum at 37°C in a humidified CO2 (5%) incubator

see Affymetrix GeneChip Expression Analysis Manual and Microarray Analysis Suite 5.0 Software. Affymetrix. Reference 701001rev2. 2001
Affymetrix 11 µm feature
parameter settings: alpha 1 = 0.05, alpha 2 = 0.065, tau = 0.15

Affymetrix MAS 5.0, trimmed mean (trimming off the top and bottom 2%) set to 150

Qiagen RNeasy protocol following the manufacturer's recommendations

NuGEN Ovation protocol following the manufacturer's recommendations

BMDM culture: Bone marrow cells were plated overnight to remove stromal cells and mature resident macrophages. Non-adherent cells were transferred to new plates and differentiated with 30% L929 supernatant-conditioned media over 7 days. 70 million cells/ml macrophages was allowed to adhere overnight and stimulated with 1ug/ml LPS.

The images are analyzed using Microarray Suite version 5.0 (MAS 5.0) and comparison analysis are carried out according to the instructions provided by Affymetrix.

Fragmented cRNA is hybridized to the test array for 16 hours at 45C. The test array is then washed and stained with streptavidin-phycoerythrin (SAPE) using the fluidics station.

First strand cDNA is synthesized by reverse transcription using the poly(A) RNA present in the starting total RNA sample. Single stranded cDNA is then converted into double stranded cDNA and purified using the Affymetrix Cleanup Module. An in vitro transcription (IVT) reaction is then carried out overnight in the presence of biotinylated UTP and CTP to produce biotin-labeled cRNA from the double stranded cDNA. The resulting cRNA is fragmented in the presence of heat and Mg+2 before hybridization to the test array.

Total RNA extracted from SH-SY5Y treated with 1mM nicotine for 24 hour.
Treatment, type=time_course, measurement=24.0 h

The glass slides were scanned using an Agilent G2565BA microarray scanner.

The microarray experiments were then carried out using competitive hybridization experiments with Cy5-labeled heart RNAs as a test RNA and with Cy3-labeled pooled heart RNA (Sample N) as a template control for normalization.

200ng of total RNA was used for T7 RNA polymerase-based cRNA labeling.

Cardiac muscles from patients with DCM or specific cardiomyopathy as well as non-disease control hearts

Normal myocardium sold commercially;myocardium sold commercially

HUES6 VGLL4 were transduced with a lentivirus carrying the human VGLL4 open reading frame.

HUES6 were plated on irradiated murine embryonic fibroblasts (MEFs) and grown in media containing KO-DMEM (Invitrogen), 10% Knockout Serum Replacement (KOSR, GIBCO), 10% human plasma fraction (Talecris), 2 mM L-glutamine (Invitrogen), 0.1 mM non-essential amino acids (GIBCO), 0.055 mM β-Mercaptoethanol (GIBCO), and 10 ng/ml bFGF (Invitrogen).

normalized in BeadStudio using the using the average normalization.

Cells were trypsinized and RNA was purified from total cultures in quadruplicates (biological replicates) using a Qiagen RNeasy kit and 200 ng of starting material were used as input for the Illumina TotalPrep Amplification Kit.

human embryonic stem cells cultured with mouse embryonic fibroblasts

Cells were transfected with the annealed siRNAs for 72 h with the use of the Lipofectamine RNAi MAX reagent (Invitrogen) according to manufacturer's recommendations.

HCT116 cells were cultured under 5% CO2 at 37°C in Dulbecco’s modified Eagle’s medium–nutrient mixture F-12 supplemented with 10% fetal bovine serum.

Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10% ).

The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_10_Apr08 and Grid: 014868_D_F_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

RNA was prepared using the NucleoSpin RNA XS (MACHEREY-NAGEL GmbH & Co. KG,Düren) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 25x fragmentation buffer and 10x blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55ul of 2xGE hybridization buffer(HI-RPM) was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

25ng total RNA was amplified by MessageAmp™ II aRNA Amplification Kit#1751(Ambion), and 0.2 ug aRNA labeled Cyanine-3 (Cy3) using the One-Color Quick Amp Labering kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

Gene expression data from HCT116 cells transfected with a control siRNA.

Gene expression data from HCT116 cells transfected with CD44 siRNA.

The details for the hyb/wash/stain are in the Affy protocol: http://media.affymetrix.com/support/downloads/manuals/wt_term_label_ambion_user_manual.pdf.  Briefly, the hybridization cocktail was made with the Affy Hyb buffer, DMSO, Oligo B2, and 20X eukaryotic controls and hybridized to the gene arrays for 17hrs at 45C. The arrays were then washed and stained with SAPE (Streptavidin Phycoerythrin binds to the biotin) and scanned.

Agent: HGF (Hepatocyte Growth Factor)
Treatment dose: 50 nM
Treatment time: 2 hour

Cell Culture Protocol
Media: 1:1 DMEM and HAM's F12 supplemented with ITS
Other: Primary hepatocytes were seeded at 2x106 in 10 cm dishes in the plating medium supplemented with 10% FBS . After 4 hours, the plating medium was replaced to serum-free medium. The following day cells were treated with 50 ng/ml of rhHGF for 0.5, 2, 12 and 24 h. Triplicate cell cultures were established from three individual mice.

After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

NCI Oligo Microarray Hybridization
Other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42øC for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 ul COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100øC for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42øC just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42øC in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), and spin for 3 minutes at 650 rpm to dry. (Refer to "NCI Microarray Manual")

C57BL;male;9-10 weeks;liver;adult;Primary hepatocytes;C57BL;male;9-10 weeks;liver;adult;Primary hepatocytes;Genotype/Genetic variation Alb-Cre +/-

C57BL;male;9-10 weeks;liver;adult;Primary hepatocytes;129SV/C57BL6;male;9-10 weeks;adult;Primary hepatocytes;Genotype/Genetic variation gene knock out;Alb-Cre +/-; Met Fl/Fl

C57BL;male;9-10 weeks;liver;adult;Primary hepatocytes;129SV/C57BL6;male;9-10 weeks;liver;adult;Primary hepatocytes;Genotype/Genetic variation gene knock out;Alb-Cre +/-; Met Fl/Fl

cells were plated in fresh medium and incubated for 4h at 37°C before stimulation with 20 µg/ml CyP (Cyanobacterial Product), for 1h

CD14+ cells from PBMC were cultured for five days in 6-well plates in RPMI, 10% fetal bovine serum (Hyclone) supplemented with GM-CSF 50ng/ml and IL-4 1,000 U/ml. On day 5 monocyte-derived dendritic cells were harvested and replated at 0.5 106 cells/ml (1.5 106 cells/well).

standard Affymetrix procedures, washes performed using Fluidics Station 400

Affymetrix GeneChip Expression 3’ Amplification One-Cycle Target Labeling kit from about 5ug of total RNA

Monocyte derived dendritic cells were generated by culturing human monocytes isolated from buffy coats using CD14 microbeads (Miltenyi)

cells were plated in fresh medium and incubated for 4h at 37°C before stimulation with 0.5 µg/ml S. abortus equi S-form LPS, pure TLR4 agonist (Alexis), together with 20 µg/ml CyP (Cyanobacterial Product) for 3h

cells were plated in fresh medium and incubated for 4h at 37°C before stimulation with 0.5 µg/ml S. abortus equi S-form LPS, pure TLR4 agonist (Alexis), for 3h

cells were plated in fresh medium and incubated for 4h at 37°C before stimulation with 20 µg/ml CyP (Cyanobacterial Product), for 3h

cells were plated in fresh medium and incubated for 4h at 37°C. Cells were left untreated for additional 3h.

Gene expression profile of HT29 cells sensitive to Methotrexate.

LOX-1:221401;LOX1_oxLDL_12hr:221401;Classification:Good;Gradient Severity:0.03;Distortion Severity:0.04;Defective Area (%):0.03;Outlier Area (%):0;3'/5' Mean:1.66;Background Mean Dev.:1.41;Absent (%):59.78;Absent (%) Dev.:1.19;Scaling Factor:0.62;Scaling Factor Dev.:0.08;LOX1;12 hours;Oxidized LDL;221401;HAECT;50 ug/ml;Endothelial;Human:Homo sapiens;LOX1_oxLDL_12hr;282295803

Wild Type ovaries were carefully disected and immediately flash frozen in liquid nitrogen before RNA isolation.

GeneChips were scanned using a GeneArray Scanner at an excitation wavelength of 488nm. Light emissions at 570nm are proportional to the bound target at each oligonucleotides position on the GeneChip® array.

Target RNA is reverse transcribed into cDNA and in-vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization. Hybridized target cRNA is stained with streptavidin phycoerythrin and arrays are scanned using a GeneArray Scanner at an excitation wavelength of 488nm. Light emissions at 570nm are proportional to the bound target at each oligonucleotides position on the GeneChip® array.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

Wild Type mice was euthanized with CO2 and whole ovaries were collected and immediately preserved in liquid nitrogen before RNA isolation.

Genotype: FORKO (FSH Recptor Knock Out). FORKO mice was generated by deleting all variants of FSH-Receptor

The data were normalised using quantile normalisation with Illumina Genome Studio

RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplif Kit

Total RNA was extracted from lymphoblastoid cells of 01-19 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;01-19 is a male with autism and duplication of 15q11-13.

Total RNA was extracted from lymphoblastoid cells of 03-43 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;03-43 is a male with autism and duplication of 15q11-13.

Total RNA was extracted from lymphoblastoid cells of 02-07 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;02-07 is a male with autism and duplication of 15q11-13.

Total RNA was extracted from lymphoblastoid cells of AU006504 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;AU006504 is a male with autism and duplication of 15q11-13.

Total RNA was extracted from lymphoblastoid cells of 98-19 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;98-19 is a male with autism and duplication of 15q11-13.

Total RNA from dissected TM tissues and RNA later-fixed cultured HTM cells at passage three was isolated using RNeasy kit (Qiagen Inc., Valencia, CA) following the manufacturer’s protocol. After DNase treatment, RNA yields were determined using the RiboGreen® fluorescent dye (Molecular Probes Inc, Eugene, OR).  RNA quality was confirmed using the Agilent 2100 Bioanalyzer.

RNA samples were amplified using the OvationTM Biotin RNA amplification and Labeling System (NuGEN Technologies Inc., San Carlos, CA) according to the manufacturer’s instructions. Briefly, total RNA (20 ng) was reverse transcribed into cDNA using a reverse transcriptase and a DNA/RNA chimeric primer. This strand is copied by a DNA polymerase with reverse transcriptase activity to give double-stranded cDNA with an RNA-DNA heteroduplex at one end. This double-stranded cDNA is amplified using the novel isothermal linear amplification method Ribo-SPIA. The cDNA amplification products were fragmented and labeled to generate biotinylated cDNA targets. Biotinylated cDNA targets were hybridized on Affymetrix Human Genome U133 Plus 2.0 high density microarrays following the manufacturer’s instructions.

GeneChips were scanned using the Affymetrix GeneChip Scanner 8000.

The data were analyzed with GeneChip Operating Software version 1.4 (GCOS1.4) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

Total RNA was obtained with Trizol extraction and purified with RNeasy Micro Kit according to the manufacturer's instructions.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 30 ng total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

Gene expression data from microdissected epithelial cells of IPMA

pancreas;epithelial cells;intraductal papillary-mucinous adenoma (IPMA)

peripheral blood;Control;PAXgene Globin reduced;Globin-depleted RNA

T165;Mouse tumorgraft, cohort 0;Male;40;Clear-cell renal cell carcinoma;wild type;mutant;mutant

Gene expression profiling of mouse tumorgraft, cohort 0 of patient T165

Total RNA was extracted immediately following microdissection using the PicoPure RNA isolation kit (Arcturus, Mountain View, CA, USA) according to the manufacturer’s instructions.

Biotin-labeled nucleotides were incorporated to obtain biotin-labeled aRNA required for Affymetrix microarray hybridization.

T144;Mouse tumorgraft, cohort 7;Male;74;Clear-cell renal cell carcinoma;wild type;wild type;mutant

Gene expression profiling of mouse tumorgraft, cohort 7 of patient T144

T158;Mouse tumorgraft, cohort 1;Female;82;Clear-cell renal cell carcinoma;wild type;mutant;mutant

Gene expression profiling of mouse tumorgraft, cohort 1 of patient T158

T158;Mouse tumorgraft, cohort 2;Female;82;Clear-cell renal cell carcinoma;wild type;mutant;mutant

Gene expression profiling of mouse tumorgraft, cohort 2 of patient T158

Stain

For each array, in a new, sterile RNase-free 1.5mL microfuge tube, combine the following:

600.0µl of 2X MES Stain Buffer
48.0µl Acetylated BSA (50mg/mL)
12.0µl Streptavidin Phycoerythrin (SAPE) (1mg/mL)
540.0µl water, Molecular Biology Grade

Total volume is 1200µl.

Divide into two aliquots of 600µl each to be used for stains 1 and 3.

Antibody

300.0µl 2X MES Stain Buffer
24.0µl Acetylated BSA (50mg/mL)
6.0µl Norma Goat IgG (10mg/mL)
3.6µl Biotinylated antibody (0.5mg/mL)
266.4µl water, Molecular Biology Grade

Total volume is 600µl.

After 16 hours of hybridization, remove 250µl of sample (in hybridization cocktail) and put back into eppendorf, containing fragmented cRNA sample.
Fill the array with 250µl of Non-Stringent Wash Buffer (Wash A)

Now ready for Fluidics Station, followed by scanning.

-Thaw components of the Eukaryotic Hybridization Control Kit.
Heat 20X Eukaryotic Hybridization Control to 65°C for 5 minutes to denature cRNA controls.
Equilibrate desired probe array to room temperature.
In a new, sterile RNase-free 1.5mL microfuge tube, add the following components:

-20µl fragmented cRNA
-5µl Control Oligonucleotide B2 (3nM)
-15µl 20X Eukaryotic Hybridization Controls
-3µl Herring Sperm DNA (10mg/mL)
-3µl Acetylated BSA (50mg/mL)
-150µl 2X Hybridization Buffer
-104µl RNase-free water

Total hybridization volume is 300µl

Heat hybridization cocktail to 95°C for 5 minutes, followed by heating at 45°C for 5 minutes.
In a new, sterile RNase-free 1.5mL microfuge tube, combine a volume of 2X Hybridization Buffer with an equal volume of RNase-free water (make 1X Hybridization Buffer).
Wet the probe array by filling it with 250µl of 1X Hybridization Buffer and incubate in Hybridization Oven 640 set at 45°C for 10 minutes with rotation setting at 60rpm.
Centrifuge hybridization cocktail for 5 minutes at max. speed to spin down any insoluble material.
Remove 1X Hybridization Buffer from probe array and fill with 250µl of hybridization cocktail, taking care not to pipette any insoluble material.
Place probe array in Hybridization Oven 640, heated to 45°C and with rotation setting at 60rpm for 16 hours.

Synthesis of Biotin-Labeled cRNA
Thaw components of the ENZO BioArray RNA Transcript Labeling Kit and purified cDNA mixture from the previous day.
In a new, sterile, 1.5mL RNase-free microfuge tube, add the following components:

10µl purified cDNA
12µl RNase-free water
4µl 10X HY Reaction Buffer (vial#1)
4µl 10X Biotin-Labeled Ribonucleotides (vial#2)
4µl 10X DTT (vial#3)
4µl 10X RNase Inhibitor Mix (vial#4)
2µl 20X T7 RNA Polymerase (vial#5)

Total reaction volume is 40µl

Gently mix and spin down.
Incubate in a 37°C water bath for 4 hours.

Cleanup of IVT Reaction

Take out 1ul of the reaction mix for gel electrophoresis inspection.
Using the GeneChip Sample Cleanup Module, add 60µl of RNase-free water to the reaction.
Mix for 3 seconds.
Add 350µl IVT cRNA Binding Buffer and mix for 3 seconds.
Add 250µl of 100% ethanol and mix well (do not centrifuge).
Add sample (~700ul total) to the IVT cRNA Cleanup Spin Column sitting in a 2mL Collection Tube.
Centrifuge for 15 seconds at 10,000rpm.
Discard flow-through and Collection Tube.
Transfer spin column to a new 2mL Collection Tube.
Add 500µl IVT cRNA Wash Buffer to spin column.
Discard flow-through.
Add 500µl of 80% ethanol onto spin column.
Open the cap of the spin column and centrifuge for 5 minutes at max. speed.
Transfer spin column to a new 1.5mL Collection Tube and pipet 11µl of RNase-free water directly onto the spin column membrane.
Centrifuge for 1 minute at max. speed to elute.
Add another 10µl of RNase-free water directly onto spin column membrane and centrifuge for 1 minute at max. speed to elute.

Use spectrophotometric analysis to determine cRNA yield and purity using a 1:100 dilution of purified cRNA (A260/A280 ratio should be close to 2.0 for pure RNA).

Calculate the adjusted cRNA yield using the following:

adjusted cRNA yield = RNAm (total RNAi)(y)

RNAm = amount of cRNA measured after IVT (µg)
total RNAi = starting amount of total RNA (µg)
y = fraction of cDNA reaction used in IVT

For fragmentation, adjusted cRNA concentration must be at least 0.6µg/µl.
The final concentration of RNA in the fragmentation mix can range from 0.5µg/µl to 2µg/µl.

For standard arrays, 15µg of fragmented cRNA is required.
Fragmentation
In a thermal cycler compatible microfuge tube, combine 4µl 5X Fragmentation Buffer (supplied in GeneChip Sample Cleanup Module), 15µg cRNA (variable) and RNase-free water for a final volume of 20µl.
Incubate in a thermal cycler at 94°C for 35 minutes.
Place mixture on ice.
Take out 1ul of fragmented cRNA for gel electrophoresis inspection.

Run crude cRNA and fragmented cRNA samples, along with a 1Kb ladder on a 1% agarose gel for visual inspection.

Protocol taken from the web site of CINJ Core Expression Array Facility where the samples were processed.

Tumor was harvested from animals at day eight of the treatment. RNA was extracted using RNeasy kit.

OVA-induced asthma model:OVA challenged and agonist of PGE receptor EP3 subtype treated  #1

24 hour incubation in Hybridoma SFM media with 10% fetal bovine serum

According to standard Affymetrix protocol.  Affymetrix 1-step IVT

Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau = 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call. A weighted mean of probe fluorescence (corrected for nonspecific signal by subtracting the mismatch probe value) was calculated using the One-step Tukey's Biweight Estimate. This Signal value, a relative measure of the expression level, was computed for each assayed gene. Global scaling was applied to allow comparison of gene Signals across multiple microarrays: after exclusion of the highest and lowest 2%, the average total chip Signal was calculated and used to determine what scaling factor was required to adjust the chip average to an arbitrary target of 150. All Signal values from one microarray were then multiplied by the appropriate scaling factor.

Cell line was established and described in LLano et al. (2004). J. Virol. 78(17):9524-9537.

293T cells stably transfected with 1 scramble shRNA construct. Control cell line for 293TsiLL cell line (LEDGF transcript knockdown - PSIP1 gene).

235;Asacol Predfoam Lanzoprazole;1/9/47;M;CAUCASIAN;6/24/97;8/26/97;FALSE;FALSE;FALSE;NO;FALSE;FALSE;2/11/05;5;0;0;0;0;0;0;0;TRUE;0;BOTH;BOTH;unknown;unknown;unknown;2/11/05;BOTH;BOTH;BOTH;BOTH;BOTH;5/31/05;FAILURE OF THERAPY;ex;1/1/97;15-24;TURP;UC;8-9-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

Passage P3 confluent MEF culture was collected for microarray profiling.

MEF cells were isolated from embryonic day E15.5 male embryos and cultured as described in “Manipulating the mouse embryo: a laboratory manual (2003, CSHL Press)”.

Processed arrays were scanned on Illumina iScan System array reader according to the manufacturer's instructions.

Raw array data were imported and preprocessed in GenomeStudio V2011.1 software (Illumina) using background subtraction and cubic spline normalization. Subsequent differential expression analysis of the grouped replicate samples was performed within GenomeStudio on the probe level utilising the Illumina custom error model with FDR multiple-testing correction.

Total RNA was isolated using the RNeasy mini kit with on-column DNase digest (Qiagen) following the supplied protocol, quantified with a Thermo NanoDrop and quality tested on Agilent Bioanalyzer.

Microarrays were hybridized following Illumina's standard hybridization protocol.

Biotinylated cRNA was prepared with the Ambion TotalPrep kit for Illumina arrays.

C57BL/6;male;embryonic day E15.5;Ing1-/-;mouse embryonic fibroblasts (MEF cells)

cells were transfected with siRNA using INTERFERin 48 hours before RNA extraction.

FA6 transiently transfected with non-targeting siRNA, transfection B

extraction of total RNA was performed using Ambion RNAqueous kit according to the manufacturer's instructions

Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

gene expression data frompancreatic cancer cell line FA6 transiently transfected with non-targeting siRNA

pancreatic cancer cell line FA6 transiently transfected with non-targeting siRNA

gene expression data from pancreatic cancer cell line MiaPaCa2 stabley transfected with empty vector pCEP4

pancreatic cancer cell line MiaPaCa2 stabley transfected with empty vector pCEP4

pancreatic cancer cell line MiaPaCa2 containing empty vector pCEP4

Patients with type 2 diabetes were treated with diet therapy alone or insulin; no patients were receiving any oral hypoglycaemic agent. Participants receiving statins, ACE inhibitors or angiotensin II receptor blockers were excluded.

Hepatic tissues were obtained with percutaneous needle liver biopsy, and immediately frozen in liquid nitrogen and stored at −80°C until use.

A scanned image was quantified using GCOS version 1.1.1 (GeneChip Operating Software; Affymetrix) with the default parameters for the statistical algorithm and all probe sets scaled to a target intensity of 100.

Total RNA was extracted with a kit (Micro RNA Isolation Kit; Stratagene, La Jolla, CA, USA), purified with RNeasy MiniElute Cleanup Kit (Qiagen, Hilden, Germany).

Ten micrograms of labelled and fragmented cRNA was hybridised onto a Human Genome U133 Plus 2.0 Array (Affymetrix) for 16 h at 45°C.

A total of 100 ng of total RNA was labelled according to the small sample labelling protocol recommended by the manufacturer.

gene expression data from pancreatic cancer cell line MiaPaCa2 stabley transfected with AGR2 overexpressing vector pCEP4 -AGR2

pancreatic cancer cell line MiaPaCa2 stabley transfected with AGR2 overexpressing vector pCEP4 -AGR2

pancreatic cancer cell line MiaPaCa2 containing AGR2 overexpressing vector pCEP4 -AGR2

Full description found in Eliezer Masiliah, Eleanor S. Roberts, Dianne Langford, Ian Everall, Leslie Crews, Anthony Adame, Edward Rockenstein, and Howard S. Fox. (2004) Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis.

NB195

total RNA extracted from cells obtained using biopsy in a patient having colon adenoma

rat hippocampus
Treatment, type=time_course, measurement=240.0 h

NB171
Medulloblastoma cell line D425 with inducible shOTX2 at different time points after induction. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0.

Medulloblastoma cell line D425;doxycyline inducible shRNA against OTX2;48 hrs;3

NB172

Medulloblastoma cell line D425;doxycyline inducible shRNA against OTX2;96 hrs;3

221;Prednisolone 7mg Asacol Adcal Seretide Fe SO4;1/29/86;F;CAUCASIAN;12/10/01;12/10/01;FALSE;FALSE;TRUE;NO;FALSE;FALSE;12/14/04;4;0;0;0;0;0;0;0;TRUE;0;BOTH;BOTH;BOTH;BOTH;BOTH;12/14/04;BOTH;BOTH;BOTH;BOTH;BOTH;3/7/05;FAILURE OF THERAPY;never;unknown;Asthma Eczema;UC;5-25-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

215;Prednisolone 5ng Balsalazide Lansoperazole;5/6/60;M;CAUCASIAN;5/1/02;8/16/02;FALSE;FALSE;FALSE;NO;FALSE;FALSE;11/16/04;3;0;0;0;0;0;0;0;TRUE;0;BOTH;BOTH;BOTH;BOTH;unknown;11/16/04;unknown;unknown;unknown;unknown;unknown;5/31/05;DISEASE IN REMISSION;ex;1/1/03;1/1/04;5-14;None;UC;5-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

209;AZA 150mg/d, Mesalazine 800mg TDS;3/27/80;F;CAUCASIAN;1/1/89;1/1/89;FALSE;FALSE;FALSE;YES;FALSE;TRUE;10/15/04;1;0;0;0;0;0;0;0;FALSE;0;11;12;12;12;12;11;11;11;11;BOTH;unknown;unknown;unknown;unknown;11/15/04;BOTH;BOTH;BOTH;BOTH;BOTH;12/16/04;FAILURE OF THERAPY;never;unknown;None;UC;1-25-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

204;AZA 200mg, Insulin, Asprin, Atenolol, Simvastatin;8/15/43;M;CAUCASIAN;7/1/02;8/1/02;FALSE;FALSE;FALSE;YES;FALSE;TRUE;11/1/04;5;0;0;0;0;0;0;0;FALSE;0;11;12;12;12;0;0;0;0;0;BOTH;BOTH;BOTH;unknown;unknown;11/1/04;BOTH;BOTH;BOTH;unknown;unknown;12/16/04;FAILURE OF THERAPY;ex;1/1/58;1/1/01;25+;Type 2 DM 02/2004.-Gout.;UC;1-25-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

214;NONE;1/10/37;M;CAUCASIAN;1/1/59;1/10/61;FALSE;FALSE;TRUE;NO;FALSE;FALSE;11/12/04;0;0;0;0;0;0;0;0;TRUE;1;BOTH;BOTH;BOTH;BOTH;BOTH;11/12/04;BOTH;BOTH;BOTH;BOTH;BOTH;12/9/04;FAILURE OF THERAPY;never;unknown;CENTRAL RETINAL VEIN OCCLUSION 01/04;UC;5-25-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

212;Pred 10mg, AZA150mg, ADCAL D3;8/3/76;F;CAUCASIAN;1/1/97;9/1/01;FALSE;FALSE;FALSE;YES;FALSE;TRUE;11/9/04;7;0;0;0;0;0;0;0;TRUE;0;0;11;12;11;12;11;11;11;11;BOTH;BOTH;unknown;unknown;unknown;11/9/04;BOTH;BOTH;unknown;unknown;unknown;12/16/04;FAILURE OF THERAPY;never;unknown;None;UC;5-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

233;Asacol 1.2g Asprin 75mg Amilodipine 10mg;2/2/29;M;CAUCASIAN;1/1/92;1/1/92;FALSE;FALSE;FALSE;NO;FALSE;FALSE;2/1/05;3;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;unknown;unknown;unknown;2/1/05;BOTH;BOTH;unknown;unknown;unknown;3/7/05;DISEASE IN REMISSION;ex;1/1/86;15-24;MI 1986, Prostate cancer 1994;UC;6-2-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

233;Asacol 1.2g Asprin 75mg Amilodipine 10mg;2/2/29;M;CAUCASIAN;1/1/92;1/1/92;FALSE;FALSE;FALSE;NO;FALSE;FALSE;2/1/05;3;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;unknown;unknown;unknown;2/1/05;BOTH;BOTH;unknown;unknown;unknown;3/7/05;DISEASE IN REMISSION;ex;1/1/86;15-24;MI 1986, Prostate cancer 1994;UC;6-2-01;terminal ileum;Uninflamed;total RNA from 10 human cell lines

203;Asacol 800mg BD, Simvastatin;1/10/35;M;CAUCASIAN;11/1/92;3/23/93;FALSE;FALSE;TRUE;NO;FALSE;FALSE;10/1/04;1;0;14;0;147;6;4;0;FALSE;0;HISTOLOGICAL;HISTOLOGICAL;HISTOLOGICAL;unknown;unknown;10/1/04;BOTH;BOTH;unknown;unknown;unknown;12/9/04;DISEASE IN REMISSION;ex;1/1/50;1/1/57;25+;None;UC;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

202;Sulphasalazine 3g/d, Folic Acid 5mg/d, HRT, DF118;10/3/50;F;CAUCASIAN;1/1/68;1/1/69;TRUE;TRUE;FALSE;YES;FALSE;FALSE;9/30/04;2;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;BOTH;BOTH;BOTH;9/30/04;unknown;unknown;unknown;unknown;unknown;12/9/04;DISEASE IN REMISSION;never;unknown;Polymyalgia rheumatica;UC;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

WI-38 cells, at 24 h after exposure to 0.5 uM BPDE, biological rep3

The microarrays were scanned using a GeneChip® Scanner 3000 (Affymetrix) and subsequent image analysis was performed using Affymetrix GCOS software using standard Affymetrix protocols.

The resulting .cel files were normalized with the robust multichip average (RMA) method.

Total cellular RNA was prepared using the RNeasy Mini Kit from (Qiagen), treated with TURBO DNA-freeTM (Ambion) and RNA integrity analyzed using Agilent Bioanalyzer 2100.

Gene expression data from WI-38 cells exposed to DMSO vehicle control

Normal human diploid WI-38 lung fibroblasts, CCL-75(TM), passage 7-12.

WI-38 cells, at 24 h after exposure to 0.1 uM BPDE, biological rep1

WI-38 cells, at 24 h after exposure to 0.1 uM BPDE, biological rep2

WI-38 cells, at 24 h after exposure to 0.1 uM BPDE, biological rep3

Cells were plated at a density of 2 × 105 cells/dish in p60 cell culture dishes 24 hours before the assay. Then, cells were cultured for 48  hours under three conditions: control (0.03% ethanol), RES150 (150 μM of resveratrol in 0.03% ethanol)  and RES250 (250 μM  of resveratrol in 0.3 % ethanol). At the end of the 48 hours treatment period cells were harvested for further RNA extraction.

The MCF-7 human breast cancer cells (ATCC) were maintained in DMEM (Dulbecco´s Modified Eagle´s Medium) supplemented with 10% fetal bovine serum (FBS), in a 5% CO2 incubator at 37°C

Genechips were scanned using the Affymetrix Command Console software  and the Affymetrix Genechip Scanner 3000  7G.

The data was analyzed using Partek Genomic Suite. Raw intensity probes wer imported by setting up RMA background correction and the differential gene expression intensities were calculated with the default  one way ANOVA parameters.

RNA was extracted using the TRIzol reagent as per  manufacturers instructions and a second round of purification was performed using the Rnaeasy Mini Kit columns (Qiagen).

After fragmentation,  700 ng of terminal labeled cDNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cDNA was prepared according to the standard Affymetrix protocol from 300 ng total RNA  for each sample ( Gene Chip Whole transcript labeling manual ,2005-2007, Affymetrix).

RNA from 3 MCF7 cell culture plates treated with 250 mM of resveratrol (SIGMA St. Louis MO)

RNA from 3 MCF7 cell culture plates treated with 150 mM of resveratrol (SIGMA St. Louis MO)

RNA from 3 MCF7 cell culture plates treated with vehicle (ethanol 0,3%).

The results were quantified and analyzed using GCOS 1.2 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity = 500; Normalization, All Probe Sets; Parameters, all set at default values).

HeLa cells grown in 100 mm dishes were transiently transfected with negative control siRNA or SON siRNA (400 pmol siRNA / dish) using Lipofectamine 2000 reagent. RNAs were isolated after 66 hours.

Standard Affymetrix recommended protocols were followed for all hybridization, wash, stain and scanning steps.

The data were analyzed using the RMA algorithm with RMAExpress version 0.5. Affymetrix default analysis settings and global scaling were used as normalization method.

Qiagen RNeasy Mini column extraction of total RNA was performed according to the manufacturer's instructions.

Standard Affymetrix recommended protocols were followed for all hybridization, wash, stain and scanning steps (see the attached EXP files).

Biotinylated cRNA were prepared using MessageAmp II-Biotin Enhanced kit according to the manufacturer's instructions from 1.5 ug total RNA (MessageAmp II-Biotin Enhanced Kit Instruction Manual, 2006, Ambion).

500ng total RNA was used initially

Quadriceps muscles were extracted and directly frozen in liquid nitrogen

Mice were kept under a 12h dark-light period and provided with a standard chow-diet and water ad libitum

GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA)

Arrays were processed in Bioconductor, using RMA background correction, quantile normalization and RMA summarization.

RNA from quadriceps muscles was extracted using a protocol combining TRIzol reagent (Invitrogen) and RNAeasy® minikit columns (Qiagen) following manufacturer's instructions

2.2 µg of cDNA was hybridized per microarray for 16 hours of hybridization at 45ºC, washing and staining of microarrays was performed using a Fluidics Station 450 (Affymetrix, Santa Clara, CA)

25 ng total RNA per sample was processed using isothermal amplification SPIA Biotin System (NuGEN Technologies, Inc.)

M327 QV RNA
Gene expression data from quadriceps muscle of 4-month-old male mouse

M464 - QV RNA

Mice were fed a standard rodent chow (Test Diet No. 5001) and water ad libitum in temperature-controlled (23°C) and virus-free facilities.

M303 QV RNA

M304 QV RNA

M322 QV RNA

M323 QV RNA

M325 QV RNA

Fibroblasts are dissociated with 0.05% trypsin at 37°C, 5% CO2 for 5minutes and collected by centrifugation; iPSCs are dissociated with 1mg/ml collagenase IV at 37°C, 5% CO2 for 5minutes, manually detached and collected by centrifugation

Fibroblasts and iPSCs are cultured in 1:1 ratio of DMEM/F12 medium supplemented with 20% KSR at 37°C, 5% CO2 until confluence

iPSC derived from CCALD patient fibroblast CCALD1, biological rep2

WebArray software was used to generate log2-transformed gene expression values using the RMA algorithm

iPSC derived from CCALD patient fibroblast CCALD1, biological rep3

iPSC derived from healthy control fibroblast WT3, biological rep8

iPSC derived from CCALD patient fibroblast CCALD1, biological rep1

iPSC derived from CCALD patient fibroblast CCALD1, biological rep4

iPSC derived from CCALD patient fibroblast CCALD2, biological rep5

42 hours post-transfection, cells were treated for 48 hours with 5nM R1881 or ethanol vehicle

LNCaP cells were cultured under androgen deprived conditions for 48 hours, and transfected with control siRNA or siRNA directed against SRF

The software R was used along with bioconductor.  The GC corrections steps were used from GCRMA, then the PM probes were normalized using fastlo, and then the median-polish portion of rma was used to summarize the expression values into probesets.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix 1-Cycle protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

LNCaP androgen-sensitive human prostate  adenocarcinoma cell line;control siRNA;EtOH vehicle

Each cRNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured. These measures provided the basis of subsequent biostatistical analysis.

The DNA Chip Analyzer (dChip) was used to normalize all CEL files to a baseline array with overall median intensity, and the model-based expression (perfect match minus mismatch) was used to compute the expression values.

B220+ splenic B cells were isolated using magnetic microbeads from Miltenyi Biotec. Plasma cells were isolated from human bone marrow mononuclear cells from healthy donors (Cambrex BioScience) using immunomagnetic bead selection with mouse anti-human CD138 monoclonal antibodies as described (Zhan, et al., 2002), except that we used LS MACS separation columns (Miltenyi Biotec) and before incubating the bone marrow mononuclear cells to CD138-coated magnetic beads, we removed contaminating histiocytes and macrophages by preloading and washing out the cells in the magnetic columns and field. Total RNA was isolated from control and transgenic B220+ splenic mononuclear cells or myeloma tumors using TRIzol Reagent.

The biotinylated complementary RNA (cRNA) was purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA was quantified spectrophotometrically and purity of the cRNA was also assessed by spectrophometric measurements.

The purified cRNA was fragmented in order to facilitate the subsequent hybridization step. The cRNA was purified from the fragmentation reaction using phenol/chloroform extraction and ethanol precipitation.

The fragmented cRNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C.

The chips were then transferred to a fluidics instrument that performed washes to remove cRNA that had not hybridized to its complementary oligonucleotide probe. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were then added using biotinylated anti-streptavidin antibody and additional SAPE.

RNA was converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis was then carried out.

The double-stranded cDNA was used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and  UTP in addition to the four unmodified ribonucleoside triphosphates.

Analysis of the raw gene expression profiling was performed using dChip software. Please see the following paper for details.
Klose RJ, Yan Q, Tothova Z, Yamane K, Erdjument-Bromage H, Tempst P, Gilliland DG, Zhang Y, Kaelin WG. The retinoblastoma binding protein RBP2 is an H3K4 demethylase. Cell  (2007)

Total RNA isolation using RNeasy mini kit with on-column DNase digestion (Qiagen).

Study the effect of RBP2 inactivation in gene expression
Analysis name: WK2006060805

Subconfluent wild type primary mouse embryonic fibroblasts at passage 3.

RMA gene level analysis with Expression Console (Affymetrix) using standard settings (Sketch-Quantile)

Whole transcript Sense Target Labeling kit - 100 ng protocol (Affymetrix)

ko_04.CEL
Gene expression data from lung tissue of Ifitm1-deficient mice

For the intratracheal administration of mepenzolate, mice were maintained under anesthesia with chloral hydrate (500 mg/kg) and mepenzolate in PBS was administered via micropipette.

The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.

Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA).

Hybridization and signal detection of  Mouse Gene 1.0 ST Arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.

The cDNA was prepared using GeneChip WT Terminal Labeling Kit (Affymetrix).

To knockdown Grhl2 gene expression, a replication incompetent, VSV-G pseudotyped lentiviral vector that contained a GFP tracking reporter gene along with either a non-targeting control shRNA (RHS4346) or the shRNA targeting Grhl2 (V2LMM_20130) was employed (Open Biosystems). Lentiviruses were packaged and concentrated as described previously (19). MLE-15 cell infections with lentiviral vectors were performed for 16 h in the presence of polybrene (5 μg/ml) at a multiplicity of infection of 50. Stable cell lines were generated by puromycin dihydrochloride (5 μg/ml, Sigma) selection for 6 days.

MLE-15 cells (provided by Dr. J. Whitsett, Children’s Hospital Medical Center, Cincinnati, OH) are murine lung epithelial cells produced from tumors in transgenic mice expressing the SV40 large tumor antigen under transcriptional control of the human surfactant protein C promoter (SP-C) (34). Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) (Life Technologies, Inc.), 10% heat-inactivated fetal bovine serum (FBS) (Life Technologies, Inc.), 100 units/ml penicillin G, 100 mg/ml streptomycin sulfate.

CEL files were summarized using Affymetrix Expression Console (current version 1.1). Expression estimates were derived from the probe level hybridization intensities using the Robust Multi-Array Analysis (RMA) algorithm.  Differential expression between experimental and control samples was examined using Welch's T-test and a False Discovery Rate correction.

Total RNA was isolated using QIAGEN’s RNeasy kit (Qiagen) and the sample integrity was verified using RNA 6000 Nano Assay RNA chips run in Agilent 2100 Bioanalyzer (Agilent Technologies).

The labeled fragmented DNA was hybridized to the GeneChip Mouse Gene Array 1.0ST (Affymetrix) for 16-18 h in a GeneChip Hybridization oven 640 at 45°C with constant rotation (60 rpm). The hybridized samples were washed and stained using Affymetrix fluidics station 450. The first stain with streptavidin-R-phycoerythrin (SAPE) was followed by signal amplification using a biotinylated goat anti-streptavidin antibody and another SAPE staining (Hybridization, Washing and Staining Kit, Affymetrix).

The total RNA (300 ng) was reverse transcribed using Whole Transcript cDNA Synthesis kit (Affymetrix). The cDNA obtained was used as a template for in vitro transcription using a Whole Transcript cDNA Amplification Kit (Affymetrix). The antisense cRNA obtained was purified using GeneChip Sample Cleanup Module (Affymetrix) and used as a template for reverse transcription (Whole Transcript cDNA Synthesis kit, Affymetrix) to produce single-stranded DNA in the sense orientation. During this step, dUTP was incorporated. Then, the DNA was fragmented using uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1), labeled with DNA Labeling Reagent and covalently linked to biotin using terminal deoxynucleotidyl transferase (TdT, Whole Transcript Terminal Labeling kit, Affymetrix). IVT and cDNA fragmentation quality controls were performed by an mRNA Nano assay in the Agilent 2100 Bioanalyzer.

At age of 4 weeks HMGN1 wildtype and knockout males received an injection of 10 µg/g body weight of N-nitrosodiethylamine or saline as a control.

Hmgn1+/+ and Hmgn1-/- littermates were generated by crossing heterozygous Hmgn1+/- male and female, DNA-tail-genotyping F1 mice and further propagating Hmgn1+/+ and Hmgn1-/- homozygotes separately

Mouse Genome 430 2.0 array has 45101 probe sets associated with approximately 20000 Mouse Genome Informatics (MGI) gene identifiers. Probe sets were mapped to MGI identifiers using information provided by the Jackson Laboratory (http://www.informatics.jax.org/). Values in the Sample data tables were derived from MAS5 algorithm.

Total RNA was isolated from frozen liver tissue with TRIzol followed by purification using RNeasy Kit.

GeneChip Hybridization, Wash and Stain Kit: Affymetrix, P/N 900720, suppliers recommendations, mouse 430.2 Affymetrix expression array

GeneChip One-Cycle Target Labeling and Control Reagents (Affymetrix, P/N 900493).

Liver;Hmgn1+/+;injection of 10 µg/g body weight of N-nitrosodiethylamine

Liver;Hmgn1-/-;injection of 10 µg/g body weight of N-nitrosodiethylamine

Peripheral blood was drawn and PBMC were isollated over Ficoll.  Samples were stored in Trizol at -80oC until extracted according to manufacturers directions.

Peripheral blood mononuclear cells;systemic JIA;LT6;65min;White;Male;242

Peripheral blood mononuclear cells;systemic JIA;LT6;70min;White;Female;176

Peripheral blood mononuclear cells;systemic JIA;LT6;110min;Black/African American;Male;222

Peripheral blood mononuclear cells;systemic JIA;LT6;95min;White;Male

Peripheral blood mononuclear cells;systemic JIA;LT6;120min;White;Female;218

Peripheral blood mononuclear cells;systemic JIA;GTE6;70min;White;Male;248

Asynchronously growing NT and CBFbeta knockdown cells were used for the RNA isolation.

Lentiviral infected PPC1 cells were maintained in RPMI containing 10% fetal calf serum, pen/strep, L-glutamine and 1 microgram/ml puromycin. Cells were subcultured 1:2 every 3 to 4 days.

Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

Total RNA was extracted and purified using Ribopure (Ambion) RNA isolation

1 µg of purified cRNA was fragmented to uniform size and applied to Agilent Whole Human Genome microarrays (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a rotating incubator, and washed at 37° C for 1 min.

First and second strand cDNA was prepared from the total RNA samples.  cRNA target was prepared from the DNA template and verified on the Bioanalyzer.  cRNA was fragmented to uniform size and verified on the Bioanalyzer.

Gene expression data from primary liposarcom cultures incubated with PBS as control for 24 h

female;70 years;upper arm;3x5x6;atypical lipoma;low;G1;primary tumor;no;no

female;69 years;lower arm;4.5x3.5x2.2;atypical lipoma with partly dedifferentiated areas;low;G2;local recurrence;no;no

male;53 years;thigh;10x3x5;atypical liposarcoma;low;G2;local recurrence;yes;no

female;67 years;thigh;35x15x12;atypical lipoma;low;G1;primary tumor;no;no

female;76 years;thigh;38.5x17.5x6;atypical lipoma;low;G1;primary tumor;no;no

HL-60 cell line infected with GSK3A Construct 5 shRNA, biological rep1
Sample name: HL60_GSK3A_5-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A05_596562.CEL

HL-60 cell line infected with GSK3B Construct 2 shRNA, biological rep2
Sample name: HL60_GSK3B_2-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A09_596622.CEL

Statistical analysis was undertaken using R (www.r-project.org) and Bioconductor
(www.bioconductor.org) software. The expression values were checked for quality and consistency using statistical quality assessment and were normalized using the RMA algorithm. Control probes and a small number (147) of probe-sets showing no variability between arrays were filtered out before subsequent analysis. For the differential expression analysis, the Deaf-1 and control samples for each clone were treated as paired observations, to reflect the biological variation between clones. Statistical significance was assessed using empirical Bayes moderated paired t-tests as implemented in the limma package within the Bioconductor software.

Total RNA was harvested from two independent clones (C1 and E1) infected with either control or Deaf-1-expressing retrovirus.  RNA was purified using using the QIAGEN RNeasy Kit (Qiagen, Hilden, Germany)
and quality assessed by spectrophotometry and gel electrophoresis before
hybridisation to Affymetrix slides.

Arrays were processed at the Australian Genome Research Facility (AGRF).

The Ebs at Day 2.5 were treated with Activin(50ng/ml) or 10 mM SB431542.

Ebs were set up by growing mouse ESCs in medium without LIF in ultra-low attachment dishes.

Differentially expressed genes were identified using a Bayes model Implemented by the limma package of R.

Human mammary epithelial MCF10A cells grown in 3-D Matrigel for 15 h after depletion of CTIP by viral RNAi

Highly enriched breast cancer cells procured by LCM.

Clinical information: Sample.ID=317;Tumor.type=D;Size=1.2;Grade=3;Nodes=1/10;ER=Pos;PR=Neg;HER2=Neg;Age=71;DFS=5;Status=recur

Clinical information: Sample.ID=297;Tumor.type=D;Size=0.8;Grade=2;Nodes=1/16;ER=Pos;PR=Pos;HER2=ND;Age=66;DFS=169;Status=non-recur

Clinical information: Sample.ID=295;Tumor.type=D;Size=3.5;Grade=2;Nodes=3/21;ER=Pos;PR=Pos;HER2=Neg;Age=52;DFS=118;Status=recur

Clinical information: Sample.ID=289;Tumor.type=D;Size=3;Grade=2;Nodes=0/15;ER=Pos;PR=Pos;HER2=Neg;Age=75;DFS=63;Status=recur

Clinical information: Sample.ID=280;Tumor.type=D;Size=2.2;Grade=3;Nodes=0/12;ER=Pos;PR=Pos;HER2=Neg;Age=66;DFS=44;Status=recur

Clinical information: Sample.ID=260;Tumor.type=D/L;Size=0.9;Grade=2;Nodes=1/13;ER=Pos;PR=Pos;HER2=Neg;Age=73;DFS=42;Status=recur

Human mammary epithelial MCF10A cells grown in 3-D Matrigel for 15 h after depletion of BRCA1 by viral RNAi

total RNA from biosource CC#34*

total RNA from biosource CC#21*

total RNA from biosource CC#12

total RNA from biosource CC#11*

total RNA from biosource CC#4*

total RNA from biosource CC#11S

total RNA from biosource CC#7S

total RNA from biosource CC#5S

total RNA from biosource CC#3S

total RNA from biosource CC#41

After a baseline tumor biopsy, patients were randomized to receive Anastrazole/fulvestrant(AF) or anastrazole/Fulvestrant/Gefitinib (AFG) for 3 weeks, then a second biopsy was obtained. After that all patients received the AFG treatment.

Expression were estimated using BRB Array Tools software, GCRMA method

RE1_H7_1349_U133Plus2.0.CEL
Gene expression data from human breast cancer

Low density BM cells were isolated with Histopaque1083, Cells were stained for LSK and sorted by flow cytometry (FACSAiraII, BD Bioscineces, CA)

Scanning was carried out in the CCHMC Affymetrix Core using standard procedures

affymetrix-algorithm-name = rma-gene-default; program-name = Expression Console.
Data analysis was performed using Genespring GC11 (Agilent Technologites). Differentially expressed genes in response to Klf5 KO versus WT BM LSL cells were identified using an unpaired Student t-test. Changes in gene expresssion were considered statistically signifiant if their p value was < 0.05 and fold change was greater than 1.15
'Cancelas_April_2011RMA-GENE-DEFAULT - Group 1.txt' contains normalized expression values from samples MxlCre_KLF5KO 2, MxlCre_KLF5KO 3, MxlCre_KLF5KO 4, MxICre_KO 5, MxlCre_KLF5WT 1, MxlCre_KLF5WT 2, MxlCre_KLF5WT 3, MxlCre_KLF5WT 4, MxlCre_KLF5WT 5.
'Cancelas_10_10_AnnotationsRMA-GENE-DEFAULT - Group 1RMA-GENE-DEFAULT - Group 1.TXT' contains normalized expression values from samples MxCre_KLF5KO, MxCre_KLF5WT.

Hybridisation was carried out in the CCHMC Affymetrix Core using standard procedures

Labeling was carried out in the CCHMC Affymetrix Core using standard procedures

this sample is from a 16-week-old male mdx mice gastrocnemius muscle

Histidine decarboxylase null myeloid-derived suppressor cell from colon tumor, rep1

MDSC HDCKO-colon tumor
Technical replicate 1 of 2.

Splenocytes from E2-2+/- mice and wild-type littermates were pooled, stained with antibody conjugates, and PDC (CD11b- CD11clow B220+ Bst2+) were flow-sorted directly into Trizol Reagent (Invitrogen).. Total RNA was isolated and quantified using the Quant-IT RNA Assay Kit (Invitrogen), and equal amounts of each RNA sample were used for reverse transcription and two-round linear aRNA amplification.

The aRNA was amplified without labeling in the first round, and then labeled with Biotin-16-UTP/Biotin-11-CTP in the second round. Labeled aRNA was fragmented in RNA Fragmentation Buffer (QIAGEN) prior to hybridization.

Summarization algorithm: RMA. Normalization: Quantile. Baseline transformation: median of control samples

Gene expression profile of HeLa cells transfected with 100nM siRNA against Sp1 (siSp1) for 48h.

HeLa;human Cervical Carcinoma;siRNA directed against Sp1 mRNA (siSp1)

Quadriceps muscle;P.q.7;Pompe;rhGAA;12 Weeks;F;5.3m;Walking;Decreased;Positive Clinical Outcome

Recombinant lentiviruses that we used to infect subconfluent SK-N-SH cells were described previously by Rastegar et al.(Rastegar et al., 2009). These are self-inactivating lentiviruses encoding either MECP2_e1, MECP2_e2 or eGFP under the control of the EF1a promoter.

Cells were grown in Eagle's Minimal Essential Medium (Invitrogen, Carlsbad, CA, USA) supplemented with 10% FBS (Wisent, St. Bruno, QC, Canada) and Penicillin-Streptomycin (Invitrogen, Carlsbad, CA, USA). Neuronal differentiation of infected SK-N-SH cells was achieved by treatment of cells with retinoic acid (Cedarlane Laboratories, Burlington, ON, Canada) and herbimycin A (Cedarlane Laboratories, Burlington, ON, Canada), using a modification of the protocol previously described (Preis et al., 1988). Retinoic acid was added to the medium at 10 uM concentration seven days post-infection, and cells were grown in the presence of retinoic acid for 96 h, with medium being replaced with fresh retinoic-acid containing medium every two days. Retinoic acid treatment increases the number of neuronally committed cells in the SK-N-SH culture (Preis et al. 1988). After 96 hours, herbimycin A was added to the growth medium at 236 nM concentration, and cells were grown in the presence of both herbimycin A and retinoic acid for 72 hours, with medium being replaced with fresh medium after 48 hours. Herbimycin A was used to clear the undifferentiated cells from the culture(Preis et al., 1988).

Feature Extraction Version 10.7; Extraction protocol GE2_107_Sept07

RNA was isolated from stably infected neuronally differentiated cells and from stably infected primary mouse fibroblasts using TRIzol (Invitrogen, Carlsbad, CA, USA), in accordance with the manufacturer’s protocol. The concentration of total RNA was determined by NanoDrop® spectrophotometry. Isolated RNA was stored at -80°C. The reverse transcription was performed using 2 mg of total RNA, SuperScript III reverse transcriptase (Invitrogen, Carlsbad, CA, USA) and random primers (Invitrogen, Carlsbad, CA, USA) in accordance with the manufacturer’s instructions

performed as service through the UHN Microarray Centre, Toronto, ON (www.microarrays.ca)

HIV seropositve, samples used to test the trend (increase or decrease) of CD4 cells

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D1;13

type: ap-cyto

Sample_ID:n22 // Patient:J-287 // Histology:Normal // Metastasis:NA // p53_mut:NA // E-cadherin_mut:NA // beta-Catenin_mut:NA

Sample_ID:n23 // Patient:J-n23 // Histology:Normal // Metastasis:NA // p53_mut:NA // E-cadherin_mut:NA // beta-Catenin_mut:NA

Sample_ID:n04 // Patient:J-133 // Histology:Normal // Metastasis:NA // p53_mut:NA // E-cadherin_mut:NA // beta-Catenin_mut:NA

Sample_ID:n03 // Patient:J-290 // Histology:Normal // Metastasis:NA // p53_mut:NA // E-cadherin_mut:NA // beta-Catenin_mut:NA

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D21;11

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D42;11

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D7;5

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D14;5

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D21;5

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D42;5

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D72 (30 days post-EBRT);5

male;non-metastatic prostate cancer;peripheral blood;white blood cells;baseline;6

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D1;6

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D7;6

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D14;6

Scanning procedures were carried out as described by Affymetrix, Santa Clara.

The data were analyzed with DChip using invariant set normalization and PM-only MBEI model settings.

Semen was collected then treated with Somatic Cell Lysis Buffer (0.1% sodium dodecyl sulfate [SDS], 0.5% Triton X-100) on ice for 30 minutes.  Lack of somatic cell contamination and sperm count were established by microscopic examination.  RNA was isolated from sample using Trizol.  Samples were then treated with RNase-free DNase I.

Hybridization to Affymetrix U133plus2 GeneChips , staining and washing were carried out as described (Affymetrix, Santa Clara).

JLI_84

GeneChips were scanned using the Affymetrix GeneChip Scanner 3016

The data were analyzed with robust multi-array (RMA) for background correction, normalization and polishing.

Following fragmentation, cRNA were hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

GeneChips were scanned using the Affymetrix GeneChip Scanner 3017

GeneChips were scanned using the Affymetrix GeneChip Scanner 3014

GeneChips were scanned using the Affymetrix GeneChip Scanner 3015

GeneChips were scanned using the Affymetrix GeneChip Scanner 3018

GeneChips were scanned using the Affymetrix GeneChip Scanner 3019

Mice were fasted for 24 h, and phenobarbital sodium solved in PBS was intraperitoneally injected to mice at a dose of 100 mg/kg body weight.

Mice were kept at 12 h light/dark cycle. Feed and drinking water were supplied ad libtum.

Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

Total RNA was extracted from livers using Trizol reagent (Invitrogen) and purified with QIAGEN RNAeasy kit (QIAGEN).

For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

Gene expression after 6 h in PBS-treated WT mouse liver
251486838940_1_1

Gene expression data from spleen of Npc1+/- mouse1 of age 67 days

Gene expression data from spleen of Npc1-/- mouse1 of age 55 days

Gene expression data from spleen of Npc1-/- mouse1 of age 67 days

Gene expression data from spleen of Npc1+/- mouse1 of age 54 days

Gene expression data from spleen of Npc1-/- mouse1 of age 25 days

Air
1
0.5

Gene expression data from spleen of Npc1+/- mouse1 of age 55 days

Gene expression data from spleen of Npc1-/- mouse1 of age 71 days

Olfactory epithelium microdissected, frozen in liquid nitrogen;tissue pulverized in Tri-Reagent (Molecular Probes), processed through a QIAshredder column (Qiagen), total RNA extracted and purified with RNeasy Mini-Kit (Qiagen)

Cells were seeded in 100 mm dishes in triplicate. 24 hours before ligand treatment, media was changed to DMEM/F12 + 100ng/ml cholera toxin + 500ng/ml hydrocortisone + 10microgram/ml insulin. RNA was harvested 48 hours after addition of ligand.

Cells are maintained in DMEM/F12 + 5% horse serum + 20ng/ml EGF + 100ng/ml cholera toxin + 500ng/ml hydrocortisone + 10microgram/ml insulin

Hybridized cRNA was detected using streptavidin coupled to phycoerythrin. Genechips were scanned using Genechip Scanner 3000 7G Plus 2 and Genechip Operating System (Affymetrix)

Default values were used to grid images (.DAT) and generate .CEL and .CHP files.
RMA

5.5 ug biotinylated cRNA was fragmented and hybridizied to an Affymetrix Genechip Human Gene 1.0 ST array

GeneChip One-Cycle Target Labeling and Control reagents kit (Affymetrix)

Gene expression data from cells treated with Heregulin for 48 hours

normal breast cell line with stably transfected full-length chimeric human HER2 receptor with FKBP and HA tags;MCF10A;Heregulin

Total RNA from testis of Ku86(+/+);G3-Terc(-/-) mice; experiment 1
Keywords = telomerase
Keywords = Ku86
Keywords = stress
Keywords = DNA damage

Total RNA from testis of Ku86(-/-);Terc(+/+) mice; experiment 2

Total RNA from testis of Ku86(+/+);Terc(+/+) mice; experiment 1

Total RNA from testis of Ku86(+/+);G3-Terc(-/-) mice; experiment 2

Nine mice of each genotype were either treated with a single intraperitoneal injection of PQ (30 mg/kg) in 200ul sterile saline (Experimental group), or a similar volume of sterile saline (Control group). Six hours after injection, each mouse was euthanized with CO2 and the cerebellum was immediately removed and frozen.

Mice were housed in positive pressure-ventilated racks at 25±1°C with a 12 h light/dark cycle, fed ad libitum with a standard rodent pellet diet and allowed free access to filtered and UV-irradiated water

After washes, the arrays were incubated with anti-biotin streptavidinphycoeritrin antibody and scanned with an Affymetrix GeneChip Scanner 7G.

Software=GEPAS suite. Background correction=RMA. Normalization:Quantiles.PM correction=PM-only.Summary=Medianpolish

Tissue was homogenized in TRIzol (Invitrogen), and total RNA extracted. A second purification using the RNeasy miniKit (Quiagen) was employed to prepare the Array probes from high-quality RNA samples. Equimolar amounts of total RNA from three randomly selected mice for each genotype and experimental condition were pooled, rendering three biological replicates to hybridize with the arrays.

Ten micrograms of the biotinylated and fragmented probes were hybridized to Affymetrix GeneChip Mouse Genome 430A 2.0 arrays at 45ºC for 16 h, following the manufacturer’s protocols.

The generation, labeling and purification of cRNA was performed using the IVT kit (Affymetrix, Santa Clara, CA).

Gene expression data from cerebellum of ApoD gain-of-function transgenic mouse

male;adult (80±5 days-old);cerebellum;Human-ApoD transgenic gain of function mutant

Total RNA from testis of Ku86(+/+);Terc(+/+) mice; experiment 2

Gene expression data from cerebellum of ApoD loss-of-function mouse

Cell were grown to log phase prior to RNA extraction in DMEM media containing 10% fetal bovine serum, L-glutamine and penicillin/streptomycin

GCOS 1.3 was used to convert intensities using Expression Analysis settings :Parameters -default, Baseline - default, Probemask - default, Normalization - all probe sets, Scaling - all probe sets, Target Signal: 2500

GeneChips were washed and stained in the Affymetrix Fluidics Station 450

Where indicated, cells were treated with 10 nM 17-β-estradiol for 6 hours.

Cells were transfected with siRNAs, grown for 24 h in DMEM containing 10% bovine growth serum then grown in phenol-red free DMEM containing 5% charcoal-dextran treated FBS for 24 hours prior to treatment with estrogen for 6 h.

log2 transformation of signal intensity, quantile normalization, R/Bioconductor, BeadStudio

Illumina Whole-Genome Gene Expression Direct Hybridization Assay Guide (11286331)

Illumina TotalPrep RNA Amplification Kit (Ambion, Inc., Cat # IL1791); 200ng total RNA input

The software used was Expression Console from Affimatrix and normalization algorithm used was MAS5.

FVB/C57B6 mixed backgroud;primary KrasG12D Pten L/+ pancreatic ductal epithelial cells, P4;Pdx1-Cre;LSL-KrasG12D L/+;Pten L/+

FVB/C57B6 mixed backgroud;primary KrasG12D pancreatic ductal epithelial cells, P7;Pdx1-Cre;LSL-KrasG12D L/+

Monolayers of astrocytes were treated with Fasudil (diluted in astrocytic medium pre-warmed at 37ºC) and the volume was maintained at 0.5 ml per well. Vehicle-treated cultures were run in parallel to serve as controls.

Cells plated in 24-well plates (2.6 × 104 cells/cm2) and incubated in a humidified incubator at 36.5ºC with 5% CO2.

Gene expression data was exported from Bead Studio using median shift normalization such that the lowest value is 1 and log2 transformed with the ‘Partek report plug-in’ (Partek® Inc., St. Louis, Missouri, U.S.A.) and analysed in Partek Genomics Suite.  The resultant export file in project file format (.ppj) included log transformed signal intensity data and annotation. This file was then imported into Partek Genomics suite Version 6.3 (Partek® Inc., St. Louis, Missouri, U.S.A.). The normalised expression data was then exported from Partek, signal p values were not available for normalised expression values.

Total RNA was extracted in one batch using the RNeasy Mini Kit and quality of the extracted RNA was determined using E-gene HAD-GT12 genetic analyser (John Morris Scientific, Melbourne, Australia).

RNA was amplified using the Illumina® TotalPrep RNA Amplication Kit. Total RNA sample was reverse transcribed using T7 Oligo(dT) primer to generate first strand second strand cDNA. Biotinylated cRNA was generated from the double-stranded cDNA templates via in vitro transcription.

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;Control;2h;1;4421339030

LaserPower: 2.56;; 1.56
Temperature: 40.72

B6129;male;12 weeks;liver;adult;B6129;male;20 weeks;liver;adult;Alb-Cre +/-

LaserPower: 2.61;; 1.33
Temperature: 42.1

LaserPower: 2.57;; 1.29
Temperature: 38.93

LaserPower: 2.57;; 1.35
Temperature: 41.32

LaserPower: 2.52;; 1.29
Temperature: 38.4

LaserPower: 2.58;; 1.35
Temperature: 41.05

LaserPower: 2.56;; 1.41
Temperature: 39.94

LaserPower: 2.6;; 1.34
Temperature: 41.77

LaserPower: 2.53;; 1.58
Temperature: 39.54

LaserPower: 2.58;; 1.55
Temperature: 41.5

After hybridization, gene chips were washed and stained in the GeneChip Fluidics Workstation 400 (Affymetrix) using the EukGE-WS2v4 protocol and subsequently scanned with the GeneChip Scanner 3000 (Affymetrix). Image analysis was performed by use of Affymetrix GeneChip operating software.

Expression values were computed with the Affymetrix Microarray Suite (MAS) 5.0 software. The amount of transcripts in a sample that scored present, absent, or marginally detectable was assessed, also with the MAS 5.0 software.

Whole testes were obtained from animals at different ages depending on the experiment. Immediately after removal, testis samples
were snap-frozen and stored in liquid nitrogen. Before RNA extraction, testis samples were weighed and homogenized in a Dounce homogenizer (Kontes Co., Vineland, NJ). Thereafter, RNA was isolated with the RNeasy Kit (Qiagen, Chatsworth, CA) according to the manufacturer’s instructions, encompassing an on-column deoxyribonuclease I (DNase I) treatment of the RNA. For quantitative RT-PCR analyses, 5ng luciferase mRNA (Promega Corp., Madison, WI) were added to each testis sample before RNA preparation as an external standard.
The quality of all testis RNA samples was monitored by measuring the 260/280 and 260/230 nm ratios with a Nano-Drop spectrophotometer (NanoDrop Technologies, Centreville, DE) and by means of the Agilent 2100 BioAnalyzer (Agilent, Palo Alto, CA). Only RNA showing no signs of degradation or impurities (260/280 and 260/230 nm ratios, larger than 1.8) was considered suitable for microarray analysis.

After purification (GeneChip Sample Cleanup Module, Affymetrix), yield (30–120 µg) and purity (260/280 and 260/230 nm ratios, >1.8) of the labeled amplified RNA were analyzed, 20 µg quality-controlled amplified RNA was fragmented by alkaline hydrolysis and resuspended with control spikes in 300 µl hybridization buffer (Eukaryotic Hybridization Control Kit, Affymetrix).  Of this probe solution, 200 µl was used for hybridization in a rotisserie oven at 45 C.

Before target synthesis, RNA extracts from one testis of three control or three SCARKO littermates were pooled, creating paired control and SCARKO samples optimally adjusted for potential variation between litters. Five micrograms of polyadenylated RNA from each pool was reverse transcribed into double-stranded DNA with a polydeoxythymidine-T7 primer using SuperScript II RT, ribonuclease H, and DNA polymerase I (Invitrogen Life Technologies, Inc., Carlsbad, CA). From this double-stranded DNA, biotin-labeled target aRNA was generated in a T7 in vitro transcription reaction using the Affymetrix IVT Labeling Kit (Affymetrix, High Wycombe, UK).

RNA from 1 testis from three 10 day old Sertoli cell-selective androgen receptor knockout (SCARKO) mice. Immediately after removal, testis samples were snap-frozen and stored in liquid nitrogen. Before RNA extraction, testis samples were weighed and homogenized in a Dounce homogenizer. Thereafter RNA was isolated with the QIAGEN RNeasy Kit (Chatsworth, CA) according to the manufacturers instructions, encompassing an on-column DNaseI-treatment of the RNA.
Keywords = SCARKO
Keywords = spermatogenesis
Keywords = androgens
Keywords = Pem
Keywords = serine protease inhibitor

Affymetrix GeneChip® Operating Software (GCOS) was used for the control of GeneChip® Scanners were used for scanning and data acquisition, according to the manufacturer's instructions.

The gene expression values for each probe set were first estimated from the hybridization intensities using the corrected for GC content Robust Multichip Analysis (GCRMA) method as implemented in Bioconductor (61–63).  Gene expression values for each sample were estimated using the linear model of the data as implemented by the LIMMA package in BioConductor (63).  The differences in log (base 2) expression levels were evaluated by the t test as implemented by the LIMMA package in BioConductor by comparing distribution of expression values between different sample categories.

Total aortic RNA was isolated by homogenization in RNA STAT-60 (Tel-Test, Inc., Friendswood, TX) and purification by chloroform extraction, with a yield of approximately 6 ug total RNA per aorta. Quantity and quality of each samples was measured at the spectrophotometer (OD 260, 280, 260/280) and RNA integrity checked with the use of a Bioanalyzer (18s and 28s peaks) confirming good quality of the samples (Agilent 2100 Bioanalyzer, Agilent Technologies, Palo Alto, CA).

Unamplified, labeled cRNA (15 ug) was hybridized to whole mouse genome 430 2.0 microarrays(Affymetrix) according to the manufacturer's instructions.  Affymetrix GeneChip® Operating Software (GCOS) was used for the control of GeneChip® Fluidics Stations for automated washing, staining, and scanning.

Total RNA (5 ug; a separate aortic sample per microarray) was used for labeling (One-Cycle Eukaryotic Target Labeling Assay (Affymetrix P/N900493, Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions.  Total RNA was reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.

Gene expression data from ovarioectomized mouse aortae treated with estrogen or placebo.

Neonatal rat ventricular myocytes plated in fibronectin-coated dishes, incubated for 24 h with 10% serum and for next 48 h in serum-free medium
Keywords = Fibronectin hypertrophy

72 hours after transduction with MSCV-IRES-GFP, gfp positive bone marrow cells were sorted and RNA isolated

The GeneChips were processed with an Affymetrix GeneChip Scanner 3000 7G. DAT image files of the microarrays were generated using Affymetrix GeneChip Command Console (AGCC, version 0.0.0.676).

The hybridisation coctail (80microliter) containing fragmented biotin-labeled target DNA at a final concentration of 25nanogram/microliter was transfered into Affymetrix GeneChip Mouse Gene 1.0 ST Arrays and incubated at 45 degrees on a rotator in a hybridisation oven 640 (Affymetrix) for 17 hours at 60rpm. The arrays were washed and stained on a Fluidics Station 450 by using Hybridisation Wash and Stain Kit (Affymetrix, cat. nu. 900720) using fluidics procedure FS450_0007.

cDNA target was synthesized, fragmented, biotin-labeled using WT target labeling and Control Reagents (Affymetrix, vat. num. 900652) starting from 200ng total RNA, according to the procedure described in the geneChip Whole Transcript Sense Target labeling Assay Manual, Version 4 (Affymetrix, santa Clara, USA). cDNA was fragmented and the resulting fragments of approximately 40-70 nucleoides were monitored with Bioanalyzer using the RNA nano 6000 Chip.

Total RNA was extracted from frozen BA22 using a Polytron type homogenizer (YellowLine DI 25 Basic) and TriZol reagent (Invitrogen, Paisley, UK) in a ratio of 1 ml of TriZol to 20 mg of tissue. RNA was further purified using RNeasy mini-columns (Qiagen, Valencia, CA, USA) including on-column DNAse-1 step and elution in water. Although pH was analysed in brain lysates using a pH meter, this was not considered to be rigorous enough to exclude or include samples and instead the RNA integrity number (RIN) was used to assess the quality of the RNA as the primary inclusion criterion. The quantity of extracted RNA was determined by spectrophotometry and quality was assessed using an Agilent 2100 Bioanalyzer (South Plainfield, NJ, USA) to determine the RIN. Based on the RIN, samples were classified into three quality groups—pass (RIN >7.0); borderline (RIN 6.0–7.0); fail (RIN<6.0). Following classification, there were 41 pass (RIN range of samples 7.0–9.0: average=7.7), 16 borderline (RIN range of samples 6.0–6.9; average=6.4) and 5 fail samples. Samples in the fail category were excluded from the study, and the remaining samples were randomized into four batches, containing an equal number of schizophrenic/control and male/female samples, for target generation and hybridization.

Female;67;6h;6.7;control;superior temporal cortex (Brodmann Area 22, BA22)

Female;46;4h;6.6;control;superior temporal cortex (Brodmann Area 22, BA22)

Female;89;5h;6.5;control;superior temporal cortex (Brodmann Area 22, BA22)

Male;91;4.5h;6.3;control;superior temporal cortex (Brodmann Area 22, BA22)

Male;60;16h;6.9;control;superior temporal cortex (Brodmann Area 22, BA22)

Male;72;12h;6.8;control;superior temporal cortex (Brodmann Area 22, BA22)

Male;38;6h;6.9;control;superior temporal cortex (Brodmann Area 22, BA22)

C57/129S;Fra-1-/-: Fra-1 KO;female;2 months;30 µl of PBS containing bleomycin (0.075U/mouse) for 5 days;lung

C57/129S;Fra-1-/-: Fra-1 KO;female;2 months;30 µl of PBS for 5 days;lung

Dulbecco’s modified Eagle’s medium - high glucose supplemented with antibiotics, 15% v/v fetal calf serum and either 103 U/ml of leukemia inhibitory factor (LIF) on gelatinized culture dishes or without LIF on feeder cell layers

Mus musculus embryonic stem cells derived from wild type embryos

bone marrow;CD34+ hematopoietic stem cells (HSC);myelodysplastic syndromes (MDS);refractory anemia (RA);monosomy7/del(7q)

bone marrow;CD34+ hematopoietic stem cells (HSC);myelodysplastic syndromes (MDS);refractory anemia (RA);del5q plus other

Cells were gently washed in warm PBS and transferred to phenol red-free DMEM/F-12 Medium (supplemented with 10% Charcoal-Stripped Fetal Bovine Serum + 1X penicillin/streptomycin) in Corning Cell Culture Cluster wells overnight and then challenged with 1pM (very low, vL), 100pM (low, L), 10nM (high, H), and 1uM (very high, vH) levels of Bisphenol A.  Prior to collection, cells were washed in warm PBS, resuspended & briefly incubated in TRI-Reagent, & finally collected (in quintuplicate replicates) at each specific time point: 8 hours, 24 hours, and 48 hours.

Ishikawa cells were maintained and grown (to confluency or at a desired cell density between 500,000 - 1 million cells/mL) in DMEM/F-12 Medium (supplemented with 10% Fetal Bovine Serum + 1X penicillin/streptomycin) in xenoestrogen-free Corning plasticware.

Total RNA was extracted using TRI-Reagent and protocol provided by supplier (Molecular Research Center, Cincinnati, OH).  Extracted RNA was further purified using Qiagen RNEasy columns and protocol provided by supplier (QIAgen, Valencia, CA).  Quadruplicate samples were advanced to target preparation and GeneChip processing.

Following fragmentation, cRNA was hybridized for 16 hr at 45C on GeneChip Human U133plus2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Purified RNA was converted to cDNA target using SuperScript Choice system (Invitrogen Corp, Carlsbad, CA) and cDNA was converted to biotinylated cRNA probes using the ENZO BioArray transcript labeling kit (ENZO Life Sciences, Farmingdale, NY).

Cells known to possess both estrogen and progesterone receptors.
vHigh_8h_3

Ishikawa;39-year-old parous Japanese female diagnosed with endometrial adenocarcinoma stage 2.;bisphenol A;1 uM;8 hours

Low_48h_4

Ishikawa;39-year-old parous Japanese female diagnosed with endometrial adenocarcinoma stage 2.;bisphenol A;100 pM;48 hours

Simple annotation: Development, androgen
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K562 cells were treated with 0.5 µM Imatinib (STI571), 0.05 µM Nilotinib (AMN107) (IC50 concentration) or DMSO as control for 24 hours.

RPMI, 10% FBS, 2 mM L-Gluthamine, 100 U/ml Penicillin, 100 µg/ml Streptomycin, 37°C humified incubator

GeneChips were scanned using the GenArray® 2500 scanner (Agilent).

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. Scaling factor was 500.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG U133 A2.0. GeneChips were washed and stained in the Gene Chips® Fluidics Station; Affymetrix.

Biotin Label Protocol GeneChip Expression 3’-Amplification One-Cycle-Target, 10 ug cRNA were used.

K562 cells (CML cell line) treated with DMSO as control for 24 hours

K562 cells (CML cell line) treated with IC50 concentration of STI571 (Imatinib) (0.5 µM) for 24 hours

112;None;7/5/81;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;12/7/04;Altered bowel habit;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

114;None;6/27/36;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;12/14/04;Altered bowel habit, Alcohol excess;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

110;None;3/13/54;M;JEWISH;FALSE;FALSE;FALSE;FALSE;FALSE;12/2/04;Diarrhoea;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

111;Paracetamol;9/5/82;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;12/3/04;FH of CD, Path Increased lymphiod in TI Bx.;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

102;Movicol 1 sachet daily;9/5/62;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;11/2/04;RIF pain, persistent anaemia.;0;TRUE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

109;None;10/10/57;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;12/2/04;FH of Colon Cancer;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

106;None;5/29/87;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;11/18/04;Abdominal pain, upper GI symptoms.;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

107;None;07/28/1060;M;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;11/25/04;FH Colon Cancer;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

115;Frusemide, Codine Phosphate;9/14/28;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;12/21/04;Diarrhoea, Also has Prostate Ca;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

116;Clomiprimine;1/19/56;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;12/21/04;FH Colon cancer;0;TRUE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

Affymetrix GeneChip experiment performed on mRNA from adrenal glands of the hypotensive mouse strain, BPL ("Blood Pressure Low"). Replicate 3 of 3.

In 6-well plates, cells were pre-incubated with 10 µM oxidized ubiquinone (Q10), or the respective vehicle controls (KANEKA Corporation, Japan). After 24 hours, cell culture medium was removed and fresh lipopolysaccharide (LPS, E. coli, O55:B5, Sigma Aldrich, Taufkirchen, Germany) containing medium (1 µg/ ml) was added for 4 hours, except in the negative control wells (-LPS).

THP-1 cells were cultivated in RPMI medium 1640 (Invitrogen, Karlsruhe, Germany) supplemented with 10% FCS and 1% antibiotics (penicillin/ streptomycin) in a humidified incubator containing 5% CO2 at 37°C. Twenty four hours before pre-incubation, cells were plated at a density of 3 x 106 per well in a 6-well plate.

Microarrays were scanned with a GeneChip® Scanner 3000 7G (Affymetrix) using GCOS software.

Cells were collected in Qiazol-lysis buffer (Qiagen, Hilden, Germany) and stored at -80 °C until isolation of total RNA.

20 µg of fragmented cRNA was hybridized to a Human Genome U133 Plus 2.0 array for 16 hr at 45 °C at 60 rpm. Arrays were washed on GeneChip®  Fluidics station 450 (Affymetrix) and stained with streptavidin-phycoerythrin

Single cell suspensions from bone marrow were obtained by crushing the bones of the hindlegs, and filtering the suspension through a 40µm cell strainer. CD71+ cells were MACS-enriched from the bone marrow of WT, CD70TG, IFNg-/- and CD70TG*IFNg-/- mice by labelling with biotin-conjugated CD71 antibodies (eBioscience) and using streptavidin-conjugated microbeads (Miltenyi Biotech).

Mice were bred and maintained on a C57BL/6 background in the animal facilities of the Academic Medical Center (University of Amsterdam, Amsterdam, The Netherlands) in specific pathogen-free conditions. Mice were given standard chow and acidified drinking water ad libitum.

According to affymetrix scan protocol, available at www.affymetrix.com using a Scanner 3000 7G. P/N 702569 Rev. 5

RMA pre-processing and baseline transformation to median of all samples using Genespring GX Software (Agilent Technologies).

FS450_0001
100-300ng of total RNA was hybridized to Mouse Gene 1.0 ST Array GeneChips, according to the manufacturer’s protocols (Affymetrix).

A comprehensive description of step-by-step instructions and lists of reagents required for the optimized Whole Transcript (WT) Sense Target Labeling Assay are described in the GeneChip Whole Transcript Sense Target Labeling Assay Manual (P/N 701880), available at www.affymetrix.com.

MPA (1mg/dam) SubQ injection for 48 hours; or the same volume of EtOH

gcrma calculated from cel files using Stratagene ArrayAssist Lite v3.4, producing chp files with unlogged signal levels and Affy flags

Following fragmentation, 2.2 ug of cDNA were hybridized for 16 hr at 45C on GeneChip mouse Genome 430V2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (WT-Ovation Pico RNA Amplification System, NuGEN Technologies).

gene expression data from pregnant mouse cervix treated with MPA

Control and STAT-deficient naïve CD4+CD44-CD62L+CD25- T cells were isolated and sorted on the flow cytometer. Cells were stimulated with IL-6 (20 ng/ml), IL-27 (20 ng/ml) or no stimulation for 3 hours.

STAT3-deficient naïve T cells stimulated for 3 hours with IL-6 3

Expression values were determined using GeneChip Operating Software (GCOS) v1.1.1 software.

The data were analyzed with GeneChip Operating Software (GCOS) v1.1.1. The trimmed mean target intensity of each array was set to 500.

Total RNA was extracted using the MirVana RNA Isolation kit from Ambion.

aRNA was hybridized to GeneChip Mouse Genome 430 2.0 Arrays from Affymetrix according the manufacturers protocol.

RNA was biotin-labeled using the MessageAmpII-Biotin Enhanced Kit from Ambion

Gene expression data from STAT3KO naïve CD4+ T cells stimulated for 3 hours with IL-6

CD4+ T;C57BL/6J;Cd4-Cre_C57BL6-STAT3<tm1Dlv> (STAT3KO);stimulated for 3 hours with IL-6 (20 ng/ml)

STAT3-deficient naïve T cells stimulated for 3 hours with IL-6 2

STAT3-deficient naïve T cells stimulated for 3 hours with IL-6 1

U2OS;osteosarcoma cells;nonspecific siRNA (SiNS);dexamethasone (Dex) for 4h

U2OS;osteosarcoma cells;none (non-infected control);dexamethasone (Dex) for 0h

U2OS;osteosarcoma cells;none (non-infected control);dexamethasone (Dex) for 2h

in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 8, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 0, Units of Dose or Concentration: ppm

nasal epithelium, formaldehyde inhalation exposure, air control, 6 hours per day, 5 days per week, 8 day time point

Rat230_2;15;ul;1.743;0.932;1.84;1:5;8.8;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;65;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;2.318;1.187;1.91;1:5;8.2;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;66;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.007;0.497;1.97;1:5;8.2;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;67;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;2.644;1.383;1.88;1:5;8.2;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;68;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

in vivo Treatment: Formaldehyde, Treatment Duration: 6, Units of Duration: hrs, Treatment Time: 6, Units of Treatment Time: hrs, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 15, Units of Dose or Concentration: ppm

nasal epithelium, formaldehyde inhalation exposure, 15 ppm, 6 h time point

Rat230_2;15;ul;2.417;1.217;1.98;1:5;7.7;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;337;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

in vivo Treatment: Formaldehyde, Treatment Duration: 6, Units of Duration: hrs, Treatment Time: 6, Units of Treatment Time: hrs, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 0, Units of Dose or Concentration: ppm

nasal epithelium, formaldehyde inhalation exposure, air control, 6 h time point

Rat230_2;15;ul;1.708;0.905;1.86;1:5;8.3;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;53;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;3.245;1.679;1.91;1:5;7.3;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;321;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;3.023;1.564;1.91;1:5;7.4;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;322;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;3.413;1.719;1.95;1:5;7.4;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;323;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;4.08;2.003;2.01;1:5;7.8;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;325;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

The Ewing sarcoma cell line A673 was grown in Dulbecco's Modified Eagle Media (DMEM) (Cellgro) with 10% Fetal calf serum (FCS) (Sigma Aldrich) and 2 mM sodium pyruvate (Cellgro) at 37C with 5% CO2.

A673 treated with cytarabine (ARA-C) for 24 hours with concentration of 0.34 uM (2 x EC50), biological rep1

Scanned per the Affymetrix Gene Chip Automated Station (GCAS) protocol (Early Access User Manual Version 1.0).

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix's default analysis settings.  The samples in the data set have been scaled so that the mean expression of all genes for each sample is equal to the mean expression of all genes for the median sample.

RNA was extracted with Trizol per the manufacturer's protocol (Invitrogen) and prepared for hybridization to Affymetrix high-throughput arrays.

3.5 ug of cRNA was hybridized to Affymetrix 96-well Gene Chip HT human array with standard hybridization, blocking, washing, and staining per the Affymetrix Gene Chip Automated Station (GCAS) protocol (Early Access User Manual Version 1.0).

Two micrograms of RNA was used for target preparation as per the Affymetrix Gene Chip Automated Station (GCAS) protocol (Early Access User Manual Version 1.0).

Gene expression data from A673 cell line that has been treated with cytarabine (ARA-C) for 24 hours with concentration of 0.34 uM (2 x EC50).

A673 cell line that has been treated with cytarabine (ARA-C) for 24 hours with concentration of 0.34 uM (2 x EC50).

A673 cell line, a human EWS/FLI translocated Ewing sarcoma cell line.

A673 treated with cytarabine (ARA-C) for 24 hours with concentration of 0.34 uM (2 x EC50), biological rep2

A673 treated with cytarabine (ARA-C) for 5 days with concentration of 0.17 uM (EC50), biological rep2

Gene expression data from A673 cell line that has been treated with cytarabine (ARA-C) for 5 days with concentration of 0.17 uM (EC50).

A673 cell line that has been treated with cytarabine (ARA-C) for 5 days with concentration of 0.17 uM (EC50).

A673 treated with cytarabine (ARA-C) for 5 days with concentration of 0.17 uM (EC50), biological rep3

A673 treated with cytarabine (ARA-C) for 3 days with concentration of 0.17 uM (EC50), biological rep3

Gene expression data from A673 cell line that has been treated with cytarabine (ARA-C) for 3 days with concentration of 0.17 uM (EC50).

A673 cell line that has been treated with cytarabine (ARA-C) for 3 days with concentration of 0.17 uM (EC50).

A673 treated with cytarabine (ARA-C) for 5 days with concentration of 0.17 uM (EC50), biological rep1

A673 treated with cytarabine (ARA-C) for 3 days with concentration of 0.17 uM (EC50), biological rep1

A673 treated with cytarabine (ARA-C) for 3 days with concentration of 0.17 uM (EC50), biological rep2

The data were analyzed with FlexArray software developed by Genome Quebec Center at McGill University and RMA as normalization method.

Following fragmentation, 10 ug of cRNA were hybridized to Affymetrix GeneChip Mouse Genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

A673 treated with cytarabine (ARA-C) for 24 hours with concentration of 0.34 uM (2 x EC50), biological rep3

A673 treated with cytarabine (ARA-C) for 3 days with concentration of 0.34 uM (2 x EC50), biological rep1

Gene expression data from A673 cell line that has been treated with cytarabine (ARA-C) for 3 days with concentration of 0.34 uM (2 x EC50).

A673 cell line that has been treated with cytarabine (ARA-C) for 3 days with concentration of 0.34 uM (2 x EC50).

SMhu016

SMhu015

Cells with stable NTAL KD were prepared by lentiviral infection of  NTAL shRNA TRCN0000127243 in pLKO.1 vector into wild type BMMCs, followed by selection in puromycin. As a negative control to these KDs, wild type BMMCs infected with empty pLKO.1 vector and selected in puromycin were used.  All four types of cells were sensitized in the medium without IL-3 and SCF supplemeted with IgE (IGEL b4 1 mAB; 1 µg/ml) for 4 hours and then half of the cells was activated with antigen (100 ng/ml TNP-BSA) for 2 hours, the other part remained nonactivated.

Bone marrow derived mast cells (BMMCs) were isolated from femurs and tibias of 8 weeks old KO or WT mice of the same littermate  on C57BL/6 background, cultured in mast cell growth media supplemented with IL-3 and SCF for 8 weeks to obtain fully differentiated mast cells.

BMMCs from NTAL WT, pLKO.1 infected, 2 h activated, biological rep1

The data were analyzed with Genomic Suite Software Partek version 6.4 (6.09.0602) using the RMA algorithm.

RNA was extracted using RNeasy kit (QIAGEN) according to a manufacturer’s protocol.

Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneTitan HT_MG-430_PM 24-Array Plate. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Affymetrix standard methods were applied using the high throughput protocol for PM arrays.

bone marrow derived mast cells;NTAL wild type;C57BL/6;lentiviral infection;pLKO.1;2 h 100 ng/ml TNP-BSA

SMhu008

SMhu007

SMhu010

SMhu009

SMhu012

SMhu011

SMhu014

SMhu013

14 days age control

whole blood;Unaffected control;Male;1;n/a;n/a;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

Cells were lysed in RLT with Beta-2-mercaptoethanol. RNA was extracted using the RNeasy Mini Kit (Qiagen), and DNA was removed with on-column DNAse digestion using RNAse-free DNAse Set (Qiagen). RNA was used for either RT-PCR or gene array.

15mg of the biotinylated cRNA was hybridized to Affymetrix Human Genome U133A 2.0 Array (22200 probe sets) (Affymetrix Inc.). The chips were washed and stained with streptavidin-phycoerythin.

For each Affymetrix genechip, 4mg total RNA was reverse-transcribed, amplified, and labeled using BioArray High Yield RNA Transcription Labeling Kit (Enzo Biochem Inc.).

Rats received a single intraperitoneal injection of irinotecan while under light halothane anaesthetic (2% in 1.5 L O2). At the specified time point, rats were killed by exsanguination and cervical dislocation. The GIT was removed immediately and flushed with chilled isotonic saline.  Sections of whole stomach, jejunum and colon were snap frozen in LN2 and stored at -70C until extraction.

Rats were housed individually with free access to food and water

Chips were scanned using the Affymetrix GeneChip Scanner 3000. The scanner operating software, GCOS, converts the signal on the chip into a DAT file, which is used for generating subsequent CEL and CHP files for analysis.

Data was normalised using robust multiarray average approach with additional background adjustment using sequence information to estimate probe affinity for nonspecific binding

Extraction of RNA was carried out by NucleoSpin RNA II kit (Machery Nagel, Germany) as per manufacturer's instructions. Rat total RNA was quality ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol.

A total hybridisation volume of 300ul was prepared for each sample and 200ul loaded into a Rat 230 version 2.0 GeneChip.  The chip was hybridised at 45C for 16 hours in an oven with a rotating wheel at 60rpm.  After hybridisation the chip was washed using the appropriate fluidics script in the Affymetrix Fluidics Station 450.

A total of 7ug was labelled using the Affymetrix One Cycle cDNA synthesis kit (Millenium Sciences cat no. 900431).  The subsequent cDNA was cleaned using the Affymetrix GeneChip Sample Cleanup kit (Millenium Sciences cat no. 900371). Biotin was incorporated into the resultant cRNA using the Affymetrix IVT labelling kit (Millenium Sciences cat no. 900449).  After the IVT process, the labelled cRNA was cleaned using the above GeneChip Sample Cleanup kit. A total of 20ug of labelled cRNA was then fragmented to the 50-200bp size range and quality control checked using the Bioanalyser 2100 using the NanoChip protocol.  Samples were then prepared for hybridisation to the Rat 230 version 2.0 GeneChip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that includes 1x Hybridisation Buffer (100mM MES, 1m NaCl, 20mM EDTA, 0.01% Tween-20), 0.1mg/ml Herring Sperm DNA, 0.5mg/ml BSA, and 7% DMSO.

Gene expression data from large intestine treated with irinotecan

The data were processed and normalised using quantile normalisation with BeadStudio software

L-540;Human Hodgkin Lymphoma;10 µM Perifosine + 5 µM Sorafenib for 24hrs

Unaffected MZ twin pair 3 (Unaffected patient of MZ twin pair CCN3)

Unaffected MZ twin pair 4 (Unaffected patient of MZ twin pair CCN4)

Unaffected MZ twin pair 5 (Unaffected patient of MZ twin pair CCN5)

Animals were injected i.p. vehicle (5% DMSO in corn oil). After 10h they were sacrificed.

Animals had free acess to food (standard laboratory chow) and drinking water. They were mantained in 12-hour light/12-hour dark cycle.

Raw data were normalized using the Robust Multichip Average (RMA) algorithm as described. After transformation to non-logarithmic data, the expression estimates were scaled to the average expression levels in the control group analyzed using GeneSpring software (Silicon Genetics, Redwood, USA).

Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer protocol and purified by RNeasy Mini Kit (Qiagen). The total RNAs of two animals were pooled in equal amounts.

After fragmentation, the cRNA was hybridised to the Gene Chips for 16 hours, followed by a standard amplification with biotin/streptavidin/phycoerythrin.

All was done according to the Affymetrix recommendations. Briefly, double-stranded cDNA was synthesised using 10mg of total RNA with a (dT)24-T7 primer and amplified with T7 RNA polymerase in the presence of biotinylated nucleotides to cRNA.

C57BL/6;male;9 - 12 weeks;liver;vehicle only (5% DMSO in corn oil)

Animals were injected i.p. 50 mg/kg of phenobarbital in vehicle (5% DMSO in corn oil). After 10h they were sacrificed.

Animals had free acess to food (standard laboratory chow) and drinking water. They were mantained in 12-hour light/12-hour dark cycle. Seven days prior treatment they were on 1% (w/w) cholesterol diet (Provimi Kliba SA, Kaiseraugst, CH).

C57BL/6;male;9 - 12 weeks;liver;vehicle only (5% DMSO in corn oil);1% cholesterol diet

GeneChip One-Cycle cDNA Synthesis Kit (Affymetrix; manufacturer’s recommendations), amount of RNA labeled: 1µg

H69 cells were treated with DMSO (control),  PIK75 (100 nM) or TGX221 (1 mM) for 24 hrs at 37 °C in complete RPMI medium.

The human SCLC cell line H69 was cultured in RPMI medium containing 10% heat-inactivated FCS, 1% L-Glutamine and 1% penicillin/streptomycin at 37°C/5% CO2 (humidified atmosphere).

Scanning was done with the GeneChip® Scanner 3000 7G (Affymetrix) using the Affymetrix Command Console as instrument control software.

Quality control and microarray data analysis was done using R/Bioconductor [Gentleman RC et al., 2004; R Development Core Team, 2011; http://www.bioconductor.org/]. Expression values were computed RMA (robust multi array average) [Irizarry et al., 2003a, b] as processing algorithm.

Total cellular RNA was extracted using the RNeasy Mini  Kit (QIAGEN) according to the manufacturer's instructions.

PAX5 expression was induced in the cell line L428-PAX5 prior to the treatment with 5-aza-2′-deoxycytidine (5-aza-dC; Sigma-Aldrich, St. Louis, MO, USA), a DNA demethylating reagent and Trichostatin A (TSA; Sigma-Aldrich), a histone deacetylase inhibitor. After 2 days of incubation with 0.25 nM mifepristone, the medium was partially replaced and only the freshly added medium was supplemented with mifepristone. 5-aza-dC was subsequently added at a concentration of 3 µM and the cells were incubated for further 3 days. TSA was added at concentration 640 nM 24 h prior to harvesting.

The Burkitt lymphoma cell lines Raji and Namalwa (designated as B-cell lines throughout the manuscript) and the Hodgkin cell line L428 were grown in RPMI 1640 (PAA Laboratories) supplemented with 10% fetal calf serum (PAN-Biotech). For the cultivation of the cell line L428-PAX5, 25 mM HEPES (Life Technologies/Invitrogen) was added supplementary. The cell lines were incubated at 37 °C and 5% CO2.

Affymetrix CEL files were imported into Partek Genomic Suite Software (Version 6.5, Partek Inc., St. Louis, USA) and processed by the implemented RMA workflow (median polish probe set summarization, RMA background correction, quantile normalization).

2.5 ug of ss cDNA were hybridized for 16 hr at 45°C on Human Gene ST 1.0 Arrays (Affymetrix). Arrays were washed and stained with standard protocols in the Affymetrix Fluidics Station 450.

Single strand cDNA was prepared from 250 ng total RNA according to the standard Ambion protocol (WT Expression kit) and fragmentation and biotin labeling  was done according to the standard Affymetrix protocol (WT terminal labeling kit)

thymuses were harvested from individual mice, single cell suspensions were made and cells were stained with antibodies for CD4 and CD8 before sorting.

The data were analyzed using Expression File Creator module on Gene Pattern Suite and RMA as normalization method.

wild-type double positive cells sorted from thymus of 8 week old mouse

Cells were treated daily with fresh media containing 200 uM Lacciac Acid A

Cells were cultured in DMEM + 10 % Fetal plex media in 6 well plates at 37C, 5% C02 for 7 days total

Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade

Data were collected using the using the GeneChip operating software (GCOS) v1.4. The data was then analyzed using Partek Genomics Suite software version 6.5 using Robust Mulitchip Average (RMA) for data normalization.

Gene expression data from E2A-deficient double-positive thymocytes

E2A-deficient double positive cells sorted from thymus of 8 week old mouse

Cells expressing IkBa dominant negative cultured in absence of dox, no TNF stimulation

Small intestinal tissue was harvested, washed in PBS, and stored in RNALater until RNA preparation.

Left ventricular myocardium in patients with Dilated cardiomyopathty (33)

Left ventricular myocardium in patients with Dilated cardiomyopathty;myocardium sold commercially

human peripheral blood derived monocytes, 24 hour LPS stimulation, biological rep2

According to the Affymetrix standard protocol (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array).

The data were analyzed with Robust Multichip Average (RMA) procedure using quantile normalization .

type: unknown

Extract Protocol Extract Protocol Extraction protocol Total RNA (TRNA) was isolated from the heart samples utilizing Trizol Reagent (GIBCO/BRL) following the manufacturer's protocol. The quality of TRNA was assessed using the Agilent 2100 Bioanalyzer (version A.02.01S1232, Agilent Technologies). Only RNA with the OD ratio of 1.99-2.0 at 260/280 was used for microarray analysis.

Cyclophosphamide-treated peripheral blood leukocytes 2 days - Biological Replicate 2 - Technical Replicate 1

Biological replicate 2 of 4. Technical Replicate 1 of 2. Peripheral blood leukocytes,  CTX-treated day 2

Peripheral blood leukocytes;DBA/2;pool of untreated bone marrow cells;DBA/2;reference

Cyclophosphamide-treated peripheral blood leukocytes 2 days - Biological Replicate 2 - Technical Replicate 2

Biological replicate 2 of 4. Technical Replicate 2 of 2. Peripheral blood leukocytes,  CTX-treated day 2

Cyclophosphamide-treated peripheral blood leukocytes 1 day - Biological Replicate 4 - Technical Replicate 1

Biological replicate 4 of 4. Technical Replicate 1 of 2. Peripheral blood leukocytes,  CTX-treated day 1

Cyclophosphamide-treated peripheral blood leukocytes 1 day - Biological Replicate 4 - Technical Replicate 2

Biological replicate 4 of 4. Technical Replicate 2 of 2. Peripheral blood leukocytes,  CTX-treated day 1

Cyclophosphamide-treated peripheral blood leukocytes 2 days - Biological Replicate 1 - Technical Replicate 1

Biological replicate 1 of 4. Technical Replicate 1 of 2. Peripheral blood leukocytes, CTX-treated day 2

Cyclophosphamide-treated peripheral blood leukocytes 2 days - Biological Replicate 1 - Technical Replicate 2

Biological replicate 1 of 4. Technical Replicate 2 of 2. Peripheral blood leukocytes,  CTX-treated day 2

Cyclophosphamide-treated peripheral blood leukocytes 1 day - Biological Replicate 2 - Technical Replicate 1

Biological replicate 2 of 4. Technical Replicate 1 of 2. Peripheral blood leukocytes,  CTX-treated day 1

Cyclophosphamide-treated peripheral blood leukocytes 1 day - Biological Replicate 2 - Technical Replicate 2

Biological replicate 2 of 4. Technical Replicate 2 of 2. Peripheral blood leukocytes,  CTX-treated day 1

Cyclophosphamide-treated peripheral blood leukocytes 1 day - Biological Replicate 3 - Technical Replicate 1

Biological replicate 3 of 4. Technical Replicate 1 of 2. Peripheral blood leukocytes,  CTX-treated day 1

Cyclophosphamide-treated peripheral blood leukocytes 1 day - Biological Replicate 3 - Technical Replicate 2

Biological replicate 3 of 4. Technical Replicate 2 of 2. Peripheral blood leukocytes,  CTX-treated day 1

FA6 transiently transfected with non-targeting siRNA, transfection C

FA6 transiently transfected with non-targeting siRNA, transfection A

gene expression data frompancreatic cancer cell line FA6 transiently transfected with AGR2 siRNA

pancreatic cancer cell line FA6 transiently transfected with AGR2 siRNA

Ulcerative colitis patient, biopsy taken from the colon, no macroscopic signs of inflammation.

Ulcerative colitis patient, biopsy taken from the sigmoideum, no macroscopic signs of inflammation.

Cells captured via Arcturus LCM system, amplified (RiboAmp, 2 rounds) and labeled (Enzo) for hybridizaton to Affymetrix MG_U74Av2 arrays, using manufacturers protocols in each step.

Control subject, biopsy taken from the colon, no macroscopic signs of inflammation.

KDM5A/LSD1 knockdown by siRNA was performed according to a published protocol (Schulte et al., Cancer Research, 2009 (PMID 19223552)).
Cells were harvested 48 h after KDM5A/LSD1 knockdown.

ONS76 cells were cultivated as described (Kuenkele et al., Neuro Oncol, 2012 (PMID 22591662)).

Signal intensities were normalized using the RMA normalization feature in Partek Genomics Suite (Partek, Inc.).

Hybridisation to human arrays was performed according to the manufacturer's recommendations (Affymetrix).

Mice were housed in a temperature controlled room with 12 h light:dark cycle. Water and food were given ad libitum.

GeneChips were scanned with the Affymetrix GeneChip Scanner 3000.

Probe level data from the .CEL files were analyzed using Partek Genomics Suite v6.5. Probes were imported and summarized using RMA and ANOVA was used to determine fold changes and p-values.

Total RNA was extracted and purified using the RNeasy Plus Mini kit (Qiagen) according to the manufacturer's instructions.

10 μg of labeled cRNA was hybridized to Affymetrix Mouse 430 2.0 arrays for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual. GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 450.

Biotinylated cRNA was prepared from 10 ug of total RNA as per the Affymetrix GeneChip Technical Analysis Manual.

Balb/C;female;pancreas;30 days old;Isocaloric low protein diet;sham

Mice (backcrossed C57Bl/6J background) were housed in QBP vivarium (University of Queensland, St. Lucia, Queensland, Australia) with 12h light–dark cycle and fed a standard diet containing 4.6% total fat (from Specialty Feeds, Glen Forrest, Western Australia) and water provided ad libitum.

Data was compiled using BeadStudio v2.3.41 (Illumina). Normalized data was produced using GeneSpring GX version 11 via normalization to control genes, where control genes were represented by all genes with an Illumina detection score equal to one in at least three out of the six samples (7730 control genes in total).

Mice were overnight fasted and then sacrificed at 9:00AM in the morning. RNA was extracted from snap frozen quadriceps femoris with tri-reagent (Sigma), followed by treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser 2100.

Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification kit (Ambion)

Transgenic mice contained a truncated version of human RORalpha1 (RORalpha1delDE) where the entire E region and part of the hinge/D region have been removed. This transgene is driven by a skeletal muscle specific human skeletal alpha-actin (HSA) promoter.
4068846001_D

4068846001_E

4068846001_F

Imaging steps were performed in the Lombardi Comprehensive Cancer Center Macromolecular Shared Resource.
Pixel Size	 3
Filter	570
Scan Date	11/06/02  14:59
Number of Scans	2

Hybridization and washing steps were performed in the Lombardi Comprehensive Cancer Center Macromolecular Shared Resource.
Protocol	EukGE-WS2v4
Station	1
Module	1
Hybridize Date	11/06/02  14:22

Data processed with Partek Genomics Suite using RMA background correction and quantile array normalisation.

Total RNA was extracted using Trizol from Invitrogen for lysis of cells and phase separation according to the manufacturers instructions. RNA was then purified from the aqueous phase using the Qiagen RNeasy Mini Kit. The protocol for RNA clean up was used according to the manufacturer’s instructions.

Genechips  were hybridised overnight at 45 degrees C for 17 hours in an Affymetrix Hybridisation oven.

Total RNA was converted to biotinylated sense DNA as per the Affymetrix Genechip Whole Transcript (WT) Sense Target Labeling Assay Manual.

2-4 month male C57BL6 mice were injected with saline once hourly for 4hours, sacrificed and total RNA isolated using guanadinium isothiocianate

Approximately 10 µg of total RNA was processed to produce fluorescently labeled RNA

Affymetrix Expression Analysis Technical Manual protocol was followed

RMA-Express was used for normalization and Genepattern and Genomatix software suites were used for statistical analysis

Silica Gel column extraction of total RNA was performed according to the manufacturer's instructions.(Agilent Technologies, Waldbronn, Germany)Total RNA was isolated from microdissected  glomeruli, reverse-transcribed, and linearly amplified.

Gene expression data from glomeruli of patient after Tumor Nephrectomy - this serves as control.

Immuno-guided microdissection was performed on muscle biopsies in order to isolate MHC-I-positive myofibers.

Chips were processed on an Affymetrix GeneChip Fluidics Station 450 using Affymetrix default analysis settings and global scaling as normalization method

Total RNA extraction using Rneasy Micro kit(Qigen). Total RNA from each sample was amplified for ssDNA generation using the Ovation™ Pico WTA System (NuGEN Technologies, San Carlos, CA)

ssDNA was fragmented and labelled with the Encore® Biotin Module (NuGEN Technologies)

Partek 6.3 was used to generate the RMA data, using the core probesets only option. This option generated the 'core' probesets as defined by Affymetrix as well-defined. This option generated 28,869 probe sets. Using the CEL files you may generate the rest, but these 28,869 probe sets were all that was used for the analysis.  RMA signals were generated for the core probe sets using the RMA background correction, Quantile normalization and summarization by Median Polish. Summarized signals for each probe set were log2 transformed. These are the standard defaults used in Partek.

Trizol using 2 times recommended volume, followed by Qiagen RNeasy column

WT protocol (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay, rev. 5

Grown for 48 hours in DMEM supplemented with 10% FBS and 1X Pennicillin-Streptromycin

Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Gene expression data from HepG2 cell lines after 18 hours of growth without PCB treatment (Control).

Liver tissues were flash frozen at the time of dissection and stored at -80 C

Mice were maintained in the designated animal care facility at the Baylor College of Medicine according to the institutional guideline for the care and use of laboratory animals. SRC-2-/- and wild-type mice were ovariectomized at 6 wk of age. Two weeks later, the mice were killed by cervical dislocation after placing the mice under anesthesia, Avertin (2,2-tribromoethyl alcohol; Sigma-Aldrich,St. Louis, MO).

Normalized expression of probe level data was calculated using the Robust Multiarray Average function (RMA) implemented in Bioconductor's affy-package

Total RNA was extracted using the QIAGEN RNeasy total RNA isolation kit and transcribed to cDNA

Single cell suspension was prepared from tumors isolated from tumor bearing mice and the CD11b+Gr1+ and CD11b+Gr1- populations were labelled with anti-CD11b (Clone M1/70, eBiosciences) and anti-Gr1 (Clone RB6-8C5, eBiosciences) and purified by FACS sorting of live cells.

Scanned on an Agilent scanner, images were processed using Agilent Feature Extraction software version 10.7.

Agilent Feature Extraction software version 10.7 was used to create feature extraction files. The normal exponential convolution model was applied for the background correction, Loess and quantile were applied for within array and cross-array normalization. Gene differential expression was analyzed by the package of limma.

Total RNA was isolated using Qiagen's RNAeasy kit following the manufacturer's instructions.  RNA quality was verified by running samples on an Agilent Bioanalyzer 2100.

Samples were labeled by two-rounds of amplification using Ambion's MessageAmpII aRNA Amplification kit and Agilent's QuickAmp Labeling kit. For all samples, 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal mouse reference (Stratagene, La Jolla, CA).

SAM630148;C57BL/6;spr881;IL17RC Knock out;pooled mouse reference RNA

SAM630147;C57BL/6;spr881;IL17RC Knock out;pooled mouse reference RNA

Quadriceps muscle;P.q.5;Pompe;rhGAA;52 Weeks;M;6.9m;Walking;Decreased;Positive Clinical Outcome

Quadriceps muscle;P.q.5;Pompe;rhGAA;12 Weeks;M;6.9m;Walking;Decreased;Positive Clinical Outcome

Quadriceps muscle;P.q.6;Pompe;rhGAA;12 Weeks;M;4.3m;Walking;Decreased;Positive Clinical Outcome

Quadriceps muscle;P.q.6;Pompe;rhGAA;00 Weeks;M;4.3m;Walking;Decreased;Positive Clinical Outcome

Quadriceps muscle;P.q.7;Pompe;rhGAA;00 Weeks;F;5.3m;Walking;Decreased;Positive Clinical Outcome

Quadriceps muscle;P.q.6;Pompe;rhGAA;52 Weeks;M;4.3m;Walking;Decreased;Positive Clinical Outcome

Quadriceps muscle;P.q.7;Pompe;rhGAA;52 Weeks;F;5.3m;Walking;Decreased;Positive Clinical Outcome

Fibroblasts are dissociated with 0.05% trypsin at 37°C, 5% CO2 for 5minutes and collected by centrifugation

Fibroblasts are cultured in DMEM medium supplemented with 10% FBS at 37°C, 5% CO2 until confluence

Quadriceps muscle;P.q.8;Pompe;rhGAA;12 Weeks;M;6.4m;Standing;Decreased;Positive Clinical Outcome

Quadriceps muscle;P.q.8;Pompe;rhGAA;00 Weeks;M;6.4m;Standing;Decreased;Positive Clinical Outcome

NCI-H460;human lung large cell carcinoma cells;cisplatin and nicotine;24 hours

whole blood;Cutaneous psoriasis without arthritis;Male;2;30.2026009582478;30;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Cutaneous psoriasis without arthritis;Female;2;13.2375085557837;8;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Cutaneous psoriasis without arthritis;Male;3;3.8507871321013;30;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Cutaneous psoriasis without arthritis;Female;1;20;33;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Cutaneous psoriasis without arthritis;Female;1;39;7;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Cutaneous psoriasis without arthritis;Female;1;31;25;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Cutaneous psoriasis without arthritis;Female;1;7.97878165639973;47;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

Microarray data were normalized using the RMA function within Bioconductor (Irizarry et al., 2003).

RNA was extracted using the StrataPrep Total RNA Mini Kit (Stratagene, La Jolla, CA), and RNA quality was assayed using a bioanalyzer (Agilent Technologies, Paola Alto, CA)

medium spiny neuron, striatum, brain, mutant mouse, Ctip2, Bcl11b, affymetrix

whole blood;Cutaneous psoriasis without arthritis;Female;2;43.0;15;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Cutaneous psoriasis without arthritis;Female;2;28;16;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

Total RNA was extracted and purified using an Picopure kit (Arcturus).

cRNA was fragmented following the Affymetrix protocol,  and hybridized to the Affymetrix GeneChip Mouse Genome 430 2.0 arrays

total RNA was processed to produce biotinylated cRNA targets using Affy Small Sample Target Labeling Assay Version II.

After Herpesvirus Saimiri transformation of human primary T cells: RPMI 1640 (Life Technologies) and Panserin 401 (PAN Biotech) mixed in a ratio 1:1, supplemented with 10% FCS (PAN Biotech), 100 µg/mL gentamicin and 10 U/mL IL-2 (Roche)

Data processing was done using GeneSpring GX 11 software (Agilent). ExonPLIER16 summarization was applied to core probe set intensities.
HuGene-1_0-st-v1.r4.mps
HuGene-1_0-st-v1.r4.pgf

Samples were hybridized using Hybridization Kit materials (Affymetrix) according to the WT Terminal Labeling Protocol (P/N 702808 Rev.1, Affymetrix); Fluidics Protocol FS450_0007

Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix) according to the WT Terminal Labeling Protocol (P/N 702808 Rev.1, Affymetrix)

Transfection of siRNAs was performed according to the Oligofectamine protocol provided by the company (Invitrogen).

Hep3B cells were grwon under full media conditions for 24 hours. After transfection with siRNAs cells were cultivated for further 24 hours. RNA isolation.

The data were imported and analyzed with a commercial software called JMP Genomics, version 4, from SAS. The Raw fluorescence intensity values were normalized applying quantile normalization.

Nucleospin RNAII II (Macherey-Nagel) was used for total RNA extraction.

Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

C57Bl6;4 weeks;BCR-ABL1 transformed pre-B cells;BCR-ABL1-driven ALL;Bach2 knockout

Subconfluent hOB shEV and shRB1 cells were irradiated at 4 Gy using a 137Cesium source at a dose rate of 1.7 min/Gy and cell pelllets collected 0, 2, 4, 8, 16  and 24 hrs after irradiation

Cells were maintained at 37°C and 5% CO2 in alpha MEM (modified Eagles's medium) containing 10% (v/v) FCS, 50 U.mL-1 penicillin and 50 ug.mL-1 streptomycin, 2mM L-glutamine, 100 uM L-ascorbate-2-phosphate

Arrays were washed using Affymetrix fluidics stations and scanned using the Gene Chip Scanner 3000.

Total RNA was extracted from cell pellets using Trizol reagent (Invitrogen)  and RNAeasy isolation kit (Qiagen). The quality of RNA was measured using Bioanalyzer (Agilent Technologies).

Labelled RNA was hybridised to Human Gene 1.0 ST arrays. Hybridisation was performed according to the manufacturers instructions (Affymetrix , Santa Clara, CA).

Affymetrix Gene Chip® WT terminal labelling and hybridization was performed according to manufacturers instructions (Affymetrix , Santa Clara, CA).

RB1-383 pGIPZ (OpenBiosystems)(shRB1),  human osteoblast cell line (hOB), irradiated (IR)

Empty vector-non silencing-pGIPZ, OpenBiosystems (EV), human osteoblast cell line (hOB), irradiated (IR)

RB1-383 pGIPZ (OpenBiosystems)(shRB1),  human osteoblast cell line (hOB)

Cell lines were cultured in standard conditions, Knockout DMEM medium (10829), supplemented with 20% Knockout Serum Replacement for ES cells (10828) both things from GIBCO (Invitrogen). Penicillin/streptomycin, LIF, no essentials aminoacids and -mercaptoethanol were also added to the medium. Cells were always cultures in a monolayer of feeder cells. Cells were maintained at 37ºC in a humidified 5% CO2 chamber.

The images were processed with Microarray Analysis Suite 5.0 (Affymetrix).

Raw expression values obtained directly from .CEL files were preprocessed using the RMA method (Irizarry et al., 2003), a three-step process which integrates background correction, normalization and summarization of probe values

Only those samples with an RNA Integrity Number (RIN) >7 were used for hybridization. Samples of 500ng/l were used to perform a Affymetric mouse 430_2 expression array

Lung, Familial Idiopathic Interstitial Pneumonia (F-IIP), Nonspecific Interstitial Pneumonia (NSIP)

Cells were either left untreated (0) or stimulated with IL-13 (100 ng) for 48h

Affymetrix murine HG-U133 plus 2 gene chips were used. GeneChip CEL files were subjected to GC-RMA normalization (get reference) using the GeneSpring GX 7.3.1
GeneSpring 7.3.1 (Agilent technologies Inc. Palo Alto, California) was used to normalization, Clustering and filtering. Samples were normalized pair wise to respective unstimulated controls

Total RNA was extracted using Trizol kit (Invitrogen).
Quality control steps: RNA quality was assessed by using the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA) and only those samples with 28S/18S ratios between 1.3 and 2 were subsequently used

Full Protocol Description: Create a hybridization cocktail for a single probe array that contains  0.067 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 10% DMSO, and 1X Hybridization Buffer.  Heat hybridization cocktail to 99?C for 5 minutes, to 45C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 uL of 1X Hybridization Buffer. Incubate at 45C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45?C for 16 hrs in the Hybridization Oven rotating at 60 rpm.   Fluidics:  Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0004. Arrays were stained with phycoerythrin-conjugated streptavidin [Molecular Probes, Eugene, OR] and hybridization signals were amplified using antibody amplification with goat IgG [Sigma-Aldrich] and anti-streptavidin biotinylated antibody [Vector Laboratories, Burlingame, CA], as described in the Affymetrix GeneChip® Expression Analysis Manual

Modified Epicentre protocol (Epicentre biotchnologies) with random primer

Primary culture of esophageal epithelial cells stimulated with IL-13 100ng/mL

Mice with targeted disruption of the akt2 gene were repeatedly backcrossed (more than 7 times) with WT C57Bl/6 mice obtained from the Jackson Laboratory prior to experimentation. Progeny were screened by tail-prep PCR. Only male mice were used.

Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA.

SAM630134;C57BL/6;spr881;IL17RC Knock out;pooled mouse reference RNA

SAM630135;C57BL/6;spr881;IL17RC Knock out;pooled mouse reference RNA

SAM630136;C57BL/6;spr881;IL17RC Knock out;pooled mouse reference RNA

Minor salivary glands were removed for routine diagnostic procedures

Affymetrix Microarray Suite version 5.0 using Affymetrix software EC (Experssion Console 1.1)

RNA extraction using Trizol Reagent and further purification using Qiagen Rneasy mini-kit.

Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 30ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

brain (frontal cortex);schizophrenia;19 yr;white;295.9;18 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);schizophrenia;51 yr;white;295.9;23 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);schizophrenia;45 yr;white;295.3;34 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);schizophrenia;52 yr;white;295.9;19 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);schizophrenia;41 yr;white;295.9;20 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);schizophrenia;50 yr;white;295.3;31 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

Grown for 48 hours in DMEM supplemented with 10% FBS and 1X Penicillin-Streptromycin

Gene expression data from HepG2 cell lines after 30 minutes of PCB77 treatment.

HepG2 cell line from ATCC at 8th generation after 30 minutes of PCB77 treatment.

Cells were plated in the evening. Next day, 1ug/mL  doxycycline was added to induce shRNA expression or JQ1 to final concentration of 500 nM was added

cells grown in DMEM (high glucose, 10% FBS, 1% Pen-strep, 1% Sodium Pyruvate, 1% L-glutamine) medium in 37oC incuabtor

Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Derived from Nf1-/- P53-/- SKPs;spindle cell malignant peripheral nerve sheath tumor cell (SMPNST);JQ1 treated

Derived from Nf1-/- P53-/- SKPs;spindle cell malignant peripheral nerve sheath tumor cell (SMPNST);Vehicle treated

Gene expression data from HepG2 cell lines after 6 hours of PCB77 treatment.

HepG2 cell line from ATCC at 8th generation after 6 hours of PCB77 treatment.

Derived from Nf1-/- P53-/- SKPs;spindle cell malignant peripheral nerve sheath tumor cell (SMPNST);Brd4 shRNA

Derived from Nf1-/- P53-/- SKPs;spindle cell malignant peripheral nerve sheath tumor cell (SMPNST);control shRNA

The aRNA sample was vacuum dried to completion and resuspended in coupling buffer (Ambion, Inc).
aRNA was labeled with 20,000pmol Cy Dye Post Labeling Reactive Dyes  (Amersham Biosciences Corp., NJ) at room temperature for 30 mins followed by addition of hydroxylamine to 0.18M to quench unreacted dye, for 15 mins at room temperature protected from light. Labeled aRNA was purified using the RNeasy MinElute Cleanup kit (Qiagen).   The labeling resulted in 30-60 dye molecules/1000nt.

A pool of two pure subsets of peripheral blood B cells (CD19+ CD3- CD4- CD8- CD16- CD56-), stringently sorted by flow cytometry, from two age and gender matched healthy donors.;Pooled RNA from the total peripheral lymphocyte fraction from 20 healthy donors, used as a common reference.

Gene expression data from HepG2 cell lines before PCB77 treatment.

HepG2 cell line from ATCC at 8th generation before PCB77 treatment.

Brown preadipocyte cell lines derived from newborn wildtype littermates of IRS-2 KO mice. Preadipocytes were grown to confluence (day 0) in differentiation medium (Dulbeco’s modified Earle’s medium containing 10% fetal bovine serum supplemented with 20 nM insulin and 1 nM T3). Brown preadipocytes were synchronized by overnight serum starvation. Total RNA was isolated with ULTRASPEC RNA Isolation System (Biotecx Laboratories, Inc., Houston, TX) following the manufacture’s instruction. 28 ug of total RNA were subjected to cDNA and cRNA preparations as previously described. 15 ug of adjusted cRNA were hybridised to Affymetrix U74A-v2 arrays (Santa Clara, CA). Intensity values were quantitated by MAS 5.0 software (Affymetrix). All chips were subjected to global scaling to a target intensity of 1,500 to take into account the inherent differences between the chips and their hybridization efficiencies.
Lot batch = Joslin core 533

Lot batch = Joslin core 927

Synovial biopsies (n = 4 to 6), obtained by needle arthroscopy from the swollen knee of a patient with microcrystalline arthritis

Trizol extraction of total RNA was performed according to manufacture's instructions.

Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Genechip Mouse Genome array.

Biotinylated cRNA were prepared according to Affymetryx protocol

Brown preadipocyte cell lines derived from newborn wildtype littermates of IRS-1 KO mice. Preadipocytes were grown to confluence (day 0) in differentiation medium (Dulbeco’s modified Earle’s medium containing 10% fetal bovine serum supplemented with 20 nM insulin and 1 nM T3). Brown preadipocytes were synchronized by overnight serum starvation.  Total RNA was isolated with ULTRASPEC RNA Isolation System (Biotecx Laboratories, Inc., Houston, TX) following the manufacture’s instruction. 28 ug of total RNA were subjected to cDNA and cRNA preparations as previously described.  15 ug of adjusted cRNA were hybridised to Affymetrix U74A-v2 arrays (Santa Clara, CA).  Intensity values were quantitated by MAS 5.0 software (Affymetrix).  All chips were subjected to global scaling to a target intensity of 1,500 to take into account the inherent differences between the chips and their hybridization efficiencies.
Lot batch = Joslin core 532

HEK293 cells were transfected with pcDNAI/Neo (Invitrogen) as control plasmid. Stable transfectants were synchronized and grown in the presence of 10% FBS for 48 h. Total RNAs were purified with the mini RNeasy kit (Qiagen).

Chip was normalized using all probe sets scaling option and target signal at 500.

Synovial biopsies (n = 4 to 6), obtained by needle arthroscopy from the swollen knee of a patient with lupus arthritis

Origin of sample: Sciatic nerve of 4 day old (P4) wild type mice (mixed background), pooled from 4--7 mice.
RNA extracted with RNeasy kits (Qiagen).
Target preparation by two rounds of in vitro transcription (Hoffmann, R., Seidl, T., Neeb, M., Rolink, A. & Melchers, F. Changes in gene expression profiles in developing B cells of murine bone marrow. Genome Res 12, 98-111 (2002)).
Labeling protocol: Standard Affymetrix biotin labeling protocol (Affymetrix, Expression Analysis: Technical manual, 2000) in 2nd round of in vitro transcription.
Hybridization procedure: Standard Affymetrix protocols (Affymetrix, Expression analysis: Technical manual, 2000).
Scanning with Affymetrix scanner and MAS 5.0 software. The original images (.dat files) are available on request (mantei@cell.biol.ethz.ch) The .cel files produced by MAS 5.0 were normalized using the program dChip (smoothing spline normalization; Li, C. & Wong, W.H. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol. 2, research0032.0031-0032.0011 (2001); http://www.dchip.org). dChip was also used to calculate a probe sensitivity index for each probe on the basis of 27 arrays, and then a "model-based expression index" (MBEI) for each gene on each array (Li, C. & Wong, W.H. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl. Acad. Sci. U.S.A. 98, 31-36 (2001)).
Keywords = peripheral nervous system
Keywords = PMP22

synovial biopsies;Microcrystalline arthritis;55;m;NSAIDs/colchicine

The data were analyzed with Microarray Suite 5.0 using a scaling factor of 125 and imported into Genespring 7.0.

Fragmented, biotin labeled cDNA was hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Male Sprague-Dawley albino rats (Charles River) initially weighting approximately 200 grams were randomly assigned to one of the following:  1) olanzapine (2 mg/kg/day, I.P.) (N=20) or 2) Saline (N=20) and administered olanzapine or saline for 21 days.
Frontal cortex (N=4/group) was dissected and homogenized for microarray, QPCR and western blotting following previous methods (Fatemi et al. 2003; Brooks et al. 2003).
RNA isolation, cDNA preparation, microarray hybridization and QPCR followed previous methods (Brooks et al. 2003).

Keywords = olanzapine
Keywords = frontal cortex

GeneChip 3000 7G(Affymetrix) was used. Array images were analysed for defects with the Expression Console software (Affymetrix).

Raw data were normalized by GC RMA algorithm.GeneSpring GX 10.0 software (Agilent Technologies, Böblingen, Germany) was used for filtering and statistical data analysis. An unpaired T test FDR corrected by Benjamini Hochberg was carried out between control and experimental samples to test for differential   expression.

RNA was extracted using PureLink RNA Micro scale kit (Invitrogen). Microarray was performed with 300ng RNA. RNA integrety was tested with Agilent 2100 Bioanalyzer (Agilent Technologies).

total BM cells were stained with antibodies and LT-HSCs were sorted directly into RLT Plus buffer summplemented with 1% 2-mercaptoethanol

Animals were maintained in the animal facility at Boston Children’s Hospital

Data were processed with GenePattern (ExpressionFileCreator, V11), RMA, median scaling

Total RNA was isolated using the RNeasy Micro Plus Kit (Qiagen) according to the manufacturer's instructions.

cDNA is prepared from total RNA using a DNA/RNA chimeric primer and a reverse transcriptase and amplified using SPIA™ amplification. After purification cDNA is fragmented and labeled with Biotin.

Mixed; mostly C57BL/6 with some 129S/SvImJ (from CJ7 ES cells).;wild type;9-day old;bone marrow;long-term hematopoietic stem cells (LT-HSC);Lin-Sca1+Kit+CD48-CD150+

The chips were scanned using an Affymetrix GeneChip® Scanner 3000 7G, and each digitized image was processed using the GeneChip® Operating Software (GCOS) version 1.2 (Affymetrix).

Gene expression data was summarized, normalized, and transformed in log2-scale by the GCRMA method

Total RNA was isolated from individual human lung samples by homogenization in TRIzol® Reagent per the manufacturer’s protocol (Invitrogen, Carlsbad, CA) using Soft Tissue Omni Homogenizer Tips (Omni International; Marietta, GA).

Labeled cRNA was fragmented and hybridized to the Affymetrix GeneChip® Human Genome U133 Plus 2.0 Array as described in the Affymetrix GeneChip® protocol.

Total RNA (100 ng) was used to synthesize double-stranded cDNA using the Two-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA).  The cDNA served as a template to generate biotin-labeled antisense cRNA with an IVT Labeling Kit (Affymetrix).

PBMC isolated by Ficoll gradient centrifugation from pauciaticular course JRA patient
Biotinylated cRNA was synthesized from total RNA (Enzo; Farmingdale, NY) and processed according to the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix; Santa Clara, CA).  57 samples: 5 pauciarticular PBMC, 15 polyarticular PBMC, 11 control PMBC, 6 JSpA PBMC, 5 pauciarticular SFMC, 10 polyarticular PBMC, 5 JSpA SFMC classified by course.
Keywords = Pauciarticular course, juvenile rheumatoid arthritis (JRA), peripheral blood mononuclear cells (PBMC)

Scanned with Illumina’s BeadArray Reader using standard protocols

The data were normalised using quantile normalisation (GeneSpring GX10.0.2)

cRNA was prepared using Ambion - Illumina TotalPrep-96 RNA Amplification Kit

umbilical cord blood;CD34+/CD38- Lin- cells;mir126 overexpression

umbilical cord blood;CD34+/CD38- Lin- cells;overexpression control

expression profile pre-treatment patients with clinical diagnosis of dermatomyositis

A pool of RNA from lung from three male mice with SM22-rtTA transgene on an FVB/N background, raised at Denver altitude (nearly normoxic), fed doxycycline for 8 weeks and sac'd at 12 weeks of age.

Mouse Genome 430 2.0 microarrays (Affymetrix, Foster City, CA) were hybridized with 20 µg cRNA. Target hybridization, washing, staining, and scanning probe arrays were done following an Affymetrix GeneChip Expression Analysis Manual.

First and second strand complimentary DNA was synthesized using standard techniques.  Biotin-labeled antisense complimentary RNA was produced by an in vitro transcription reaction.

A pool of RNA from lung from three female mice with SM22-rtTA transgene on an FVB/N background, raised at Denver altitude (nearly normoxic), fed doxycycline for 8 weeks.

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 800.

Total RNA was extracted according to the standard Affymetrix protocol including Trizol extraction and Rneasy column cleanup

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133A  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Naïve OT-I T cells were transferred into isogenic recipient mice and infected with Listeria monocytogenes. Memory T cells were isolated from these recipient mice at>80 days post infection.

GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 complete with a 7G upgrade.

The data were analyzed with Partek GS v 6.4 using default RMA as normalization method.
Probe group file: MoGene-1_0-v1.r4.pgf
Meta-probeset file: MoGene-1_0-v1.r4.mps

Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by further purification on RNeasy columns.

2.5 ug of labeld cDNA were hybridized on mouse GENE 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cDNA were prepared using NuGEN WT-Ovation PicoRNA amplification system, starting from 800 pg to 50 ng of total RNA.

isolated from spleen;memory CD8 T cells;C57/BL6;wild type;over 80 days after infection

The cells were treated with vehicle, R5020 [10nM], TPA [1µM] or R5020 [10mM] + TPA [1µM] in fresh media [as given in growth protocol] for 24 hours.

The cells were starved overnight in phenol red free MEM (Minimal Essential Medium) containing 5% charcoal-stripped fetal bovine serum with NEAA (non-essential amino acids), L-glutamine , sodium bicarbonate, penicillin, streptomycin and Fungizone.

Background Correction and Quantile Normalization using 'lumi' package in R

RNA was extracted followed by clean-up and DNase I treatment using the DNA-Free RNA Kit (Zymo Research) in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanalyser.

glaucoma;no or early glaucoma;No radiation treatment;DBA/2J;Female;10.5

Trizol reagent (Invitrogen) and RNeasy kit (Qiagen) was used to isolate and purify total RNA

15ug of fragmented cRNA hybridized for 16 hours at 45C with constant rotation

The mRNA was extracted from rat livers collected 24 hour after inflicting with a burn injury

The mRNA was extracted from rat livers collected 8 hour after inflicting with a burn injury

Crohn's Disease subject (43 year old caucasian male, SAK_1315906827)

Subject Age : 43

Crohn's Disease subject (41 year old caucasian female, SAK_1304662648)

in vivo Treatment: Corn Oil, Treatment Duration: 2, Units of Duration: hours, Treatment Time: 1:32, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.178, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

KJ_0_2_48_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

in vivo Treatment: Corn Oil, Treatment Duration: 2, Units of Duration: hours, Treatment Time: 1:26, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.21, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

KJ_0_2_47_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

in vivo Treatment: Corn Oil, Treatment Duration: 1, Units of Duration: hour, Treatment Time: 1:30, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.21, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

KJ_0_1_42_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

in vivo Treatment: Corn Oil, Treatment Duration: 1, Units of Duration: hour, Treatment Time: 1:24, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.21, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

KJ_0_1_41_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

in vivo Treatment: Corn Oil, Treatment Duration: 1, Units of Duration: hour, Treatment Time: 1:18, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.21, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

KJ_0_1_40_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

Crohn's Disease subject (34 year old caucasian female, SAK_1288107729)

Subject Age : 34

in vivo Treatment: Corn Oil, Treatment Duration: 12, Units of Duration: hours, Treatment Time: 6:35, Units of Treatment Time: am, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.245, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

KJ_0_12_62_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

in vivo Treatment: Corn Oil, Treatment Duration: 12, Units of Duration: hours, Treatment Time: 6:30, Units of Treatment Time: am, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.245, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

KJ_0_12_61_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

in vivo Treatment: Corn Oil, Treatment Duration: 12, Units of Duration: hours, Treatment Time: 6:25, Units of Treatment Time: am, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.235, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

KJ_0_12_60_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

Crohn's Disease subject (58 year old caucasian female, SAK_1316890359)

Subject Age : 58

Mice at around age postnatal day 40 were sacrificed, the brain extracted and sliced on a vibratome (Leica). Slices were incubated in ACSF with pronase E (1mg/mL; Sigma) for 1 hour and desired regions were microdissected. Three Pasteur pipettes with decreasing tip size were used for tritration in a 1.5 ml Eppendorf tube. Tritrated samples were diluted 20 times with ACSF with FBS (1%) and plated on a 10cm petri dish with Sylgard substriatum. Glass pipette of tip size around 50 um was used to aspirate fluorescent cells under a fluorescent stereomicroscope (Leica). Aspirated cells were transferred to a new dish with fresh ACSF and aspirated again to purify the sample. This wash was repeated twice more (total of 3 washes). After the last wash, the sample was transfered to a 200 ul PCR tube with 50 ul of XB (extraction and lysis buffer from PicoPure RNA Isolation Kit; Arcturus).

The data were processed with GCRMA algorithm in the Bioconductor with default settings.

Total RNAs of regions of interest were prepared with an RNeasy miniprep kit according to manufacturer's (Qiagen, Valencia, CA) protocol. RNA was quantified by using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE), and quality was assessed with a 2100 Bioanalyzer (Agilent Technologies, Palo Alta, CA) and with agarose gel electrophoresis. Depending on the brain region, between 1 and 5 µg of total RNA was used to prepare double-stranded cDNA with a cDNA synthesis kit (GIBCO/BRL) for first and second strand. Biotinylated cRNA was generated from these cDNAs with a BioArray high-yield RNA transcript labeling kit (Enzo Life Sciences). It was then purified with RNeasy spin columns (Qiagen) and fragmented before hybridization

Approximately 1 to 5 µg of total RNA was processed to produce biotinylated cRNA targets.

cocaine naive, lateral hypothalamus, 0 hrs/day access to cocaine

Transfection of siRNA duplexes using Oligofectamine according to the manufacturer´s instructions

HeLa cells were transfected with siRNA specific for optineurin mRNA

knockin mouse forebrain
Treatment, type=time_course, measurement=4.0 weeks

knockin mouse cerebellum

wild-type mouse cerebellum

Monocytes were isolated from 30 ml of whole blood from 19 women, 10 with high BMD and 9 with low BMD, using monocyte negative isolation kit from Dynal Biotech Inc. Total RNA was extracted from monocytes using Qiagen RNeasy Mini Kit. Targets were produced for each subject using standard Affymetrix procedures from about 4ug of total RNA. Hybridization was made for each subject. Comparison was performed between 10 high BMD and 9 low BMD subjects.
MCI-001 is the sample from a premenopausal high BMD women.
Keywords = monocyte
Keywords = osteoporosis
Keywords = HDC
Keywords = CCR3
Keywords = GCR

MCI-003 is the sample from a premenopausal high BMD subjects.

MCI-004 is the sample from a premenopausal high BMD women.

ApoE-/- RAGE-/-;C57BL/6;Ann Marie Schmidt laboratory, Columbia University;Male;9 weeks;Total aorta from root to bifurcation.;diabetic

Aorta from ApoE-/- RAGE -/- mouse with diabetes sacrificed at 9 weeks.

BMDCs were stimulated with tumor-derived DNA using Lipofectamin for 7 hours.

Bone marrow derived dendritic cells were generated by culturing bone marrow cells in the presence of GM-CSF for 9-12 days.

GeneChips were scanned using Affymetrix Gene Chip Scanner 3000 7G and CEL.

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) and dChip software using Affymetrix default analysis settings and global scaling as normalization method. The genes scored as "absent" or with signal intensity <100 were first filtered out.

Total RNA was isolated with Rneasy kit (Qiagen) using manufacture`s instruction.

129/SvEv;wild type;bone marrow derived dendritic cells (BMDCs);purified tumor-cell derived DNA

129/SvEv;wild type;bone marrow derived dendritic cells (BMDCs);none (unstimulated control)

129/SvEv;STING knockout;bone marrow derived dendritic cells (BMDCs);purified tumor-cell derived DNA

0.065% DMSO or 650nM MLN4924 were added to 2 million A375 cells and incubated for 1, 2, 4, 8, or 24 hours before recovery for RNA isolation and Gene Expression.

A375 cells were maintained at 37oC in DMEM medium supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine and 100 U/ml penicillin/100 g/ml streptomycin (Invitrogen).

The data were analyzed with Expression Console software from Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

Cells were precipitated, PBS washed, lysed using Qiagen RLT Buffer, and then RNA was extracted with Ambion MegaMax kit using King Fisher automated platform. All protocoles were executed following manufacturers recommendations.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133Plus 2.0 Array in an Affymetrix Model 640 hybridization oven . GeneChips were washed and stained on an Affymetrix FS450 station.

Biotinylated cRNA were prepared using modified MesageAmp-based protocols (Ambion Inc) from 1.5ug total RNA.

Gene expression data from TH GFP labeled neurons from the locus coeruleus (LC), Mecp2 null

see Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001).

Software – Affymetrix Microarray Suite 4.0
Scanning Hardware = HP GeneArray Scanner.

Probe level measurements produced by Affymetrix Microarray Suite 4.0. Analysis performed at level of raw average difference. A GCOS absolute expression analysis was performed for each GeneChip genome array hybridization. Following the initial analysis, the absolute analyses were rerun using global scaling to an average target intensity of 200.  The scaling allows for the direct comparison of hybridization values from the different targets analyzed in this project (and with any additional GeneChip sample assays you run using the same array type). For each analysis, scaled or unscaled, the parameters ALPHA 1 and ALPHA 2 are set to 0.1 and 0.15 respectively.  These parameters set the point at which a probe set is called present (P), marginal (M), or   undetectable (A).  This call is based on the Detection p-value of the probe set.

Total RNA from each sample was isolated and purified using RNeasy Mini Columns and DNase On-Column digestion (Qiagen, Valencia, CA) according to the manufacturer’s specifications. RNA quality was assessed by OD reading and 1% formaldehyde agarose gel. Because there was not enough RNA material, samples from the two 8-year-old brains were pooled and used as a single sample.

Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001)
Standard Affymetrix external spikes added to hybridization mixture: BioB, BioD, and CreX at 5.0pm, 25pm and 100pm respectively.

gene expression data from the Brain area 8/9 of two 8 year-old girls suffering from from Rett Syndrome (RTT), RNA labeled and hybridized Dec. 2001

Brain area 8/9 from two 8 year-old girls suffering from Rett Syndrome.

Total RNA was isolated and purified using RNeasy Mini Columns and DNase On-Column digestion (Qiagen, Valencia, CA) according to the manufacturer’s specifications. RNA quality was assessed by OD reading and 1% formaldehyde agarose gel

gene expression data from the Superior Frontal Gyrus of 10year-old normal girl, RNA labeled and hybridized Dec. 2001

Superior Frontal Gyrus from a 10 year-old girl not suffering from Rett Syndrome and therefore considered as a normal subject.

Chips were processed on an Affymetrix GeneChip Fluidics Station 450. Background adjustment by Robust Multi-Array (RMA) algorithm was applied to probes intensities. Raw probes gene level expression were summarized from the corrected intensities and then quantile normalized.

Total RNA was extracted from fresh peripheral blood mononuclear cells using an RNeasy kit (Quiagen, Santa Clarita, USA)

Samples were hybridized using Affymetrix hybridization kit materials.

Samples were chemically fragmented and biotinylated using the IVT Labelling Kit (Affymetrix).

Female;36;PBMC;Patient 113;REBIF;12 month of REBIF;multiple sclerosis;NAB-

Female;36;PBMC;Patient 113;REBIF;24 month of REBIF;multiple sclerosis;NAB-

Female;36;PBMC;Patient 113;baseline;baseline;multiple sclerosis;NAB-

Female;36;PBMC;Patient 113;REBIF;3 month of REBIF;multiple sclerosis;NAB-

Female;35;PBMC;Patient 112;REBIF;12 month of REBIF;multiple sclerosis;NAB-

Female;35;PBMC;Patient 112;REBIF;24 month of REBIF;multiple sclerosis;NAB-

Female;35;PBMC;Patient 112;baseline;baseline;multiple sclerosis;NAB-

Female;35;PBMC;Patient 112;REBIF;3 month of REBIF;multiple sclerosis;NAB-

Female;33;PBMC;Patient 108;BETAFERON;12 month of BETAFERON;multiple sclerosis;NAB-

Female;33;PBMC;Patient 108;BETAFERON;24 month of BETAFERON;multiple sclerosis;NAB-

Ikf/f Rosa26-CreERT2+ mice after daily intraperitoneal injections of tamoxifen (50 mg/kg weight of mouse, dissolved in sunflower oil) for 4 days. Mice were analyzed 24h after the last injection.

The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 1.56 µm.

CEL files were processed using Robust Multi-array Average (RMA) algorithms from Bioconductor with default settings to calculate probe set signal intensities

10 μg of cRNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse 430 2.0 arrays (Affymetrix)

Biotinylated cRNA targets were prepared according to Affymetrix recommendations in  GeneChip Expression Analysis Technical Manual  (P/N 702232 Rev.2) starting from [100 ng (A810) ; 50 ng (A1052) ; 15-100 ng (A1031)] of total RNA  in a two cycle target labeling assay

Day: 1; Drug: Methamphetamine; Phase: Drug treatment; Replicate: 3

Day: 6; Drug: Methamphetamine; Phase: Drug treatment; Replicate: 3

A549 cells were transfected with pcDNA-NME2-MYC or pcDNA-MYC (control).

A549 cells were procured from ATCC. Cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) (Sigma, USA) supplemented with 10% FBS and 5% CO2 at 37°C

The data were normalised using quantile normalisation with BeadStudio

Data processing cel files were normalized with 'gcrma' function of the Bioconductor package (v2.4) 'gcrma' in R.2.9.1

For total RNA extraction cryopreserved liver tissue samples were homogenized in TRIzol reagent (Invitrogen, San Diego, CA, USA) using pestle and nuclease-free 1,5ml reaction tubes (Ambion). Total RNA was then extracted following the manufacturers guidelines and quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).

Human CD4+ and CD8+ T cell were isolated by negative selection using Miltenyi beads and MACS Vario magnetic cell separation apparatus. T-cell purity was assessed by FACS using anti-CD4-FITC and anti-CD8-PE (Miltenyi) using CellQuest software.

All steps of data preprocessing including background correction, normalization and expression set summaries were performed using the RMA algorithm in R/Bioconductor rma package.  Batch effects corrected using the ComBat R package.  Data was filtered to remove probes which had low expression in all arrays (rma signal value of < 4 was removed).  Differential gene regulation was determined by taking the output from a shrinkage t-test ('st' R package), and then computing the p-values and q-values (FDR) using 'fdrtool' R package.

Total RNA was extracted using the mirVanaTM miRNA isolation kit (Ambion Europe) eluted in 50 ul RNase-free water (Promega UK) and purity was measured using a BioTek PowerWave XS (SSi Robotics, U.S.A.) spectrophotometer and Agilent Bioanalyser, which showed RIN values > 9.5.

Gene expression data from circulating T cells of severe asthmatic

female;1;55;Severe_4;65;81;Prednisolone 10mg od,Spiriva 18mcg od,Methotrexate 12.5mg wkly, Seretode 500 1pbd,Fosamax 70mg once/wk,Folic acid 5mg od,Calchichew,Cocodamol prn;CD8+ T-cells

female;1;54;Severe_5;44;61;Prednisolone 5mg od,Montelukast 10mg od,Symbicort 400/12 2pbd,Omeprazole 20mg od,Uniphyllin 400mg bd,Bricanyl prn;CD8+ T-cells

female;1;21;Severe_2;105;101;Prednisolone 8mg - 1mg for 5wks(stopped 30/5/08),seretide 500mcg 1pbd,Singular 10mg bd,Phyllocontin 225mg am 450mg pm,Ventolin prn;CD8+ T-cells

male;1;32;Severe_3;98;113;prednisolone 15mg od,Seretide 500mcg 2pbd,Montelukast 10mg nocte,Ventolin prn,Phyllocontin 450mg bd,Flixonase od;CD8+ T-cells

Gene expression data from circulating T cells of non severe asthmatic

This is second run of normal bladder cells treated with APF. Membrane B is used.

second run of normal bladder treated with mock APF. Membrane A is used.

female;1;54;Severe_6;55;69;Prednisolone 10-20mg od,Combivent neb 2-4/day,Cetirizine 10mg od,Terbutaline 500mcg od,Budesonide 400mcg 2pbd, Aminophylline SR 450mg bd, Formoterol 12mcg 2pbd;CD8+ T-cells

female;1;45;Severe_7;71;105;Prednisolone 10mg od, Insulin S/C,Seretide 500mcg 2pbd, Metformin,Nexium, Flixonase,Tramacet,Calcium,Valsartan,Amitriptyline;CD8+ T-cells

Cells were seeded in dup[licate 10cm dishes at 1,000,000 cells per dish and incubated for 24h then cells were treated with vehicle (0.1% DMSO) or Vemurafenib (Vem; PLX4032) for a further 24h.

A375 human melanoma cells grown in a monolayer in a 37°C humidified 5%CO2 incubator. Cells were grown in RPMI 1640 + HEPES containing 10% FBS, 2 mM L-alanyl-L-glutamine, 1% penicillin/streptomycin and 250 ng/ml amphotericin B

Raw data were RMA normalized after which differentially expressed genes were detected using a 2-way ANOVA using Partek software. The batch date of the different replicates was controlled for and the log fold change between control and Vem-treated samples was estimated. Normalized data was also subjected to gene set enrichment analysis (provided online by the Broad Institute) using c2 curated gene sets (Molecular signatures database v3.1) to identify enrichment of entire gene sets in either the control of Vem-treated samples

Total RNA was extracted using a Qiagen miRNeasy Mini kit according to the manufacturer's protocol.

5μg of fragmented, labeled cRNA was hybridized at 45°C for 16h onto GeneChip® 1.0 ST human gene arrays then washed and stained using the Affymetrix GeneChip Fluidics Station 450

Biotinylated cRNA was prepared from an input of 250ng RNA using an Ambion WT kit followed by the Affymetrix terminal labelling kit according to the manufacturer's instructions.

Gene expression data from A375 melanoma cells treated with 10 μM vemurafenib

Gene expression data from A375 melanoma cells treated with vehicle control (0.1% DMSO)

10 male Fischer rats, aged 24 months were trained sequentially on two tasks, SWM and OMT; hippocampal tissue collected 24 hours after a 7 day training/testing sequence
Keywords = bioinformatics
Keywords = synaptic plasticity
Keywords = myeli
Keywords = inflamation

Tacrine 2.7mg/kg/day from 5 weeks, from 5 weeks. Moclobemide 10mg/kg/day
Creatine 1%w/v added to wet mash

Lot batch = 5241

Immature, ovariectomized C57BL/6 mice were treated with sesame oil (vehicle) or with 0.1mg/kg 17-alpha-ethynylestradiol (EE) for the length of time indicated. Mice received one dose, except for the 3x24hr samples, which received 3 consecutive daily doses and were sacrificed 24hr after the final dose.
Keywords = estrogen, uterus, mouse, ovariectomized, gavage

Gene expression data from mouse embryonic fibroblasts isolated from 13.5 day C57BL/6 Rap1 knockout embryos, immortalized with SV40LgT

Gene expression data from mouse embryonic fibroblasts isolated from 13.5 day C57BL/6 wildtype embryos, immortalized with SV40LgT

Diclofenac sodium, carbamazepine, nefazodone and ketoconazole were obtained from Sigma (Zwijndrecht, the Netherlands). Methotrexate was from Acros Organics (Geel, Belgium). Human recombinant TNFα was acquired from R&D Systems (Abingdon, United Kingdom).

Human hepatoma HepG2 cells were obtained from American Type Culture Collection (ATCC, Wesel, Germany), cultured in DMEM supplemented with 10% (v/v) FBS, 25 U/mL penicillin and 25 µg/mL streptomycin and used for experiments between passage 5 and 20.

Scanning of the Array Plates was performed using the Affymetrix GeneTitan scanner

BRB Array Tools software was used to normalize the CEL data using the Robust Multichip Average (RMA) method. Significantly differentially expressed genes (p-value < 0.001) between the various experimental conditions were identified with an ANOVA test followed by calculation according to Benjamini and Hochberg (Benjamini and Hochberg, 1995).

RNA was isolated using the RNeasy® Plus Mini Kit (Qiagen, Venlo, the Netherlands) and RNA integrity and quality was assessed using the Agilent bioanalyser (Agilent Technologies, Palo Alto, CA, USA).

cRNA was denaturized to prepare for the hybridization on the array. The fragmented cRNA with a concentration of 0.0375 μg/μl was finally utilized for the hybridization on the Affymetrix HT HG U133 plus PM.  The Affymetrix HWS Kit (#901530) was used for the hybridization, washing and staining of the chips.

The Affymetrix 3' IVT-Express Labeling Kit (#901229) was used to synthesize Biotin-labeled cRNA. From each RNA sample 100 ng was used as input for the labeling reactions.

diclofenac;5;5;Human liver slices (diameter 4 mm, thickness 250 µm)

control;5;5;Human liver slices (diameter 4 mm, thickness 250 µm)

diclofenac;4;30;Human liver slices (diameter 4 mm, thickness 250 µm)

control;4;30;Human liver slices (diameter 4 mm, thickness 250 µm)

diclofenac;7;53;Human liver slices (diameter 4 mm, thickness 250 µm)

control;7;53;Human liver slices (diameter 4 mm, thickness 250 µm)

Immune; Lymph Node_Comprlete Freunds Adjuvant stimulated

Immune; Lymph Node_unstimulated

Immune; normal adult(2X+)

cel files were quantile normalized and signal estimates generated using RMA (Affymetrix package, Bioconductor)

Macro-dissected renal cystic epithelial tissue from Fh1 knockout mouse

Macro-dissected renal epithelial tissue from wild-type littermate controls

F9 cells were treated with DMEM supplemented with etoh for 24hrs. RNA was harvested using Tri-reagent. RNA was Dnase treated and purified using RNeasy spin columns. Samples were submitted to Center for Functional genomics microarray core facility where they followed affymetrix hybridization protocol. Raw data was then entered into GeneSpring for Data analyzation

hESCs that were seeded one day before were transfected with 2ug of the OCT4 or Luciferase shRNA using 6ul of Fugene in 100ul optimen. After 20mins, the transfection mix were added to the cells.

H1 hESCs were grown at 37degress for 5 days before the cells were passaged for OCT4 and Luciferase transfection. Samples were harvested after 2 or 3 days after transfection.

The data were normalized using median (MeV) by performing log2 transformation, followed by median centering on samples and median centering of genes across the samples.

Data were generated using the Affymetrix Expression Console Software using Affymetrix default analysis settings. Data were RMA normalized and analyzed with Partek Genomics Suite 6.5.

Total RNA from biospecimens was extracted using the Quagen RNeasy mini kit according to the manufacturer's instructions and integrity of RNA was checked using the Agilent Bioanalyzer.

Following fragmentation, 6 ug of cDNA were hybridized for 17 hr at 45C on GeneChip HuGene-1.0-st arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

Sample name: TM-827-12R
Gene expression data from PTC with a BRAF mutation

Sample name: TM-824-12R

Sample name: TM-892-11R

Sample name: TM-857-12R

Sample name: TM-1152-12R

Sample name: TM-1064-11R

Sample name: TN-247-13R
Gene expression data from normal thyroid tissue

Sample name: TN-157-12R

Sample name: TN-726-11R

Sample name: TN-720-11R

E9.5 Embryos were collected/dissected and immediately lyzed  in RNA extraction buffer.

The animals were maintained in accordance with the guidelines of the University of Gent Care and Use ethical Committee.

Data were normalized using RMA normalization. The package affy in Bioconductor was used for this.

RNeasy. RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technolgies) and RNA integrity was assessed using the Bioanalyser 2100 (Agilent).

Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.

RNA from 6 different Cop-null embryos were mixed and subdivided into KO pool 1 and pool 2.

Arrays were washed and stained in the Genechip Fluidics Station 450 (Affymetrix) following the manufacturer’s instructions.  Chips were scanned with the Affymetrix GeneChip Scanner 3000 using GeneChipOperating System 1.4

RMA expression values were generated using the R Bioconductor package.

RNA was extracted from micro-dissected tumor and matched normal tissue using the PureLink Micro-to-Midi Total RNA Purification System (Invitrogen, Carlsbad, CA).

U251 GBM cells were transduced with the lentiviral shRNA (shCON or shCypB) for 5 days before total RNA extraction. The pLKO1.5 vectors (shCON encoding non-target control sequence and shCypB to target CypB gene) were used to generate lentiviral particles.

Fastlo [1] normalization was used to preprocess the data. In the quality control step, the Principal Components Analysis (PCA) graph and the hierarchical clustering plot (based on Pearson’s dissimilarity) showed a plate effect, which was removed later using Partek’s batch removal tool[2]. 1. J. E. Eckel, C. Gennings, T. M. Therneau, L. D. Burgoon, D. R. Boverhof, and T. R. Zacharewski. Normalization of two-channel microarray experiments: a semiparametric approach. Bioinformatics (2005) 21(7): 1078-1083.    2. Removing Batch Effects in Partek. Partek® software On-line Help, version 6.5, build 6.10.0915. Copyright © 2010 Partek Inc., St. Louis, MO, USA.

Total RNA was isolated using the miRNeasy RNA isolation kit from Qiagen

According to Buermans HP, et al. Physiol Genomics 2005;21:314-23

ImaGene feature extraction (Biodiscovery Ltd, Marina del Rey, CA, USA) was used to record spot intensities. The signal mean was taken to represent the actual spot intensity, after subtraction of the mean background values. All spot were log2 transformed and intensities lower than 10, typical for the empty spots, were classified as missing. Next for each micro-array, the spot intensities were Z score normalized (Cheadle C, et al. J Mol Diagn  2003;5:73-81), while missing values (some 6% overall) were handled so as to minimize their effect on statistics. Specifically, such values were set equal to the mean of the micro-array distribution after Z score normalization, thus equal to zero. So for each micro-array, Z scores were computed for each green labeled spot intensity according to(2log(G) - mu) / sigma, where mu is the mean and sigma the standard deviation of all 2log(G) of the micro-array. Likewise the Z score was computed for each red labeled spot intensity and the result subtracted from the 'green' Z score for each spot on the micro-array. These differences were then again Z score normalized to obtain the so called Z ratio for each spot.This information will soon be available in a publication.

lymphoblastoid cell line from F6.04, one out of seven of sensitive group;Pooled RNA from a number of lymphoblastoid cell lines (with and without bleo treatment) and head and neck cancer cell lines.

For raw microarray data, we used the RMA (robust multi-array average) method to summarize expression values from probe pair values; data were background-adjusted, quantile normalized (global scaling across multiple arrays). Expression measures were summarized based on log transformed PM (perfect match) values using Median Polish algorithm. Then, we used locally weighted scatterplot smoothing (LOWESS) to do within-array normalization. RMA and LOWESS were performed in Genedata Expressionist Pro3.1® (Basel, Switzerland).

BOEC (blood outgrowth endothelial cells) from individuals that do not have sickle cell anemia

Peripheral blood was drawn into heparin-containing sterile tubes and peripheral blood mononuclear cells were prepared by Ficoll (Amersham) density gradient centrifugation for immediate use. B cells were labeled with a biotin anti-CD19 monoclonal antibody (HIB19 clone, Pharmingen) at 4°C and revealed by phycoerythrin-labelled streptavidin (Biomeda) before immediate B cell sorting with high speed cell sorter (FACS Diva, Beckton-Dickinson).

Raw Affymetrix data were analyzed using R (R Development Core Team, 2008; The Comprehensive R Archive Network: http://cran.r-project.org/) and Bioconductor (Bioconductor: http://www.bioconductor.org/) softwares. The quality of the 27 Affymetrix genechips and RNA was assessed using the Bioconductor AffyPLM and simpleaffy packages, with qc, AffyRNAdeg, fitPLM, image, RLE and NUSE functions. For normalization and background correction.  Raw values were pre-processed with RMA or GCRMA (library simpleAffy).
The Sample data table shows genes that are considered as expressed by affy (P) at least in one of the patients and controls, thus, reporting ~65% of the  data rows in the U133 Plus 2.0 Array.

Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix GeneChip human genome U133 plus 2.0 (with probe sets representing 38,572 UniGene clusters) according to the manufacturer’s instructions. After hybridization and washings, arrays were stained with PE-conjugated streptavidin (10 μg/ml) before scanning.

Gene expression data from human sorted B cells.
P17
JLP_P17_U133_2.CEL

patient17;Systemic lupus erythematosous (SLE);blood;Sorted B cell

T01
JLP_T01_U133_2.CEL

P15
JLP_P15_U133_2.CEL

patient15;Systemic lupus erythematosous (SLE);blood;Sorted B cell

P16
JLP_P16_U133_2.CEL

patient16;Systemic lupus erythematosous (SLE);blood;Sorted B cell

T04
JLP_T04_U133_2.CEL

T05
JLP_T05_U133_2.CEL

T02
JLP_T02_U133_2.CEL

T03
JLP_T03_U133_2_2.CEL

T06
JLP_T06_U133_2.CEL

Five million Panc-1 control or GSK3B shRNA cells were implanted bilaterally and subcutaneously into the flanks of 3-5 week old, female, athymic nude mice. Animals were handled according to a protocol approved by the University of Michigan Committee for Use and Care of Animals. Xenografts were grown to at least 250mm3 followed by harvesting, snap freezing, and tumor tissue microdissection.

Ann Arbor quantile-normalized trimmed-mean method (PMID: 15705192).

Total RNA was extracted from the tissue lysate using Trizol (Invitrogen) and cleanup performed with an RNeasy kit (Qiagen)

3-5 micrograms of total RNA was processed to produce biotinylated cRNA targets.

Panc-1 human pancreatic carcinoma cell line, grown in mice;control shRNA

Xenograft of Panc-1 (Human pancreatic carcinoma) cell line, in mouse

Two lines of NSun2-/- mice were generated using the ES cell line D014D11 (German Gene Trap Consortium) and the mouse line Nsun2tm1a(EUCOMM)Wtsi (The Wellcome Trust Sanger Institute).

Standard Illlumina protocol (Illumina WGGX DirectHyb Assay Guide 11286331 RevA)

Using the R beadarray package the data was corrected for spatial artefacts, logged (base 2) and quantile normalised

RNA was isolated from testis using Trizol (Life Technologies) and cDNA synthesis was performed on 1µg of RNA using the Superscript III Reverse Trancriptase kit from Invitrogen using random hexamers

250 ng of total RNA was converted to complementary RNA (cRNA) target using the Illumina TotalPrep-96 Kit (Ambion 4397949). Total RNA was reverse transcribed and converted to double-stranded cDNA using a T7 promoter-Oligo(dT) primer and purified with magnetic oligo(dT) beads. This formed the template for an in vitro transcription (IVT) reaction which included a biotinylated nucleotide / ribonucleotide mix for both cRNA amplification and biotin labeling.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix 430 2.0 Mouse Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Gene expression data from murine embryonic stem cells with calreticulin deficiency

Generation of Trim24-/- and Trim24-/-Rara+/- mice has been described previously (Khetchoumian et al., 2007). Colonies of both lines were maintained under specific pathogen-free conditions at the Mouse Clinical Institute (MCI) of the IGBMC. Harvesting of mouse liver tissues was done as described in Khetchoumian et al. (2007). All liver samples were subjected to histopathological evaluation before analysis. All animal procedures were approved by the French Ministry of Agriculture (agreement B67-218-5) according to guidelines in compliance with the European legislation on care and use of laboratory animals.

Raw data were transformed with the Mas5 algorithm, which yields a normalized expression value, and "absent" and "present" calls. Target intensity was set to 100 for all chips.

Harvesting of mouse liver tissues was done as described in Khetchoumian et al. (2007). Livers were rapidly excised, washed in cold PBS, and frozen in liquid nitrogen and stored at - 80°C until use for RNA extraction.
Qiagen RNeasy extraction of total RNA was performed according to the manufacturer's instructions.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip MOE-430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 with the EukGE_WS2v5 protocol.

100 ng of RNA from each sample was used to synthesize biotinylated probes, using 2 successive rounds of cRNA amplification with appropriate quality control to ensure full length synthesis according to standard Affymetrix protocols.

SMhu157

Standard Affymetrix protocol, standard GCOS data processing produced the values in the accompanying table

The availability of pluripotent stem cells offers the possibility of using such cells to model hepatic disease and development. With this in mind, we previously established a protocol that facilitates the differentiation of both human embryonic stem cells and induced pluritpotent cells into cells with hepatocyte characteristics. The use of highly defined culture conditions and the avoidance of feeder cells or embryoid bodies allowed synchronous and reproducible differentiation to occur. The differentiation toward a hepatocyte–like fate appeared to recapitulate many of the stages normally associated with the formation of hepatocytes in vivo. In the current study we addressed the feasibility of using human pluripotent stem cells to probe the molecular mechanisms underlying human hepatocyte differentiation. We demonstrate i) that human ES cells express a number of mRNAs that characterize each stage in the differentiation process, ii) that gene expression can be efficiently depleted throughout the differentiation time course using shRNAs expressed from lentiviruses, and iii) that the nuclear hormone receptor HNF4a is essential for specification of human hepatic progenitor cells by establishing expression of the network of transcription factors that control hepatocyte cell fate.

WAO9 human embryonic stem cells;shRNA-mediated HNF4a knockdown;subjected to a hepatic differentiation protocol;d20

WAO9 human embryonic stem cells;subjected to a hepatic differentiation protocol;d15

WAO9 human embryonic stem cells;subjected to a hepatic differentiation protocol;d10

All mice were maintained in the institute animal facility following the IACUC guidelines.

CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA) and probe set signals were generated using the RMA algorithm in ArrayAssist 3.4 (Stratagene). Differential gene expression was determined by pair-wise comparisons.

The Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from 25 ng of total RNA following manufacturer’s instructions.

Gene expression data from cardiac muscle of two-month-old mouse deficient in Neu5Gc sialic acid.
10 Cmah KO Heart

Gene expression data from cardiac muscle of two-month-old mouse deficient in dystrophin.
340 mdx Heart

5 Cmah KO Heart

7 Cmah KO Heart

Gene expression data from cardiac muscle of two-month-old WT mouse.
61 WT Heart

66 WT Heart

Gene expression data from skeletal muscle of two-month-old mouse deficient in Neu5Gc sialic acid and dystrophin.
8Cmah KO mdx Skeletal Muscle

65 WT Heart

82 mdx Heart

336 mdx Heart

Total RNA was extracted by using Trizol (GIBCOyBRL). RNA pellets were resuspended at 1 ug RNA/ul diethyl pyrocarbonate-treated water.

After purification and fragmentation, 15ug of cRNA was used in a 300 ul hybridization mixture containing spiked IVT controls. Approximately 200 ul of mixture was hybridized on chips for 16 h at 45°C. Standard posthybridization wash and double-stain protocols used an Affymetrix GeneChip Fluidics Station 400.

8 ug of total RNA was used in a reverse transcription reaction (SuperScript II; Life Technologies, Rockville, MD) to generate first-strand cDNA. After second-strand synthesis, double-strand cDNA was used in an in vitro transcription (IVT) reaction to generate biotinylated cRNA.

The design of the study was a randomized cross-over design with two different treatments: placebo and resVida (150mg/day trans-resveratrol). Subjects were instructed to take the first supplement on the day after baseline measurements (d1) and the last supplement in the evening on day 29. In the morning of day 30, after a 36h in the respiration chamber, a muscle biopsy was taken, which was followed by the withdrawal of a fasting blood sample.

Ten healthy obese men (age 45–65 years; BMI 30-35 kg/m2) participated in a double-blind randomized cross-over study. Exclusion criteria were unstable body weight (weight gain or loss > 3 kg in the last three months), total body fat (%) < 25%, fasting plasma glucose > 6.1 mmol/l, hemoglobin < 7.8 mmol/l, engagement in programmed exercise > 2 hours total per week, impaired kidney and/ or hepatic function, first- or second-degree family member with type 2 diabetes mellitus, any medical condition requiring treatment and/or medication use, intake of dietary supplements except vitamins and minerals, unwilling to restrict high-resveratrol-containing foods, current alcohol consumption > 20 grams/day, participation in another biomedical study within 1 month before the first screening visit, a contraindication to MRI scanning. All subjects were informed about the nature of the study and written informed consent was obtained before study participation. The local Medical Ethical Committee of Maastricht University Medical Centre approved the study protocol.

Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.16.0).

Skeletal muscle biopsies were taken in the morning of day 30 after an overnight fast. Biopsies were obtained from the vastus lateralis muscle under local anesthesia of the skin and fascia using the Bergström method with suction, cleaned from any visible fat and blood, immediately frozen in isopentane at its melting point, and stored at −80C until analysis.

The Affymetrix GeneChip Human Gene 1.1 ST 24-array plate consists of 24 single Gene 1.1 ST arrays arranged into the standard 96 well plate format. For this experiment 20 arrays were used. Array hybridization, washing and scanning were performed on a GeneTitan Instrument according to the manufacturer’s recommendations.

The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit (P/N 900652) was used for the preparation of labelled cDNA from 100ng of total RNA without rRNA reduction. A detailed description can be found in the User Manual, Chapter 3 (P/N 701880, revision 5).

0.5mM VPA was added to the cell medium in the indicated samples for 4 hrs.

Blood was collected on CPT tubes (Vacutainer® with Sodium Citrate; BD). Whole blood specimens were preserved on RNALater buffer (Ambion) and stored in -80oC

Scanning was performed on a 7th generation GeneChip Scanner 3000, and the Affymetrix GCOS software was used to perform image analysis and generate raw intensity data.

RMA normalization was performed using Expression Console software.

RNA was isolated using the RiboPure-Blood kit (Ambion) and alpha and beta globin mRNA was depleted by GLOBINclear™ Kit (Ambion) according to the manufacturer’s protocol. All RNA samples were checked for purity using a ND-1000 spectrophotometer (NanoDrop Technologies) and for integrity by electrophoresis on a 2100 BioAnalyzer (Agilent Technologies).

Two-round in vitro transcription amplification and labeling was performed starting with 50 ng intact, total RNA per sample, following the Affymetrix protocol. Samples were hybridized on Human U133 Plus 2.0 Arrays (using GeneTitan platform).

Total RNA sample quality was evaluated by spectrophotometer to determine quantity, protein contamination and organic solvent contamination, and an Agilent 2100 Bioanalyzer was used to check for RNA degradation. Two-round in vitro transcription amplification and labeling was performed starting with 50 ng intact, total RNA per sample, following the Affymetrix protocol.

Whole Blood of Dengue infected patient at acute infection time point

prefrontal cortex from adult APP knock-out mouse;back-crossed to C57BL/6 for 6 generations;male

sex=female
ID = C564
Stage 1B
Total RNA
Keywords = cervical cancer
Keywords = cervix

ID = C567
Stage 2B (DOD)
Total RNA

ID = C542
Stage 1B
Total RNA

ID = C555
Stage 1B (NED)
Total RNA

ID = C579
Stage 1B
Total RNA

Total RNA was isolated from tissues with the mirVana RNA Isolation labeling kit (Ambion, Inc.) according to the manufacturer protocol. RNA quality and integrity were confirmed by the ExperionTM Automated Electrophoresis System (BIO-RAD).

Labeled, amplified material (750 ng per array) was hybridized to the Illumina mouse-6 V2.0 expression BeadChip according to the manufacturer's instructions (Illumina, Inc., San Diego, CA).

Cells were grown under standard cell culture condition (95% air, 5% CO2, 37C)

Samples were processed in CINJ Core Expression Array Facility according to Affymetrix protocol.

SKI-DLCL cells were treated with Aplidin 1.5 nM and AraC 5.0 nM combination for 24h. Total RNA was isolated.

C2C12 myoblast cells were maintained in growth medium(DMEM containing 10% fetal bovine serum). To induce differentiation, cells were reseeded in 12-well dishes and after reaching ~90% desity, the medium was changed to DMEM containing 2% horse serum(differentiation medium)

C2C12(ATCC, CRL-1772) cells were cultured using standard protocols provided by the ATCC

The stained chips were read and analyzed with GeneChip Scanner 3000 (Affymetrix).

RMA signal estimates from Expression Console software
probe group file: MoGene-1_0-st-v1.r2.pgf

Total RNA was isolated using RNeasy mini kits(QIAGEN) according to the manufacturer's protocol

Following fragmentation, cRNA were hybridized for 16 hr at 45C (GeneChip® WT Terminal Labeling and Hybridization User Manual, P/N 702808 Rev.5, Affymetrix). GeneChips were washed and stained according to the standard Affymetrix protocol(GeneChip® Expression Wash, Stain and Scan User Manual For Cartridge Arrays,P/N 702731 Rev.3,Affymetrix).

Biotinylated cRNA were prepared according to the standard Affymetrix protocol (GeneChip® WT Terminal Labeling and Hybridization User Manual, P/N 702808 Rev.5, Affymetrix).

C2C12 cells were seeded in same numbers and cultured in same condition.

Serum-starved Control and shCDK8 expressing HCT116 cells were either not treated or treated with 10%FBS McCoy's 5A for 30 minutes in duplicate before RNA was isolated as below.

HCT116 cells were routinely passaged in 10% FBS McCoy's 5A medium . Cells were serum-starved for 40 hours in McCoy's

CEL files were imported into SpotFire (TIBCO), normalized using Robust Multi-chip Average (RMA) and analyzed using the Spotfire Decision Site.

Total RNA was isolated using RNeasy kit from Qiagen per the manufacturers protocol.

Samples were hybridized to Affymetrix GeneChip® Human Gene 1.0 ST arrays using an Affymetrix GeneChip® Hybridization Oven 640.  Each array was washed and stained using a GeneChip® Hybridization, Wash and Stain kit (Invitrogen) and an Affymetrix Fluidics station 450.

Gene expression data from serum-starved shControl HCT116 cells treated with 10% FBS McCoy's 5A for 30 minutes

The microarrays were scanned on an Agilent G2565 scanner (Agilent Technologies) and images were extracted and quality assessed with the Agilent Feature Extraction software (Agilent Technologies), using "Lowess" processing.

Data from individual hybridizations were normalized using the RMA algorithm, and the data were then further analyzed using the microarray software package Genespring GX 7.3software (Agilent Technologies).

Mycroarrays were hybridized using the Agilent 60-mer oligo microarray processing protocol. Version 4.1. April 2004.

Standard Agilent protocol for use with 11K, 22K, and 44K Agilent oligo microarrays. Version 4.0.1 February 2006. Agilent Low RNA Input Fluorescent Linear Amplification Kit was used.

Stratagene Human Universal Reference Pool;C33KD2 is a stable clone derived from C33 cervical carcinoma cell line. These cells express a shRNA that knockdown the expression of the gene CHD8. Expression of the shRNA is induced upon addition of doxycycline.

At postnatal day 70, mice were sacrificed by CO2 asphyxiation and whole brain tissue were dissected using RNAse-free tools.  Brains were snap-frozen in liquid nitrogen and stored at -80 degrees C until RNA isolation.

Mice were raised in standard same-sex housing conditions (14/10-hour light/dark cycle, 40-60% humidity,21°C to 24°C temperature).  Mice were sacrificed at postnatal day 70.

GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 using Command Console v1.1

The data were analyzed with Partek Genomics Suite software v6.6.  Probes  were quantile-normalized using the GeneChip-Robust Multiarray Averaging and log2 transformed. All other settings were left as default.

Trizol extraction of total RNA was performed according to the manufacturer's instructions and cleaned using Rneasy Mini kit (QIAGEN).

5.5 ug of single-stranded cDNA was hybridized for 16 hours at 45 degrees C to the array.  Liquid handling steps were performed by a GeneChip Fluidics Station 450.

Single-stranded cDNA was synthesized using 200 ng of total RNA using Ambion WE Expression Kit for Affymetrix GeneChip Whole Transcript WT Expression Arrays and labelled using the Affymetrix GeneChip WT Terminal Labeling kit.

24 hours prior to transfection, 2102Ep and NTera-2 cells were seeded on 6-well plates in normal growth medium without antibiotics. For transfection, old media were replaced with reduced-serum Opti-MEM I medium. siRNA previously incubated with Lipofectamine 2000 (2102Ep cells) or Lipofectamine RNAiMAX (NTera-2 cells) in Opti-MEM I were added to the cells and these were incubated under transfection conditions for 6 hours. After transfection, media were replaced with normal growth medium and sample incubated for 72 hours with daily medium refreshing.

2102Ep and NTera-2 cell lines were grown in normal growth medium containing Dulbecco's Modified Eagle's Medium supplemented with 10% foetal bovine serium and 2% Penicillin-Streptomycin mixture. Cells were kept at 37°C and 5% CO2.

GeneChips were scanned with an Affymetrix GeneChip Scanner 3000 7G

Data was analysed with R/CRAN statstical software with the Bioconductor 2.9 package and the Linear Models for Microarray Data (limma) plugin

Samples were extracted with the Ambion miRVana PARIS kit as per manufacturers protocol.

Hybridisation was performed for 17 hours at 45°C in a Affymetrix GeneChip Hybridization Oven 640. Chips were washed with the Affymetrix GeneChi Hybridization, Wash and Stain Kit on a Affymetrix GeneChip Fluidics Station 450.

Labelling was performed with the Affymetrix GeneChip WT Terminal Labeling Kit as per manufacturer's protocol.

transfected with Ambion Silencer Select Negative Control #1;embryonal carcinoma;2102Ep;35-50

2102Ep cells transfected with Ambion Silencer Select Negative Control #1

Category: Cell-line
Subcategory: HMEC
Scanning Software: unknown
Software version: unknown
Lot batch = 0090-5k

Lot batch = 0088-5k

transfected with Ambion Silencer Select SOX2 siRNA;embryonal carcinoma;2102Ep;35-50

Scanning Software: ScanAlyze
Software version: 2.44
Lot batch = 0106-5k

Lot batch = 0083-5k

Lot batch = 0097-5k

Lot batch = 0134-5k

Lot batch = 0087-5k

Lot batch = 0164-5k

Lot batch = 0119-5k

Lot batch = 0111-5k

Test Compound: Corn Oil
CAS #:  8001-30-07
Delivery Volume:  1mL/kg
Exposure Duration:  Single, Acute

Test Compound Concentration:  1 mg/mL

The just.gcRMA normalization with normalize.ExpressionSet.lvs function from FLUSH.LVS.bundle package of the Bioconductor project was used. Low signal probesets were filtered out according to expression of probesets assigned to Y chromosome in female samples (expression lower than 95 percentile of Y-chromosome probesets in at least 20 samples), differential probesets were selected with Kruskal-Wallis test.

Extraction of total RNA was performed using the RNeasy Plus Mini Kit (cat. 74134) according to Qiagen's instructions.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed (Fluidics Scripts FS450_001) and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual With Specific Protocols for Using the GeneChip® Hybridization, Wash, and Stain Kit, 2005-2009, Affymetrix).

gastrointestinal stromal tumor;Male;LOW;PDGFRA mutation detected

11B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

10B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

12B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

C57BL/6;Lineagelow Sca1+cKit high Cells;mutant JAK2V617F (heterozygous)

Total RNA was isolated from whole brains using TRI REAGENT (Sigma-Aldrich, St. Louis, MO) according to the manufacturer's instructions, and further purified on a Qiagen RNeasy mini kit (Qiagen Sciences, Germantown, MD)

The data were normalised using quantile normalisation with Beadarray and analyzed with Limma package in R

RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN miRNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

mouse in the same generation maintained in the same SPF animal facility of Emory University following IACUC protocol

Arrays were scanned at the Emory Integrated Genomics Core at Emory University following manufacturers instructions.

The data was analyzed by the Emory Integrated Genomics Core at Emory University using mean polish and RMA with GC content adjustment.

Labeled, fragmented RNA hybridized to Affymetrix Mouse Gene 1.0 ST Gene Arrays at the Emory Integrated Genomics Core at Emory University following manufacturers instructions.

RNA was biotin labeled at the Emory Integrated Genomics Core at Emory University following manufacturers instructions.

Gene expression data from Klf5-KO 6-month mouse dorsal prostate with Pten-null upon PB-Cre4 mediated floxed fragment deletion

NCCIT cells were cultured in McCoy’s 5A medium (Invitrogen) supplemented with 2 mm L-glutamine (Mediatech) and 10% heat-inactivated fetal bovine serum (Hyclone).

Intensities of arrays have been quantile-normalized using Partek Genomic Suite (v6.6).  Differential expressions were calculated using ANOVA of Partek package.

Following labeling, cDNAs were hybridized for 16 hr at 45C on Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cDNAs were prepared according to the standard Ambion and Affymetrix protocol from 250 ng total RNA (The Ambion WT Expression Kit and GeneChip Terminal Labeling Kit, Affymetrix).

RNA from NCCIT human cells treated with a control non-targeting siRNA

GeneChip Expression 3’-Amplification One-Cycle-Target Labeling & Control Reagents
(Affymetrix; 900493)

Trizol standard protocol
Total RNA (TRNA) was isolated utilizing Trizol Reagent (GIBCO/BRL) following the manufacturer's protocol. The quality of TRNA was assessed using the Agilent 2100 Bioanalyzer (version A.02.01S1232, Agilent Technologies). Only RNA with the OD ratio of 1.99-2.0 at 260/280 was used for microarray analysis.

Labeling was performed according to standard Affymetrix instructions at the Genomic Core Facility at the Hospital for Sick Children.
Affymetrix standard protocol

All the chips were controlled for presence of any defect before scanning.

Murine 3T3-L1 progenitor adipocytes cell cultures, Control 1 (untreated with resveratrol)

Lateral prostates were dissected from euthanized mice at 12 months of age by use of a stereomicroscope and placed in RNAlater solution. Tissues were homogenized using a Polytron homogenizer. Total RNA was extrected using RNeasy (QIAGEN).

The data were analyzed with GeneSpring 7.3 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1.

The tissue was pulverized in liquid nitrogen to a powder. Total RNA was extracted using TRIzol Reagent (Invitrogen, Carlsbad, CA). The purity and integrity of the RNA were assessed by the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) and its quantity was determined by NanoDrop spectrophotometer (NanoDrop Technologies, Wilmington, DE).

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix Human Genome U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001,

LaserPower: 2.56;; 1.61
Temperature: 38.73

B6129;male;12 weeks;liver;adult;129SV/C57BL6;male;12 weeks;liver;adult;genotype/variation gene knock out;Alb-Cre +/-; Met Fl/Fl

LaserPower: 2.56;; 1.29
Temperature: 37.67

Exponetially growing MEFs were infected with control or Cre adenovirus and total RNA was extracted from cells after 3 days of infection

Ada3FL/FL MEFs were grown in DMEM medium supplemented with 10% FCS

The data were analyzed with Affymetrix Expression Console using Robust Multi-chip Averaging (RMA) background correction as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 50.

Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA was prepared using Ambion Expression Kit according to the manufacturer's instructions from 200 ng total RNA.

Gene expression data of asynchronous cells after 3 days of control adenovirus infection

Gene expression data of asynchronous cells after 3 days of Cre adenovirus infection

U-33 cells stably transfected with an empty vector control (U-33/c cells);24 hrs;No Rosiglitazone present

U-33 cells stably transfected with an empty vector control (U-33/c cells);24 hrs;Rosiglitazone present

U-33 cells stably transfected with an empty vector control (U-33/c cells);72 hrs;No Rosiglitazone present

Approximately10-14Gastrin Knockout mice were dissected and the fundus was used to isolate parietal cells and purified by flow cytometry. Total RNA was extracted from the purified parietal cells by Trizol followed by an RNeasy kit (Qiagen).

NCI-H460;human lung large cell carcinoma cells;radiation and nicotine;2 hours

NCI-H460;human lung large cell carcinoma cells;radiation and cigarette smoke extract;2 hours

NCI-H460;human lung large cell carcinoma cells;cisplatin;2 hours

The images were captured by the Agilent High-Resolution Microarray Scanner Bundle (catalog #G2565CA) reader according to the parameters recommended for bioarrays and extracted by Agilent Feature Extraction software version 9.5.3.

Among the 45,015 spots present in each array, only those with none or only one flag (i.e. low intensity, saturation, controls, etc.) were selected for analysis using the R software version 2.9.2 (R Development Core Team, 2009). Fold change was calculated using the following formulae: =sign(group A mean - group B mean)*2^ABS(group A mean - group B mean). Group mean was calculated by the summation of each group component divided by number of group components. We selected as differentially expressed transcripts those presenting a p-value Â£ 0.05 (Student's t test and adjusted Bonferroni correction) and fold variation of ±2. Hierarchical clustering was based on Pearson correlation and complete linkage.

Tissue samples (20-30mg) were homogenized with TissueRupter (QIagen, cat. no. 9001272 Valencia, CA) and total RNA was extracted from the homogenates using the RNeasy Mini Kit (QIagen cat. no. 74104, Valencia, CA) according to the manufacturer's instructions.

In order to determine gene expression profiles, 44K DNA microarrrays (Agilent Technologies, cat no. G4845A Santa Clara, CA) were used. The procedures for hybridization followed the protocols provided by the manufacturer´s instructions (One-Color Microarray-Based Gene Expression Analysis - Quick Amp Labeling).

The RNA was labeled using the Cyanine CTP Dye Pack, one color, Agilent technologies, Part no. 5188-1169-P.

HIV seropositive drug naïve group, viral load low

AML blasts from bone marrow;training;mutated;M2;internal tandem duplication (ITD)

Total RNAs were extracted using Isogen (Nippon Gene, Osaka, Japan). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).

Microarray experiments were performed using whole-mouse-genome oligoarrays (Mouse430a, Affymetrix). Array data were analyzed using MAYDAY (Version 2.10). Array data were subjected to robust multi-array average (RMA) normalization. Normalized data were used for calculating fold changes of up- and down-regulated genes using Student's test. Only data with a false discovery rate (FDR) adjusted p-value <0.05 and at least 2x differential expression were included in the analysis. Data underwent z-score transformation for display.

Injection of Ketamine/xylazine (300mg/kg; 40mg/kg) before sacrifice

Specifically bound probe was detected by incubating the arrays with SAPE (Molecular Probes) and scanning the chips with a Hewlett-Packard GeneArray scanner (Affymetrix). A second scan was performed after signal enhancement with biotinylated anti-streptavidin antibody Vector Laboratories). The scanned images were analyzed using the GeneChip Analysis Suite 3.3 (Affymetrix) to identify genes differentially expressed among the RNA samples.

The hybridization mixture was prepared by mixing 15 mg biotinylated probe with control oligonucleotide B2 (final concentration 50 pM; Affymetrix), herring sperm DNA (final concentration 0.1 mg/ml; Research Genetics), acetylated bovine serum albumin (final concentration 0.5 mg/ml; Gibco BRL Life Technologies) in a final volume of 300 ml of 13 MES hybridization buffer (100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween-20; all reagents from Sigma). The hybridization mixture was denatured for 10 minutes at 99 C, incubated for 5 minutes at 45 C, and spun for 5 minutes in a benchtop microcentrifuge. The microarray was warmed to room temperature and prehybridized in hybridization buffer for 10–20 minutes at 45 C. The prehybridization solution was removed and 150 ml of the hybridization mix was added to the array. The array and probe fragments were incubated at 45 C overnight (16–20 hours).  After hybridization, nonspecifically bound probe was removed by washing with the GeneChip Fluidics station 400 (Affymetrix). In total, 10 low-stringency washes (63 SSPE, 0.01% Tween-20, 0.005% Antifoam) and 4 high-stringency washes (100 mM MES, 0.1 M NaCl, 0.01% Tween-20, 50 C) were performed (all reagents from Sigma).

Target RNA is reverse transcribed into cDNA and in-vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization.

Monitor the effect of HNF4alpha lost in mouse colonic epithelium

Total mRNA from liver tissues, strain: C57BL/6J- Lepob
Keywords = Mus musculus, liver

untrained wt control animal for training induced gene expression response

endometrial stromal cell - Jag1 retrovirus infected2, 3 days post infection

untrained plakoglobin (+/-) control animal for training induced gene expression response

prefrontal cortex from adult APPsa knock-in mouse;back-crossed to C57BL/6 for 6 generations;male

prefrontal cortex from adult APLP2 knock-out mouse;back-crossed to C57BL/6 for 6 generations;male

Data processed using Affymetrix Expression Console software using default RMA parameters, log2 scale

Cells from 10 cm plates were scraped and pelleted by centrifugation, followed by resuspension in 1 ml Trizol, incubation for 5 in at room temp, and addition of 200 ul CHCl3 with vigorous shaking by hand. After centrifugation 10 min 14,000 rpm, aqueous phase combined with equal volume of 70% EtOH, and subsequent cleanup on Qiagen RNeasy kit (Catalog# 74104)

Hybridization performed according to standard Affymetrix protocols

First Strand and Second Strand synthesis, followed by 2 rounds of SPIA amplification to generate cDNA was performed using WT-Ovation™ FFPE System V2 (Nugen Catalog#3400-60, Lot#801142-A). Fragmentaion and Biotinylation were completed using FL-Ovation™ cDNA Biotin Module V2 (Nugen Catalog# 4200, lot#709151-F)

Cells transfected with Stealth HSF1 siRNA (5'CGGAUUCAGGGAAGCAGCUGGUGCA) and subsequently treated for 6 hours with 50 uM HNE in vehicle 0.5% DMSO, in DMEM Media containing 10% FBS

RKO colon carcinoma cells (ATCC #CRL-2577), cultured in DMEM (Invitrogen Catalog#10569) containing 10% FBS (Atlas Biologicals)

RKO cells transfected with HSF1 Stealth siRNA treated 6 h with 50 uM HNE in DMSO 0.5% final

Cells were treated by mometasone furoate, some with additional formoterol

R1/E ES cells were reversely transfected in a 12well plate using 800ng esiRNA and 2ul Lipofectamine2000 (Invitrogen) and 80000cells/well. Procedure according to manufacture's protocol

The data were normalized with GC-RMA method using Partek Genomics Suite 6.4 (6.09.0129). Properties: quantile normalizytion, GCRMA background correction, median polish probe set summarization

Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Mouse 430 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

Gene expression data from mouse ESC after 48h RNAi against Luciferase

TIG3 diploid fibroblasts were were grown in DMEM media supplemented with 10% (v/v) fetal calf serum. For siRNA experiments cells were transfected with siRNA oligonucleotides specific for SUZ12 and harvested for preparation of RNA after 44 hours.

The Identification of gene expression changes in human embryonic fibroblast cells depleted of SUZ12. Sample A

TIG3 diploid lung embryonic fibroblasts were transfected with siRNA oligos specific for the Polycomb protein SUZ12. After 44 hours expression analysis was performed.

fibroblast, TSG6-knockout, TSG6+HA-treated, biological replicate 2

fibroblast, TSG6-knockout, TSG6+HA-treated, biological replicate 1

fibroblast, TSG6-knockout, TSG6+HA-treated, biological replicate 4

fibroblast, TSG6-knockout, TSG6+HA-treated, biological replicate 3

(CML) chronic myeloid leukaemia / CD34+ stem cells after 7 days of Glivec therapy

Standard Eukaryotic Affymetrix default settings and Genechip Scanner 3000.

Initially, total RNA was subjected to a single round of RNA amplification.
Amplified RNA was used as starting material for the Affymetrix hybridization protocol.

Standard Eukaryotic Affymetrix protocols as of 05-06.
Fluidics script EukGE_Ws2v5 was used with GeneChip® Fluidics Station 450.

This is WT sample number two of three.
Experiment compares 129 Wt pineal gland gene expression at P0 versus P0 pineal gland gene expression in NeuroD1 transgenic knockout mice.

F1 (C57BL6 X 129/SvEv);wild type mice;kidney;male;ANG II +NS diet

Pineal gland tissues were collected during the daytime period.
3 pineal glands were pooled per sample and total RNA extracted.

Initially, total RNA was subjected to a single round of RNA amplification using Ambion Message Amp II kit.

GeneChip® One-Cycle Target Labeling from Affymetrix.

3' In Vitro Transcription, GeneChip® One-Cycle Target Labeling from Affymetrix.

This is the homozygous sample number one of three.
Experiment compares 129 Wt pineal gland gene expression at P0 versus P0 pineal gland gene expression in NeuroD1 knockout mice.

Check paper for details. "Gene Array Expression Profiling in Acne Lesions Reveals Marked Upregulation of Genes Involved in Inflammation and Matrix Remodeling". Journal of Investigative Dermatology (JID 126:1071-1079, 2006).

This is the homozygous sample number two of three.

Amplified RNA was used as starting material for the Affymetrix hybridization.

GeneChip® One-Cycle Target Labeling and hybridization.
Washing and staining was performed on GeneChip® Fluidics Station 450.
EukGE_Ws2v5 washing script was used.

This is WT sample number one of three.
Experiment examines 129 Wt mouse pineal gland gene expression at P0 versus P0 pineal gland gene expression in NeuroD1 transgenic knockout mouse.

Rats were sacrificed seven hours after the injection with methylprednisolone

Rats were sacrificed seventy-two hours after the injection with methylprednisolone

Rats were sacrificed eight hours after the injection with methylprednisolone

dorsal neural tube was bisected along the midline with one half from each embryo used for control and the other half treated with 10-6M RA dissolved in ethanol for 6, 12, 24 or 48 h. For 6 h exposures, the explants were cultured overnight on fibronectin coated 35mm dishes (Biocoat, Becton Dickinson Labware, Bedford, MA) in DMEM with 10% horse serum in order to allow for sufficient outgrowth of neural crest cells. The RA was added the following morning; RMA Express 0.2 used to initially normalize data; GeneSpring (Silicon Genetics, Inc.) used for subsequent analysis
24 hour RA treated, replicate 2

24 hour RA treated, replicate 3

24 hour control, replicate 4

24 hour RA treated, replicate 1

24 hour control, replicate 2

24 hour control, replicate 3

12 hour RA treated, replicate 3

24 hour control, replicate 1

12 hour RA treated, replicate 1

12 hour RA treated, replicate 2

Animals were of the following genetic background: 129S7/SvEvBrd-Hprtb-m2, F2, 1 backross to C57BL/6N. Mice were weaned at the age of 4 weeks, and afterwards supplied with standard nutrition until sacrification.

The data were normalised using quantile normalisation with BeadStudio Software. Data were exported to Microsoft Excel for applying student´s t-test on analysis groups of Cldn16 -/- and Cldn16 +/+ animals. Data with a p-value of < 0.05 were considered as significant.

Poles were removed from freshly dissected kidneys, followed by immediate snap-freezing.
Total RNA was extracted with Trizol reagent, followed by DNAse treatment and purification via RNEasy columns. RNA purity and concentration was assessed with a Bioanalyzer.

Biotinylated cRNA was prepared with the AMIL1791 Illumina® TotalPrep™ RNA Amplification Kit.

female;juvenile, 8 weeks (P58);Sv129 / C57BL/6N mixed background;Cldn16 +/+;renal tissue

female;juvenile, 8 weeks (P59);Sv129 / C57BL/6N mixed background;Cldn16 +/+;renal tissue

Lung from SM22-dnBMPR2 inducible transgenic males activated 1 week

Lung tissues were flash-frozen in liquid nitrogen within minutes of death, and RNA extracted using an RNeasy kit (Qiagen)

Mouse Genome 430 2.0 microarrays (Affymetrix, Foster City, CA) were hybridized with 20 �g cRNA. Target hybridization, washing, staining, and scanning probe arrays were done following an Affymetrix GeneChip Expression Analysis Manual.

A pool of RNA from lung from three male mice, raised at Denver altitude (nearly normoxic), with SM22-rtTA x tetO7-BMPR2delx4+ transgene activated for 1 week. These mice have elevated RV pressures, and dysfunctional pulmonary vascular reactivity.

Lung from SM22-dnBMPR2 inducible transgenic females activated 1 week

A pool of RNA from lung from three female mice, raised at Denver altitude (nearly normoxic), with SM22-rtTA x tetO7-BMPR2delx4+ transgene activated for 1 week

Lung from SM22-dnBMPR2 inducible transgenic males activated 8 weeks

A pool of RNA from lung from three male mice, raised at Denver altitude (nearly normoxic), with SM22-rtTA x tetO7-BMPR2delx4+ transgene activated for 8 weeks; mice are 12 weeks old when sac'd.

Lung from SM22-dnBMPR2 inducible transgenic females activated 8 weeks

A pool of RNA from lung from three female mice, raised at Denver altitude (nearly normoxic), with SM22-rtTA x tetO7-BMPR2delx4+ transgene activated for 8 weeks

heart of mouse subjected 1 week to chronic constant hypoxia (C1B)

RNA samples (60ug) were extracted from the mouse heart and retrotranscribed to cDNA labeled with Cy5 (male) and Cy3 (female) individually. The cDNAs were co-hybridized with the 27K mouse microarray slide (No: M5-62).

heart of female mouse subjected 1 week to chronic constant hypoxia (C1BF)

Total RNA was extracted from brain microvessels with TRIzol Reagent (Invitrogen), cleaned with RNeasy Mini Kit (Qiagen). The sample was pooled with the total RNA from 5 rats.

Approximately 15 µg of total RNA was processed to produce biotinylated cRNA targets.

brain microvessels from WKY treated with AT1 antagonsit (candesartan, 0.3 mg/kg/day) for 4 weeks subcutaneously by osmotic minipump.

12-week-old Wistar Kyoto (WKY), male, brain microvessels, treated with AT1 antagonsit (candesartan, 0.3 mg/kg/day) for 4 weeks subcutaneously by osmotic minipump.

TP082505-26_HG-U133A_2_IMFGN0023: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

C57Bl/6 Vert-X (IL-10-eGFP) mice were infected intracranially with 500 PFU J2.2-V-1 virus and seven days later their brain lymphocytes were isolated and negatively selected for CD8 T cells. The CD8 brain lymphocytes were then sorted for IL-10+ and IL-10- CD8 T lymphocytes using GFP as a marker.

Extraction of total RNA was achieved by purification on RNeasy columns.

Gene expression data from IL-10+CD8 T cells in a J2.2-V-1-infected mouse

brain;C57/BL6 Vert-X;IL-10eGFP;6-8 weeks;CD8 T cells that are IL-10+

Gene expression data from IL-10-CD8 T cells in a J2.2-V-1-infected mouse

brain;C57/BL6 Vert-X;IL-10eGFP;6-8 weeks;CD8 T cells that are IL-10-

Mice with intestinal epithelium-specific Pdx1 inactivation (Pdx1flox/flox;VilCre) were generated by intercross mating between VilCre and Pdx1flox/flox mouse strains. The VilCre mouse strain carries a Villin-Cre transgene and expresses Cre recombinase under the control of a 12.4 kb mouse villin 1 gene promoter fragment. Pdx1 exon 2 encoding the DNA-binding Homeodomain is flanked by loxP target sites in Pdx1flox/flox mice. Pdx1 expression is absent in the epithelium of mature Pdx1flox/flox;VilCre proximal small intestine.

Mice were fed a standard diet (4.5 % fat, Prolab RMH 3000, LabDiet) and maintained under normal, non-stressed condition.

The arrays were scanned with GeneChip Scanner 3000 7G (Affymetrix).

The fluorescence intensity image files obtained from scanning each of the arrays were reviewed and processed initially by the Stanford PAN Facility with GeneChip Operating Software (Affymetrix). The resulting .CEL files were imported into Partek Genomics Suite (version 6.4, Partek Inc., St. Louis, MO) for probe set summarization and statistical analysis.

The small intestine tissue was preserved in RNAlater (Qiagen, Valencia, CA) during harvest and before processing for RNA isolation. Total RNA was then extracted and treated with DNase I using the RNeasy Mini kit (Qiagen, Valencia, CA) according to manufacturer’s protocol.

The labeled cRNA prepared from each mouse was fragmented and hybridized to a single GeneChip Mouse Genome 430 2.0 Array (Affymetrix), according to manufacturer’s recommendation. The microarrays were washed, stained with fluorescent molecule SAPE that binds to biotin in combination of biotinylated anti-streptavidin antibody on GeneChip Fluidics Station 450 (Affymetrix).

The total RNA samples were reverse transcribed into double-stranded cDNA, followed by an in vitro transcription (IVT) reaction that produced amplified amounts of biotin-labeled antisense mRNA (cRNA) using GeneChip 3' IVT Express Kit (Affymetrix, Santa Clara, CA), according to manufacturer’s recommendation.

male;6 months old;Pdx1flox/flox (Ctrl);brother of the same litter

Mature proximal small intestine, first 5 cm immediately adjacent to the pylorus

male;6 months old;Pdx1flox/flox;VilCre (KO);brother of the same litter

Mature proximal small intestine with intestinal epithelium-specific Pdx1 inactivation, first 5 cm immediately adjacent to the pylorus

Fresh frozen samples were optaint from the Robert-Rössle-Biobank at the ECRC (Experimental and Clinical Research Center).

GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).

Rneasy lipip tissue Kit (Qiagen) was used according to the manufacturer's instructions.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Human Genome U133 Plus 2.0 Array.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 µg total RNA (GeneChip® One-Cycle Target Labelling Kit (Affymetrix)).

The data were normalized using quantile method with the Illumina function provided by beadarray Bioconductor package

Total RNA was isolated using the RNeasy Mini Kit (QIAGEN) per the manufacturer’s instructions. Quantity and quality of each RNA sample was assessed using Nanodrop and Bioanalyzer (Agilent)

Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Life Technologies) according to the manufacturer’s protocol and starting with 150 ng of total RNA

TP082505-25_HG-U133A_2_IMFGN0023: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

Crohn's Disease subject (65 year old caucasian female, SAK_1280909823)

Subject Age : 65

Crohn's Disease subject (51 year old caucasian female, SAK_1287951234)

Subject Age : 51

Crohn's Disease subject (62 year old caucasian female, SAK_1287995940)

Subject Age : 62

DNFB (1-fluoro-2,4 dinitrobenzene, Merck) was diluted in acetone/olive oil (4:1) immediately before use. Mice without any skin lesions and ear tags were sensitized by painting 50 µl of 0.2% DNFB on the shaved abdomen on two consecutive days. Controls were treated with 50 µl acetone-olive oil. For elicitation of CHS, ears of mice were painted with 10 µl of 0.3% DNFB on day 5. Ear thickness was measured 24 h, 48 h and 72 h after challenge using an engineers micrometer (Oditest, Fa. Kroeplin, Schlüchtern, Germany) and ear swelling was calculated in each mouse as the difference in ear thickness between the unchallenged control (left) and the challenged (right) ear. Experimental mice of either wildtype C57BL/6J line or CB1/CB2 double knockout mice (Cnr1-/-/Cnr2-/-) were used in the age of 8-10 weeks. Right ears of the mice were treated with DNFB, whereas left ears were untreated and used as control. All experimental animals were females. DNFB treated and control ears from three Cnr1-/-/Cnr2-/- and three Cnr1+/+/Cnr2+/+ mice were used for the gene expression analysis. Whole ear tissue was harvested 48h after the 2nd DNFB-challenge and immediately snap frozen in liquid nitrogen. Tissue was stored on –80°C until RNA isolation.

Cnr1-/-/Cnr2-/- female number 3, DNFB-treated allergic ear (#12_Ko-Tr-7)

Microarry expression values were generated using GC-RMA using software ArrayAssist® 3.0 (Stratagene). The GC-RMA-obtained log2-transformed expression values were imported into searchable database using this software.. For the treatment effects, which were independent of the genotype, all control (n=6) and DNFB-treated ears (n=6) were statistically analyzed using t-test with p ≤ 0.05 after Bonferroni correction and a differential expression higher than fourfold (given as an average log 2 ratio; ALR). The genotype effects were obtained by comparison of DNFB-treated ears of Cnr1+/+/Cnr2+/+ (n=3) versus Cnr1-/-/Cnr2-/- (n=3) with p ≤ 0.001 and ALR ≥ 1. Results for treatment and genotype effects were compared using Venn diagram.
Hierarchical clustering was performed on log2 transformed values using “ArrayAssist 3.0” (Stratagene) in two dimensions (e.g. both genes and samples).

Total RNA was isolated using Trizol (Invitrogen) and purified using RNeasy columns (Qiagen). RNA intergrity was assessed using Agilent 2100 Bioanalyzer (www.agilent.com). Five μg of total RNA was converted into double-stranded cDNA using T7-oligodT coupled primers. Ten μg of fragmented cRNA samples were hybridized to MG_430 2.0 Affymetrix GeneChips following the manufacturer´s instructions.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on MG_430 2.0 Affymetrix GeneChips . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

Cnr1-/-/Cnr2-/- female number 3, 2 months old, whole ear tissue, DNFB-treated allergic ear

whole ear tissue, DNFB-treated allergic ear 48h after 2nd challenge

Crohn's Disease subject (50 year old caucasian female, SAK_1288040656)

Subject Age : 50

Crohn's Disease subject (33 year old caucasian female, SAK_1275455680)

Cnr1-/-/Cnr2-/- female number 2, untreated control ear (#8_Ko-C-5)

Cnr1-/-/Cnr2-/- female number 2, 2 months old, whole ear tissue, untreated control ear

Cnr1-/-/Cnr2-/- female number 3, untreated control ear (#9_Ko-C-7)

Cnr1-/-/Cnr2-/- female number 3, 2 months old, whole ear tissue, untreated control ear

Cnr1-/-/Cnr2-/- female number 1, DNFB-treated allergic ear (#10_Ko-Tr-4)

Cnr1-/-/Cnr2-/- female number 1, 2 months old, whole ear tissue, DNFB-treated allergic ear

Crohn's Disease subject (34 year old caucasian female, SAK_1275478033)

Crohn's Disease subject (54 year old caucasian male, SAK_1275522739)

Subject Age : 54

Crohn's Disease subject (56 year old caucasian male, SAK_1263271818)

Subject Age : 56

Cells were infected with respective lentiviruses and RNA was isolated 2 weeks post infection when cells were confirmed fully senescent

The data were analyzed with GCRMA (Bioconductor) using Affymetrix default analysis settings and quantile normalisation as normalization method.

Gene expression data from primary human melanocytes with activated BRAFV600E

Gene expression data from primary human melanocytes with Empty Vector infection

Ewing family tumor cell-line A673 (transfected with empty vector). Experiment 3.
Lot batch =

Bone Marrow;Monoclonal Gammopathy of Undetermined Significance (MGUS) plasma cells

Ewing family tumor cell-line A673 (wild-type). Experiment 3.
Lot batch =

Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.

RNA was prepared from subconfluent asynchronously proliferating cells using TRIZOL and purified by RNeasy MinElute Cleanup kit (Qiagen).

The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix Human GeneChip 1.0 ST microarrays.  The microarrays were washed and stained in an Affymetrix Fluidics Station using  standard Affymetrix protocols.

300 ng of total RNA was used for labeling.  The probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).

glioblastoma cells;42MGBA cells;STAG2 knock-in pre-Cre clone 92 (STAG2 deficient)

glioblastoma cells;42MGBA cells;STAG2 knock-in pre-Cre clone 53 (STAG2 deficient)

Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. At P7, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.

Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. At P10, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.

monocytes were precipitated untouched from 8ml peripheral blood mononuclear cells, washed in PBS + 2mM EDTA, lysed in TriZol

The data were analyzed with GCOS 1.4 using Affymetrix default analysis settings and global scaling as normalization method.

Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133A2.0 GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

Mouse embryonic fibroblast derived from MyoD-/-/Myf5-/- animals transduced with ER-MyoD wt in differentiation media for 12hrs

The data were analyzed with the Expression Console applilcation from Affymetrix. We performed RMA to summarize the data.

Total RNA was extracted from mononuclear cell preparations of leukemic B cells obtained fromp peripheral blood prior to treatment using TRIZOL. RNA quality and quantity was assessed using the bionalyzer 2100 and nanodrop spectrophotometer

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HU133plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol using the 3' IVT Express kit from Affymetrix

Mice were placed under inhaled isofluorane with body temperature maintained at 37°C. After right nephrectomy, the left pedicle was occluded with a microaneurysm clip for 23min. The clip was then released and buprenorphine was given S.C.. Sham mice underwent the same right nephrectomy except the clip was placed underneath the pedicle. Kidneys were harvested at 4hr reperfusion.

8 wks old male mice were purchased from the Jackson Laboratory and fed ad libitum in our animal facility before surgery.

The data were analyzed with Microarray Suite version 5.0(MAS5.0) using Affymetrix default analysis and global scaling as normalization method.

Kidneys were dissected, snap-frozen in liquid nitrogen and stored at -80°C. Samples were homogenized and total RNA was extracted using the the RNeasy Midi Kit(Qiagen) according to the manufacturer's manual. RNA integrity was measured on the Agilent 2100 Bioanalyzer(RIN:9.5).

Following fragmentation, 15µg of cRNA were hybridized at 45°C  for 16 hr on the GeneChip Mouse Genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA was amplified from 1µg of total RNA using the MessageAmp II-Biotin Enhanced Kit(Ambion) protocol.

Gene expression data from TLR4-/- ischemic(23min) kidney at 4hr reperfusion(No.1)

Gene expression data from WT sham kidney at 4hr reperfusion(No.3)

Gene expression data from WT sham kidney at 4hr reperfusion(No.2)

Gene expression data from WT sham kidney at 4hr reperfusion(No.1)

Gene expression data from WT ischemic kidney(23min) at 4hr reperfusion(No.3)

Gene expression data from WT ischemic kidney(23min) at 4hr reperfusion(No.2)

Gene expression data from WT ischemic kidney(23min) at 4hr reperfusion(No.1)

Gene expression data from TLR4-/- ischemic(23min) kidney at 4hr reperfusion(No.3)

Gene expression data from TLR4-/- ischemic(23min) kidney at 4hr reperfusion(No.2)

African-American (AA);Female;Systemic lupus erythematosus (SLE) patient;Peripheral blood;CD14-PerCP;CD14 positive monocytes

0.5 mg/kg/ml Isoproterenol treatment, 24 hour time point,  biological rep 2

CHIPEXP_NAME: 230_2_050531tpj_54h

trizol extraction followed by qiagen RNeasy total RNA cleanup protocol

Intensity of hybridization for each probe pair was computed by GCOS 1.2 software (Affymetrix). (For more detailed methods, please refer to the website of the Malaria Research Institute Gene Array Core Facility (MRI-GACF) at the Johns Hopkins Bloomberg School of Public Health http://jhmmi.jhsph.edu)

BALB/c scid, gender:male, age:8wks, tissue: whole lung, condition: 2DPI

BALB/c WT, gender:male, age:8wks, tissue: whole lung, condition: 3DPI

BALB/c WT, gender:male, age:8wks, tissue: whole lung, condition: 2DPI

BALB/c scid, gender:male, age:8wks, tissue: whole lung, condition: 3DPI

The signal values were generated by statistical algorithm implanted in Affymetrix Suite Version 5.0 software (MAS5, Affymetrix, Inc.) The detection calls were calculated, based on the detection p-value, as following: probe sets with p-value of more than 0.06 were designated as absent, p-value of more than 0.04 and less than 0.06 as marginal and p-value of less than 0.04 as present. For interarray comparisons, data from each array was scaled using MAS5 software, and the mean intensity for each array was adjusted by a scaling factor to a set target intensity of 150.

Fragmented cRNAs were hybridized overnight at 45°C to Affymetrix Gene Chip Murine Genome U74Avr2 arrays (Affymetrix, Inc.).

10 mg of total RNA were used to synthesize double-stranded cDNA with the Superscript Choice System (Invitrogen, Carlsbad, CA) and 100 pmole of oligo-dT primer attached to a T7 promoter sequence (Genset, Paris, France). The double-stranded cDNAs were phenol/chloroform extracted with Phase Lock Gels tubes (Eppendorf, Hamburg, Germany). In vitro transcription (IVT) of the double-stranded cDNA products was performed with an Enzo BioArray High Yield Transcript labeling kit in the presence of biotin-labeled nucleotides (Affymetrix, Inc., Santa Clara, CA). Following purification by an RNeasy mini kit (Qiagen Sciences), the biotin-labeled cRNA products were subjected to alkaline lysis (200mM Tris-acetate pH 8.1, 500mM potassium acetate, 150mM magnesium acetate).

Total RNA was extracted from whole brain. Total RNA isolation, target preprocessing and hybridization to the U74Av2 microarray were conducted according to Affymetrix’s instructions.

Data were generated using MAS 5.0 and normalized using global scaling.

Female B6.V-lepob obese mice (n=24) aged 7 weeks were obtained from The Jackson Laboratory (Bar Harbor, ME).  Upon arrival, mice were placed on a standard chow diet and were allowed to acclimate fro 1 week before starting the experiment.  For leptin treatments, mice received daily intraperitoneal injections of either recombinant mouse leptin (R&D Systems, Minneapolis, MN) (n=12) at a dose of 5 µg/g body weight or with saline as a control (n=12) for 4 weeks.  At 12 weeks of age, mice were fasted overnight with free access to water.  The following morning the mice underwent cholecystectomy. Three gallbladders were pooled and total RNA was isolated.

Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 18 hours, replica 3

1 ug/ml doxycyline;18 h;A673;doxycyclin  inducible EWS-FLI1 knockdown;Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown construct

Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 18 hours, replica 2

Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 18 hours, replica 1

Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 0 hours, replica 4

control;0 h;A673;doxycyclin  inducible EWS-FLI1 knockdown;Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown construct

Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 53 hours, replica 1

Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 36 hours, replica 3

1 ug/ml doxycyline;36 h;A673;doxycyclin  inducible EWS-FLI1 knockdown;Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown construct

Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 36 hours, replica 2

Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 36 hours, replica 1

Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 72 hours, replica 1

1 ug/ml doxycyline;72 h;A673;doxycyclin  inducible EWS-FLI1 knockdown;Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown construct

K-rasLSL-G12D MEFs were infected with adenoviral Cre to activate K-ras.

bone marrow;CD34+ hematopoietic stem cells (HSC);myelodysplastic syndromes (MDS);refractory anemia with excess blasts 2 (RAEB2);del5q

bone marrow;CD34+ hematopoietic stem cells (HSC);myelodysplastic syndromes (MDS);refractory anemia (RA);normal

Infected myoblasts maintained in growth medium were defined as day 0. Infected myoblasts cultured in differentiation medium (DMEM, 5% FBS) for 3 days were defined as day 3.

Myoblasts isolated from Gata4-loxP mice were cultured in growth medium (Ham’s/F10, 20% FBS, 0.2 μg/ml bFGF) and adenovirally infected with nLacZ or Cre, or retrovirally infected with GATA4.

The data were normalized using mean/median scaling normalization and Welch t test with array track. Signal intensities were normalized by rank invariant method.

Labeling was performed using TotalPrep RNA Labeling Kit (Ambion).

Gata4tm1.1Sad/J;Nuclear β-galactosidase;Differentiation medium for 3 days

Gata4tm1.1Sad/J;Cre recombinase;Differentiation medium for 3 days

For transfection, the hESCs were passaged with 0.25% trypsin (Invitrogen) for dissociation and transfected with 2 µg pSUPER-Luciferase shRNA (control) or pSUPER-HERVH shRNA and 6 µl Mirus LT1 transfection reagents the following day. Cells were harvested 5-days post transfection for RNA extraction.

The H1 hESC line (WA-01, passage p32) was cultured under feeder-free conditions on Matrigel (BD) in conditioned medium, which contains 1 mM L-glutamine (Gibco), 1% non-essential amino acids (Gibco) and 0.1 mM 2-mercaptoethanol (Gibco), 4 ng/ml human basic fibroblast growth factor (bFGF) (Invitrogen), 20% Knock-out serum replacement (Gibco), 78% DMEM/F12 media (Gibco), and medium was supplemented with additional bFGF (8 ng/ml) before use. For expansion, the H1 hESCs were passaged with 1 mg/ml collagenase IV (Gibco) every 5-7 days.

After washing and drying of the chip, the microarray chip was scanned with a BeadArray Reader.

Data was extracted with GenomeStudio and normalized with the rank-invariant method.

For microarray, total RNA extracted from control samples and HERVH-depleted samples using TRIzol was treated with DNase for 1 hour. RNA was then purified by the PureLink RNA mini kit (Invitrogen).

750 ng cRNA was used for hybridization to each lane of the HumanHT-12 v4 Expression BeadChip.

500 ng total RNA was used for cRNA synthesis and cRNA lableing with the TotalPrep RNA Amplification Kit (Illumina).

C3H denotes C3H/HeJ mice whereas C57 denotes C57Bl/6 mice
T00 denotes baseline time point, whereas T04 means 4 weeks on diet, T08 means 8 weeks on diet and so on.
HF denotes high-fat diet, whereas NC is normal chow diet
Keywords = mouse aorta
Keywords = cross strain comparison

Raw Signal intensities were extracted with Feature Extraction v10.6 software.

mTECs were sorted based on the following markers: DAPI-, CD11c-, CD45-, Ly51-, EPCAM+, Class II+.  RNA was isolated using Qiagen’s RNeasy Micro Plus Kit and amplified using Sigma Whole transcriptome amplification kits.

Labeled Cy3-cDNA was assesed using the Nanodrop ND-8000 (nanodrop Technologies, INC, Wilmington DE), and equal amounts of Cy3 labeled target were hybridized for 17hrs to Agilent whole mouse genome 4x44K ink-jet arrays.

Cy3-CTP labeling was performed using NimbleGen one-color labeling kits (Roche-NimbleGen Inc, Madison, WI)

shRNA mediated knock-down of VEGFR-2 was done in LN-308 and U138MG glioma cells.

LN-308 and U138MG glioma cell lines were cultured in Dulbecco´s ;odified Eagle´s Medium (DMEM) containing 10 % fetal bovine serum, 100 IU/ml penicillin and 100 mg/ml streptomycin.

The data were analyzed using Bioconductor and package Affy, using the JustRMA() function with default setting (quantile normalization and RMA background correction).

Chirgwin's extraction of total RNA (Chirgwin JM et al., 1979) performed on fresh tissues.

Fifteen micrograms of fragmented cRNA were hybridized for 16 hrs at 45°C under constant rotation. After hybridization, chips were processed using the Affymetrix GeneChip Fluidic Station 450 (protocol FS450_0007). Staining was made with streptavidin-conjugated phycoerythrin (SAPE, Molecular Probes), followed by amplification with a biotinylated anti17 streptavidin antibody (Vector Laboratories), and followed by a second round of SAPE.

Total mRNA was RNase H reduced and labelled with the SuperScript One-Cycle cDNA Kit following manufacturer's instructions (Invitrogen).

Gene expression data from Deltoid, control, cohort 20, subject 20U

Gene expression data from Deltoid, control, cohort 21, subject 21U

Gene expression data from Biceps, control, cohort 21, subject 21U

skeletal muscle;insulin sensitive;untreated;0.85;172;63;1500;70;21.2;51.4;1484

human skeletal muscle from insulin sensitive individuals after insulin therapy

Clinical information: Sample.ID=1279;Tumor.type=D;Size=2;Grade=2;Nodes=0/12;ER=Pos;PR=Pos;HER2=Neg;Age=68;DFS=102;Status=non-recur

Clinical information: Sample.ID=1218;Tumor.type=D;Size=4.5;Grade=1;Nodes=3/16;ER=Pos;PR=Pos;HER2=Neg;Age=62;DFS=10;Status=recur

Clinical information: Sample.ID=1260;Tumor.type=D;Size=3.5;Grade=2;Nodes=0/14;ER=Pos;PR=Pos;HER2=Neg;Age=58;DFS=79;Status=non-recur

Clinical information: Sample.ID=1205;Tumor.type=D;Size=2.7;Grade=2;Nodes=1/19;ER=Pos;PR=Pos;HER2=Neg ;Age=71;DFS=88;Status=non-recur

Clinical information: Sample.ID=1206;Tumor.type=D;Size=4.1;Grade=3;Nodes=0/15;ER=Pos;PR=Neg;HER2=Neg;Age=84;DFS=56;Status=recur

Clinical information: Sample.ID=1093;Tumor.type=D;Size=1;Grade=3;Nodes=1/14;ER=Pos;PR=Pos;HER2=Neg ;Age=66;DFS=85;Status=non-recur

Clinical information: Sample.ID=1125;Tumor.type=D;Size=2.6;Grade=2;Nodes=0/18;ER=Pos;PR=Neg;HER2=Neg;Age=54;DFS=123;Status=non-recur

Clinical information: Sample.ID=1047;Tumor.type=D/L;Size=2.6;Grade=2;Nodes=0/18;ER=Pos;PR=Neg;HER2=Neg;Age=70;DFS=128;Status=non-recur

Clinical information: Sample.ID=1085;Tumor.type=D;Size=4.7;Grade=2;Nodes=0/8;ER=Pos;PR=Pos;HER2=Neg;Age=48;DFS=101;Status=recur

Gene expression data under ER stress from lymphoblastoid cells of twin 1706:1 treated with DMSO.

lymphoblastoid cell line;1706;GM14414;Twin number 1;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1710:2 treated with DMSO.

lymphoblastoid cell line;1710;GM14433;Twin number 2;DMSO;4 hours

Arrays were scanned on an Illumina BeadArray Reader.  Laser power and PMT voltage were kept constant for Cy3 scans.

Images were quantitated by Illumina Beadscan, v3.  Quantitated data was imported into Beadstudio software.  On-slide spot replicates were averaged by Beadstudio and individual spot data was reported

RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA) as per manufacturer’s protocol.

750ng of each aRNA in water (10ul) was suspended in Illumina “HYB” buffer (20ul) and heated to 65C for five minutes, then allowed to cool to room temperature.  The samples were applied to HumanHT12v3 Expression Beadchips and hybridized at 58C for 16-20 hours at high humidity.  Arrays were washed according to Illumina standard protocol.  Immobilized, biotinylated aRNAs were then detected by staining with cy3 Steptavidin (1ug cy3-SA per 1 ml of Illumina “Block E1”) for 10 minutes at room temperature.  Arrays were washed and dried according to Illumina standard protocol.

RNA samples were labeled with biotin according to Manufacturer's instructions.

OCI-Ly7;diffuse large B-cell lymphoma (DLBCL);LZRS-IRES-YFP;negative control

OCI-Ly10;diffuse large B-cell lymphoma (DLBCL);LZRS-IRES-YFP;negative control

OCI-Ly1;diffuse large B-cell lymphoma (DLBCL);LZRS-FOXP1-IRES-YFP;FOXP1 overexpression

OCI-Ly1;diffuse large B-cell lymphoma (DLBCL);LZRS-IRES-YFP;negative control

GeneChip Operating Software (GCOS) with Affymetrix Microarray Suite 5.0 (MAS5) algorithm was used to define the probe cells and compute intensity for each cell. The Expression ConsoleTM software was used to enable probe set summarization and to verify if the hybridization results and initial data were of sufficient quality for secondary analysis.

The Sample data table represents the GCOS data. The GCOS and Expression Console (EC) CHP files are attached to the Sample record as supplementary files.

Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 array. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Affymetrix GeneChip Expression Analysis Technical Manual).

Gene expression data from wild-type mice 8 h after cecal ligation and puncture surgery.
B-3

lung;Balb/c;wild-type;cecal ligation and puncture surgery;8-10 weeks

mouse wild-type lung 8 h after cecal ligation and puncture surgery

Gene expression data from PPTA knockout mice 8 h after sham surgery.
MS-1

Gene expression data from wild-type mice 8 h after sham surgery.
BS-1

B-1

B-2

BS-2

BS-3

Three-month-old mice were killed and tissues were collected and snap frozen in liquid nitrogen.

Animals were maintained on standard mouse chow diet at 22oC on 12 h light-dark cycle allowed ad libitum access to food and tap water.

Kinin B1 receptor knockout with selective rescue in fat, biological rep3

Data were analyzed using Affymetrix GCOS v. 1.3, MAS5.0 algorithm, and globally scaled with the trimmed mean target intensity set to 1500.

6µg of biotinylated cRNA were hybridized for 16hr at 45C to the Affymetrix Mouse Genome 430 2.0 array.  Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 450.

Biotinylated aRNA synthesis was performed using the MessageAmp III aRNA Amplification Kit (Ambion)

Kinin B1 receptor knockout with selective rescue in fat, biological rep1

Kinin B1 receptor knockout with selective rescue in fat, biological rep2

This is from a study of femoral fracture healing in female rats 16 weeks old at fracture to compare intramedullary nailing, screw and plate fixation, and sham surgery.  This sample is from the nail (intramedullary rod) group collected 6 weeks after fracture.  Each sample is a pool of RNA from three rats.  The middle third of the femur was collected with the cortical bone, fracture callus, and marrow elements.  Mid-diaphyseal, simple, transverse fractures were induced by a Gigli saw.

This is from a study of femoral fracture healing in female rats 16 weeks old at fracture to compare intramedullary nailing, screw and plate fixation, and sham surgery.  This sample is from the group repaired with a plate and screws(rigid fixation) collected 1 day after fracture.  Each sample is a pool of RNA from three rats.  The middle third of the femur was collected with the cortical bone, fracture callus, and marrow elements.  Mid-diaphyseal, simple, transverse fractures were induced by a Gigli saw.

HCT116 cells stably expressing NFX1-91 shRNA or control β-Galactosidase shRNA were delivered by lentiviral vector FUGW.

HCT116 cells were grown in Dulbecco’s modified Eagle’s medium (DME medium, GIBCO-BRL) + 10% FBS + penicillin-streptomycin

GeneChIP scanner 3000 7G, as described in the affymetrix technical manual

The data were analyzed with dChIP using Affymetrix default analysis settings and global scaling as normalization method.

Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was purified using an RNeasy kit from Qiagen.

The target preparation and hybridization were conducted as described in the Affymetrix technical manual.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

This is from a study of femoral fracture healing in female rats 16 weeks old at fracture to compare intramedullary nailing, screw and plate fixation, and sham surgery.  This sample is from the nail (intramedullary rod) group collected 2 weeks after fracture.  Each sample is a pool of RNA from three rats.  The middle third of the femur was collected with the cortical bone, fracture callus, and marrow elements.  Mid-diaphyseal, simple, transverse fractures were induced by a Gigli saw.

Cultures were maintained in DMEM with L-glutamine and high glucose (Invitrogen) plus 10% heat-inactivated FBS (Invitrogen) and 100 U/mL penicillin streptomycin (Invitrogen) at 37 oC and 5% CO2. Cells were passaged at confluence by 0.25% trypsin EDTA (Invitrogen).

B6; gender: mix; age: 0-2d; tissue: rib cartilage; passage #: 4; treatment: control; biological replicate: 2

This is from a study of femoral fracture healing in female rats 16 weeks old at fracture to compare intramedullary nailing, screw and plate fixation, and sham surgery.  This sample is from the nail (intramedullary rod) group collected 4 weeks after fracture.  Each sample is a pool of RNA from three rats.  The middle third of the femur was collected with the cortical bone, fracture callus, and marrow elements.  Mid-diaphyseal, simple, transverse fractures were induced by a Gigli saw.

According to the manufacturer's instructions. See Moreno CS et al (2005). Cancer Res 65(22):10214-10222.

Briefly,total RNA (100 ug) was purified, using the RNeasy Mini Kit (Cat.No.74104, QIAGEN Inc., Valencia, CA) with minor modifications. Total RNA was eluted twice with 50 ul of 65 C DEPC-treated water.

Biotin-labeled cRNA was produced with Enzo BioArray High Yield RNA Transcription Labeling kit according to the manufacturer's instructions. See Moreno CS et al (2005). Cancer Res 65(22):10214-10222.

This is from a study of femoral fracture healing in female rats 16 weeks old at fracture to compare intramedullary nailing, screw and plate fixation, and sham surgery.  This sample is from the group repaired with a plate and screws (rigid fixation) collected 2 weeks after fracture.  Each sample is a pool of RNA from three rats.  The middle third of the femur was collected with the cortical bone, fracture callus, and marrow elements.  Mid-diaphyseal, simple, transverse fractures were induced by a Gigli saw.

HepG2 cell cultures were incubated with quercetin (3μM) for 4 hours after overnight serum starvation.

RMA normalization was performed with the raw data using Genespring GX V9.0 (Agilent, Foster City, CA).

Total RNA was isolated using NucleospinII columns (Macheray-Nagel, Dttren, Germany), according to the manufacturer’s instructions.

Hybridization was perfoermed according to the Affymetrix protocol (Affymetrix Gene-Chip Expression Analysis Technical Manual) by the Laboratoire Transcriptome of CHU Montpellier, France

RNA was labeled according to the Affymetrix protocol (Affymetrix Gene-Chip Expression Analysis Technical Manual) by the Laboratoire Transcriptome of CHU Montpellier, France.

This sample was part of a time course experiment of the effect of quercetin on HepG2 cells gene axpression

HepG2 cell cultures were incubated with serum free medium for 4 hours after overnight serum starvation.

HepG2 cell cultures were incubated with quercetin (3μM) for 12 hours after overnight serum starvation.

HepG2 cell cultures were incubated with serum free medium for 12 hours after overnight serum starvation.

HepG2 cell cultures were incubated with quercetin (3μM) for 24 hours after overnight serum starvation.

HepG2 cell cultures were incubated with serum free medium for 24 hours after overnight serum starvation.

plaque type psoriasis;epidermis;67;male;< 1 y;phototherapy;pre-UV

plaque type psoriasis;epidermis;59;male;> 20 y;phototherapy;pre-UV

plaque type psoriasis;epidermis;17;male;> 10 y;phototherapy;pre-UV

plaque type psoriasis;epidermis;43;male;> 10 y;phototherapy;pre-UV

plaque type psoriasis;epidermis;47;female;> 10 y;phototherapy;pre-UV

plaque type psoriasis;epidermis;74;female;2 y;phototherapy;pre-UV

plaque type psoriasis;epidermis;46;female;> 10 y;phototherapy;pre-UV

plaque type psoriasis;epidermis;28;female;> 10y;phototherapy;pre-UV

plaque type psoriasis;epidermis;33;female;> 10 y;phototherapy;pre-UV

WT and RORasg/sg mice were fed with high fat diet (HFD; 35% fat)

Liver and white adipose tissue (WAT) from WT and RORasg/sg mice fed with a high fat diet (HFD; 35% fat) for 6 weeks

Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters

For each sample, 1.65ug of Cy3 labeled cRNA was fragmented and hybridized for 17 hours in a rotating hybridization oven.

Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol

Agilent TIFF High File = US23502387_251486824233_S01_H.tif
Agilent TIFF Low File = US23502387_251486824233_S01_L.tif
RNA samples from WT mice fed with a HFD

C57BL/6;wild type;male;5 Month old;White adipose tissue (WAT);35% Fat Diet (High Fat Diet; HFD)

Agilent TIFF High File = US23502387_251486824232_S01_H.tif
Agilent TIFF Low File = US23502387_251486824232_S01_L.tif

RNA samples from Staggerer mice fed with a HFD

C57BL/6;RORasg/sg;male;5 Month old;White adipose tissue (WAT);35% Fat Diet (High Fat Diet; HFD)

Agilent TIFF High File = US23502387_251486824231_S01_H.tif
Agilent TIFF Low File = US23502387_251486824231_S01_L.tif

Hypoxia adeno treated sample (wild type) for evaluation of hypoxic response in hepatocytes

Human glioblastoma cells were cultured in DMEM supplemented with 10% FCS and standard antibiotics in an incubator at 37°C and 5% CO2 humidified atmosphere.

Expression values were estimated using the GC-RMA implementation found in Genedata’s Refiner 4.1 (Genedata) package. Data-mining and visualization was performed using Genedata’s Analyst 4.1 package.  Only median fold ratio values with P < 0.05 using t test were used for subsequent analysis. All samples were quintile normalized and median scaled to correct for minor variations in their expression distributions.

Total RNA was extracted from the primary tumor samples using Trizol reagent, according to manufacturer’s instructions, and resuspended in diethylpyrocarbonate (DEPC) treated water.  Total RNA was further purified using the RNeasy kit (Qiagen) and following the protocol for Total RNA cleanup.  Cultured cells were collected when plates were 70-80% confluent and RNA was extracted using RNeasy Mini kit (Qiagen).

Samples were hybridized to Affymetrix U133v2.0 GeneChips and scanned as per manufacturer’s instructions.

RNA was then amplified and labelled using the Affymetrix 2-cycle amplification protocol as per manufacturer’s instructions (Affymetrix).

Hypoxia treated sample (HIF-1alpha null) for evaluation of hypoxic response in hepatocytes

A HID I_B048

A HID I_B047

A HID U_B045

A HID I_B044

A HID U_B081

A HID I_B052

A HID I_B051

A HID I_B050

this sample is from a 16-week-old male normal mouse gastrocnemius muscle

A HID I_B083

A HID B_B082

this sample is from a 16-week-old male mdx mouse gastrocnemius muscle

Sample name: CSB_CR_3

C57BL/6;Csbm/m;male;cerebellum;1 year;40% caloric restriction of SD diet

Sample name: CSB_CR_2

Sample name: CSB_CR_1

vastus lateralis biopsy, 63 year-old trained COPD patient (male #64).

vastus lateralis biopsy,65 year-old sedentary COPD patient (male #48).

The mice were then fed for 2 weeks with AIN93G (control group) or AIN93G containing 0.1%, 0.5% or 1% quercetin.

Six-week-old male BALB/c mice were obtained from the Institute for Animal Reproduction, Charles River Japan Inc. (Ibaraki, Japan). The mice were housed under conditions of 24± 1°C, 55 ± 5% humidity, and 12 hour light/dark photocycles (dark period from 0800 to 2000) with free access to water and a standard nonpurified diet (NMF, Oriental Yeast Co., Tokyo, Japan) for a week prior to the experiment.

After hybridization, the gene chips were washed and stained using a GeneChip Fluidics Station 450 (Affymetrix) and then scanned (GeneChip Scanner; Affymetrix) with the GeneChip Operation Software Ver. 1.3 (Affymetrix).

Data analysis was performed with a GeneChip Operating Software (Ver. 1.3) using Affymetrix default analysis settings and global scaling as normalization method..

Fifteen microgram aliquots of fragmented cRNA were hybridized to an array (Mouse Genome 430 2.0 array, Affymetrix) at 45°C for 16 h.

Gene expression data from liver after 14 day feeding of 0.1% quercetin diet

Gene expression data from liver after 14 day feeding of control AIN93G diet

Treatment time: 0.5 hour

Psoriasis;m;30s;African American;disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 34;YES, subject has history of AR (allergic rhinitis), asthma or both: no;normal (120-300 cells/ml): 360;normal (0-48.5 kIU/L): 224;detects IgE that reacts specifically with suspected or known allergens: positive;Skin culture positive or negative for S. Aureus: neg

Atopic Dermatitis;f;30s;Caucasian;disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 4.5;YES, subject has history of AR (allergic rhinitis), asthma or both: YES;normal (120-300 cells/ml): 100;normal (0-48.5 kIU/L): 36;detects IgE that reacts specifically with suspected or known allergens: positive;Skin culture positive or negative for S. Aureus: neg

Psoriasis;f;30s;Caucasian;disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 9.1;YES, subject has history of AR (allergic rhinitis), asthma or both: YES;normal (120-300 cells/ml): 10;normal (0-48.5 kIU/L): 49.3;detects IgE that reacts specifically with suspected or known allergens: positive;Skin culture positive or negative for S. Aureus: neg

Psoriasis;m;20s;Caucasian;disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 3;YES, subject has history of AR (allergic rhinitis), asthma or both: no;normal (120-300 cells/ml): 110;normal (0-48.5 kIU/L): 31.2;detects IgE that reacts specifically with suspected or known allergens: negative;Skin culture positive or negative for S. Aureus: neg / positive to Strep. Viridans

Atopic Dermatitis;m;50s;Caucasian;disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 34.6;YES, subject has history of AR (allergic rhinitis), asthma or both: YES;normal (120-300 cells/ml): 510;normal (0-48.5 kIU/L): 710;detects IgE that reacts specifically with suspected or known allergens: positive;Skin culture positive or negative for S. Aureus: neg

Atopic Dermatitis;m;20s;Native American;disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 11.6;YES, subject has history of AR (allergic rhinitis), asthma or both: YES;normal (120-300 cells/ml): 990;normal (0-48.5 kIU/L): 4136;detects IgE that reacts specifically with suspected or known allergens: positive;Skin culture positive or negative for S. Aureus: pos

Atopic Dermatitis;f;40s;Caucasian;disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 11.3;YES, subject has history of AR (allergic rhinitis), asthma or both: YES;normal (120-300 cells/ml): 430;normal (0-48.5 kIU/L): 319;detects IgE that reacts specifically with suspected or known allergens: positive;Skin culture positive or negative for S. Aureus: pos

Atopic Dermatitis;f;20s;African American;disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 15.2;YES, subject has history of AR (allergic rhinitis), asthma or both: YES;normal (120-300 cells/ml): 290;normal (0-48.5 kIU/L): 2578;detects IgE that reacts specifically with suspected or known allergens: positive;Skin culture positive or negative for S. Aureus: neg

Nonatopic Control;m;20s;Caucasian;disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 0;YES, subject has history of AR (allergic rhinitis), asthma or both: no;normal (120-300 cells/ml): 90;normal (0-48.5 kIU/L): 70.8;detects IgE that reacts specifically with suspected or known allergens: negative;Skin culture positive or negative for S. Aureus: neg

Psoriasis;f;30s;Caucasian;disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 6.6;YES, subject has history of AR (allergic rhinitis), asthma or both: no;normal (120-300 cells/ml): 140;normal (0-48.5 kIU/L): 18.2;detects IgE that reacts specifically with suspected or known allergens: negative;Skin culture positive or negative for S. Aureus: neg

Gene expression in CD71+ bone marrow cells from CD70TG*Ifng-/- mice

Gene expression data from left lung samples from C57BL/6 male mice exposed to 0.3 ppm O3  for 72 hours

C57BL/6;Il10+/+;6-8 weeks;Male;Left lung;Jackson Labs, Bar Harbor, ME;72 hours;ozone;0.3 ppm O3;10028-15-6

Gene expression data from left lung samples from B6.129P2-Il10tmlCgn/J male mice exposed to 0.3 ppm O3  for 72 hours

B6.129P2-Il10tmlCgn/J;Il10-/-;6-8 weeks;Male;Left lung;Jackson Labs, Bar Harbor, ME;72 hours;ozone;0.3 ppm O3;10028-15-6

Wild type or CHIP knockout C57BL/6J mice were injected DOX at1dose of 15mg/kg,and the hearts were taken out after 5 days.

Eight to ten-week-old wild type or CHIP knockout C57BL/6J male mice were kept at least 5 days at 22°C and 55% relative humidity in a 12-h day/night lighting environment with free access to food and water.

Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-8 ug total RNA

Gene expression data from CHIP knockout mouse herat DOX treated for 1dose of 15mg/kg

Gene expression data from CHIP knockout mouse heart with no DOX treatmeant

Gene expression data from wild type mouse heart with no DOX treatmeant

Gene expression data from wild type mouse heart DOX treated for 1dose of 15mg/kg

Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

All procedures performed on animals were done in accordance with guidelines of the American Physiological Society and were approved by The University of Texas MD Anderson Cancer Center Institutional Animal Care and Use Committee (Richard R. Behringer, IACUC Protocol Number: 02-90-01735).  Mice carrying a targeted Lim1 null allele (Lim1lacZ), a Lim1 conditional null allele (Lim1flox) and an Rarb2-Cre transgene in which Cre is expressed in the metanephric mesenchyme of the developing kidney, were used in this study.  Lim1lacZ/+ and Lim1flox/flox mice were maintained on a C57BL/6J x 129/SvEv genetic background.  Rarb2-Cre transgenic mice were initially generated on a C57BL/6J x SJL/J genetic background. (Reference: BMC Nephrol. 7(1):1, 2006, PMID: 16464245)

To obtain mouse embryos with metanephric mesenchyme-specific Lim1 deficient (Lim1flox/lacZ; Rarb2-Cretg/+) kidneys, timed matings between Lim1+/lacZ; Rarb2-Cretg/+ males and Lim1flox/flox females were established.  Kidney samples of two different embryonic stages (E14.5 and E18.5) were isolated.  Their genotypes were assigned unambiguously using real time PCR assays detecting the presence of lacZ and Cre alleles, which were established in the M. D. Anderson Cancer Center DNA Analysis Core Facility.  For the E14.5 time point, a total of 71 embryos were collected, 17 of them were genotyped as conditional mutants (Lim1flox/lacZ; Rarb2-Cretg/+).  Kidneys from 23 Lim1flox/+; Rarb2Cretg/+ embryos were used as “control” kidneys.  For the E18.5 time point, a total of 39 embryos were harvested, 9 of them were genotyped as conditional mutants and 14 of them were genotyped as controls. (Reference: BMC Nephrol. 7(1):1, 2006, PMID: 16464245)

The arrays were stained with phycoerythrin-coupled avidin and scanned using a GeneArray Scanner 3000.  The resultant output was analyzed using Affymetrix Microarray Suite software and examined for excessive background or evidence of RNA degradation.  All microarray processing was performed in the Murine Microarray and Affymetrix Facility at the University of Texas M. D. Anderson Cancer Center. (Reference: BMC Nephrol. 7(1):1, 2006, PMID: 16464245)

dChip2004, scaled to 250. (Reference: BMC Nephrol. 7(1):1, 2006, PMID: 16464245)

Embryonic kidney tissue from each individual was placed in a separate tube with 0.5 ml TRIzol (Invitrogen, Carlsbad, CA) and stored at –75oC until the corresponding visceral tissue could be genotyped.  After a genotype was unambiguously assigned to each individual, TRIzol preserved kidneys of the same genotype were pooled and total RNA was prepared as per the manufacturer’s instructions.  Total RNA was then processed using a QIAGEN RNeasy Midi Kit before in vitro transcription-labeling reaction per Affymetrix (Santa Clara, CA) recommendation.  Once purified, RNA quality was determined by electrophoretic methods using an agarose gel or analysis using an Agilent Bioanalyzer 2100 (Palo Alto, CA) and by spectroscopy at 260 and 280 nm. (Reference: BMC Nephrol. 7(1):1, 2006, PMID: 16464245)

The target was then fragmented and hybridized to Mouse Genome 430 2.0 Affymetrix GeneChip Arrays (Affymetrix, Santa Clara, CA) in duplicates using an Affymetrix GeneChip Fluidics Station 400, according to the manufacturer’s standard protocols. (Reference: BMC Nephrol. 7(1):1, 2006, PMID: 16464245)

Five to forty micrograms of total RNA from each pooled embryonic kidney sample was used to produce the cRNA target for the microarray.  The target was created using a reverse transcription reaction to produce cDNA (Supercript Choice System, Gibco), which was subsequently subjected to in vitro transcription with biotinylated cytidine-5’-triphosphate and uridine-5’-triphosphate using the ENZO BioArray High Yield RNA Transcript Labeling Kit to produce biotinylated cRNA. (Reference: BMC Nephrol. 7(1):1, 2006, PMID: 16464245)

After scanning, all probe sets were scaled to a signal intensity of 250 and relative levels of expression of each transcript (signal) were determined using Microarray Suite 5.0 software (Affymetrix).  The images of all arrays were inspected for physical anomalies and for the presence of excessive background hybridization.  Generally, all array results used in this study were of good quality, and no major manufacturer’s defects or abnormalities were detected. (Reference: BMC Nephrol. 7(1):1, 2006, PMID: 16464245)

129 / C57BL/6 / SJL/J mixed, Genotype: Lim1flox/lacZ; Rarb2Cretg/+; Gender: mixed; Age: embryonic day 18.5; Tissue: whole kidneys from 9 embryos. (Reference: BMC Nephrol. 7(1):1, 2006, PMID: 16464245)

129 / C57BL/6 / SJL/J mixed, Genotype: Lim1flox/+; Rarb2Cretg/+; Gender: mixed; Age: embryonic day 18.5; Tissue: whole kidneys from 14 embryos. (Reference: BMC Nephrol. 7(1):1, 2006, PMID: 16464245)

129 / C57BL/6 / SJL/J mixed, Genotype: Lim1flox/lacZ; Rarb2Cretg/+; Gender: mixed; Age: embryonic day 14.5; Tissue: whole kidneys from 17 embryos. (Reference: BMC Nephrol. 7(1):1, 2006, PMID: 16464245)

129 / C57BL/6 / SJL/J mixed, Genotype: Lim1flox/+; Rarb2Cretg/+; Gender: mixed; Age: embryonic day 14.5; Tissue: whole kidneys from 23 embryos. (Reference: BMC Nephrol. 7(1):1, 2006, PMID: 16464245)

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10 days old tumor spheroids were processed for RNA isolation using the Quiagen RNeasy Micro Kit.

HepG2 spheroids were grown from 1x106 cells in coated (Sigmacote) 250-mL spinner flasks (Integra Biosciences, Fernwald, Germany) with 250 mL complete medium (MEM with 10% FCS, 2 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin, 0.1 mM non-essential amino acids) in a Cell Spin stirrer system (22.5 rotations/min, Integra Biosciences). 125 mL cell culture medium was replaced every second day.

Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project. Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al.
probe group file: Unsupported Human Gene 1.0 ST Array CDF Files
meta-probeset file: HuGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 30 (11 MB 01/22/10)

total RNA was isolated using Quiagen RNeasy Kit, RNA was amplified using the One-direct-Kit from NUGEN applied for 250 microdissected cells

Human Gene 1.0 ST arrays (Affymetrix) were hybridized with 5.5 mg labelled cDNA.

Samples were labelled with Encore biotin module (NUGEN) washed and stained using the HWS Kit (Affymetrix).

HepG2;Human hepatocellular liver carcinoma cells;HIF-2α knockdown;10 days old tumor spheroids

Cells transfected with H133W mutant sirtuin 6 and stimulated with TNFa, biological rep1

Gene expression data from HEK293 cells transfected with H133W construct  and stimulated with TNFa

HEK293 cells transfected with H133W construct  and stimulated with TNFa

Gene expression data from HEK293 cells transfected with H133W construct  and unstimulated

Biopy protocol: 8 biopsies evaluated as acceptable by the research assistant were taken from bronchi of the right lung using alligator forceps (Olympus FB-15C-1). Biopsies were obtained from the  ubsegmental and segmental bronchial carinae of the lower (3 to 5 biopsies) and upper (1 to 2 biopsies) lobes, as well as the lobar carinae of the middle (2 biopsies) and upper (1 to 2 biopsies) lobes to provide adequate samples of the large airways (3rd to 5th bronchial generation). The samples were immediately placed in RNAlater.

Scanning was done using a GeneArray Scanner at the McGill University and Genome Quebec Innovation Centre (www.genomequebec.mcgill.ca) and was performed in parallele for control and asthmatic samples

The scanned images were analyzed using the Microarray Analysis Suite 5.0 (MAS5, Affymetrix) and the raw image fils obtained (.CEL) were used for statistical analyses. To calculate gene expression, the robust multiarray analysis (RMA) was used. To identify significant differences in gene expression, a pairwise comparison between control and allergic asthmatic subjects was performed with the microarray results, in the first case with the Limma package available in Bioconductor. However, no correction was applied when using the U133A GeneChips since the RMA method is more stringent. However, Smyth’s moderated t test was used.

The samples were mechanically homogenized (Rotor/Stator homogenizer; PowerGen) and total RNA was extracted using the RNEasy kit (Qiagen) according to the manufacturer’s instructions.

Hybridation was done at the McGill University and Genome Quebec Innovation Centre (www.genomequebec.mcgill.ca) and was performed in parallele for control and asthmatic samples

Probe labelling was done at the McGill University and Genome Quebec Innovation Centre (www.genomequebec.mcgill.ca) and was performed in parallele for control and asthmatic samples.

non allergic non asthmatic subject, without any stimulation;bronchial biopsies

Total RNA was isolated with the RNeasy kit (Qiagen) from macrophages incubated at normoxia (21% oxygen) or hypoxia (0% oxygen) for 24 h. Two μg RNA from 4 donors incubated at normoxia and 4 donors at hypoxia was pooled respectively and these 2 pools were used for the target preparation and analyzed on duplicate DNA microarrays (Hu95A; Affymetrix).

Human mononuclear cells were isolated by Ficoll-Paque centrifugation in a discontinuous gradient from buffy coats from healthy blood donors. Cells were differentiated in macrophage-SFM medium supplemented with 70 U/ml human granulocyte macrophage colony-stimulating factor. After 3 days, the medium was changed to macrophage-SFM without GM-CSF and cells were cultured up to 8 days

lung tissue;CD-1_Nrf2 -/-;13 weeks + 2 month;fresh air, treatment over 2 month, 4x1h exposure per day

lung tissue;CD-1;13 weeks + 2 month;2R4F whole mainstream smoke 750 µg/ml, treatment over 2 month, 3x1h exposure per day

Fresh biopsy was placed on ice in the Trizol solution (Invitrogen).

GeneChips were scanned using the Hewlett-Packard GeneArray Scanner (Affymetrix).

The DNA-Chip Analyzer (dChip) software (Li, C. and Wong, W.H. 2001) was used to normalize the image data and calculate the expression value.

Total RNA was extracted using TRIzol reagent according to the manufacturer's instructions.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC on GeneChip U95Av2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Colonic biopsy was collected during endoscopy from affected area of a patient with ulcerative colitis (UC). The standard Affymetrix protocols were followed to prepare target from 5ug of total RNA. The expression profiles generated from normal individuals were compared to that from patients with different types of disease.

disease affected colon of an adult with ulcerative colitis (UC).

colonoscopic biopsy from adult with affected colon from adult with UC

Colonic biopsy was collected during endoscopy from unaffected area of a patient with Crohn's disease (CD). The standard Affymetrix protocols were followed to prepare target from 5ug of total RNA. The expression profiles generated from normal individuals were compared to that from patients with different types of disease.

colonoscopic biopsy from adult with unaffected colon with Crohn's disease

Cells were transfected with 60 nM of the corresponding double-stranded siRNAs (siC or siLsd1; Applied Biosystems, Foster City, CA) using Metafectene Pro (Biontex, Martinsried, Germany) at a 1:3 w:v ratio with the siRNA. RNA was extracted at 24h and 48h after transfection, without any media changes.

Mouse 3T3-L1 preadipocytes were maintained in Dulbecco's modified Eagle's Medium (DMEM) supplemented with 10% calf serum (all products from Sigma). Cells (1x10^6) were trypsinized 1h before transfection and seeded into 60 mm dishes.

Array normalization, modeling and statistical analysis of gene expression was perform using Dchip software.

Total RNA was extracted and purified with the RNeasy Mini Kit (Qiagen GMbH, Hilden, Germany) according to the instructions of the manufacturer.

cRNA hybridization was done according to standard Affymetrix protocols.

cRNA labelling was done according to standard Affymetrix protocols.

According to paper: Multiple adaptive mechanisms to chronic liver disease revealed at early stages of liver carcinogenesis in the Mdr2-knockout mice.

Gene expression data from purified clock negative bulge stem cells

Dorsal skin bulge epidermal stem cells;Venus GFP negative Bulge cells (alpha6bright/CD34+/Venushigh population)

Venus GFP negative Bulge cells (alpha6bright/CD34+/Venushigh population) isolated from the dorsal skin of P18-19 mice

GCRMA normalized data (Wu et al. Journal of the American Statistical Association, 2004 vol 99 page 909)

To understand the different steps leading to thyroid carcinoma, we analyzed thyroid gene expression in two transgenic strains at different ages (2, 6, 10 months) by microarray technology

HaCat cells infected with a control lentiviral construct. Replicat 3

Control frontal cortex 3

Control frontal cortex 5

Control frontal cortex 6

Control frontal cortex 7

transfected with pSuper-shMTDH, cultured with HMVEC-L and then purified by FACS;Purchased from Stratagene, Inc.

The R statistical software was applied for data analysis. The RMA method was used for global background correction and qspline was used for normalization. Gene expression index calculation was done using model based index calculation (MBEI). Only perfect match probes were included in data analysis. Welch two sample t-test was used to calculate p-values.

Affymetrix GeneChip scanner 3000 (00-0074)
Affymetrix GeneChip Operating Software (GCOS) ver. 1.1 (690036)
Standard Affymetrix parameters

Standard QIAGEN procedure for total RNA extraction using RNeasy Lipid Tissue Midi kit (QIAGEN)

Standard Affymetrix procedures for hybridization, blocking and washing, including any post-processing steps

Standard Affymetrix procedure for biotin labeling. Approximately 2 micro-g of total RNA was processed to produce biotinylated cRNA targets.

The caudate nucleus from a neurologically normal Jpanese male (aged 60 yr).

Brain tissue from Fisher 344 male rat, Animal #256, 200mg/kg D-Serine

Male;82;5h;6.2;schizophrenic;superior temporal cortex (Brodmann Area 22, BA22)

Male;63;30h;6.5;schizophrenic;superior temporal cortex (Brodmann Area 22, BA22)

Male;87;3.5h;6;schizophrenic;superior temporal cortex (Brodmann Area 22, BA22)

"Whole blood cell RNA was isolated at baseline, 3 h, 6 h, 24 h , and 7days after intravenous endotoxin challenge using PAXgene blood RNA tubes.  Total RNA was extracted and treated with DNase 1 as per PAXgene Blood RNA kit protocol with the following modifications: after 2 h incubation at room temperature, blood samples were kept for minimum 24 h at 4°C and total RNA precipitated overnight with 3M NaAc and 100% ethanol.  All samples were processed within 72 h from time of collection. Double stranded cDNA was synthesized from total RNA (5 to 20 µg) using 7-d(T)24  primer and SuperScriptä Double-Stranded cDNA Synthesis Kit and purified by phase lock gel-phenol/chloroform extraction followed by ethanol precipitation. Biotin-labeled cRNA was prepared by in vitro transcription using HighYieldä RNA Transcript Labeling Kit followed by fragmentation with 5X fragmentation buffer.  Fragmented cRNA (10 µg) was hybridized to Affymetrix Hu95Av2 oligonucleotide probe arrays for 16 h at 45°C.  After removal of hybridization fluid, the arrays were washed, stained with streptavidin phycoerythrin (SAPE), and signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400.  Probe set signals were measured using Agilent GeneArray Scanner (Affymetrixâ, Santa Clara, CA)."

"female subject, 18-45 yrs, whole blood cells 6 h after intravenous endotoxin challenge"

"female subject, 18-45 yrs, whole blood cells 24 h after intravenous endotoxin challenge"

"male subject, 18-45 yrs, whole blood cells 24 h after intravenous endotoxin challenge"

"male subject, 18-45 yrs, whole blood cells 168 h after intravenous endotoxin challenge"

"female subject, 18-45 yrs, whole blood cells prior to (baseline - 0 h) intravenous endotoxin challenge"

Total mRNA from liver tissues, strain: C57BL/6J- Lepob, subjected to intermittent hypoxia for 12 weeks
Keywords = Mus musculus
Keywords = liver

"male subject, 18-45 yrs, whole blood cells prior to (baseline - 0 h) intravenous endotoxin challenge"

J1 mouse ES cells were cultured in monolayer on gelatin-coated dishes containing ES medium (Dulbecco's Modified Eagle's Medium supplemented with 10% ES cell qualified fetal calf serum (Invitrogen, Carlsbad, CA), 2 mM glutamine, 100 units/ml penicillin, 100 µg/ml streptomycin, 1 mM sodium pyruvate, 100 µM MEM nonessential amino acids, and 0.1 mM ß-mercaptoethanol).

"male subject, 18-45 yrs, whole blood cells  6 h after intravenous endotoxin challenge"

K562 (Iscoves + 10% FCS) and TF-1 (RPMI + 10%FCS + rhGM-CSF.  Cells were cultured at 37oC, 5% CO2 and split every 3 to 4 days. The CREB specific shRNA sequences were selected and validated based on accepted parameters established by Tuschl et al.

K562 (Iscoves + 10% FCS) and TF-1 (RPMI + 10%FCS + rhGM-CSF.  Cells were cultured at 37oC, 5% CO2 and split every 3 to 4 days. . The CREB specific shRNA sequences were selected and validated based on accepted parameters established by Tuschl et al.

0.5 mg/kg/ml Isoproterenol treatment, 72 hour time point,  biological rep 1

CHIPEXP_NAME: 230_2_050531tpj_58h
SAMPLING_TIME: 72

CHIPEXP_NAME: 230_2_050531tpj_21h

CHIPEXP_NAME: 230_2_050531tpj_18h

CHIPEXP_NAME: 230_2_050531tpj_17h

0.5 mg/kg/ml Isoproterenol treatment, 24 hour time point,  biological rep 1

CHIPEXP_NAME: 230_2_050531tpj_53h

0.5 mg/kg/ml Isoproterenol treatment, 24 hour time point,  biological rep 4

CHIPEXP_NAME: 230_2_050531tpj_57h

0.5 mg/kg/ml Isoproterenol treatment, 24 hour time point,  biological rep 3

CHIPEXP_NAME: 230_2_050531tpj_55h

CHIPEXP_NAME: 230_2_050531tpj_20h

CHIPEXP_NAME: 230_2_050531tpj_19h

the fourth run of normal bladder cell treated with mock APF. Membrane A is used

Cells were treated with vehicle (DMSO), 1 µM lapatinib, 0.1 µM GSK1363089 (foretinib) or a combination of 1µM lapatinib and 0.1 µM foretinib for 24h.

Cells were plated in RPMI medium containing 10% FBS overnight at 37ºC, 5%CO2.

RNA microarray signals were normalized by MAS5. QC and data analysis were performed using Omicsoft microarray analysis tools (http://www.omicsoft.com/).

Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Response Genetics, Inc.)

BT474-J4;breast cancer;acquired lapatinib-resistant;HER2-positive;DMSO

BT474-J4;breast cancer;acquired lapatinib-resistant;HER2-positive;foretinib

Five days post-plating, primary hippocampal neurons from NSE-CD46+ mice and NSE-CD46+/STAT1-KO mice were treated with murine IFNγ (BD Transduction Labs), diluted in B27-free Neurobasal Media, added to the cultures (100 U/ml final concentration) and incubated for the indicated times prior to collection.

Primary hippocampal neurons were prepared from embryonic (E15-16) mice as previously described {Banker and Goslin, 1991, Rall, et al, 1997). Neurons were plated on 15mm glass coverslips or in 12-well plates coated with poly-L-lysine (Sigma) at a density of 2.5x105 cells/well.  Neurons were incubated at 37°C in a humidified incubator with 5% CO2 for 5d prior to IFNγ treatment or infection to allow for full differentiation.

Microarray images were processed using Agilent Feature Extraction software (version 9.5). Data were background corrected using normexp (offset=25), followed by quantile normalization. Control probes, probes lacking Entrez ID, and probes with intensity close to background across all arrays were removed.

RNA was purified from whole cell lysates using the RNeasy Mini kit (Qiagen), and contaminating DNA was removed using an RNase-Free DNase set.

Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed according to Agilent protocol.

500 ng total RNA was amplified and labeled using the Low RNA input linear amplification kit (Agilent). Labeled cRNA targets were hybridized onto Agilent 4×44k mouse whole genome arrays. Microarray images were processed using Agilent Feature Extraction software (version 9.5).

Gene expression at 3h after treatment with IFNg in WT mouse neurons

Peripheral blood from B-CLL patients as well as from healthy donors were firstly separated by Ficoll gradient (GE Healthcare), obtained peripheral mononuclear cells (PBMC). PBMC were shortly incubated in IMDM (Isove’s Modified Dulbecco’s) medium supplemented with 10% fetal calf serum, 1% non essential amino acids, 1% antibiotics. PBMCs from healthy donors were separated by autoMACS Pro Separator and anti FITC microbeads, CD19 human FITC antibody were used.

GeneChips were processed using the Agilent GeneArray Scanner 3000 7G system in the Genomics Facility of the New York University Cancer Institute.

Data were summarized using GeneSpring implementation of RMA algorithm and expression data were normalized on median of control samples.

Total RNA was extracted by TRIzol Reagent following the manufacturer protocol.   Precipitation by isopropyl alcohol (0.5mL per 1mL TRIzol) was done over night. As carrier of the aqueous phase the Acrylamide was used. The RNA pellets were washed with 75% ethanol (1mL per 1mL TRIzol) and dry pellets were resuspend in 20 uL of RNAse free water.

RNA was proceeded according to Affymetrix 3‘ – IVT Express Kit protocol. cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station.

RNA was proceeded according to Affymetrix 3‘ – IVT Express Kit protocol. cDNA were prepared using the recommended Affymetrix reagents and kits.

Additional information and characteristics in the referred paper supplement xls table.

Cells expressing IkBa dominant negative cultured in presence of dox, TNF stimulation for 6h

The data were analyzed with GCRMA package in the bioconductor project (gcrma version 2.32.0).

Extraction of total RNA was performed using RNeasy® Mini Kit (Qiagen)

Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the Affymetrix small sample amplification protocol from app. 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

Gene expression data from control mouse cerebral microvascular fragments

advanced thymic tumor from a homozygote mouse with a hypomorphic Ikaros mutation

genotype: Tgfbr2fl/fl
age: E14.5

vLow_24h_4

Ishikawa;39-year-old parous Japanese female diagnosed with endometrial adenocarcinoma stage 2.;bisphenol A;1 pM;24 hours

vLow_48h_1

Ishikawa;39-year-old parous Japanese female diagnosed with endometrial adenocarcinoma stage 2.;bisphenol A;1 pM;48 hours

A pool of two pure subsets of peripheral blood CD56dim natural killer cells (CD19- CD3- CD56dim Cd16+), stringently sorted by flow cytometry, from two age and gender matched stage IV (American Joint Committee on Cancer) melanoma patients.;Pooled RNA from the total peripheral lymphocyte fraction from 20 healthy donors, used as a common reference.

Tacrine 2.7mg/kg/day from 5 weeks
Moclobemide 10mg/kg/day

Lot batch = 5211

vLow_48h_3

Gene expression data under ER stress from lymphoblastoid cells of individual GM12751 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12750 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12750 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12717 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12717 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12716 treated with DMSO 8 hours.

mononuclear cells were isolated from fresh peripheral blood samples (Lyphoprep, Invitrogen, Karlsruhe, Germany). CD3-positive cells were enriched employing anti-CD3 magnetic microbeads (MIdiMACS, Miltenyi, Bergisch-Gladbach, Germany)

Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 13.5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

Gene expression data from immunomagnetically purified CD3+ normal donor derived peripheral blood cells

CD3-purified cells from normal peripheral blood sample. >95% purity

Following washing and staining, the chips were scanned using a GeneChip Scanner 3,000 6 G in the UNMC microarray core facility

Raw .cel files were processed using Robust Multichip Average (RMA) from GenePattern Software to create a .res file that was subjected to further analysis.

1)  Place freshly isolated tissue directly in TriReagent (1ml/50-100mg of tissue).
2)  Immediately homogenize tissue and transfer to a sterile 50 ml centrifuge tube.
3)  Cap the tube securely, shake, vortex vigorously, and incubate at room temperature 5 min. to assure dissociation of nucleoproteins.
4)  Add 0.1 ml BCP/ ml of TriReagent used.  Cap the tube, shake, and vortex.  Incubate at RT for 10 min.  Centrifuge at 3200 rpm in Sorvall tabletop centrifuge or equivalent (1800 g) for 30 min. at 40 C.
5)  Of the three phases seen, RNA remains in the topmost aqueous phase.  Transfer the aqueous layer to a fresh tube being careful not to disturb the protein-rich interface.
6)  Precipitate the RNA by adding isopropanol (molecular biology grade) at 0.5 ml / ml TriReagent used.  Shake vigorously, vortex, and leave at room temperature 10-15 min.
7)  Centrifuge at 3200 rpm for 45 min. to one hour at 40 C.
8)  Decant the isopropanol and wash the pellet gently with 10ml ice cold 75% ethanol (made with 100% ethanol (molecular biology grade) and HPLC grade-H2O).  Centrifuge at 3200rpm for 20 min. at 4ºC.
9) Carefully decant the ETOH.  Draw off the last with a pipet and allow excess ethanol to evaporate 5-10 min.  Do not permit the pellet to completely dry as this will decrease its solubility.

10) Bring the volume of the sample up to 250ul (or appropriate volume) with HPLC-H20.  Transfer the RNA sample to a 1.5ml microfuge tube.
15) Decant the ethanol mixture and wash the RNA pellet with 100μl 75% ethanol. Spin at top speed of microfuge for 10 minutes at room temperature.   Draw off the supernatant with pipet and repeat the wash step.  After drawing off the second 75% wash, invert the tube 5-10 min. to partially dry the sample.  Do not completely dry the RNA pellet as this will decrease its solubility.

Resultant cRNA probes were hybridized to the Affymetrix (Santa Clara, CA) Mouse Genome 430 2.0 Array per manufacturer's suggestion.

Expression analysis of white adipose tissue from a KSR2-/- mouse.

Expression analysis of white adipose tissue from a wild type mouse.

Eight week old C57Bl/6 male mice were injected i.d. with 100 ul type II Collagen in 100 ul of Complete Freunds ajuvant at day 24 were injected with LPS and sacrifice by decapitation at day 31 h

Mice were housed in HEPA filtered air racks (Tecniplast, Italy) with food and water ad libitum

Images were obtained with a VersArray ChipReader system (BioRad) at 10 um resolution and 16bit depth. Each slide was scanned three times, each time with a 5% increment in the sensitivity of the scanner. The data integration for multipole scanning were calculated by M = log2(cy3 / cy2) and A = 0.5 * log2(cy2 * cy3) values for all the possible combinations between channels among the three scannings. Quality score for each couple of channels was calculated as QS = min(QScy2, QScy3). The resulting 9 sets of A and M values were averaged using the QS as weights to obtain the integrated A and M sets.

Data was log2 transformed and normalizaed with an intensity- and location-dependent loess fit

Slides were prehybridised at 42°C in 2X SSC, 0.1% SDS, 1% BSA. Labeled probes were mixed with hybridization buffer containing 30% formamide and hybridized overnight at 42°C

RNA was reversed transcribed using Superscript II RT (Invitrogen) with oligo dT primers and random primers, both in the presence of aa-dUTP (Sigma). The cDNA was labeled with Cy3 or Cy5 dyes (Amersham), resuspended in DMSO, and incubated for 1 hr at room temperature in the dark. The probes were purified using the SNAP Gel Purification Kit (Invitrogen) following manufacturer instructions with the following modification: at the initial step, 500 ul of loading buffer (2.25 M guanidinium HCl in 70% isopropanol) were added to the sample, placed in a SNAP column and incubated for 4 min before the first centrifugation

Pre-frontal cortex from male C57Bl/6 mice 31 d after i.d. injection of Complete Freunds adjuvant;Pre-frontal cortex from male C57Bl/6 mice 31 d after i.d. injection of Type II collagen in Complete Freunds adjuvant

Eight week old C57Bl/6 male mice were injected i.d. with 200 ul of Complete Freunds ajuvant at day 24 were injected with LPS and sacrifice by decapitation at day 31 h

Pre-frontal cortex from male C57Bl/6 mice 31 d after i.d. injection of Type II collagen in Complete Freunds adjuvant;Pre-frontal cortex from male C57Bl/6 mice 31 d after i.d. injection of Complete Freunds adjuvant

Ulcerative colitis patient, biopsy taken from the descending colon, macroscopic inflammation vissible

Cells transfected with Stealth Negative Control siRNA (Invitrogen Catalog# 12935-300) and subsequently treated for 6 hours with 0.5% DMSO in DMEM Media containing 10% FBS

RKO cells transfected with NEG Stealth siRNA treated 6 h with vehicle DMSO 0.5%

Cells transfected with Stealth Negative Control siRNA (Invitrogen Catalog# 12935-300) and subsequently treated for 6 hours with 50 uM HNE in 0.5% DMSO final, in DMEM Media containing 10% FBS

RKO cells transfected with NEG Stealth siRNA treated 6 h with 50 uM HNE in DMSO 0.5% final

breast cancer derived cell line treated with 0.3 mM of 5-Fluorouracil for 36hours

immortalized human mammary epithelial cell line treated with fresh medium for 12 hours

breast cancer derived cell line treated with 3.0 mM of 5-Fluorouracil for 24 hours

immortalized human mammary epithelial cell line treated with 0.06 mM of 5-Fluorouracil for 12 hours

Samples were scanned according to Illumina's Whole-Genome Gene Expression Direct Hybridization Assay Guide

The bead-level data were preprocessed using BASH (Cairns et al. (2008) Bioinformatics 24(24):2921-2), a function from the beadarray package (Dunning et al (2007) Bioinformatics 23(16):2183-4) in Bioconductor, and normalised using variance stabilising data transformation (vsn) method (Huber et al. (2002) Bioinformatics 18: S96–S104) from the beadarray package

Total RNA was isolated using Trizol (Invitrogen), purified and on-column DNAse treated using Rneasy mini kit  (Qiagen) according to manufacturer's protocol.

Samples were hybridised according to Illumina's Whole-Genome Gene Expression Direct Hybridization Assay Guide

100ng of total RNA was labelled using Illumina TotalPrepTM-96 RNA Amplification Kit (Ambion) according to manufacturer's protocol.

Replicate_1
6816115008_A
Samples were enriched for epithelial cells by scraping epithelium off the muscle wall

Murine small intestine (jejunum);VillinCreERT2+_Apcfl/fl_Brg1fl/fl

6816115008_C

Murine small intestine (jejunum);VillinCreERT2+_Apcfl/fl_Brg1+/+

Replicate_2
6816115008_B

6816115008_E

6816115008_D

horns at 24 hours after injection.  8 uterine horns from 4 mice were

horns at 18 hours after injection.  8 uterine horns from 4 mice were

horns at 15 hours after injection.  8 uterine horns from 4 mice were

horns at 12 hours after injection.  8 uterine horns from 4 mice were

Experiments were performed on adult (2 months old) male Sprague–Dawley rats and rat pups (10 days postnatal age, P10) and carried out in accordance with the United Kingdom Animal (Scientific Procedures) Act 1986. Spared nerve injury and sham surgery were performed under halothane general anaesthesia with antiseptic conditions. After skin preparation, the sciatic nerve and its three terminal branches were exposed in the upper lateral thigh. Axotomy and ligation of the common peroneal and tibial branches was performed under direct vision, leaving the sural nerve intact. Muscle and skin were closed in two layers. In the sham operation, the procedures were the same but the nerves were only exposed and not cut or ligated. In all cases great care was taken not to stretch the nerve, or its branches, nor to damage the intact nerves.

After the surgery, the animals were returned to their cages and litters and maintained on a 12 hour light/dark cycle at constant ambient temperature in the Biological Services Unit with free access to food and water for 7 days post surgery (ps) until DRGs collection.

The data were analyzed with 'R software' loaded with the 'Bioconductor' platform using GC-RMA normalisation and Limma test to contrast the experimental groups.

Seven days post surgery, animals were sacrificed with 0.1 mL of Euthanal®, the fresh DRGs were snap frozen on liquid nitrogen and stored at –80o C until RNA extraction. L4 and L5 DRGs ipsilateral to the lesion were collected and pooled from 3 animals per adult experimental group and 4 animals per P10 group, (i.e. n= 6 DRGs per adult sample , n=8 per P10 sample) to minimise inter-animal differences. RNA was extracted using Trizol® reagent (Invitrogen®) and QIAshredder column (Qiagen®) for homogenisation according to manufacturer’s protocols. Additionally, the RNA was cleaned by ”RNA purification column” (Qiagen®) and a final volume of 50 uL obtained according to manufacturer protocol. The amount of RNA was measured with a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Inc.) and its quality assessed with Experion RNA HighSens StdSens analysis kit (Bio-Rad®). Then, the RNA was precipitated and dissolved to obtain a final concentration of 1 µg/µL and stored at -80°C until for cRNA synthesis or amplification by quantitative real-time polymerase chain reaction (qPCR).

For the mRNA high-throughput screening we used the GeneChip ® Rat expression  230 version 2.0 arrays and the GeneChip® Hybridization, Wash and stain kit from Affymetrix®. The protocol of hybridisation, according to manufactured indications was the 49/64 formats, which corresponds to the selected type of array. The control oligonucleotides were: B2 and the Eukaryotic bioB, bioC, bioD and cre. Then, the samples were washed and stained on the Fluidics Station 450 (Affymetrix®) monitored with the GeneChip® Operating Software (Affymetrix®) according to manufactured instructions (using the protocol FS450_003 which corresponds to rat 230 v2.0 array).

cRNA synthesis First strand cDNA synthesis; 2 g (for qPCR) or 10 ug (microarray analysis) of total RNA and 100 pmol/uL of the T7(dT)24 primer (5’-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3’) were combined for annealing at 70o C for 10mins and chilled on ice for 2mins. Then, the SuperScript III kit (Invitrogen®) was added according to manufacturer indications to synthesize the cDNA.  Second strand cDNA synthesis; the whole amount of the cDNA produced was used as template for the second strand synthesis plus 10 units of E. coli DNA ligase, 40 units of E. coli DNA polymerase (Invitrogen®), 3uL of 10 mM dNTPs and 2 units of Rnase H (Invitrogen®). The reaction was stopped by addition of 10 uL of 0.5M EDTA. The double stranded cDNA was then purified and precipitated and the resuspended in 10uL of nuclease free water.  Synthesis of biotin-labelled cRNA; we used the Enzo-Bioarray kit (Enzo Life Sciences, Inc) for synthesis of the cRNA according to manufacturer protocol. The resulting cRNA was purified with Rneasy kit (Qiagen®). The concentration was measured on a spectrophotometer and 20 µg of each sample was fragmented in 200 mM tris-acetate (pH= 8.1), 500mM potassium acetate and 150 mM magnesium acetate for 35mins at 95°C, then chilled on ice and stored at -80°C until microarray hybridisation

The L4/L5 dorsal root ganglia in the sham group are those ganglia ipsilateral to the surgery

L4/L5 dorsal root ganglia from adult rats (2 months old) 7 days after sham surgery

The L4/L5 dorsal root ganglia in the contralateral group are those ganglia contralateral to the surgery in the spare nerve injury group

Sprague-Dawley;Dorsal root ganglia;2 months;Spare nerve injury;Adult Contralateral

L4/L5 dorsal root ganglia from adult rats (2 months old) 7 days after SNI surgery

Swiss;adult mouse intestine, kidney, and liver plus fetus tissue;C57BL/6J;IL10-/-;12 weeks;colon epithelium

Swiss;adult mouse intestine, kidney, and liver plus fetus tissue;C57BL/6J;IL10-/-;6 weeks;colon epithelium

Swiss;adult mouse intestine, kidney, and liver plus fetus tissue;C57BL/6J;wildtype;6 weeks;colon epithelium

Agent: Azoxymethane (AOM), Dextran Sodium Sulfate (DSS)
Treatment dose: AOM (10mg/kg), DSS (2%)
In-vivo treatment: Mice six to eight weeks of age were injected i.p. with AOM (10 mg/kg) in 0.2 ml saline. One week after AOM administration, DSS at 2% was administered in the drinking water for 3 consecutive days, thereafter mice were euthanized.

Affy Scanning Protocol
Other: Scanning was performed by the Affymetrix GeneChip Scanner 7G.

BRBArray Tools Data Processing Protocol
Calculation Method: Resulting data files analyzed using BRBArrayTools, developed by the Biometric Research Branch, National Cancer Institute (Rubinfeld et al., 1997) (http//:linus.nci.nih.gov/BRB-ArrayTools.html. Data were normalized using median over the entire array as the reference because single color labeling technology was used. Gene ratios were average corrected across experimental samples and displayed according to an uncentered correlation algorithm (Ross et al., 2000).

Extraction Protocol
Other: Total RNA was extracted using Qiagen reagent according to the manufacturer’s instructions. RNA was digested using the RNase-Free Dnase Set and amplified into anti-sense RNA (aRNA) according to the Affymetrix gene expression protocol. The quality of both, total RNA and secondarily amplified RNA was tested using an Agilent Bioanalyzer 2000 (Agilent Technologies, Palo Alto, CA).

Hybridization Protocol
Other: Test aRNA was loaded into Affymetrix whole genome mouse arrays 430 2.0 and hybridized overnight in a hybridization oven.

Labeling Protocol
Other: Post-hybridization arrays were labeled using an Affymetrix fluidics wash and stain station.

Rats were sacrificed 30 minutes after the injection with methylprednisolone

Rats were sacrificed thirty hours after the injection with methylprednisolone

Rats were sacrificed 2 hours after the injection with methylprednisolone
Lot batch =

Rats were sacrificed one hour after the injection with methylprednisolone

Wee1 inhibitor II was synthesized and 17-AAG was obtained from the National Cancer Institute (Bethesda, MD). Drug treatments were performed as follows unless otherwise stated. Cells were plated in growth media at 10% confluency 1 day prior to initiation of treatment. On the first day of treatment, Wee1 inhibitor was added to the medium so that the final concentration was 2.5 μM. Twentyfour hours later, 17-AAG was added to the medium so that the final concentration was 40 nM. For controls, an equivalent amount of vehicle was administered. Cells were harvested for analysis 48 hrs after administration of 17-AAG.

The human prostate cancer cell line PC3 (ATCC) was cultured in Dulbecco's modified Eagle's minimal essential medium (DMEM; Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS; Invitrogen). Cells were propagated at 37°C in an atmosphere containing 5% CO2.

Data were collected using Affymetrix AGCC software.Statistical and clustering analysis was performed with Partek Genomics Suite (6.5) software using RMA normalization algorithm.

Samples were hybridized to Affymetrix GeneChip microarrays overnight

RNA (100 ng) was reverse transcribed and labeled with biotin using Affymetrix 3’ IVTexpress Labeling kit following manufacturer’s protocol.

Gene expression data from PC3 cells treated with Wee1inhibitorII

RNA interference: siRNA (either an empty vector control or a construct targeting the intracellular domain of the cadherin-11 wild type isoform) is stably expressed in MDA-MB-231 breast cancer cells.

Cells were maintained in DMEM containing 5% fetal bovine serum and 1mg/ml hygromycin for stable selection, and grown in a humid 5% CO2 incubator at 37 degrees C.

Performed by Microarray Shared Resources Core at Georgetown University Medical Center (please contact for further information).

Seven U133A Affymtrix GeneChip arrays were run in this study. Three of these were hybridized with RNA prior to treatment, while the remaining four were hybridized with treated RNA (gene knockout). Our data analysis began with preprocessing of the probe-level Affymetrix data (.cel files). To accomplish this, we applied low-level analysis methods that have been recently optimized to perform better than those provided by the Affymetrix’s software, MicroArray Suite (MAS 5.0). Note that Affymetrix data preprocessing involves three major steps: i) background adjustment to minimize the effect of non-specific binding and optical noise, ii) normalization to ensure that the measurements from different arrays are comparable; and iii) summarization to obtain an expression value for a probeset by combining multiple probe intensities. Recent studies have shown that the performance of MAS 5.0 in accomplishing the above three preprocessing steps is suboptimal and new approaches have been proposed (Bolstad, 2004).
For background adjustment, Irizarry et al. (2003) proposed a robust multi-array analysis (RMA) method that employs the perfect match probe data only. RMA estimates background based on a convolution model that is motivated by the distribution of probe intensities (Bolstad et al., 2003). It models the observed intensity as the sum of a signal and a background component, S = X + Y, where X and Y denote the signal and the background, respectively. The model assumes that X and Y are independent with X following an exponential distribution and Y a normal distribution truncated at 0, i.e. Y ≥ 0. The corrected probe intensities is estimated as E(X | S = s).
Normalization methods such as quantile and cyclic loess use information from across all arrays to produce the normalization. For example, quantile normalization uses this approach to give the same distribution to each array. These methods have been shown to outsmart the baseline methods such as MAS 5.0’s scaling method that select one array to represent the typical array and all other arrays are scaled to have the same mean intensity as this array.
Several methods of summarization procedures have been used including single-chip methods (e.g. averages and robust averages) and multi-chip models such as the model-based expression index (MBEI) (Li and Wong, 2001), Tukey's median polish, and the robust multi-array average (Irrizary et al., 2003).
In our low-level analysis, we used RMA for background adjustment, quantile method for normalization, and a robust multi-array average for summarization. These methods have provided better performance than MAS 5.0 and MBEI in detecting known levels of differential expression using spike-in Affymetrix data (Irizarry et al., 2003; Bolstad, 2004). They are implemented in several statistical tools including Bioconductor and BRB-ArrayTools (NCI, Bethesda, MD).
We analyzed the preprocessed data to identify those that were differentially expressed between the untreated and treated groups. The random variance model implemented in BRB-ArrayTools was used for this analysis. The random-variance t-test is an improvement over the standard separate t-test as it permits sharing information among genes about within-class variation without assuming that all genes have the same variance (Wright and Simon, 2003). Probesets were considered statistically significant if their p-value was less than 0.001. A stringent significance threshold was used to limit the number of false positive findings. With this threshold, 28 probesets were found statistically significant (p<0.001). A less stringent significance threshold of p<0.01 produced 236 differentially expressed probesets.
Furthermore, we performed statistical analysis to determine which gene ontology (GO) categories were differentially expressed between the untreated and treated groups. This was performed using a functional class scoring analysis as described by Pavlidis et al. (2004). For each gene in a GO class, the p value for comparing treated versus untreated groups samples was computed. The set of p values for a class was summarized by two summary statistics: (i) The LS summary is the average log p values for the genes in that class and (ii) the KS summary is the Kolmogorov-Smirnov statistic computed on the p values for the genes in that class. The statistical significance of the GO class containing n genes represented on the array was evaluated by computing the empirical distribution of the above two summary statistics in random samples of n genes. We considered a GO category significantly differentially regulated if either significance level was less than 0.005. We considered all GO categories with between 5 and 100 genes represented on the array. Some of the categories were overlapping. 92 GO categories are significant at the 0.005 level of the LS permutation test or KS permutation test. Functional class scoring is a more powerful method of identifying differentially expressed gene classes than the more common over-representation analysis or annotation of gene lists based on individually analyzed genes. The functional class scoring analysis for Gene Ontology classes was performed using BRB-ArrayTools.

Trizol/RNeasy hybrid protocol from Affymetrix was used to extract total RNA from these samples.  Briefly, cells were washed with PBS, resuspended in 1ml of Trizol for 5 minutes at RT, then scraped into a 1.5 ml Eppendorf tube.  200ul of chloroform was added to each sample, shaken vigorously for 15 seconds, allowed to sit for 2-3 minutes prior to spinning at 12,000xg for 15 minutes at 4 degrees C.  Aqueous phase was very carefully removed so as not to disturb any of the aqueous/organic interface and placed into a fresh tube.  An equal amount of cold 70% EtOH was added and mixed with aqueous solution.  Sample was loaded into RNeasy column (Qiagen Mini Kit) and processed according to their protocol (washes, then spins, with RWI and RPE buffers, prior to elution of RNA using RNase-free H2O).

Fragmented cRNA was analyzed for quality and given to the Microarray Shared Resources Core at Georgetown University Medical Center for hybridization to Affymetrix U133A gene chips (please contact for further information).

Enzo BioArray High Yield RNA Transcript Labeling Kit (Affymetrix) was used for generating labeled cRNA.  Briefly, template cDNA (assessed for quality and quantitated) was mixed very carefully with kit reagents to include ddH2O, HY buffer, Biotin-labeled ribonucleotides, DTT, RNase inhibitor mix, and T7 RNA polymerase.  The mixed contents were incubated in 37 degree C water bath for 4-5 hours with contents mixed gently every 30-45 minutes.  cRNA was cleaned-up and fragmented according to protocol using the GeneChip Sample Cleanup Module.

This study involved seven arrays (3 control, 4 treated) to assess genetic differences in breast cancer cells when cadherin-11 was stably depleted.  Cadherin-11 expression is associated with tumor progression and metastasis in various cancers, including basal-like breast carcinoma and advanced prostate cancer, and invasive cell lines, yet is absent in normal epithelium.  Cadherin-11 attenuation in aggressive breast and prostate cancer cells results in marked decreases in proliferation, migration, and invasion.  Cadherin-11 depletion in MDA-231 cells prevents tumor growth in mice and alters gene expression and survival outcome associated with poor prognosis malignancies, as observed through publically available data mining.  This study was aimed at uncovering possible mechanisms associated with these facts.

MDA-MB-231 breast cancer cells stably expressing empty vector control siRNA (RNAi 1B)

Cadherin-11 wt pooled stable knockdown cells (RNAi 4A)

Depletion of Cadherin-11 in MDA-MB-231 breast cancer cells

MDA-MB-231 breast cancer cells;cadherin-11 knockdown;FRAG.cRNA-4A

male;grape extract (B);12 months;Isolated peripheral blood mononuclear cells (PBMCs)

Isolated PBMCs from diabetic male patient_Grape extract group_12 months

RES-enriched Grape extract group, Time 0 (basal), patient number 13

male;resveratrol-enriched grape extract (C);day 0 (basal);Isolated peripheral blood mononuclear cells (PBMCs)

Isolated PBMCs from diabetic male patient_RES-enriched Grape extract_basal expression level

RES-enriched Grape extract group, Time 0 (basal), patient number 41

RES-enriched Grape extract group, Time 0 (basal), patient number 51

RES-enriched Grape extract group, Time 0 (basal), patient number 22

RES-enriched Grape extract group, Time 0 (basal), patient number 28

RES-enriched Grape extract group, Time 0 (basal), patient number 62

male;resveratrol-enriched grape extract (C);6 months;Isolated peripheral blood mononuclear cells (PBMCs)

Isolated PBMCs from diabetic male patient_RES-enriched Grape extract_6 months

C57BL/10J, Gender: Male, Age: 2 months, Tissue: Gastrocnemius Muscle, Deficient in Dystrophin

C57BL/6J, Gender: Male, Age: 2 months, Tissue: Gastrocnemius Muscle

C57BL/6J, Gender: Male, Age: 2 months, Tissue: Gastrocnemius Muscle, Galgt2 Transgenic

Cells were treated with Cas II-gly in 6-well microplates by 6h. In order to diminish biological variability, pools of 3 wells were made and combined into a single sample before proceeding to chip hybridization.

HeLa cells were mantained at room temperature in 5% CO2 under sterile conditions in  DMEM, Sigma),  supplemented with 10% fetal bovine serum (Sigma).

Scanning procedure was carried out as described by Affymetrix, Santa Clara.

Data pre-processing was performed by using the affy library in BioConductor running under [R].

Hybridization to Affymetrix U133plus2 GeneChips, staining and washing were carried out as described (Affymetrix, Santa Clara).

Biotinylated cRNA were prepared according to Affymetrix, Santa Clara CA Inc. protocol from 400 ng total RNA.

Gene expression data from HeLa cells treated with Cas-II-gly.
Cas_II-gly-3

CONTROL MYOTUBES
C2C12 mouse myoblasts (American Type Culture Collection, Manassas, VA) were maintained in growth medium (DMEM supplemented with 10% Fetal Bovine serum, Invitrogen Corporation, Carlsbad, CA) in 5% CO2.  Cells were plated at a density of 40-50% in 100mm dishes.  When cells reached ~90% confluency 24 hours later, they were switched to differentiation media (DMEM containing 2% horse serum; GIBCO, Invitrogen Corporation, Carlsbad, CA) which was subsequently changed every 48 hours. All cells were allowed to differentiate for 4 days with feeding every two days (day 0, 2, and 4).  Beginning at day 4, control cells were re-fed every 48 hours whereas experimental cells were not re-fed.  After an additional 4 days (8 days post differentiation), cells were harvested and total RNA was isolated from control and "starved" (non re-fed cells)
Keywords = skeletal muscle
Keywords = atrophy

Cas_II-gly-1

Cas_II-gly-2

Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V4.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.

Over the span of four days, embryoid bodies were treated for 12h with DMSO or ATRA (5 mikromol final concentration).

mESCs (siSCR and siPRMT1) were cultured as described in the article. ES medium contained 15% ES qualified FBS.  For induction of EB formation mES cells were aggregated in 100-mm bacteriological dishes (Greiner) at a specific density (4x10^6 cells/ 15 ml) in the abscence of LIF.

D3;scrambled sequence control (siSCR);undifferentiated embryonic stem cells

D3;scrambled sequence control (siSCR);4d_old aggregated embrioid bodies

D3;scrambled sequence control (siSCR);4d_old aggregated embrioid bodies;DMSO for 12hr

tissue: Epithelial cells were collected by bronchial brushing and cultured.
media: For culture, cells were washed once in RPMI-1640 media and the cell pellet resuspended in bronchial epithelial basal media (BEBM, Clonetics, CA) supplemented with bovine pituitary extract (50 mM), insulin (5 mM), hydrocortisone (0.5 mM), gentamicin (0.001%, v/v), amphotericin B (0.0005%, v/v), retinoic acid (0.1 µM), transferrin (10 mM), triiodothyronine (6.5 µM), epinephrine (6.5 µM) and human recombinant epidermal growth factor (EGF: 0.5 µM).
plating: The plate was incubated for 20 minutes (37C, 5% CO2) to allow the macrophages to adhere. The suspended epithelial cells were aspirated from the plate, and the macrophages removed using trypsin (0.25%) for subsequent analysis.
passage: The cells were seeded into a culture vessel (25 cm2 growth surface area) pre-coated with a mixture of fibronectin, collagen and bovine serum albumin, and maintained at 37C in a humidified incubator. Twenty-four hours post-isolation, unattached cells were collected. These cells were reseeded into the same culture vessel, with fresh media containing Ultroser G (2% v/v; BioSepra, CA), a serum substitute. The collection and reseeding of viable unattached cells was repeated at both 48 and 72 hours post isolation. Subsequent cultures were fed every second day and were usually passaged every 13–16 days.

RTotal RNA was extracted from epithelial cells using the QIAGEN RNeasy kit (Vic, Australia).

For microarray hybridization, RNA was processed for hybridization to Affymetrix GeneChip® Human HG-U133A Arrays according to the manufacturer’s instructions.

Male;25;12h;6.6;control;superior temporal cortex (Brodmann Area 22, BA22)

D3;scrambled sequence control (siSCR);4d_old aggregated embrioid bodies;ATRA (5 mikromol final conc.) for 12hr

GeneChips were scanned using Affymetrix GeneChip Scanner 3000 (GCS3000)

The data were analyzed with Affymetrix Expression Cosole (v.1.1). The normalization used in RMA is quantile normalization.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA

(BALB/c x C57BL/6J) F1 obtained by breeding heterozygote mice(+/-) with a C57BL/6J and BALB/cA background;Shn2 deficient;adult;male;hippocampus

MEFs were infected with adenoviral Cre to activate K-ras and delete Wt1

A mouse colonic epithelial cell line, MCE301, derived from transgenic mice harboring a temperature-sensitive simian virus 40 large T-antigen was used. MCE301 cells were treated with 2 mM sodium butyrate (SB) for 12 h.

A mouse colonic epithelial cell line, MCE301, derived from transgenic mice harboring a temperature-sensitive simian virus 40 large T-antigen was used. MCE301 cells were treated with 2 mM sodium butyrate (SB) for 24 h.

A mouse colonic epithelial cell line, MCE301, derived from transgenic mice harboring a temperature-sensitive simian virus 40 large T-antigen was used. MCE301 cells were treated with 2 mM sodium butyrate (SB) for 0 h.

A mouse colonic epithelial cell line, MCE301, derived from transgenic mice harboring a temperature-sensitive simian virus 40 large T-antigen was used. MCE301 cells were treated with 2 mM sodium butyrate (SB) for 6 h.

decitabine treated 48h
3237_H1299_0.3uM-Dac_2.CHP
H1299 0.3D
3237_H1299_0.3uM-Dac_2.CEL

3238_H1299_1uM-Dac_1.CHP
H1299 1D
3238_H1299_1uM-Dac_1.CEL

3229_H1299_0.3uM-Aza_2.CHP
H1299 0.3A
3229_H1299_0.3uM-Aza_2.CEL

3230_H1299_1uM-Aza_1.CHP
H1299 1A
3230_H1299_1uM-Aza_1.CEL

DMSO treated
3225_H1299_VEH_2.CHP
H1299 VEH
3225_H1299_VEH_2.CEL

3228_H1299_0.3uM-Aza_1.CHP
H1299 0.3A
3228_H1299_0.3uM-Aza_1.CEL

3233_H1299_3uM-Aza_2.CHP
H1299 3A
3233_H1299_3uM-Aza_2.CEL

3236_H1299_0.3uM-Dac_1.CHP
H1299 0.3D
3236_H1299_0.3uM-Dac_1.CEL

3231_H1299_1uM-Aza_2.CHP
H1299 1A
3231_H1299_1uM-Aza_2.CEL

3232_H1299_3uM-Aza_1.CHP
H1299 3A
3232_H1299_3uM-Aza_1.CEL

CEL files were imported into RMA Express version 1.0 for background correction, quantile normalization and log transformation.

Samples were processed at the Case Western Reserve University Cancer Center Gene Expression Array Core Facility

Cells were transfected with human precursor mir-221 or negative control oligonucleotides using lipofectamin following the manufacturer’s instructions (Apllied Biosystems). The optimal miRNA oligonucleotide concentrations were titrated for optimal transfection results. In all experiments the final miRNA concentration was 10 nmol/L.

PC-3 cells were purchased from the American Type Culture Collection (ATCC) and were grown in medium as indicated by ATCC instructions.

GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000

The data were analyzed with Bioconductor packages (under R) and vsn as normalization method using perfect match only

RNA was isolated using the Rneasy Mini Kit from Qiagen (including Dnase digest)

Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on HG U 133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station_450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (GeneChip® Expression Analysis Manual, Affymetrix).

Cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with Ham’s nutrient mixture F-12 with 1% ITS+Premix and 2.5% Nu-Serum at 37°C in a 5% CO2 atmosphere.

Probe arrays were scanned once at 570 nm using an Affymetrix GeneChip scanner (Affymetrix, Santa Clara, California, USA) and the fluorescence intensity of the scanned image registered in CEL intensity files.

DNA-Chip Analyser (dChip) software (Li and Wong 2001 PNAS, 98:31) was used to automatically select probes, detect outliers/artefacts, normalise the fluorescence intensity over multiple arrays and calculate model-based expression values from CEL intensity files using the PM/MM values.

After treatment, T-RNA was extracted using QIAGEN RNeasy Mini kit according to the manufacturer’s instructions. T-RNA concentration was determined by measuring the absorbance of a 1:100 diluted solution at 260 nm in a GeneQuant II RNA/DNA calculator spectrophotometer (Pharmacia Biotech, Cambridge, UK), assuming that if A260 = 1, the content equals 40 µg/ml of RNA. T-RNA integrity was investigated in the Agilent 2100 Bioanalyzer, by assessing size distribution of the T-RNA using the Eukaryote Total RNA Nano assay (Agilent Technologies, Palo Alto, California, USA), according to the manufacturer’s specifications.

Fragmented, labelled cRNA (15 µg) was added to 15 µl of 2× hybridisation buffer (final 1× concentration is 100 mM 2-Morpholinoethanesulfonic acid (MES), 1 M [Na+], 20 mM EDTA, 0.01% Tween 20), 3 µl of 10 mg/ml herring sperm DNA (Promega, Southampton, UK), 3 µl of 50 mg/ml acetylated bovine serum albumin (BSA) (Invitrogen, Paisley, UK) and 30 µl of DMSO. The hybridisation buffer was spiked with 5 µl of 3nM control oligonucleotide B2 and 15 µl of the 20× eukaryotic cRNA controls bioB, bioC, bioD and cre (final concentration is 1.5, 5, 25 and 100 pM, respectively), all controls were from the GeneChip Eukaryotic Hybridisation Control Kit (Affymetrix, Santa Clara, California, USA). The hybridisation mixture was heated to 99 °C for 5 minutes, cooled to 45 °C for 5 minutes and centrifuged at 14,000 × g for 5 minutes to remove any insoluble material from the hybridisation mixture. Each hybridisation mixture containing 10 µg of fragmented biotin-labelled cRNA (200 µl) was hybridised to a pre-wetted (with hybridisation buffer) GeneChip Human U133 Plus 2.0 array (Affymetrix, Santa Clara, California, USA) for 16 hours at 45 °C with permanent rotation at 60 rpm in a Hybridisation Oven 640 (Affymetrix, Santa Clara, California, USA). Probe array washing and staining were performed according to EukGE-WS2v5 Gene Chip protocol (Affymetrix, Santa Clara, California, USA) in the Fluidics Station 400 (Affymetrix, Santa Clara, California, USA). Briefly, arrays were washed in a non-stringent wash buffer containing 6× SSPE (0.9 M NaCl, 0.06 M NaH2PO4, 0.006 M EDTA) (Cambrex, Berkshire, UK) and 0.01% Tween-20 at 25 °C, then with a stringent buffer containing 100 mM MES, 0.1 M [Na+], 0.01% Tween-20 at 50 °C. Following this wash, the probe arrays were stained with a solution containing 10 µg/ml of streptavidin-phycoerythrin (SAPE) conjugate (Invitrogen, Paisley, UK) and 2 mg/ml acetylated BSA (Invitrogen, Paisley, UK) dissolved in a buffer containing 100 mM MES, 1 M [Na+], 0.05% Tween 20. Following staining, the probe arrays were exposed to 3 µg/ml goat biotinylated anti-streptavidin antibody (Vector laboratories, Peterborough, UK) in a buffer as above containing 0.1 mg/ml normal goat IgG (Sigma, Poole, UK) and 2 mg/ml acetylated BSA (Invitrogen, Paisley, UK). Finally, the probe arrays were re-stained with SAPE as described above.

The One-cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, California, USA) was used to convert the mRNA in the T-RNA samples into ds-cDNA by reverse transcription with an oligo-dT primer. Initially, first strand cDNA was formed in a reaction containing 6 g of T-RNA, 2 µl of diluted poly-A RNA controls, 2 µl of 50 µM T7-oligo (dT) primer and RNase-free water to a final volume of 12 µl. This mixture was incubated at 70 °C for 10 minutes and chilled at 4 °C for 5 minutes, after which the following reagents were added: 4 µl of first strand reaction mix, 2 µl of 100 mM dithiothreitol (DTT) and 1 µl of 10 mM dNTP. Tubes were placed at 42 °C for 2 minutes to equilibrate the temperature prior to the addition of Superscript II reverse transcriptase (1µl) and further incubated for 1 hour at 42 °C. The second strand cDNA synthesis was performed by adding, to the solution containing the first strand cDNA, 3 µl of 10mM dNTP, 1 µl of E. coli DNA ligase, 4 µl of E. coli DNA polymerase I, 1 µl of E. coli RNase H, 30 µl of second strand reaction buffer and 91 µl of RNase-free water. The reaction was incubated for 2 hours at 16 °C. Following this incubation, 2 µl of T4 DNA polymerase were added and incubated for 5 minutes at 16 °C. The reaction was stopped by the addition of 10 µl of 0.5 M EDTA. The resulting ds-cDNA was cleaned up using the Sample Cleanup Module (Affymetrix, Santa Clara, California, USA), according to the manufacturer’s instructions.
Synthesis of biotin labelled cRNA was performed by in vitro transcription using the IVT labelling kit (Affymetrix, Santa Clara, California, USA). Briefly, the ds-cDNA synthesised above (12 µl) was used as template, and added to 4 µl of 10× IVT labelling buffer, 12 µl of Labeling NTP mix, 4 µl of IVT Labeling Enzyme mix and 8 µl of RNase-free water. The reaction was incubated at 37 °C for 16 hours. This step was followed by cRNA cleanup with the Affymetrix Sample Cleanup Module, according to the manufacturer’s specifications. Quantification of cRNA was performed in a spectrophotometer by measuring the absorbance at 260 nm and the adjusted cRNA yield calculated taking into account the carryover of unlabelled T-RNA by the following formula: adjusted cRNA yield = RNAm – (T-RNAi)(y), where RNAm is the amount of cRNA measured after the IVT reaction, T-RNAi is the starting amount of T-RNA and y is the fraction of cDNA used in the IVT reaction. Size distribution of the labelled transcripts was investigated in the Agilent 2100 Bioanalyzer using the Eukaryote Total RNA Nano assay (Agilent Technologies, Palo Alto, California, USA). The appropriate amount of cRNA (20 µg) was fragmented by adding 8 µl of the fragmentation buffer provided in the Sample Cleanup Module and RNase-free water to a final volume of 40 µl, and incubating at 94 °C for 35 minutes. Fragmentation efficiency was confirmed by analysing the size distribution of the fragmented, labelled transcripts in the Agilent 2100 Bioanalyzer using the Eukaryote Total RNA Nano assay (Agilent Technologies, Palo Alto, California, USA).

Cells were exposed to 10 µM of 2-OH-BDE47 dissolved in 0.1% dimethyl sulfoxide (DMSO) for 24 hours.

All experiments were carried out in accordance with the animal care guidelines of the University of Kiel (acceptance no.: V 742-72 241.121-3 (20-2/04) and (76-7/00)). Mice were maintained in a 12-h light-dark cycle under standard conditions and were provided with food and water ad libitum. Procedures involving animals and their care were conducted in conformance with national and international laws and policies. Blood was drawn from the mice by cardiac puncture under general anesthesia.

Image aquisition was performed according to the standard Affymetrix protocol for Mouse Gene 1.0 arrays using the AGCC (Affymetrix) software.

Data was processed using the AGCC (Affymetrix) software and normalized using the RMA method. Signals, that were not stronger than the 95th percentile of all intron probes on the array were excluded from further analysis.
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.r4.mps

Qiagen RNA extraction (Rneasy) according to the manufacturers guidelines

Hybridization was performed according to the standard Affymetrix protocol for Mouse Gene 1.0 arrays, using the AGCC (Affymetrix) software.

Biotinylated cRNA was prepared according to the standard Affymetrix protocol for Mouse Gene 1.0 arrays.

Control or Wnt3A conditioned medium was added to the cells and incubated for 4, 7 or 9 hours before RNA extraction.

HEK293T cells are seeded on 6-well plates and transfected with control/human TNIK 15nM siRNA for 72 hours.

Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

Total RNA was extracted using RNeasy mini kit (Qiagen) following manufacturer's instructions.

The synthesized cRNA was then purified with RNeasy mini kit (Qiagen). 825ng of the corresponding Cy3 and Cy5 cRNA was fragmentated at 60°C for 30 min in the presence of blocking agent and fragmentation buffer (Agilent), then combined with 55ul 2X hybridization buffer (Agilent) and applied to 4X44k human expression microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

2µg of total RNA were primed with 1.2 µl of T7 promoter primer at 65°C for 10 min together with control spike A/B, then reversed transcribed at 40°C for 2hrs in the presence of MMLV RTase (Agilent), and dNTP mix. It was then followed by the cRNA transcription at 40°C for 2hrs in the presence of T7 RNA polymerase, inorganic pyrophosphatase, NTP mix, DTT, PEG and Cy3/Cy5-labeled-CTP.

Sample 2
Dye swap of 1. 293T cells transfected with si-control, induced with Wnt3A vs control medium for 4 hours.

Sample 3
293T cells transfected with si-control, induced with Wnt3A vs control medium for 7 hours.

Sample 1
293T cells transfected with si-control, induced with Wnt3A vs control medium for 4 hours.

Sample 4
Dye swap of 3. 293T cells transfected with si-control, induced with Wnt3A vs control medium for 7 hours.

Sample 5
293T cells transfected with si-control, induced with Wnt3A vs control medium for 9 hours.

Female;68;6h;6.4;control;superior temporal cortex (Brodmann Area 22, BA22)

Pineal tissues collected during the daytime period.

This is WT sample number three of three.

Cells were treated for 4 hours or 24 hours with 1 micromnolar dexamethasone dissolved in ethanol

Primary cultured human airway smoothmuscle were grown in Hams/F12 with 10% FBS

raw signal intensities were extracted with Feature Extraction v9.1 software

RNA was extracted using Trizol frolloed by purification with Invitrogne midilink columns

Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays for 14 hours

RNA was labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol

human airway smooth muscle gene expression, 24 hours dexamethasone

no history of asthma;smooth muscle cells;dexamethasone for 24 hr

cultured human airway smooth muscle, 24 hour dex treatment, replicate 3

cultured human airway smooth muscle, 24 hour dex treatment, replicate 2

human airway smooth muscle gene expression, 4 hours dexamethasone

cultured human airway smooth muscle, 4 hour dex treatment, replicate 2

cultured human airway smooth muscle, 4 hour dex treatment, replicate 1

cultured human airway smooth muscle, 24 hour dex treatment, replicate 1

cultured human airway smooth muscle, 4 hour dex treatment, replicate 3

Primary hepatocytes isolated from Donor 4 treated with Wy14643 for 6h

Primary hepatocytes isolated from Donor 3 treated with DMSO for 24h

Primary hepatocytes isolated from Donor 4 treated with Wy14643 for 24h

Primary hepatocytes isolated from Donor 4 treated with DMSO for 6h

Primary hepatocytes isolated from Donor 5 treated with Wy14643 for 6h

Primary hepatocytes isolated from Donor 4 treated with DMSO for 24h

Primary hepatocytes isolated from Donor 5 treated with Wy14643 for 24h

Primary hepatocytes isolated from Donor 5 treated with DMSO for 6h

Primary hepatocytes isolated from Donor 6 treated with Wy14643 for 6h

Primary hepatocytes isolated from Donor 5 treated with DMSO for 24h

European-American (EA);Female;Systemic lupus erythematosus (SLE) patient;Peripheral blood;CD4-FITC;CD4 positive T cells

CD11c+ dendritic cells were purified from the spleen by flow cytometry and then lyzed in RNA extraction buffer.

Wild-type and Map3k7-CreER mice were treated with tamoxifen in vivo for 3 days to induce deletion of Map3k7 (TAK1).

Signals on arrays were summarized using the RMA method as implemented in the Affymetrix Expression Console software v1.1

RNA was extracted using the Qiagen RNeasy micro kit according to the manufacturer's recommended protocol.

5 micrograms of biotin-labeled cRNA was hybridized to an Affymetrix HT_MG-430_PM array using the Affymetrix GeneTitan system

100 ng of total RNA was converted to biotin-labeled cRNA using the Affymetrix 3'-IVT Express protocol as per the manufacturer's recommendations

splenic CD11c+ dendritic cells;C57Bl/6strain: C57Bl/6;Map3k7CreER;tamoxifen

Gene expression of mouse (ATF6aKO) colon after 3days treatment of 3% DSS

C57BL/6, ADNP+/- Gender: mixed Age:E9 Tissue: whole embryonic body;Activity-dependent neuroprotective protein: a novel gene essential for brain formation.;83-90.;12888219 [PubMed - indexed for MEDLINE]

Gene expression of mouse (ATF6bKO) colon after 3days treatment of 3% DSS

Placental biopsies were obtained during Caesarean section from early onset Preeclampsia. A mixture of 3 placentas from normal subjects were used for a template control.

Placental tissue from early onset Preeclampsia;A mixture of placental tissue from normal pregnancy

Gene expression at 24h after treatment with IFNg in STAT1-KO mouse neurons

Gene expression at 6h after treatment with IFNg in STAT1-KO mouse neurons

Gene expression at 3h after treatment with IFNg in STAT1-KO mouse neurons

Samples were processed by RMA normalization and log2-scaled expression values were generated through the WebArray tool (URL: http://www.webarraydb.org/webarray/index.html) with default options. p-values for significance testing were adjusted using the SPLOSH (Spacings LOESS Histogram) method as implemented by WebArray.

Embryo was harvested at embryonic day 15.5 of development. Total RNA was extracted with the Qiagen RNeasy Plus Mini Kit according to manufacturer's protocol from anterior or posterior palatal tissue, from either mutant or control mice as designated.

Whole genome transcriptome profile of murine posterior palatal tissue, collected at E15.5, from control mice.

Sample name: TM-279-08R

IS patient;male;69;65;Mirandela;Hypertension, diabetes, hypercholesterolemia;ever drinker

IS patient;male;74;73;Mirandela;Hypertension, hypercholesterolemia;ever drinker

IS patient;female;54;49;Vila-Real;Hypertension, diabetes, hypercholesterolemia;ever drinker

IS patient;female;49;48;Porto;Diabetes, hypercholesterolemia;ever smoker, ever drinker

IS patient;male;71;65;Porto;Hypertension;ever smoker, ever drinker

IS patient;male;54;53;Mirandela;Diabetes, hypercholesterolemia;ever drinker

A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factor can be identified. This entry corresponds to the RNA isolated from uninduced INS-1 cell line #1 containing hepatocyte nuclear factor-4a2 (HNF4a2).
Keywords = HNF4a

A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factor can be identified. This entry corresponds to the RNA isolated from tet-induced INS-1 cell line #1 containing hepatocyte nuclear factor-4a2 (HNF4a2).

A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and induced cells, target genes of introduced transcription factor can be identified. This entry corresponds to the RNA isolated from uninduced INS-1 cell line #2 containing hepatocyte nuclear factor-4a2 (HNF4a2).
Keywords = b-cell

A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and induced cells, target genes of introduced transcription factor can be identified. This entry corresponds to the RNA isolated from tet-induced INS-1 cell line #2 containing hepatocyte nuclear factor-4a2 (HNF4a2).

A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and induced cells, target genes of introduced transcription factor can be identified. This entry corresponds to the RNA isolated from uninduced INS-1 cell line #1 containing hepatocyte nuclear factor-6 (HNF6; onecut1).

A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and induced cells, target genes of introduced transcription factor can be identified. This entry corresponds to the RNA isolated from tet-induced INS1 cell line #1 containing hepatocyte nuclear factor-6 (HNF6; onecut1).

Clinical information: Sample.ID=633;Tumor.type=D;Size=2.7;Grade=3;Nodes=0/11;ER=Pos;PR=Pos;HER2=Neg;Age=61;DFS=20;Status=recur

Clinical information: Sample.ID=638;Tumor.type=D;Size=2;Grade=2;Nodes=1/24;ER=Pos;PR=Pos;HER2=Neg;Age=67;DFS=148;Status=non-recur

6816115008_G

Cells were grown in DMEM/F12 plus 10%FBS in 5%CO2 at 37C. Cells were trypsinized and harvested when in log-growth phase.

Scanning was performed at the core technician at the microarry core facility at the University of Kentucky School of Medicine.

Data processing was performed at the core technician at the microarry core facility at the University of Kentucky School of Medicine.

Total RNA was extracted from cells using the Qiagen RNA purification kit following the manfacturer's protocol.

Hybridization was performed at the core technician at the microarry core facility at the University of Kentucky School of Medicine.

Labeling was performed at the core technician at the microarry core facility at the University of Kentucky School of Medicine.

Gene expression array of less metastatic breast tumor cell line.

total RNA from biosource CC#10S

total RNA from biosource CC#6S

total RNA from biosource CC#2S

total RNA from biosource CC#35

total RNA from biosource CC#40

Gene expression data from ERα-positive breast tumor with PIK3CA mutation

primary unilateral non-metastatic postmenopausal ERα-positive breast tumor;woman;46 years

primary unilateral non-metastatic postmenopausal ERα-positive breast tumor;woman;73 years

primary unilateral non-metastatic postmenopausal ERα-positive breast tumor;woman;53 years

54;Adenocarcinoma of breast, ductal, recurrent;G3;IIA;T2;N0;0;0;13;0;0

57;Adenocarcinoma of breast, ductal;G2;IIA;T2;N0 (i-);1;1;35;0;0

Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

RNA was prepared using the Rneasy lipid tissue mini kit(Quiagen).

1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

The BeadChips were scanned according to the protocol described in the Illumina Whole Genome Gene Expression for BeadStation Manual v3.2, Revision A using scanning software BeadScan 3.5.31.

Variance stabilization normalization was applied. The statistical software R and Bioconductor libraries lumi and vsn were used.

Total RNA was isolated in accordance with Qiagen protocols for the extraction of PAXgene tube-treated whole blood.

Synthesis, amplification and purification of anti-sense RNA was performed using 300 ng of enriched mRNA per sample and  the Illumina TotalPrep RNA Amplification Kit (Ambion/Applied Biosystems) following the Illumina Sentrix Array Matrix expression protocol.

Male Sprague-Dawley rats weighing 280-300 g were anesthetized with 1.75% to 2.5% isofluorane and instrumented with two arterial catheters, one externalized for blood withdrawal and the other (not externalized) attached to the Data Sciences International (DSI) PhysioTel (St. Paul, MN, model C50-PXT) monitoring device placed intraperitoneally and used in monitoring blood pressure, temperature, and electrocardiogram data via telemetry.  After 7 to 10 days of recovery, and only after the animals had begun to gain weight, the experiment was performed.  At the beginning of hemorrhage (H), blood was withdrawn manually through the externalized catheter with 1-ml syringes at l ml/min.  Total blood volume was estimated to be 6.5% of the body weight and 40% of this (2.6 ml/100g) was removed to effect the hemorrhage.
Keywords = rat lung hemorrhage

Pooled RNA of equal amounts from 10 organs (liver, lung, kidney, spleen, heart, skeletal muscle, skin, jejunum, and brain) of untreated control animals

MO-B10-WT 7
Gene expression data from MeV-infected NT mice brain at 10 d.p.i.

C57BL/6;non-transgenic;brain (right cerebral hemisphere);12 days;measles virus (MeV);10

MO-B10-WT 8

MO-B10-WT 5

MO-B10-WT 6

MO-B10-WT 1
Gene expression data from MeV-infected NT mice brain at 5 d.p.i.

C57BL/6;non-transgenic;brain (right cerebral hemisphere);7 days;measles virus (MeV);5

MO-B10-WT 2

Data were obtained and processed with the Agilent Feature Extraction Software (v9.5). The resulting data were imported into Rosetta Resolver (v7.0) and normalized intensities were exported.

Neuroserpin expression was induced in 'on' samples with 2 ug/ml doxycycline 48 hours before collection.  'off' samples remained untreated.

250,000 Cells per well were grown in six well plates for 72 hours.  The cells were cultured in DMEM supplemented with 10% v/v Tet-free approved FBS (Clontech), 200 µg/ml Geneticin and 100 µg/ml Hygromycin B (both selective antibiotics from Invitrogen, Paisley, UK), at 37°C and 5% v/v CO2 in a humidified incubator.

Raw data were pre-processed using R software (http://www.r-project.org) and the bioconductor (http://www.bioconductor.org) package lumi (Du et al., 2008).  Probes were removed from the data set where the Illimuna detection p-value was greater than 0.01.  The data were then transformed using the variance stabilisation transformation algorithm (VST) and normalised using the quantile normalisation method.  Differentially expressed genes for each condition (wild-type neuroserpin ‘on’ versus wild-type neuroserpin ‘off’, G392E neuroserpin ‘on’ versus G392E neuroserpin ‘off and Δ neuroserpin ‘on’ versus Δ neuroserpin ‘off’’) were identified by fitting linear models with the bioconductor R package limma (Smyth, 2004).  To account for multiple hypotheses testing, p-values were adjusted using the Benjamini & Hochberg False Discovery Rate (FDR) correction (Benjamini and Hochberg, 1995).  In order to assess the gene expression profiles at a pathway level, Gene Set Enrichment analysis (Subramanian et al., 2005) was performed on the normalised gene expression values for each group. Gene Set Enrichment analysis uses a priori defined gene sets to determine pathway differences between two phenotypic states.  Gene expression data is therefore evaluated at the pathway level rather than the single gene. Gene Set Enrichment analysis first ranks the genes according to their relative difference in gene expression.  The ranked list is then compared to gene sets (pathways) and an enrichment score (ES) is calculated for each gene.  When a gene is present in the gene set of interest, the running enrichment score is increased.  If the gene is absent the running enrichment score is decreased.  The enrichment statistic is the maximum deviation of the running enrichment score from zero.  Statistical significance is assessed by performing a permutation test procedure.  To account for the differences in gene set size, a normalised enrichment score (NES) is calculated.  Estimated significance levels are also adjusted for multiple hypothesis testing.  False Discovery Rate (FDR) is the estimated probability that a gene set with a given enrichment statistic represents a false-positive finding.  A total of 639 pathways (gene sets) were analysed from Kyoto Encyclopedia of Genes and Genomes, Reactome, and BioCarta databases (http://www.genome.jp/kegg/pathway.html, http://www.reactome.org/ and http://www.biocarta.com/genes/index.asp respectively). Gene sets containing less than 15 and greater than 500 genes were filtered out, along with gene sets containing no genes from the input data set.

Cells were collected by trypsinisation and pelleted at 700 g for 10 min at 4⁰C.  RNA was isolated with Tri Reagent (Sigma).  RNA amplification was performed using Ambion Total Prep kit (Ambion, UK)

Hybridization was carried out following the beadchip manufacturer's instructions (Illumina)

Sample was labelled with biotin as part of the Ambion Total Prep kit (Ambion, UK) protocol.

Standard Illumina iScan N240 scanning protocol
scan_setting: Direct Hyb

The data were quantile normalisation and background corrected using GenomeStudio software

Illumina®Totalprep-96RNA Amplification kit 4397949 RevC, (Modification of Amplification kit v 2.2)

K562 cell line was mock treated.  RNA was extracted using Trizol plus Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA and included suggested level of Affymetrix RNA spike controls.
Keywords = Human, leukemia, mock treated

K562 cell line treated for 24 hours with one micromolar imatinib. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA and included half the standard level of Affymetrix RNA spike in controls.

GBM sphere samples (GBM146, GBM157, and GBM 206) were treated with 1 µM Siomycin A or control (DMSO) for 24 hours

Cells derived from GBM surgical tissues (GBM146, GBM157, and GBM206) were established in Dr. Harley Kornblum’s laboratory at UCLA and were cultured as previously described

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and quantile normalization  as normalization method.

Total RNA was extracted using the RNeasy Mini Kit according to the manufacturer’s protocol (Qiagen).

A pool of two pure subsets of peripheral blood B cells (CD19+ CD3- CD4- CD8- CD16- CD56-), stringently sorted by flow cytometry, from two age and gender matched stage IV (American Joint Committee on Cancer) melanoma patients.;Pooled RNA from the total peripheral lymphocyte fraction from 20 healthy donors, used as a common reference.

Mice were produced and housed in a specific pathogen-free (SPF), AAALAC-certified barrier facility. Animals are housed in plastic 27 cm x 27 cm cages which are held in HEPA-ventilated cage racks (maximum of 7 animals per cage). Animals are also housed in half-cages (maximum of 3 animals). Cages, bedding (Sani-chip hardwood bedding) and food (Purina Lab Chow # 5010) are sterilized by autoclaving. Food and water (also sterilized) are provided ad libitum. The same food is used for all animals, including pregnant and nursing mothers and weaned pups. Bedding is changed once per week. A light-dark cycle of 12 hours is used (7 AM On, 7 PM Off). Temperature is maintained at 70°F, and humidity at 50%.

Arrays were scanned on a 3000 G7 scanner running  AGCC v3.2.4 software

The data from all expression arrays were normalized using the Affymetrix Expression Console software package, and expression values for all genes were generated using the built-in RMA algorithm.

Fragments of tissues in the range of 20-50 mg were removed from samples kept at -80°C, carefully weighed on dry ice, and homogenized in Trizol reagent (Invitrogen) according to the supplier's instructions. Two homogenization methods were used. In the first, the tissue was hand-ground to a powder using a plastic homogenizer (Fisher 02-542-09) chilled in liquid nitrogen, and the powder was vigorously vortexed with Trizol reagent at room temperature. In the second, the tissue fragment was homogenized directly in Trizol reagent in a Fisher PowerGen 125 motorized homogenizer at room temperature. Equal amounts of total RNA from 5 to 8 male animals were pooled to create a representative sample with a final concentration of 100 ng/ul. The same animals were used for the analysis of all tissues. The pooled RNA samples were converted to cRNA targets using the 3' IVT Express kit from Affymetrix, hybridized to Mouse 1.0 Gene ST arrays, and scanned on a 3000 G7 scanner, all according to the manufacturer’s protocols.

The Hybridization Wash Stain kit from Affymetrix was used for hybridization according to the manufacturer's protocols.

The WT amplification kit from Life Technologies and the WT terminal labeling kit from Affymetrix were used according to the manufacturer's protocols.

Cells were trypsinized, washed tree times with PBS and stored in -80 C.

Trypsin-2 overexpressing HSC-3 cells and control vector HSC-3 cells were cultured 48 h in a humid atmosphere of 5% CO2 and 95% air at 37°C in 1:1 DMEM (Lonza) and Ham’s Nutritient Mixture F-12 supplemented with 10% heat-inactivated fetal calf serum, 1 mM natrium pyruvate, 250 ng/ml fungizone (Invitrogen), 100 units/ml penicillin, 100 µg/ml streptomycin, 2 mM L-Glutamine and 0.4 ng/ml hydrocortisone (Sigma-Aldrich ).

MAS5-analysis was done to the data.  Scaling parameters: scale to all probe sets; TGT 100. Detection parameters: Alpha1 0.05, Alpha2 0.065, Tau 0.015.

RNA was extracted by Qiagen RNeasy mini kit according to the manufacturer's instruction.

Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Probe Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2007, Affymetrix).

HSC-3;human tongue squamous cell carcinoma;control vector (no trypsin-2 expression)

HSC-3;human tongue squamous cell carcinoma;overexpressing trypin-2

The pMSCV retroviral expression vector (Clonetech, Palo Alto, CA, USA) was utilized enforce the expression of Irf7 or empty plasmid in 4T1.2 cell line. These constructs were transfected into HEK-293 packaging cells using lipofectamine (Invitrogen, Carlsbad, CA, USA). Conditioned media was filtered and incubated with target 4T1.2 cells. 4T1.2 cells were then selected using puromycin, single cell cloned and multiple clones pooled. Stably transfected cells were cultured in α-MEM supplemented with 5% FCS and grown at 37 ºC in a humidified incubator with 5% CO2.

Slides were scanned immediately after washing on the Agilent DNA microarray scanner (G2505B) using one color scan settings for 4x44k array slides (scan area 61x21.6mm, scan resolution 5um, dye channel is set to Green and Extended Dynamic range selected at 100% and 10% Green PMT)

The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (protocol GE1-v1_95 and Grid: 014868_D_F_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

Total RNA was extracted using Qiagen RNeasy mini columns according to the manufacturers instructions.  The protocol includes an on-column DNAse digestion step.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer

1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent gene expression hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Quick Amp Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

BALB/c;4T1.2;pMSCV retroviral expression vector system with IRF7;IRF7;Mammary Tumour

Embryo was harvested at E13.5 and palatal mesenchyme cells were placed into culture. Total RNA was extracted with the Qiagen RNeasy Plus Mini Kit according to manufacturer's protocol from a culture of primary mouse embryonic palatal mesenchyme after undergoing 2 passages.

Whole genome transcriptome profile of cultured primary palatal mesenchyme cells, collected at E13.5 and cultured at P2, with a conditional inactivation of Tgfbr2 in the cranial neural crest.

C57BL/6J;Tgfbr2 fl/fl; Wnt1-Cre;Primary palate mesenchyme;E13.5  + P2

E13.5 Wnt1-Cre;Tgfbr2 Conditional Knockout Mouse Model Primary Palate Mesenchyme collected after 2 passages in culture

Whole genome transcriptome profile of cultured primary palatal mesenchyme cells, collected at E13.5 and cultured at P2, from control mice .

E13.5 Tgfbr2 Wildtype Mouse Model Primary Palate Mesenchyme collected after 2 passages in culture

SMhu140

SMhu139

SMhu138

SMhu137

SMhu136

SMhu135

SMhu134

SMhu133

SMhu142

SMhu141

CG
32 mg
72

CG
32 mg
72

CG
32 mg
0.5

CG
32 mg
0.5

RNA was extracted using the Qiagen RNeasy Midi Kit according to the manufacturer guidelines

Extraocular Muscle is Defined by a Fundamentally Distinct Gene Expression Profile

(BALB/c x C57BL/6J) F1 obtained by breeding heterozygote mice(+/-) with a C57BL/6J and BALB/cA background;wild type;adult;male;hippocampus

immortalized human mammary epithelial cell line treated with 0.01 mM of 5-Fluorouracil for 12 hours

immortalized human mammary epithelial cell line treated with 0.01 mM of 5-Fluorouracil for 36hours

breast cancer derived cell line treated with 3.0 mM of 5-Fluorouracil for 36hours

immortalized human mammary epithelial cell line treated with 0.5 uM of Doxorubicin for 12 hours

breast cancer derived cell line treated with 3.0 mM of 5-Fluorouracil for 12 hours

breast cancer derived cell line treated with 0.9 uM of Doxorubicin for 12 hours

breast cancer derived cell line treated with 0.4 uM of Doxorubicin for 36hours

immortalized human mammary epithelial cell line treated with 0.06 mM of 5-Fluorouracil for 36hours

T22;Mouse tumorgraft, cohort 0;Male;67;Clear-cell renal cell carcinoma;wild type;wild type;mutant

Gene expression profiling of mouse tumorgraft, cohort 0 of patient T22

Microarray data were normalized with Affymetrix Microarray Suite (MAS 5.0)

EYFP positive GMPs were sorted into RLT buffer (Qiagen, Venlo, the Netherlands). RNA was extracted with the RNeasy Micro Kit (Qiagen).

Cebpa-Cre;R26-LSL-Eyfp;Dicer1wt/fl/Dicer1fl/fl (donror), C57BL/6 (recipient);Dicer wild type;YFP-positive  granulocyte-macrophage progenitor

Cebpa-Cre;R26-LSL-Eyfp;Dicer1wt/fl/Dicer1fl/fl (donror), C57BL/6 (recipient);Dicer heterozygous deletion;YFP-positive  granulocyte-macrophage progenitor

Cebpa-Cre;R26-LSL-Eyfp;Dicer1wt/fl/Dicer1fl/fl (donror), C57BL/6 (recipient);Dicer null;YFP-positive  granulocyte-macrophage progenitor

Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=1 and B=0 (Non-acute rejection).

Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=1 and B=1 (Acute rejection).
One of two samples from the same patient, different visits.

Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=2 and B=0 (Acute rejection).

Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=2 and B=1 (Acute rejection).
One of two samples from the same patient, different visits

HL-60 cell line infected with GSK3A Construct 6 shRNA, biological rep1
Sample name: HL60_GSK3A_6-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A06_596738.CEL

HL-60 cell line infected with GSK3A Construct 5 shRNA, biological rep2
Sample name: HL60_GSK3A_5-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A10_596670.CEL

THP-1 cell line infected with scrambled control shRNA, biological rep1
Sample name: THP1_CTRL-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B01_596662.CEL

When cells were 80% confluent,  cells were transfected with the pcDNA3 (control) or the pcDNA3-Pit-1 overexpression vector for 48 hours.

MCF-7 cells were grown in DMEM with 10% of FBS,100 mU/mL penicillin, 100 μg/mL streptomycin, and 2 mM l-glutamine in a 5% CO2 atmosphere at 37°C.

For the microarray data analysis, Affymetrix CEL files from each of the two microarray hybridization experiments for the four conditions (pcDNA3, control, C1 and C2, and  pcDNA3-Pit-1 (+1 and +2) were imported into the dChip software (v.2010.01; Dana Farber Cancer Institute, Boston, MA). Normalization of all arrays was done against the array with median overall intensity.

Total RNA was extracted and purified using the PureLink Micro-to-Midi kit (Invitrogen).

The labeled RNA was fragmented and hybridized to human oligonucleotide arrays (HU 1.0 ST Array) using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640 and GeneChip Fluidics Station 450)

Double-stranded cDNA and biotinylated cRNA were synthesized using a T7-polyT primer and the BioArray RNA labeling kit (Enzo Life Sciences, Farmingdale, NY), respectively.

THP-1 cell line infected with GSK3B Construct 2 shRNA, biological rep2
Sample name: THP1_GSK3B_2-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B09_596702.CEL

THP-1 cell line infected with GSK3B Construct 2 shRNA, biological rep1
Sample name: THP1_GSK3B_2-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B04_596688.CEL

Using the affy package of functions of statistical scripting language 'R' integrated into the Bioconductor project data from cel files of each sample were normalized by variance stabilizing transformations (VSN) Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics 2002;18:96-104.

age	26;gender	female;disease	CML;disease phase	chronic phase;previous therapy	no;bcr-abl/G6PDH ratio (%)	9.3;leukocyte count (/nl)	25.7;hemoglobin (g/dl)	13.9;platelet count (/nl)	915

age	34;gender	male;disease	healthy control;disease phase;previous therapy	no;bcr-abl/G6PDH ratio (%)	n.a.;leukocyte count (/nl)	6.3;hemoglobin (g/dl)	14.5;platelet count (/nl)	293

age	54;gender	female;disease	healthy control;disease phase;previous therapy	no;bcr-abl/G6PDH ratio (%)	n.a.;leukocyte count (/nl)	5.1;hemoglobin (g/dl)	13.8;platelet count (/nl)	284

age	26;gender	male;disease	healthy control;disease phase;previous therapy	no;bcr-abl/G6PDH ratio (%)	n.a.;leukocyte count (/nl)	6.1;hemoglobin (g/dl)	14.6;platelet count (/nl)	217

age	24;gender	female;disease	healthy control;disease phase;previous therapy	no;bcr-abl/G6PDH ratio (%)	n.a.;leukocyte count (/nl)	5.2;hemoglobin (g/dl)	12.5;platelet count (/nl)	235

age	31;gender	male;disease	healthy control;disease phase;previous therapy	no;bcr-abl/G6PDH ratio (%)	n.a.;leukocyte count (/nl)	8.3;hemoglobin (g/dl)	14.9;platelet count (/nl)	269

age	43;gender	male;disease	healthy control;disease phase;previous therapy	no;bcr-abl/G6PDH ratio (%)	n.a.;leukocyte count (/nl)	6.8;hemoglobin (g/dl)	14;platelet count (/nl)	311

age	29;gender	female;disease	healthy control;disease phase;previous therapy	no;bcr-abl/G6PDH ratio (%)	n.a.;leukocyte count (/nl)	7.3;hemoglobin (g/dl)	12.9;platelet count (/nl)	257

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA using one-cycle amplification (Expression Analysis Technical Manual, 2001, Affymetrix).

Procedures are described in Paulsen et al. (2011). For generation of iPS cells, human primary fibroblasts were transduced overnight with equal amounts of concentrated supernatants containing each of the four retroviruses, supplemented with 8 μg/ml polybrene. Twenty-four hours after transduction, virus-containing medium was replaced by the second round of supernatant. Two days after transduction, 50 μg/ml of L-ascorbic acid (USB Corporation) was added to cultures. Six days after transduction, cells were replated (5 × 10^4 cells per six-well plate) on mitotically inactivated mouse embryonic fibroblasts (MEFs). In the following day, medium was replaced by mTeSRTM1 and changed every day. Eight days after transduction, 1 mM of valproic acid (VPA, Sigma) was added to the medium for another 7 days. About 20 days after transduction, colonies were picked up and transferred to six-well plates coated with Matrigel in mTeSRTM1. Pluripotent-like colonies were selected based on morphological criteria, and pluripotency was verified by RT-PCR analyses and immunostaining assays using OCT3/4 (Santa Cruz Biotechnology; mouse, 1:100), stage-specific embryonic antigen 4 (SSEA4; Chemicon; mouse, 1:100), TRA-1-60 (Chemicon; mouse, 1:100), and TRA-1-81 (Chemicon; mouse, 1:100) primary antibodies. Generation of neural precursor cells (NPCs) was performed using retinoic acid (RA), and immunological analyses were done using primary antibodies for nestin (Chemicon; mouse, 1:100), βIII-tubulin (Sigma; mouse, 1:100), and NeuN (Chemicon; mouse, 1:100). The cell lines derived in this work, as well as controls, are available in the cell bank of the National Laboratory for Embryonic Stem Cell Research at Federal University of Rio de Janeiro, LaNCE-RJ (Brazil).

Scanned images of the arrays were processed using Feature Extraction 10.7.3.1 software (Agilent Technologies) with default parameters.

Self-self experiments were performed by labelling the SCZP hiPSC with either Cy3 or Cy5 dyes and hybridizing simultaneously on the same microarray slide to determine the intensity-dependent cut-offs. These cut-offs were applied to the non-self-self experiments, (NPCxhIPSC SCZP) and (NPCxhIPSC CON).
R (programming language) and Bioconductor package Limma were used.

Total RNA was isolated using TRIzol (Sigma) according to the manufacturer’s instructions. RNA quantity and integrity were assessed by spectrophotometry (Nanodrop) and microfluidics-based electrophoresis (Bioanalyzer, Agilent 2100), respectively, and obtained OD of ~2.0 and RIN>9.

Samples were hybridized for microarrays in the Agilent SureHyb chambers (Agilent Technologies) for 20 h at 55°C, and the platforms were washed with the manufacturer’s washing buffers.

Samples were prepared according to the Agilent mRNA Microarray System protocol using 250ng of total RNA for amplification and labelling using the Agilent Low RNA Input Fluorescent Linear Amplification Kit.

Technical replicate of patient with schizophrenia.
Patient was a 48-year-old woman with DSM-IVTR schizophrenia defined as treatment-resistant under clozapine treatment (SZCP).

neuron progenitor cells (NPC);schizophrenia;human induced pluripotent stem cells (hiPSC);schizophrenia

Microarray scanning and data extraction was perfomed by Expression Analysis, Inc. (Durham, NC).  The Affymetrix GeneChip Scanner 3000 7G was used. GeneChip Command Console (Affymetrix) was used to drive the scanners.  Expression Console (Affymetrix) was used to extract data from the scanned images.

Expression file matrix data was generated using Genepattern Software for the Broad Institute (http://genepattern.broadinstitute.org/gp) with the ExpressionFileCreator Module.  GCRMA method was used with quantile normalization.

RNA isolation was peformed by Expression Analysis, Inc. (Durham, NC).  RNA was purified using the RNeasy Mini Kit (QIAGEN) according to the manufacturer's protocol, including the on-column DNase I digestion.  RNA integrity and quantity was measured using an Agilent Bioanalyzer 2100.

RNA hybridization to Affymetrix HG-U133 Plus 2 arrays was performed by Expression Analysis, Inc. (Durham, NC).   Standard Affymetrix protocols were used with the Affymetrix FS450 Fluidics Station and the Affymetrix Hybridization, Washing and Staining kits.

RNA labeling was peformed by Expression Analysis, Inc. (Durham, NC).  Total RNA was converted cDNA and in vitro transcribed to biotin-labeled anti-sense RNA, using the Enzo Single Round RNA Amplification and Biotin Labeling System (Enzo # ENZ-42420-10) according to the manufacturer’s protocol.

Gene expression data from Vehicle treated, DAY 6, biological rep.3, MOLM-13 cells

MOLM-13;acute myeloid leukemia (MLL-AF9 rearrangement);RPMI with 10% FBS;Vehicle;day 6;3

Gene expression data from Vehicle treated, DAY 6, biological rep.2, MOLM-13 cells

MOLM-13;acute myeloid leukemia (MLL-AF9 rearrangement);RPMI with 10% FBS;Vehicle;day 6;2

For transfection with siRNA oligonucleotides (all invitrogen), cells were cultured to 70% confluence and transfected with a combination of three FoxP1-targeting siRNAs or an irrelevant control oligonucleotide (all from invitrogen) according to the manufacturers instructions.

Human umbilical vein endothelial cells (HUVECs) were isolated from donated umbilical cords, pooled from two donors and cultivated up to passage 5.

Agilent arrays were washed using Agilent's gene expression wash buffer 1 and 2 according to Agilent's instructions. Scanning was performed using an Agilent DNA microarray Scanner and Agilent's Scan Control Software (version A.8.3.1).

Primary data analysis was performed using Agilent's Feature Extraction Software (version 10.5.1.1).

Total RNA was isolated from HUVECs 48h after transfection with TRIzol (Invitrogen) according to the manufacturers instructions.

1.65 µg of Cy3-labelled cRNA were fragmented according to the manufacturer´s instructions, and 1.5 µg of fragmented cRNA hybridized to an Agilent 4x44K array. Hybridization conditions: 65°C, 10 rpm, 17 h; in an Agilent hybridization oven

Kit: Quick Amp Labeling Kit, One Color (#5190-0442), using 200 ng of total RNA as starting material, according to the manufacturer's instructions (Manual .One-color microarray-based gene expression analysis, version 5.5, February 2007). cRNA synthesis was regarded successful provided that .1.65 µg of cRNA with a Cy3-incorporation rate .8.0 pmol/µg cRNA were synthesized.

21-day-old felmale C57BL/6 mice from Harlan (Indianapolis, IN) were ovariectomized on day 26 and fed with phytoestrogen-free diet two days later (AIN-93G purified rodent diet, Dyets, In., Bethlehem, PA). Experimental treatments began on day 30. Animals were fed with a diet containing 1500 ppm genistein (Indofine Chemicals, Somerville, NJ) ad libitum by adding genistein to the AIN-93G diet.. RNA were extracted at day 3 after experiment started. Total 6 animals were treated. RNA samples were pooled from 3 animals, resulting two independent biological replicates.

21-day-old felmale C57BL/6 mice from Harlan (Indianapolis, IN) were ovariectomized on day 26 and fed with phytoestrogen-free diet two days later (AIN-93G purified rodent diet, Dyets, In., Bethlehem, PA). Experimental treatments began on day 30. Animals were fed with a diet containing 1500 ppm genistein (Indofine Chemicals, Somerville, NJ) ad libitum by adding genistein to the AIN-93G diet.. RNA were extracted at day 2 after experiment started. Total 6 animals were treated. RNA samples were pooled from 3 animals, resulting two independent biological replicates.

21-day-old felmale C57BL/6 mice from Harlan (Indianapolis, IN) were ovariectomized on day 26 and fed with phytoestrogen-free diet two days later (AIN-93G purified rodent diet, Dyets, In., Bethlehem, PA). Experimental treatments began on day 30. Animals received daily subcutaneous injections of 125 ng of E2 (Signma-Aldrich, St. Louis, MO) in 0.02 ml corn oil. RNA were extracted at day 6 after experiment started. Total 6 animals were treated. RNA samples were pooled from 3 animals, resulting two independent biological replicates.

21-day-old felmale C57BL/6 mice from Harlan (Indianapolis, IN) were ovariectomized on day 26 and fed with phytoestrogen-free diet two days later (AIN-93G purified rodent diet, Dyets, In., Bethlehem, PA). Experimental treatments began on day 30. Animals received daily subcutaneous injections of 125 ng of E2 (Signma-Aldrich, St. Louis, MO) in 0.02 ml corn oil. RNA were extracted at day 3 after experiment started. Total 6 animals were treated. RNA samples were pooled from 3 animals, resulting two independent biological replicates.

Microarray data were analyzed using GeneSifter with a quality cut-off of 0.5 and a fold-change between groups of at least 1.2.  Raw data were normalized by median scaling of P-calls.

Extraction of total RNA was performed using the Qiagen RNeasy Lipid Tissue Kit according to the manufacturer's instructions.

20 µg of cRNA was fragmented and hybridized for 16H at 45ºC on Mouse 430 2.0 chips.  Chips were then washed and stained using the Affymetrix Fluidics Station 400

Biotinylated cRNA was prepared from 5 µg total RNA using Affymetrix One-Cycle Target Labeling protocol (GeneChip Expression Analysis Technical Manual 1999-2004, Affymetrix)

Total RNA was extracted from omental  adipose tissue from a control subject

Total RNA was extracted from omental  adipose tissue from a PCOS subject

Total RNA was extracted from omental  adipose tissue from a PCOS patient

Total RNA was extracted from omental adipose tissue from a control subject

Animals received humane care according to the criteria outlined in the “Guide for the Care and Use of Laboratory Animals” of the National Academy of Sciences. All animals were maintained in accordance with the institutional guidelines of the Massachusetts General Hospital Subcommittee on Research Animal Care. Male Wistar rats received weekly IP injections of diethylnitrosamine (DEN) at 50 mg/kg or vehicle control (PBS) for 18 weeks. A subset of rats received either daily (5X a week) IP injections of 2 mg/kg erlotinib or vehicle control during weeks 13 - 18. Animals were sacrificed at 9, 13 and 19 weeks after a one-week washout period to eliminate acute effects of DEN. At the time of sacrifice, the non-tumor liver tissues were collected in RNase-free tubes and snap-frozen in liquid nitrogen. Frozen tissues were stored at -80°C until RNA extraction.

Standard Illumina protocol, refer to the Illumina beadarray Assay System Manual

For each probe, replicated mesurements (beads) were averaged after removing outliers. Data were were then normalized using the cubic spline algorithm.

Using frozen non-tumor liver tissues, total RNA was extracted using TRIzol (Invitrogen).

rat, hepatocellular carcinoma (DEN 50mg), treated with vehicle (week 18)

Confocal scanner used to collect fuorescence signal.  The average signal from 2 sequential scans wa scalculated for each microarray feature.

Affy cel files were processed using GC-RMA in Stratagene ArrayAssist Lite version 3.4, MAS5 flags were calculated simultaneously and both the gc-rma expession value and the MAS5 detection flag were included in the .chp files. Default paramters were used.

The cRNA products were fragments to 200 bp or less, heated for 5 min (100-C) and hybridized for 16 hours at 45-C.  Arrays washed at low and hi strigency and stained with streptavidin coupled with fuorscent marker.

Standard Affymetrix protocol using 5 micorgrams total RNA, Superscript II RT.  Second strand synthesis and in vitro amplification and incorporation with biotynalted CTP and UTP.

Comparison of GATA6 null tissue and wild type controls to determine the role GATA6 plays in lung development and regeneration.

Data were obtained and processed with the Agilent Feature Extraction Software (v9.5).  The resulting data were imported into Rosetta Resolver (v7.1) and log2 intensities were exported.

Clinical information: Sample.ID=1343;Tumor.type=D;Size=2.5;Grade=3;Nodes=ND;ER=Pos;PR=Pos;HER2=Neg;Age=79;DFS=21;Status=recur

Clinical information: Sample.ID=1363;Tumor.type=D;Size=2.1;Grade=2;Nodes=0/15;ER=Pos;PR=Pos;HER2=Neg ;Age=56;DFS=114;Status=non-recur

Sodium arsenite at prescribed concentrations was added to food, which was repelleted, or sodium arsenite was added to water. Injections were intraperitoneal in a normal saline solution.

6wk male C57BL/6 male mice were acclimated to their respective diets for 2 wk prior to treatments.

After hybridization, the arrays were stained with streptavidin-phycoerythrin in the GeneChip Fluidics station and then scanned using Affymetrix GeneChip Scanner (laser filter set at 570 nm; pixel size 2.5 um). The array image data were acquired, and the fluorescent signal intensities were quantified using Affymetrix® GCOS v. 1.2 software with following settings of quantitation parameters: Alpha1=0.05, Alpha2=0.065, Tau=0.015, Gamma1H=0.0045, Gamma1L=0.0045, Gamma2H=0.006, Gamma2L=0.006, Perturbation=1.1, Target Intensity=150.

CEL file data were normalized using RMA as implented in Bioconductor simpleaffy. Genes were selected by  Rank Product (Breitling, R., 2004, FEBS Letter, 57383-92) implemented in Bioconductor RankProd at  p < .05 and by ANOVA.

RNA was extracted from frozen lung samples and homogenized using QiashredderTM and RNeasy® Mini Kits (Qiagen, Valencia, CA) per manufacturer's protocol. Contaminating genomic DNA was removed using DNA-free kits
(Ambion, Austin, TX) and total RNA was quantified with a NanoDrop®ND-1000 Spectrophotometer (NanoDrop Technologies, Rockland, DE). RNA quality was determined with the RNA 6000 LabChip kit Nano Assay (Agilent Technologies, Inc., Santa Clara, CA).

The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling. Biotinylated cRNA (15 ug) targets were then cleaned up, fragmented, and hybridized to GeneChip® array during the overnight incubation at 45oC in rotating hybridization oven.

Total RNA was first reverse-transcribed using T7-oligo(dT) promoter primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double stranded cDNA was purified and served as a template in the subsequent in vitro transcription (IVT) reaction.

Mouse Lung AIN Diet 5wk Control, biological replicate D
AN080806_Sample 69.CEL

Sodium arsenite added to food: None; Injection: None; Diet: AIN-76A; Sodium arsenite added to drinking water: None

Mouse Lung AIN Diet 8hr Saline Injection, biological replicate C
AN080406_Sample 68.CEL

Sodium arsenite added to food: None; Injection: IP 8hr saline only; Diet: AIN-76A; Sodium arsenite added to drinking water: None

Mouse Lung AIN Diet 5wk 10ppb As Food Exposure, biological replicate C
AN080306_Sample 67.CEL

Sodium arsenite added to food: 10 ppb, 5wk; Injection: None; Diet: AIN-76A; Sodium arsenite added to drinking water: None

Mouse Lung AIN Diet 5wk 10ppb As Drinking Water Exposure, biological replicate E
AN080306_Sample 66.CEL

Sodium arsenite added to food: None; Injection: None; Diet: AIN-76A; Sodium arsenite added to drinking water: 10 ppb, 5wk

Clinical information: Sample.ID=1368;Tumor.type=D;Size=2.6;Grade=2;Nodes=ND;ER=Pos;PR=Pos;HER2=Neg ;Age=82;DFS=63;Status=non-recur

Clinical information: Sample.ID=1370;Tumor.type=D;Size=2;Grade=2;Nodes=ND;ER=Pos;PR=Pos;HER2=Neg;Age=73;DFS=61;Status=non-recur

WT and Crem-/- animals of the mixed strain (129Pas x C57Bl/J ) [Nantel F, Monaco L, Foulkes NS, Masquilier D, LeMeur M, Henriksén K, Dierich A, Parvinen M, Sassone-Corsi P: Spermiogenesis deficiency and germ-cell apoptosis in CREM-mutant mice. Nature 1996, 380:159-162] were maintained in a temperature and humidity controlled room under a 12:12 h light:dark cycle (light on at 7:00 am, light off at 7:00 pm) with free access to food (Harland Tekland 2916) and water.

GeneChip data was processed and analyzed using R/Bioconductor packages. Data were summarized (w.r.t. core meta-probeset annotations and AFFX control probes, probes grouped to the level of transcripts) and quantile-normalized (background computed from antigenomic probes) using RMA algorithm from XPS package.

8 weeks old mice were sacrificed with cervical dislocation at 7 am (0h circadian time). Tissue samples from adrenal glands were excised, snap frozen in liquid nitrogen and stored at -80°C for subsequent analysis. Samples were homogenized in 500 μl of TRI Reagent (Sigma) and total RNA was isolated according to the manufacturer’s instructions. RNA quantity and quality were assessed with NanoDrop and Agilent 2100 Bioanalyzer instruments, all samples isolated fulfilled the minimum requirements (OD260/280 and OD230/280 > 1.8) for microarray hybridization.

100 ng of total RNA was used for hybridization of Affymetrix Gene Chip Mouse 1.0 ST Arrays according to manufacturer’s instructions (Genechip® Whole Transcript (wt) Sense Ttarget Labeling Assay Manual – P/N 701880 Rev 4). Labled samples were injected into Affymetrix arrays and hybridized at 45°C and 60 rpm for 16 h in an Affymetrix Hybridization Oven. Arrays were stained and washed in the Affymetrix GeneChip Fluidic Station 450.

Total RNA was used to synthesize double-stranded cDNA with random hexamer primers tagged with a T7 promoter sequence. The double-stranded cDNA was subsequently used as a template and amplified by T7 RNA polymerase producing cRNA. In the second cycle of cDNA synthesis, random hexamers were used to prime reverse transcription of the cRNA and dUTP was incorporated to produce single-stranded DNA. This single-stranded DNA sample were then treated with a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) that specifically recognized the unnatural dUTP residues and broke the DNA strand. DNA was labeled by terminal eoxynucleotidyl transferase (TdT) with the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.

8 weeks old mice were sacrificed with cervical dislocation at 7 am (0h circadian time). Tissue samples from testis were excised, snap frozen in liquid nitrogen and stored at -80°C for subsequent analysis. Samples were first pulverized and then homogenized in 1000 μl of TRI Reagent (Sigma) and total RNA was isolated according to the manufacturer’s instructions. RNA quantity and quality were assessed with NanoDrop and Agilent 2100 Bioanalyzer instruments, all samples isolated fulfilled the minimum requirements (OD260/280 and OD230/280 > 1.8) for microarray hybridization.

Affymetrix Microarray Suite MAS 5.0. Images were scaled to an average hybridization intensity of 250. Further data analysis was performed using GeneSpring software.

hybridized to Affymetrix HG U95 Av2 GeneChip using Affymetrix fluidics station according to the instructions of the manufacturer

Labeled cDNA was prepared with BioArray High Yield RNA Transcription Kit (Enzo Life Sciences, Farmingdale,NY)

Total RNA was prepared using TRIzol reagent from the entire pancreas one 57 day old male mouse.  The genotype was gastrin+/-, CFTR+/+ on 95% black6, 5% 129Sv background.  Mice were fed Peptamen from age 10 days to prevent intestinal obstruction.

This was a non-interventional study. Juvenile idiopathic arthritis patients were treated with methotrexate and samples collected prior to treatment and after 6 months on therapy.

Total RNA was extracted from 3x10e6 PBMC using TRIzol reagent (Invitrogen, UK)

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix GeneChip Human U133 2.0 array. GeneChips were washed and stained on the Affymetrix Fluidics Station 450.

RNA was coverted to cDNA (Roche) using an oligod(T) primer and converted to cRNA using In Vitro Triscription labelling kit (Affymetrix

The data were normalised using quantile normalisation and log2 transformed with 'beadarray' Bioconductor package in R

Oligonucleotide arrays were scanned using a confocal laser scanner (GeneArrayTM, Hewlett Packard, Palo Alto, CA).

We used the Affymetrix GeneChip Suite 5.0 software (MAS 5.0) to calculate raw expression values for each of the 22,283 probe sets on the U133A oligonucleotide arrays.

protocol used in (Gehring et al., Mol.Cell, 2003); PMID: 12718880

HeLa cells were treated in three independent experiments with UPF1 siRNAs or luciferase siRNAs as a negative control. To positively control for the effect of RNAi the efficient depletion of UPF1 was ascertained by immunoblotting. RNA isolated from these cells was analyzed on Affymetrix HG_U133A GeneChips™. The data here correspond to the third experiment (UPF1 siRNA transfection).

MC3T3-E1 OB cells grown in 6-well plates and either left untreated or treated with 50 micrograms of Ascorbic Acid (AA) for 5 days.  Media was replenished every 2nd day.

MC3T3-E1 subclone 4 was obtained from American Type Culture Collection (ATCC). The MC3T3-E1 steoblastic cell line was routinely cultured in α-MEM supplemented with heat inactivated 10% FBS and incubated in a humidified atmosphere at 37oC with 5% CO2.

Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Mouse MOE430 2.0 array.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

Mc3T3-E1_T0-1
MOE4302_042809H_RH1_Ctl1
Gene expression data from control Mc3T3-E1 cells

The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

After FACS isolation the cells were immediately resupended in Trizol

Biotinylated cRNA was prepared according to the standard 3'IVT expression kit (cat. #901229) Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

3rd Gen.FVB/N from 129Sv/Ev and Black Swiss mix;8 Weeks;Mammary Gland;Epithelial Cells;MMTV-cre; PtenloxP/loxP

Epithelials cells isolated from mouse mammary glands with Pten deletions

2nd Gen. FVB/N from 129Sv/Ev and Black Swiss mix;13.5 days;whole body;Fibroblasts;Ptenloxp/loxp

C57BL/6;male;embryonic day E15.5;wild type;mouse embryonic fibroblasts (MEF cells)

DNA chip technology was used to systematically search for genes differentially expressed in early onset CRC. We report a panel of 7 over-expressed genes in the normal appearing colonic mucosa of young patients without dominant family history compared to that of HC that could potentially predict early onset CRC.

biopsies from healthy individuals undergoing colonoscopic examination, snap-frozen immediately, stored at -80ºC

human immortalized mesenchymal stem cells;RNF40;5 days osteoblast differentiation

human immortalized mesenchymal stem cells;RNF40;2 days osteoblast differentiation

human immortalized mesenchymal stem cells;RNF40;undifferentiated

human immortalized mesenchymal stem cells;control;5 days adipocyte differentiation

5491021070_K
Down's Syndrome;induced pluripotent stem cell;CCL54 C11;rep2

induced pluripotent stem cell;Down's Syndrome;CCL54;male;P12;C11

5491021070_J
Down's Syndrome;induced pluripotent stem cell;CCL54 C11;rep1

5445316039_D
normal;induced pluripotent stem cell;CRL-2429 C11;rep1

5491021070_L
Down's Syndrome;induced pluripotent stem cell;CCL54 C11;rep3

5445316039_F
normal;induced pluripotent stem cell;CRL-2429 C11;rep3

5445316039_E
normal;induced pluripotent stem cell;CRL-2429 C11;rep2

Cells were grown for 1 days on irradiated feeders after trypsinisation and either cultured for 1 more day under these conditions or induced for 24h by the addition of DOX.

Cells were passaged according to standard procedures with standard ES medium (Non essential AA, Pyruvate, PSG, LIF, 15% serum, beta-mercaptoethanol)

The data were analyzed using the RMA method of background correction, quantile normalization, and summarization of cell signal intensity

After 2 days of culture, cells were trypsinized, resuspended in 15ml of medium, allowed to settle for 10 minutes to eliminate feeders. The top 50% of the suspension was used for RNA preparation/Trizol.

Cells were grown for 3 days on irradiated feeders after trypsinisation and cultured in the presence of hygromycin

After 3 days, cells were trypsinized, resuspended in 15ml of medium, allowed to settle for 10 minutes to eliminate feeders. The top 50% of the suspension was used for RNA preparation/Trizol.

Monocytes were isolated from 30 ml of whole blood from each of 19 women, 10 with high BMD and 9 with low BMD, using monocyte negative isolation kit from Dynal Biotech Inc. Total RNA was extracted from monocytes using Qiagen RNeasy Mini Kit. Targets were produced for each subject using standard Affymetrix procedures from about 4ug of total RNA. Hybridization was made for each subject. Comparison was performed between 10 high BMD and 9 low BMD subjects.
MCI-015 was from a premenopausal low BMD woman.

Lacrimal Gland 7 days after greater superficial petrosal nerve sectioning.

The mice were then intraperitoneally injected with STZ (Wako Pure Chemical Industries, Osaka, Japan, 185 mg/kg in 0.05M citrate buffer, pH 4.5).  Mice (n=6) in the untreated control group did not receive any treatment.  Tail vein blood was sampled weekly and the blood glucose levels of the samples were immediately measured using a blood glucose test meter (Glucocard, Arkray, Kyoto, Japan).  After 1 week, 18 mice showing non-fasting blood glucose levels of 230-400 mg/dL were divided into 3 groups: one group was fed with AIN93G only (control group), the others with an AIN93G diet containing 0.1% or 0.5% quercetin (Funakoshi, Tokyo, Japan) for 2 weeks. All mice had access to food and water ad libitum during the experimental period.

Data analysis was performed with a GeneChip Operating Software (Ver. 1.3) using Affymetrix default analysis settings and global scaling as normalization method.

Gene expression data from STZ-treated mouce liver after 14 day feeding of 0.1% quercetin diet

Gene expression data from STZ-treated mouce liver after 14 day feeding of 0.5% quercetin diet

Gene expression data from STZ-treated mouce liver after 14 day feeding of control AIN93G diet

224;Salazopyrin BFZ Losartan Thyroxine Doxazosin;2/21/38;F;CAUCASIAN;1/1/77;1/1/77;FALSE;FALSE;FALSE;NO;FALSE;FALSE;1/6/05;1;0;0;0;0;0;0;0;FALSE;0;12;12;12;12;12;11;12;11;11;BOTH;unknown;unknown;unknown;unknown;1/6/05;BOTH;BOTH;unknown;unknown;unknown;3/4/05;DISEASE IN REMISSION;never;unknown;Hypertension Hashimoto's Thyroditis;UC;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

223;Prednisolone 20mg Asacol 2.4g;1/18/44;F;CAUCASIAN;3/1/04;3/15/04;FALSE;FALSE;FALSE;NO;FALSE;FALSE;12/16/04;2;0;0;0;0;0;0;0;TRUE;0;BOTH;BOTH;unknown;unknown;unknown;12/16/04;BOTH;BOTH;BOTH;unknown;unknown;5/31/05;DISEASE IN REMISSION;unknown;unknown;None;UC;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

217;Asacol 1.2g daily;2/9/57;M;CAUCASIAN;1/1/79;1/10/79;FALSE;FALSE;FALSE;NO;FALSE;FALSE;11/26/04;1;0;0;0;0;0;0;0;TRUE;0;12;12;12;11;11;11;11;11;11;BOTH;unknown;unknown;unknown;unknown;11/26/04;BOTH;BOTH;BOTH;unknown;unknown;3/4/05;DISEASE IN REMISSION;never;unknown;None;UC;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

216;NONE;5/10/36;M;CAUCASIAN;2/19/66;8/20/66;FALSE;FALSE;FALSE;NO;FALSE;FALSE;11/18/04;0;0;0;0;0;0;0;0;FALSE;0;11;11;11;11;11;11;11;11;12;BOTH;BOTH;BOTH;unknown;unknown;11/18/04;unknown;unknown;unknown;unknown;unknown;12/9/04;DISEASE IN REMISSION;never;unknown;NONE;UC;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

220;Asacol 800mg BFZ 2.5mg Metformin Simvastatin;6/28/48;M;CAUCASIAN;1/10/95;3/25/95;FALSE;FALSE;FALSE;NO;FALSE;FALSE;12/10/04;0;0;0;0;0;0;0;0;TRUE;0;BOTH;BOTH;BOTH;BOTH;BOTH;12/10/04;BOTH;BOTH;BOTH;BOTH;BOTH;3/7/05;DISEASE IN REMISSION;ex;1/1/90;5-14;Type 2 DM.;UC;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

218;Sulphasalazine Asprin Metoprolol Atorvastatin;9/27/24;F;CAUCASIAN;1/1/58;1/1/58;FALSE;FALSE;FALSE;NO;FALSE;FALSE;12/3/04;0;0;0;0;0;0;0;0;TRUE;0;BOTH;unknown;unknown;unknown;unknown;12/3/04;BOTH;unknown;unknown;unknown;unknown;3/4/05;DISEASE IN REMISSION;never;unknown;Breast cancer;UC;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

206;Asacol 800mg BD;9/10/59;F;CAUCASIAN;1/1/79;1/1/80;FALSE;FALSE;TRUE;NO;FALSE;FALSE;10/8/04;3;0;0;0;0;0;0;0;FALSE;2;BOTH;unknown;unknown;unknown;unknown;10/8/04;BOTH;unknown;unknown;unknown;unknown;12/9/04;DISEASE IN REMISSION;ex;1/1/94;5-14;None;UC;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

201;None;4/12/56;M;CAUCASIAN;6/19/03;7/4/03;FALSE;FALSE;FALSE;NO;FALSE;FALSE;9/30/04;1;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;BOTH;BOTH;BOTH;9/30/04;BOTH;HISTOLOGICAL;unknown;unknown;unknown;12/7/04;FAILURE OF THERAPY;ex;1/1/70;1/1/99;25+;None;UC;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

213;PRED 7MG, ATENOLOL 100MG, ASPRIN 75MG, SIMVASTATI;11/1/43;M;CAUCASIAN;3/1/82;2/2/83;FALSE;FALSE;FALSE;YES;FALSE;FALSE;11/12/04;0;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;unknown;unknown;unknown;11/12/04;COLONOSCOPIC;unknown;unknown;unknown;unknown;12/9/04;DISEASE IN REMISSION;ex;1/1/74;unknown;ISCHEAMIC HEART DISEASE;UC;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

210;Mesalazine 800mg B, Prednisolone Supps;6/28/56;M;CAUCASIAN;1/1/73;1/10/74;FALSE;TRUE;FALSE;NO;FALSE;FALSE;10/19/04;2;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;BOTH;unknown;unknown;10/14/04;BOTH;unknown;unknown;unknown;unknown;12/9/04;DISEASE IN REMISSION;never;unknown;Scarlet Fever 1964;UC;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

121;Cp-tenedone, Enalapril, Loperamide.;4/8/59;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;2/1/05;Diarrhoea, Blastocytitis on stool cultures.;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

nomal skeletal muscle from a female 30 year-old healthy volunteer.

nomal skeletal muscle from a male 30 year-old healthy volunteer.

Gene expression data from microdissected epithelial cells of invasive cancer originating in IPMN

pancreas;epithelial cells;intraductal papillary-mucinous neoplasm (IPMN)

microdissected epithelial cells from invasive cancer originating in IPMN 3

microdissected epithelial cells from invasive cancer originating in IPMN 2

Gene expression data from microdissected epithelial cells of IPMC

pancreas;epithelial cells;intraductal papillary-mucinous carcinoma (IPMC)

microdissected epithelial cells from invasive cancer originating in IPMN 1

117;Loperamide;3/31/67;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;12/21/04;IBS type symptoms;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

To obtain transient pre-miR-148b (PM10264, Ambion) expression, cells were plated in 6-well plates at 30-50% confluency and transfected 24h later using RNAiFect (QIAGEN, Stanford, CA) reagent, according to manufacturer’s instructions, with 75 nM pre-miR-148b. Cells were tested for miR overexpression 48h later.

MDA-MB-231 cells were from American Type Culture Collection and maintained in standard conditions: Dulbecco's Modified Eagle's Medium containing 10 mM Glutamax and 4.5 g/mLglucose (DMEM Glutamax™, GIBCO Invitrogen Life Technologies, Carlsbad, CA), supplemented with 10% heat-inactivated FCS (Seromed, GmbH), 1 mM sodium pyruvate, 25 mM HEPES pH 7.4 and 100 μg/mL gentamicin (all from GIBCO Invitrogen Life Technologies, Carlsbad, CA).

Slides were scanned on an Agilent microarray scanner (model G2565CA) at 100% and 10% sensitivity settings.

Only spots with signal minus background flagged as positive and significant (flag=1) were used in the following analysis as “detected” spot while probes with flag equal to 0 were noted as “null”. Probes with less than 73% of detected spots across all arrays were removed from the analysis. Background corrected intensities of replicated spots on each array were averaged. Data were inter-array normalized with Quantile normalization (Bolstad BM et al., Bioinformatics (2003), 19(2):185-93) and then log2-transformed. Principal component analysis, cluster analysis and profile similarity searching were performed with tMev that is part of the TM4 Microarray Software Suite (Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, Howe EA, et al. Methods in Enzymology. 2006;411:134-93). Identification of differentially expressed genes was performed with one and two class Significance Analysis of Microarray (SAM) program (Tusher VG, Tibshirani R, Chu G. Proc Natl Acad Sci USA 2001;98:5116-121) with default settings. SAM uses a permutation-based multiple testing algorithm and identifies significant genes with variable false-discovery rates (FDR). This can be manually adjusted to include a reasonable number of candidate genes with acceptable and well defined error probabilities.

Total RNA was isolated from 106 cells by using Trizol® Reagent (Invitrogen) according to the manufacturer’s protocol. Total RNA was quantified using the ND-1000 spectrophotometer (Nanodrop), while RNA integrity and content of microRNAs (%) in each samples were assessed by capillary electrophoresis using the RNA 6000 Nano LabChip using the Agilent Bioanalyzer 2100 (Agilent Technologies). Only total RNA samples with R.I.N. (RNA Integrity Number) values of 6, or higher, were used for microarray analysis.

Samples were hybridized to Whole Human Genome Microarray 4 x 44K (G4112F, Agilent Technologies). 1.65 ug of Cy3 labelled aRNA were hybridized for 17 hours at 65ºC in a hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies). Arrays were washed with Agilent Gene Expression wash buffers and Stabilization and Drying Solution as suggest by the supplier.

Eight hundred nanograms of total RNA were labelled with “Agilent One-Color Microarray-Based Gene Expression protocol” (Agilent) according to the manufacturer’s instructions. The synthesized cDNA was transcribed into cRNA and labelled with cyanine 3-labelled nucleotide. Labelled cRNA was purified with RNeasy Mini columns (Qiagen). The quality of each cRNA sample was verified by total yield and specificity calculated with NanoDrop ND-1000 spectrophotometer measurement (NanoDrop Technologies).

Agilent Feature Extraction software version 10.5.1.1 was used for image analysis.

122;Venlafaxine;7/10/61;M;JEWISH;FALSE;FALSE;FALSE;FALSE;FALSE;2/10/05;FH Colon Ca;0;TRUE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

Cells were incubated with the piperazine designer drugs at EC20 for 24 h.

Microarrays were scanned with an Affymetrix Gene-Chip Scanner-3000-7G controlled by GCOS software.

Data were processed using the statistical programming language ‘R-version 2.15.1’. For the normalisation of the entire set of Affymetrix gene expression arrays was used the Robust Multi-array Average (RMA) algorithm

QIAzol extraction of total RNA was performed according to the manufacturer's instructions.

12.5 μg of labeled and fragmented cRNA were hybridized to Rat Genome 430 2.0 AffymetrixGeneChips

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA

Arthritic mice were intraperitoneally injected with 150 ul of K/BxN serum on days 0 and 2. Mice were killed for ankle RNA extraction on day 7 after serum injection.

The chips were scanned using an Affymetrix  7G Genechip Scanner 3000 with GeneChip Command Console 1.1 software (Affymetrix)

Data were processing by RMA algorithm using Partek Genomic Suite

Ankle joints were pulverized in presence of liquid nitrogen and total RNA was extracted with Rneasy mini kit and QIAshredder (Qiagen) according to the manufacturer’s instructions.

Samples were hybridised to Affymetrix Mouse Gene 1.0 ST genechip using Affymetrix standard hybridization protocol  (GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cDNA were prepared from 300 ng of total RNA, using the WT cDNA synthesis and amplification kit (Affymetrix) following the GeneChip whole transcript (WT) sense target labelling assay manual of Affymetrix

Gene expression data from 36M2 trated with Carboplatin for 30hrs

Gene expression data from 36M2 trated with Carboplatin for 36hrs

Gene expression data from 36M2 trated with Carboplatin for 24hrs

Gene expression data from 36M2 trated with Vehicle-Control for 24hrs

Gene expression data from 36M2 trated with Vehicle-Control for 30hrs

Dams were randomly distributed among two groups (3 dams per group) and exposed by caudal injection (0.3 ml/kg body weight) from GD 15 to PND 20 every 5 days (a total of 6 injections/dam). Dams of the control group received vehicle: ethanol 95%, Cremophor EL, and sterile water (1:1:8, v/v); dams of exposed group 1 received 0.002 mg/kg body weight (BW) of BDE-47 in vehicle, and dams of exposed group 2 received 0.2 mg/kg body weight (BW) of BDE-47 in vehicle. Dams and pups were kept together until weaning on PND 21.

We obtainedtimed pregnant Wistar rats (250–300 g; Charles River Laboratories, St. Constant, Que., Canada) on gestational day (GD) 14 and housed them individually in plastic cages with sawdust bedding, under regulated temperature (21 ± 2 ° C), relative humidity (50 ± 10%) and a 12-hour light/dark cycle. Food (Rodent chow 5075; Charles River Laboratories) and water were provided ad libitum. All animals received care in compliance with the Guide to the Care and Use of Experimental Animals from the Canadian Council of Animal Care and the protocol was approved by our institutional animal research ethics review board.

The raw data were pre-processed and normalized with the lumi Bioconductor package

All tissues were snap-frozen in liquid nitrogen, and stored at -80°C until RNA extraction. RNA was extracted with the RNeasy Mini Kit (Qiagen, Maryland, USA) according to the manufacturer’s instructions.

Gene chips were scanned using an Affymetrix GeneChip Scanner 3000 7G.

Gene chips were analyzed using affymerix power tools using MAS 5 background correction, RMA probeset summarization, and median normalization (-a mas5-bg,med-norm,pm-only,med-polish).

total RNA was harvested with Trizol according to manufacturer's instructions

Fragmented cRNA are hybridized using a GeneChip Fluidics Station 450 in aGeneChip Hybridization Oven 640.

total RNA was labeled with the Ambion Affymetrix WT expression kit for Affymetrix whole transcript arrays, product #4411974.  Product number 4411974

cell lines were subcloned from WT and IKK2-/- primary tumors by serial dilution

BALB/c BMDM stimulated overnight with 50 IU/ml IFN-g and infected with WA(pYV)

skeletal muscle;insulin resistant;untreated;0.9;206;35;1380;73;30.7;47.4;2241.1

Semen was collected then treated with Somatic Cell Lysis Buffer (0.1% sodium dodecyl sulfate [SDS], 0.5% Triton X-100) on ice for 30 minutes.  Lack of somatic cell contamination and sperm count were established by microscopic examination.  RNA was isolated from sample using a modified RNeasy protocol (Qiagen Inc. Valencia, CA).  RNA was eluted from collection columns using 50 microL of nuclease-free water twice for a final volume of 100 microL.  Dithiothreitol (DTT) was added to eluted samples to a final concentration of 10 mM.  A total of 40 units RNase block (Strategene, La Jolla, CA) was added to each sample prior to a 20-minute treatment with RNase-free DNase I (Ambion, Austin, TX) at 37°C.

Spermatozoal RNA profile from an infertile individual with a consistent severely teratozoospermic semen profile.  The individual demonstrated no other abnormal semen characteristics.

Human Sperm from an infertile male with a consistent severe teratozoospermia

JLI_47

JLI_46

JLI_49

JLI_48

A catalytic antioxidant (AEOL 10150) attenuates expression of inflammatory genes in stroke.

White and grey matter in the distribution on the middle cerebral artery 6 hours after administration of saline (control); first replicate; pooled mRNA from 6 brains.

JLI_42

White and grey matter in the distribution on the middle cerebral artery 6 hours after administration of saline (control); third replicate; pooled mRNA from 6 brains.

White and grey matter in the distribution on the middle cerebral artery 6 hours after administration of the catalytic antioxidant AEOL 10150; second replicate; pooled mRNA from 6 brains.

White and grey matter in the distribution on the middle cerebral artery 6 hours after administration of the catalytic antioxidant AEOL 10150; third replicate; pooled mRNA from 6 brains.

JLI_53

JLI_50

Mice were maintained in a pathogen-free facility, with 4–5 animals per cage in a temperature-controlled room with a 12-h light/dark cycle and access to food and water ad libitum. Age and sex matched littermate cohorts were used for all the experiments to account for potential strain differences.

Gene expression data under ER stress from lymphoblastoid cells of individual GM06993 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM06994 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM06985 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM06993 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM06985 treated with 4 ug/ml tunicamycin 8 hours.

NB125

Medulloblastoma cell line D425;doxycyline inducible shRNA against OTX2;0 hrs;1

NB126

Medulloblastoma cell line D425;doxycyline inducible shRNA against OTX2;8 hrs;1

NB127

Medulloblastoma cell line D425;doxycyline inducible shRNA against OTX2;16 hrs;1

NB128

Medulloblastoma cell line D425;doxycyline inducible shRNA against OTX2;24 hrs;1

T-ALL1, CEM, KOPT-K, DND41 and HPB-ALL cells lines have been treated with control peptide or IKKg NEMO binding domain (NDB) inhibitory peptide at 100mM for 16 hours

Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was done by the RMA algorithm using GeneSpring 7.2 program. No further adjustments were made to the data in the table.

15 mcg of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

20 ng total RNA converted to cDNA using Affymetrix GeneChip® Two-Cycle cDNA Synthesis Kit and in vitro transcription resulting into biotin-labeled cRNA, fragmented prior to hybridization (Affymetrix Expression Analysis Technical Manual, as described).

Twenty samples were analyzed: human T-ALL, CEM, KOPT-K, DND41, HPB-ALL cells lines have been treated at 100uM for 16 hours with control peptide or IKKγ Nemo binding domain (NBD) inhibitory peptide, that specifically block the canonical NF-κB activity by disrupting the interaction of IKKγ to IKKβ and IKKα

JCRB0086 [TALL-1];human T-ALL cell line;IKKγ Nemo binding domain (NBD) inhibitory peptide

Affymetrix GeneChip® Scanner 3000 according to the manufacturer's recommended protocols

initial step used Trizol extraction of RNA, following manufacturer's recommended protocols, followed by Qiagen RNeasy Mini Kit per manufacturer's recommended protocols

Affymetrix Hybridization Oven 640 and GeneChip® Fluidics Station 450 according to the manufacturer's recommended protocols

GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols

SNU-398 human HCC cells were maintained in RPMI medium supplemented with 10% fetal bovine serum (FBS) at 37°C in a humidified atmostphere of 5% CO2

The data were summarized with the RMA and normalized with the Cross-correlation method.

Tissue and tumor samples were excised and subjected to manual disruption prior to total RNA extraction

The arrays were scanned using an Affymetrix GeneChip Scanner 3000 enabled for High-Resolution Scanning, and the raw images were converted to .CEL files using Affymetrix GCOS software

The MAS5 algorithm was used to accomplish the mean scaling normalization and scaling to 500.

Trizol extraction of total RNA was performed according to the manufacturer's instructions and was further purified using RNeasy kit (Qiagen)

cRNA (15 ug) was fragmented following the Affymetrix protocol, added to 270 ul of hybridization buffer, and hybridized to the Affymetrix GeneChip Mouse Genome 430 2.0 arrays (P/N 900495)

labeled target RNA was prepared from total tissue RNA using the One-Cycle Target Labeling Kit and Control Reagents

VAL;diffuse large B-cell lymphoma (DLBCL) cells;non-targeting siRNA

KARPAS-231_siRNA_R2
Gene expression data from a DLBCL cell line.

KARPAS-231;diffuse large B-cell lymphoma (DLBCL) cells;LITAF-specific siRNA

DLBCL cell line KARPAS-231 transfected with a LITAF-specific siRNA

KARPAS-231_siRNA_R1

KARPAS-231_siRNA_R3

KARPAS-231;diffuse large B-cell lymphoma (DLBCL) cells;non-targeting siRNA

DLBCL cell line KARPAS-231 transfected with a non-targeting siRNA

SC-1;diffuse large B-cell lymphoma (DLBCL) cells stably transfected with a tetracycline-inducible LITAF expression vector;doxycycline

DLBCL cell line SC-1 stably transfected with a tetracycline-inducible LITAF expression vector, presence of doxycycline

Control and LIRKO mice aged 2-3 months were fed ad libitium with a normal chow diet

Data were analyzed with the Bioconductor packages affy to normalize and background correct using RMA

Cells were stimulated for 24 hours with interferon- (IFN; 100 units/ ml), were left untreated for 24 hours, or were treated for 3 hours with lipopolysaccharide (LPS; 10 ng/ml)

SPeripheral blood samples were diluted with phosphate buffered saline (PBS), then underlaid with Ficoll-Paque Plus (Amersham Biosciences, Piscataway, NJ), and centrifuged under standard conditions to separate mononuclear cells.  PBMCs were removed and plated in nonsupplemented Cellgro RPMI 1640 (Mediatech, Herndon, VA) at 37°C for 2 hours. Following removal of nonadherent cells and media, the attached cells were cultured in R-10 (day 0), which consisted of RPMI 1640 supplemented with 10% fetal bovine serum (Hyclone, Logan, UT), HEPES (Sigma, St. Louis, MO), penicillin/ streptomycin (Gibco), and L-glutamine (Fisher Scientific, Pittsburgh, PA), and which was supplemented with recombinant human granulocyte–macrophage colony-stimulating factor (GM-CSF; 100 units/ml) (PeproTech, Rocky Hill, NJ). Every other day, 75% of the medium was removed and fresh R-10 supplemented with GM-CSF was added.

Cells were suspended in TRIzol (Invitrogen, Carlsbad, CA) and processed according to the manufacturer's instructions

Macrophages were derived from the peripheral blood of 8 AS patients (median disease duration 13 years [range <1-43 years]) and 9 healthy control subjects over 7 days with the use of granulocyte-macrophage colony-stimulating factor.

FLP-IN HEK 293-NOD2wt, HEK 293-NOD2L1007fsinsC and HEK 293mock cells were cultivated in medium without FCS for 7 h before stimulation with 10 µg/ml MDP for 0h, 2h and 6h. Cells were harvested simultaneously.

NOD2wt and NOD2-L1007fsinsC expressing cells were generated with the FLP-IN system (Invitrogen, Carlsbad, CA, USA). HEK 293 cells containing the recombination site were purchased from Invitrogen. Wildtype and mutated NOD2 were inserted to the genomic recombination site by FLP-recombinase enzyme. A control cell line was generated by transfecting an empty mock vector. All stable cell lines were selected for Hygromycin B resistance and consequently cultured in MEM + 10 % FCS + 1% Penicillin/Streptomycin + 50 μg/ml Hygromycin B (Invitrogen).

GeneChips were scanned using the Affymetrix GeneChip Scanner  3000.

The data were analyzed with Gene Chip Operating Software 1.1. Represents the relative level of expression of a transcript. The median of the data is identified and each datum is weighted by how far it is from the median using One-step Tukey's Biweight Algorithm. A weighted mean is then calculated.

Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array in a Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station.

Hybridization and data collection were carried out by the Microarray facility at the Institute of Molecular and Cell Biology in Singapore.

Peripheral blood mononuclear cells;healthy control;GTE6;75min;White;Male

Peripheral blood mononuclear cells;healthy control;GTE6;120min;UK;Female

Peripheral blood mononuclear cells;healthy control;GTE6;70min;White;Male

Peripheral blood mononuclear cells;healthy control;GTE6;95min;White;Female

Peripheral blood mononuclear cells;healthy control;GTE6;87min;White;Male

Peripheral blood mononuclear cells;healthy control;LT6;UKmin;White;Male

Peripheral blood mononuclear cells;healthy control;GTE6;105min;White;Female

Peripheral blood mononuclear cells;healthy control;LT6;98min;White;Male

The data were analyzed with dChip 2004. After array normalization (default analysis settings)  the model-based expression values were calculated using the PM-only model

TRIzol extraction of total RNA and further purified using the RNeasy Mini Kit (Qiagen) was used according to the manufacturers’ instructions.

After fragmentation of the cRNA, 15 μg cRNA in 200 μl hybridisation cocktail was hybridised onto Affymetrix MOE430 2.0 microarray chip for 16 h at 45 °C. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Swegene Microarray Resource Centre (Lund, Sweden).

gene expression data from 4 weeks old laminin alpah 2 chain deficient mouse hind limb skeletal muscle

dy3K/dy3K, mouse model for congenital muscular dystrophy type 1 A

Tamoxifen was administered via 5 mg daily gavage for three days.

Cells were cultured in RPMI 1640 with 20% FBS and the following cytokines: IL-3 (10 ng/mL), IL-6 (10 ng/mL), SCF (10 ng/mL)

Zfx wt/y CreER;infected with control retrovirus with GFP selectable marker

Sorted Zfx wt myeloid progenitors overexpressing only GFP selectable marker

Zfx fl/y CreER;infected with control retrovirus with GFP selectable marker

Sorted Zfx ko myeloid progenitors overexpressing only GFP selectable marker

Zfx wt/y CreER;infected with Myc expressing and control retrovirus with GFP selectable marker

Sorted Zfx wt myeloid progenitors overexpressing Myc using GFP selectable marker

Zfx fl/y CreER;infected with Myc expressing and control retrovirus with GFP selectable marker

Sorted Zfx ko myeloid progenitors overexpressing Myc using GFP selectable marker

MDA-LM2-shTARBP2 cells were transduced with shZNF395 and shControl lentiviral particles and selected for short-hairpin expression.

Cells were grown in DMEM-based media supplemented with 10% FBS, 1% L-glutamine, 1% Sodium Pyruvate, and 1% Pen/Strep

Data were quantile-normalized and processed using the Lumi package.
Non-normalized values indicate the average probe hybridization signal (supplementary file linked to Series record).
Normalized values are quantile-normalized.
Final processed values are logFC of average normalized signals in shZNF395 relative to siControl (supplementary file linked to Series record).

48hr post-transfection, total RNA was extracted and on-column Dnase treated using Norgen Biotek total RNA extraction kit (per manufacturer instructions).

Samples were biotin-labeled using the TargetAmp-Nano Labeling Kit for Ilumina Expression BeadChip

2_DMSO-2_(Mouse430_2)

Bone marrow-derived macrophages (BMMs) from wild type mice were treated with IFN-gamma (10 ng/ml) for 4 h. Total RNA was prepared with RNA-STAT60 (TEL-TEST) and purified with the RNeasy kit (Qiagen). Double stranded complementary DNA was synthesized from 20 ug of total RNA according to Affymetrix methodology, and purified with Phase Lock Gels (Eppendorf). Biotin-labeled RNA was synthesized with the BioArray High Yield RNA Transcript Labeling Kit (Enzo). Samples were cleaned, fragmentated and hybridized to murine genome (MGU74Av2) Genechips (Affymetrix) as instructed. GeneChips were stained with phycoerythrin-streptavidin (Molecular Probes) and scanned with a GeneChip scanner (Affymetrix). Data were analyzed with the GeneSpring software.

Bone marrow-derived macrophages (BMMs) from wild type mice were untreated. Total RNA was prepared with RNA-STAT60 (TEL-TEST) and purified with the RNeasy kit (Qiagen). Double stranded complementary DNA was synthesized from 20 ug of total RNA according to Affymetrix methodology, and purified with Phase Lock Gels (Eppendorf). Biotin-labeled RNA was synthesized with the BioArray High Yield RNA Transcript Labeling Kit (Enzo). Samples were cleaned, fragmentated and hybridized to murine genome (MGU74Av2) Genechips (Affymetrix) as instructed. GeneChips were stained with phycoerythrin-streptavidin (Molecular Probes) and scanned with a GeneChip scanner (Affymetrix). Data were analyzed with the GeneSpring software.

Bone marrow-derived macrophages (BMMs) from Pias1 null mice were untreated. Total RNA was prepared with RNA-STAT60 (TEL-TEST) and purified with the RNeasy kit (Qiagen). Double stranded complementary DNA was synthesized from 20 ug of total RNA according to Affymetrix methodology, and purified with Phase Lock Gels (Eppendorf). Biotin-labeled RNA was synthesized with the BioArray High Yield RNA Transcript Labeling Kit (Enzo). Samples were cleaned, fragmentated and hybridized to murine genome (MGU74Av2) Genechips (Affymetrix) as instructed. GeneChips were stained with phycoerythrin-streptavidin (Molecular Probes) and scanned with a GeneChip scanner (Affymetrix). Data were analyzed with the GeneSpring software.

Bone marrow-derived macrophages (BMMs) from wild type mice were treated with IFN-beta (500 U/ml) for 2 h. Total RNA was prepared with RNA-STAT60 (TEL-TEST) and purified with the RNeasy kit (Qiagen). Double stranded complementary DNA was synthesized from 20 ug of total RNA according to Affymetrix methodology, and purified with Phase Lock Gels (Eppendorf). Biotin-labeled RNA was synthesized with the BioArray High Yield RNA Transcript Labeling Kit (Enzo). Samples were cleaned, fragmentated and hybridized to murine genome (MGU74Av2) Genechips (Affymetrix) as instructed. GeneChips were stained with phycoerythrin-streptavidin (Molecular Probes) and scanned with a GeneChip scanner (Affymetrix). Data were analyzed with the GeneSpring software.

Bone marrow-derived macrophages (BMMs) from wild type mice were treated with IFN-beta (500 U/ml) for 4 h. Total RNA was prepared with RNA-STAT60 (TEL-TEST) and purified with the RNeasy kit (Qiagen). Double stranded complementary DNA was synthesized from 20 ug of total RNA according to Affymetrix methodology, and purified with Phase Lock Gels (Eppendorf). Biotin-labeled RNA was synthesized with the BioArray High Yield RNA Transcript Labeling Kit (Enzo). Samples were cleaned, fragmentated and hybridized to murine genome (MGU74Av2) Genechips (Affymetrix) as instructed. GeneChips were stained with phycoerythrin-streptavidin (Molecular Probes) and scanned with a GeneChip scanner (Affymetrix). Data were analyzed with the GeneSpring software.

Bone marrow-derived macrophages (BMMs) from wild type mice were treated with IFN-gamma (10 ng/ml) for 2 h. Total RNA was prepared with RNA-STAT60 (TEL-TEST) and purified with the RNeasy kit (Qiagen). Double stranded complementary DNA was synthesized from 20 ug of total RNA according to Affymetrix methodology, and purified with Phase Lock Gels (Eppendorf). Biotin-labeled RNA was synthesized with the BioArray High Yield RNA Transcript Labeling Kit (Enzo). Samples were cleaned, fragmentated and hybridized to murine genome (MGU74Av2) Genechips (Affymetrix) as instructed. GeneChips were stained with phycoerythrin-streptavidin (Molecular Probes) and scanned with a GeneChip scanner (Affymetrix). Data were analyzed with the GeneSpring software.

MLL_00233;PBMC;no Multilineage dysplasia, acute myeloid leukemia, biallelic

MLL_00237;PBMC;no Multilineage dysplasia, acute myeloid leukemia, biallelic

MLL_00266;PBMC;Multilineage dysplasia, acute myeloid leukemia, biallelic

MLL_00268;PBMC;Multilineage dysplasia, acute myeloid leukemia, biallelic

MLL_00257;PBMC;no Multilineage dysplasia, acute myeloid leukemia, biallelic

MLL_00262;PBMC;no Multilineage dysplasia, acute myeloid leukemia, biallelic

MLL_00239;PBMC;no Multilineage dysplasia, acute myeloid leukemia, biallelic

MLL_00245;PBMC;no Multilineage dysplasia, acute myeloid leukemia, biallelic

MLL_00263;PBMC;no Multilineage dysplasia, acute myeloid leukemia, biallelic

MLL_00264;PBMC;no Multilineage dysplasia, acute myeloid leukemia, biallelic

Simple annotation: Infection, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20591.gif
Infection: N
name: 20591_Infection

Common Reference 2 round amplification 2 ug;Mening UNSTIM WB NP 3b

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20590.gif
Infection: Y
name: 20590_Infection

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20558.gif
name: 20558_Infection

Common Reference 2 round amplification 2 ug;Mening SWB WB NP 12b

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20573.gif
name: 20573_Infection

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20556.gif
name: 20556_Infection

Common Reference 2 round amplification 2 ug;Mening SWB WB NP 12a

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20539.gif
name: 20539_Infection

Common Reference 2 round amplification 2 ug;Mening SWB WB SW 24b2

Crohn's Disease subject (22 year old caucasian female, SAK_1316756241)

Subject Age : 22

um-uc-3 (atcc# crl-1749) bladder cancer cells were stably transfected with gfp-tagged rhogdi2, sorted for expression of gfp-rhogdi2 by fluorescence activated cell sorting as described (moissoglu et al. cancer res 2009. pmid: 19276387). RNA was isolated for microarray hybridization from cells in log phase growth.

RMA, using its standard settings as implemented in the Bioinformatics Suite commercially available as an add on for Matlab R2009B, (The Mathworks, Natick, MA).

Total RNA was extracted using an RNeasy kit, per manufacturer instructions (Qiagen, Valencia, CA, USA).

Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA.

As a control for experimental samples transfected with and stably expressing a GFP-RhoGDI2 fusion transgene, UM-UC-3 cells were transfected with GFP (empty vector), selected using puromycin, and sorted by FACS as described before (Moissoglu et al. Cancer Res 2009. PMID:19276387). Two biological replicates were prepared, GFP Replicates A and B, which are paired (prepared at the same times) as biological replicates A and B, respectively, of the GFP-RhoGDI2 experimental samples.

um-uc-3 (atcc# crl-1749);bladder cancer cells;transfected with gfp-tagged rhogdi2

UM-UC-3 bladder cancer cells, stably transfected with GFP-tagged RhoGDI2, biological replicate A

UM-UC-3 bladder cancer cells, stably transfected with GFP-tagged RhoGDI2, biological replicate B

PZA, one of the first line anti-TB drugs, was used to treat one group of Mtb infected mice. The compound was used at 150mg/kg body weight, dissolved in distilled water and administered through gavage five days a weeks.  Treatment was started at 28 days post infection and continued up to 63 days post infection.

B6D2F1 mice were infected with Mtb CDC1551 at ~2log10 (on day 0). At28 days post infection, one group of infected mice were treated with Pyrazinamide at 150mg/kg.  Lung tissue from Uninfected, Untreated and PZA treated mice were isolated at Day 0, 28, 42 and 63 days post infection and used for total RNA isolation.

standard protocol used can be found at <http://www.cag.icph.org> from the center for advanced genomics of the Public Health Research Institute of UMDNJ was used for all the experiments

Data from the scanned images were extracted using the software from Affymetrix and processed using PARTEK Genomics Suite for further analysis

Total RNA from the mouse lungs were isolated using TRIzol reagent (Invitrogen, CA, USA) and purified using RNA mini prep columns (Qiagen, CA, USA) according to the instructions of the manufacturers

Total RNA samples were reverse transcribed and labled with biotin as suggested by the array manufacturer (affymetrix)

GeneChip arrays are scanned using default parameters. Affymetrix GeneChip  Command Console software (AGCC) was used to acquire GeneChip images and  generate .DAT and .CEL files.

Data were RMA normalized and expression changes determined as fold difference between the average signals of Yy1 vs Ctrl datasets. P-values were determined by ANOVA [The fold-change data is provided as a Series supplementary file].

Total RNA was extracted in TRIzol (invitrogen) and cleaned -up with RNAesy Quiagen purification kit.

GeneChip Hybridization, Wash and Stain Kit (Affymetrix cat #900720) is used  to prepare the Hybridization Cocktail. The kit contains mix for target  dilution, DMSO at a final concentration of 7% and pre-mixed biotin-labelled  control oligo B2 and bioB, bioC, bioD and Cre controls (Affymetrix cat  #900299) at a final concentration of 50 pM, 1.5 pM, 5 pM, 25 pM and 100 pM,  respectively. These control oligos serve as positive controls for  hybridization. Biotin-labeled sense targets were diluted in hybridization  buffer at a concentration of 25 ng/ul and denatured at 99 °C for 5 minutes.  Hybridization cocktails were incubated at 45 °C for 5 minutes and centrifuged  at maximum speed for 1 minute prior to loading into the GeneChip® array  cartridge.  Hybridizations were performed for 16 h at 45 °C in a rotisserie oven at 60  RPM. Upon hybridization, GeneChip cartridges were washed and stained with  GeneChip Hybridization, Wash and Stain Kit in the Affymetrix Fluidics Station  450 following the FS450_0007 standard protocol. The cartridge is then loaded  into the GeneChip Scanner 3000 7G.

Biotin-labeled cDNA targets were synthesized starting from 150 ng of totRNA.  Double stranded cDNA synthesis and related cRNA amplification was performed  with Ambion® WT Expression Kit (Ambion, Austin, TX). cRNA was reverse  transcribed to cDNA fragmented and terminal labeled with Affymetrix GeneChip®  WT Teminal Labeling Kit (Affymetrix, Santa Clara, CA). All steps of the  protocol were performed according to manufacturer’s specifications. Efficacy  of fragmentation procedure was checked on Agilent Bioanalyzer 2100.

Animals were maintained in the animal facility of the University of Oviedo. 3 knock-in and 3 wild-type female animals were killed, and total RNA was isolated from liver samples

Washing and scanning were performed with a Fluidics Station 400 and GeneChip Scanner (Affymetrix).

After scanning, raw data were processed with the RMAExpress program (http://RMAExpress.bmbolstad.com), using default settings.

The biotin-labeled cRNA was purified, fragmented, and hybridized to a GeneChip Mouse Gene 1.0 ST Array (Affymetrix).

Double-stranded cDNA was synthesized using the SuperScriptTM cDNA synthesis kit (Invitrogen). In vitro transcription was carried out with the Bioarray high-yield RNA transcript labeling kit (Enzo Diagnostics).

Crohn's Disease subject (34 year old caucasian female, SAK_1307702704)

Crohn's Disease subject (52 year old caucasian female, SAK_1307747342)

Subject Age : 52

microarray analysis of gene expression after transverse aortic constriction in mice - 10 days sham group No.1

Hybridized target cRNA is stained with streptavidin phycoerythrin and arrays are scanned using a GeneArray Scanner at an excitation wavelength of 488nm

Monocyte cell line terminally differentated into macrophages by PMA treatment
Gene expression data from macrophages

microarray analysis of gene expression after transverse aortic constriction in mice - 3 wks sham group No.1

microarray analysis of gene expression after transverse aortic constriction in mice - 3 wks sham group No.3

microarray analysis of gene expression after transverse aortic constriction in mice - 3 wks sham group No.2

microarray analysis of gene expression after transverse aortic constriction in mice - 3 wks TAC group No.1

microarray analysis of gene expression after transverse aortic constriction in mice - 3 wks sham group No.4

microarray analysis of gene expression after transverse aortic constriction in mice - 3 wks TAC group No.4

microarray analysis of gene expression after transverse aortic constriction in mice - 3 wks TAC group No.3

liver;Male, Wistar-derived-Liverpool John Moores University rats;7-9 weeks of age;control 72 hr

liver;Male, Wistar-derived-Liverpool John Moores University rats;7-9 weeks of age;monuron 72 hr

kidney;Male, Wistar-derived-Liverpool John Moores University rats;7-9 weeks of age;control 72 hr

Peripheral blood cells taken from survivors few hours after exposure to trauma. date: 2001

Sample name: CSB_SD_1

C57BL/6;Csbm/m;male;cerebellum;1 year;standard AIN-93G diet (SD; carbohydrate:protein:fat ratio of 64:19:17 percent of kcal) ad libitum for 8 months

Csbm/m Mouse_cerebellum_Standard diet supplemented with resveratrol_Ad Lib_Replicate-1

Sample name: CSB_Resv_1

Primary fibroblasts were transfected with shRNA constructs targeting KDM4C or a control construct (SureSilencing shRNA Plasmids, SABiosciences) and selected for stable selection of the constructs with 1ug/mL Puromycin

Primary fibroblasts were grown in MEM supplemented with 10% FBS, 2 mM L-glutamine, and 100 U/mL penicillin-streptomycin, and .5ug/mL Puromycin

RNA was extracted using the RNeasy kit (Qiagen) according to the manufacturer's instructions.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133 Plus 2 Array. Chips were washed and stained in the Affymetrix Fluidics Station 450.

gene expression data from primary fibroblasts expressing shRNA targeting KDM4C or a control constuct

neonatal foreskin;primary dermal fibroblasts;shKDM4C construct 1

primary fibroblasts expressing a shRNA construct targeting KDM4C, construct 1, clone 1

primary fibroblasts expressing a control shRNA construct, clone 2

primary fibroblasts expressing a control shRNA construct, clone 1

Non-syndromic cleft lip/palate (NSCL/P);decidous teeth dental pulp;female

primary fibroblasts expressing a shRNA construct targeting KDM4C, construct 1, clone 2

Peripheral blood mononuclear cells;oligoarticular JIA;LT6;195min;White;Male

We analyzed the lumbar spinal cord tract of transplanted nmd mice (n=3), untransplanted nmd mice (n=3) and wild-type mice (n=3) (all mice are of male gender). The latter groups underwent surgical procedure with vehicle. The surgical procedure and spinal cord-derived neural stem cell transplantation (intratechal injection) were done at P1 and the animals were sacrificed at 6 weeks of age.
Frozen tissue was stored at -80°C. Total RNA was purified from tissue, using the EUROZol Kit (EuroClone Ltd., United Kingdom) following the manufacturer’s instructions. Total RNA (5 ug) was reverse-transcribed with a cDNA synthesis kit in the presence of SuperScript II RT (Invitrogen-Life Technologies, Inc.) and an oligo dT-T7 primer (Affymetrix Inc., Santa Clara, CA). After phenol/chloroform extraction and ethanol precipitation, the cDNA pellet was air-dried and re-suspended in 12 uL of diethyl pyrocarbonate-treated water and quantified by spectrophotometer measurement. An aliquot of each sample was conserved for gel electrophoresis and for inspection of RNA quality (i.e., 28S:18S RNA ratio). 10 ul was used for the IVT (In Vitro Transcription) amplification reaction, in the presence of biotinylated nucleotides (Enzo Biochem Inc.). Labeled cRNA (15 ug) was fragmented by incubation at 94°C for 35 minutes in fragmentation buffer (GeneChip Sample Cleanup, Qiagen) and the fragmented cRNA was then hybridized competitively against the Affymetrix 430 2.0 Array oligonucleotide array. Hybridization occurred at 47°C overnight. The arrays were scanned using a GeneArray 2500 Scanner (Affymetrix) and analyzed using MicroArray Suite 5.0 (Affymetrix). All experiments were validated after direct measures of cRNA quality: 5':3' ratios for beta-actin and for GAPDH (determined from Affymetrix chip hybridization analysis) are indirect indicators of overall RNA preservation. The default parameters were used for the statistical algorithm and for probe set scaling. The target intensity was set to 1,000 to normalize expression levels across all samples.

Cells were transfected with 30nM KEAP1 or non targeting control (NTC) siRNA in heavy and light SILAC media respectively by reverse transfection.  Cells were treated with 15 µM sulforaphane (SFN) or acetonitrile vehicle in heavy and light medium respectively 24 hours after plating. RNA was collected 24 hours after plating. The SFN treatment and KEAP1 knockdown experiments each had four biological replicates

MCF10A (American Type Culture Collection, Manassas, VA) cells were cultured in (DMEM)/F12 minus L-lysine and L-arginine for SILAC. Medium was supplemented with 5% horse serum, 20ng/ml epidermal Growth Factor, 0.5 µg/ml hydrocortisone, 100 ng/ml cholera toxin and 10 µg/ml insulin at 37°C in a humidified environment with 5% CO2. For light medium 12C6 L-lysine:2HCL and 12C6 L-arginine-HCl were supplemented and for heavy medium 13C6 L-lysine:2HCl and 13C6 L-arginine:HCl were added (Cambridge Isotope Laboratories, Andover, MA).

Microarrays were scanned using an Agilent G2565A Scanner controlled by Agilent Scan Control 7.0 software.

Data were extracted with Agilent Feature Extraction 9.5.3.1 software.

Total MCF10A RNA was isolated from cell pellets using TriZol reagent (Invitrogen), followed by RNeasy mini kit with DNase on-column digestion (Quiagen, Valencia, CA). MCF10A RNA was quantified with a NanoDrop ND-1000 (Thermo Scientific) followed by quality assessment with a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) according to the manufacturer’s protocol.

Cy3-labeled samples (0.825 ug) were used for hybridization at 65ºC for 17 hours in a hybridization oven with rotation. After hybridization, microarrays were washed and dried in a walk-in ozone-controlled enclosure according to the Agilent microarray processing protocol.

Sample amplification and labeling procedures were carried out using a Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies) with minor modifications. Briefly, 0.4 µg total RNA was reverse-transcribed into cDNA by MMLV-RT using an oligo dT primer (System Biosciences, Mountain View, CA) that incorporates a T7 promoter sequence. The cDNA was then used as a template for in vitro transcription in the presence of T7 RNA polymerase and Cyanine-3 labeled CTP (Perkin Elmer, Waltham, MA). The labeled cRNA was purified using RNeasy mini kit (Qiagen). RNA spike-in controls (Agilent Technologies) were added to RNA samples before amplification and labeling according to the manufacturer’s protocol.

non tumorigenic human breast epithelial MCF10A cell line: SFN_rep4

non tumorigenic human breast epithelial MCF10A cell line: NTC siRNA_rep1

non tumorigenic human breast epithelial MCF10A cell line: NTC siRNA_rep2

non tumorigenic human breast epithelial MCF10A cell line: NTC siRNA_rep3

non tumorigenic human breast epithelial MCF10A cell line: Vehicle_rep4

non tumorigenic human breast epithelial MCF10A cell line: SFN_rep1

This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv].  Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction.  Lv2 samples are from the same region in a sham operated mouse.  Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse.  The lv and lv2 samples can be compared as both are from normal functioning hearts.  For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html

Region of the heart between the LAD artery and the apex on a mouse with myocardial infarction (The infarcted area)

Anterior pituitary gland was harvested at the time of sacrifice, weighed and flash-frozen in liquid nitrogen. Tissue was homogenized in lysis buffer by passage through an 18- and then 22-guage needle. Total RNA was isolated using the Absolutely RNA Kit from Stratagene.

Approximately 2 µg of total RNA was processed to produce biotinylated cRNA targets.

BN rats were obtained from Harlan (Indianapolis, IN). At 9 weeks of age, a silastic tubing implant containing 5mg of the synthetic estrogen diethylstilbestrol (DES) was surgically implanted subcutaneously in the interscapular region of male rats. Each animal received an intraperitoneal injection of BrdU (50mg/kg) 4 hours prior to sacrifice. Animals were sacrificed at 21 weeks of age by decapitation and pituitary glands were immediately harvested, weighed and flash-frozen in liquid nitrogen. Tissues were homogenized through a 22-gauge needle and total RNA was extracted using the Absolutely RNA Kit (Stratagene). A total of 4 DES-treated males were used, resulting in three independent biological replicates.

BN strain, male, age 21 weeks, treated with the synthetic estrogen diethylstilbestrol (DES) for 12 weeks

The data were analyzed with RMAExpress using Affymetrix default settings and were normalized according to the quantile method (Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003;19:185-93). After normalization, the intensity values below 30 were set at 30.T

Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG 133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Untreated control. nr 2.

For siRNA knockdown of mutant FOXL2, KGN cells, passage 8, were seeded at a density of 300,000 cells per well of a six well plate.  Cells were transfected with FOXL2 stealth RNAi™ (cat#HSS101080 Invitrogen, NZ) or a GC matched control using Lipofectamine 2000 and Opti-MEM serum free media (Invitrogen, NZ).  RNAi-lipid complexes were removed 7h post transfection and replaced with complete media.  For overexpression of wildtype or mutant FOXL2, COV434 cells, passage 9, were seeded at a density of 300,000 cells per well of a six well plate.  Cells were transfected with 1µg of control (empty vector), pFOXL2wt, or pFOXL2m using Lipofectamine 2000 and Opti-MEM serum free media.  Plasmid-lipid complexes were removed 7h post transfection and replaced with complete media.

Both cell lines were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine and 1% non essential amino acids, and maintained at 37°C in 5% CO2.

Cells were harvested 24h post transfection and total RNA was extracted using TRIzol® reagent (Ambion, NZ).  Chloroform was added to the TRIzol® to separate the phases, and the aqueous phase was combined with 70% ethanol and passed through an RNeasy column (Qiagen, Australia) according to manufacturer’s instructions.

8.5µg of labelled aRNA was hybridised to Affymetrix U133 Plus 2 microarrays.

105ng of total RNA from the knockdown and overexpression experiments was labelled using the MessageAmp™ Premier amplification according to manufacturer’s instructions (Ambion, NZ).

Cells expressing IkBa dominant negative cultured in presence of dox, TNF stimulation for 1 h

Cells expressing IkBa dominant negative cultured in presence of dox, TNF stimulation for 0 h

Cells expressing IkBa dominant negative cultured in presence of dox, TNF stimulation for 6 h

Cells expressing IkBa dominant negative cultured in presence of dox, TNF stimulation for 3 h

Jurkat cells were infected at a multiplicity of infection of 1 with the LTR-Tat-IRES-GFP HIV-based vector (which transduces HIV-1 Tat and eGFP) pseudotyped with vesicular stomatitis virus G protein in the presence of 4 ug/ml Polybrene for 24 hours.

Mice and diets.  One-month-old male mice of the long-lived B6C3F1 strain were purchased from Harlan (Indianapolis, IN) and maintained as described after weaning (15).  Mice were housed in groups of 4 per cage and fed a non-purified diet, PMI Nutrition International Product #5001 (Purina Mills, Richmond, IN).  At 5 months of age, the mice were individually housed, and randomly assigned to one of two groups, control (CON) or long-term CR (LTCR).  CON mice were fed 93 kcal per week of a defined control diet (AIN-93M, Diet No. F05312, BIO-SERV).  LTCR mice were fed 52.2 kcal per week of a defined CR diet (AIN-93M 40% Restricted, Diet No. F05314, BIO-SERV).  The LTCR mice consumed approximately 40% fewer calories than mice in the CON mice.  The CR diet was enriched so that the CR mice consumed approximately the same amount of protein, vitamins, and minerals per gram body weight as the control mice.  Experimental design.  At 20 months of age, cohorts of mice in the CON group were randomly assigned to one of 7 experimental groups (Fig. 1).  A CON group continued to be fed 93 kcal per week of control diet for 8 weeks.  A CR8 group was fed 77 kcal per week of CR diet for 2 weeks, followed by 52.2 kcal per week of CR diet for 6 weeks.  The remaining dietary groups were fed the control diets containing, respectively, metformin (MET; Sigma, St. Louis, MO), glipizide (GLIP; Sigma), GLIP plus MET (GM), rosiglitazone (ROS; Avandia, SmithKline Beecham) or soy isoflavone extract (SOY; NOVASOY 400, Life Extension Foundation) for 8 weeks at the dosages indicated in Table 1.  The drugs were mixed with powdered control diet and cold-pressed into one gram pellets (BIO-SERV Inc.).  At 0900, all mice were fed 2/7 of the weekly allotment of food on Monday and Wednesday and 3/7 on Friday.  The mice had free access to acidified tap water.  They were fasted for 48 hours and killed by cervical dislocation at 22 months of age.  No signs of pathology were detected in the animals used for the studies reported (n=4 per group).  Organs were removed rapidly, flash frozen, and stored in liquid nitrogen.  The weights of the mice were monitored bi-weekly.  Mouse weights are given in Table 1.
Keywords = CR mimetics
Keywords = microarray profiling
Keywords = drug discovery
Keywords = gene-expression biomarkers

Mice and diets.  One-month-old male mice of the long-lived B6C3F1 strain were purchased from Harlan (Indianapolis, IN) and maintained as described after weaning (15).  Mice were housed in groups of 4 per cage and fed a non-purified diet, PMI Nutrition International Product #5001 (Purina Mills, Richmond, IN).  At 5 months of age, the mice were individually housed, and randomly assigned to one of two groups, control (CON) or long-term CR (LTCR).  CON mice were fed 93 kcal per week of a defined control diet (AIN-93M, Diet No. F05312, BIO-SERV).  LTCR mice were fed 52.2 kcal per week of a defined CR diet (AIN-93M 40% Restricted, Diet No. F05314, BIO-SERV).  The LTCR mice consumed approximately 40% fewer calories than mice in the CON mice.  The CR diet was enriched so that the CR mice consumed approximately the same amount of protein, vitamins, and minerals per gram body weight as the control mice.  Experimental design.  At 20 months of age, cohorts of mice in the CON group were randomly assigned to one of 7 experimental groups (Fig. 1).  A CON group continued to be fed 93 kcal per week of control diet for 8 weeks.  A CR8 group was fed 77 kcal per week of CR diet for 2 weeks, followed by 52.2 kcal per week of CR diet for 6 weeks.  The remaining dietary groups were fed the control diets containing, respectively, metformin (MET; Sigma, St. Louis, MO), glipizide (GLIP; Sigma), MET plus GLIP, rosiglitazone (ROS; Avandia, SmithKline Beecham) or soy isoflavone extract (SOY; NOVASOY 400, Life Extension Foundation) for 8 weeks at the dosages indicated in Table 1.  The drugs were mixed with powdered control diet and cold-pressed into one gram pellets (BIO-SERV Inc.).  At 0900, all mice were fed 2/7 of the weekly allotment of food on Monday and Wednesday and 3/7 on Friday.  The mice had free access to acidified tap water.  They were fasted for 48 hours and killed by cervical dislocation at 22 months of age.  No signs of pathology were detected in the animals used for the studies reported (n=4 per group).  Organs were removed rapidly, flash frozen, and stored in liquid nitrogen.  The weights of the mice were monitored bi-weekly.  Mouse weights are given in Table 1.

Measurement of specific mRNA levels.  Liver total RNA was isolated as described from livers of pathology-free mice in each group (n=4 per group) (13). mRNA levels were measured using Affymetrix mouse U74Av2 arrays according to standard Affymetrix protocols (Affymetrix).
Probe set expression measurement and normalization.  After hybridization and scanning, raw image files were converted to probe set data (*.CEL files) using Microarray Suite (MAS 5.0). Probe set data from all 32 arrays were simultaneously analyzed with the Robust multichip Average (RMA) method to generate normalized expression measures for each probe set (Fig. 2; Ref. 24)  The data were further filtered to exclude probe data sets that were “Absent” across all 32 arrays according to the MAS 5.0 detection algorithm (1,47).

No treatment. Samples are from SIRT4 WT or KO littermate mice on a 129 background.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

anaplastic thyroid carcinoma (ATC);subtype spindle cell;unmatched

anaplastic thyroid carcinoma (ATC);subtype spindle cell;matched to N14

anaplastic thyroid carcinoma (ATC);subtype squamoid/giant cell;unmatched

anaplastic thyroid carcinoma (ATC);subtype spindle cell;matched to N16

anaplastic thyroid carcinoma (ATC);subtype spindle/squamoid cell;unmatched

anaplastic thyroid carcinoma (ATC);subtype squamoid cell;unmatched

This sample is from Rotavirus acute phase infection of patient #1(see Table 1 in paper)

This sample is from Rotavirus acute phase infection of patient #2(see Table 1 in paper)

This sample is from Rotavirus acute phase infection of patient #3(see Table 1 in paper)

For gene expression profiling, peripheral blood mononuclear cell (PBMC) were obtained from leukopheresis by density centrifugation over Ficoll-hypaque according to standard procedures. Briefly, heparinized blood was diluted with 1 volume of RPMI medium and gently layered over the Fycoll. Following centrifugation at 660 g for 30 minutes, cells at the interface of the gradient was collected and washed 3 times. Highly purified CD4+ and CD8+ (purity >95%) cell subsets were then sorted by flow cytometry on MoFlo high speed cell sorter (Beckman Coulter, Fullerton, CA) and frozen in Trizol (Invitrogen).

GeneChips were scanned using the Affymetrix® GeneChip® Scanner 3000.

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The statistical analysis was performed couple by couple using the Rosetta Resolver® system (Rosetta Biosoftware). The fold-change of each gene was calculated by comparing gene expression in the affected twin with that in the unaffected twin and the genes with the same trend in at least 3 twin pairs out of the 4 studied were selected as candidates to be validated by real-time RT-PCR.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

0.518518519;exon 11;GIST Tumor;Universal Human Reference RNA (Stratagene)

0.016666667;exon 11;GIST Tumor;Universal Human Reference RNA (Stratagene)

0.0625;wildtype;GIST Tumor;Universal Human Reference RNA (Stratagene)

0.017156863;wildtype;GIST Tumor;Universal Human Reference RNA (Stratagene)

Cells were grown in DMEM medium supplemented with 10% fetal bovine serum and 20 µg/ml blasticidin

The data were analyzed with Expression Console (v1.1) using Affymetrix default analysis settings and global scaling as normalization method.

total RNA was extracted using the RNeasy Mini Kit according to manufacturer's instructions (Qiagen).

Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Gene expression data from cell population of MDA-MB-231 stably transfected with pcDNA6/V5-His plasmid, cell culture 2

cell population of MDA-MB-231 stably transfected with pcDNA6/V5-His plasmid, cell culture 2

Gene expression data from cell population of MDA-MB-231 stably transfected with pcDNA6/V5-His-ZNF217 plasmid, cell culture 2

cell population of MDA-MB-231 stably transfected with pcDNA6/V5-His-ZNF217 plasmid, cell culture 2

Gene expression data from cell population of MDA-MB-231 stably transfected with pcDNA6/V5-His plasmid, cell culture 1

cell population of MDA-MB-231 stably transfected with pcDNA6/V5-His plasmid, cell culture 1

Gene expression data from cell population of MDA-MB-231 stably transfected with pcDNA6/V5-His-ZNF217 plasmid, cell culture 1

cell population of MDA-MB-231 stably transfected with pcDNA6/V5-His-ZNF217 plasmid, cell culture 1

RNA was isolated from HMEC (passage 3) after stimulation with  2 ng/ml TNF for 5 h.

3 min exposure to halothane, immediate perfusion with ice cold saline
Keywords = Eckenhoff, anesthetics

Keywords = Eckenhoff. anesthetics

Two 90 minute exposures (3 hr recovery in between) to 0.8% halothane every day for 5 days, for a total of 10 exposures

The R statistical software was applied for data analysis. VSN was used for global background correction and normalization. Gene expression index calculation was done using model based index calculation (MBEI). Only perfect match probes were included in data analysis. Welch two sample t-test for paired data was used to calculate p-values.

One µg purified total RNA was converted to biotin-labeled aRNA using the MessageAmpTM II-Biotin single round aRNA amplification kit

peritoneal macrophages were preprared from thioglycollate-injected mice.

The data were analyzed with RMA using the arrayassist program (Stratagene).

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA were prepared by NuGEN Ovation system according to the manufactuerer's inscrution.

Gene expression data from IRAK2 KO macrophages stimulated with MALP-2 for 8h

Gene expression data from IRAK2 KO macrophages stimulated with MALP-2 for 4h

Gene expression data from IRAK2 KO macrophages stimulated with MALP-2 for 2h

Gene expression data from wild-type macrophages stimulated with MALP-2 for 8h

Gene expression data from wild-type macrophages stimulated with MALP-2 for 4h

Gene expression data from wild-type macrophages stimulated with MALP-2 for 2h

Gene expression data from IRAK1/IRAK2 KO macrophages stimulated with MALP-2 for 2h

Gene expression data from unstimulated IRAK1/IRAK2 KO macrophages

C57BL/6;wild type (D4-cre/Ai9 tdTomato);retina;cone photoreceptors;postnatal day 50

T144;Mouse tumorgraft, cohort 3;Male;74;Clear-cell renal cell carcinoma;wild type;wild type;mutant

Gene expression profiling of mouse tumorgraft, cohort 3 of patient T144

T144;Mouse tumorgraft, cohort 0;Male;74;Clear-cell renal cell carcinoma;wild type;wild type;mutant

Gene expression profiling of mouse tumorgraft, cohort 0 of patient T144

T143;Mouse tumorgraft, cohort 0;Female;74;Clear-cell renal cell carcinoma;wild type;wild type;wild type

Gene expression profiling of mouse tumorgraft, cohort 0 of patient T143

T142;Mouse tumorgraft, cohort 2;Female;56;Clear-cell renal cell carcinoma;wild type;mutant;mutant

Gene expression profiling of mouse tumorgraft, cohort 2 of patient T142

T143;Mouse tumorgraft, cohort 9;Female;74;Clear-cell renal cell carcinoma;wild type;wild type;wild type

Gene expression profiling of mouse tumorgraft, cohort 9 of patient T143

T143;Mouse tumorgraft, cohort 4;Female;74;Clear-cell renal cell carcinoma;wild type;wild type;wild type

Gene expression profiling of mouse tumorgraft, cohort 4 of patient T143

T127;Mouse tumorgraft, cohort 0;Male;35;Clear-cell renal cell carcinoma;wild type;wild type;mutant

Gene expression profiling of mouse tumorgraft, cohort 0 of patient T127

T84;Mouse tumorgraft, cohort 0;Male;52;Clear-cell renal cell carcinoma;wild type;mutant;mutant

Gene expression profiling of mouse tumorgraft, cohort 0 of patient T84

T142;Mouse tumorgraft, cohort 1;Female;56;Clear-cell renal cell carcinoma;wild type;mutant;mutant

Gene expression profiling of mouse tumorgraft, cohort 1 of patient T142

T127;Mouse tumorgraft, cohort 2;Male;35;Clear-cell renal cell carcinoma;wild type;wild type;mutant

Gene expression profiling of mouse tumorgraft, cohort 2 of patient T127

lung tissue;CD-1;13 weeks + 5 month + 13 days;fresh air, treatment over 5 month + 15 days recovery, 4x1h exposure per day

lung tissue;CD-1;13 weeks + 5 month + 13 days;2R4F whole mainstream smoke 750 µg/ml, treatment over 5 month + 15 days recovery, 3x1h exposure per day

Mice were anesthetized by isofluorane. Mouse brains were briefly rinsed with PBS after dissection and hippocampi tissues were collected for RNA extraction

Mice were maintained in the pathogen-free mouse facility until sacrifice.

Procedures were performed following the protocol of the microarray Genomic and RNA Profiling Core in Baylor College of Medicine

Raw data were analyzed by Bio-conductor, RMA method was used for normalization

2-3 month old animal with brain-specific IκBα deletion ( IκBαfl/-;Nestin-Cre)

Identification of genes differentially regulated by TGFBeta1 in glomerular mesangial cells.
Keywords = hexosamine
Keywords = glucose
Keywords = mesangial
Keywords = diabetes
Keywords = diabetic glomerulopathy

A self versus self control where differentially labeled RNA from the same source was hybridized to the same slide.
Keywords = self versus self

Identification of genes regulated by low glucose, high glucose and glucosamine treatments

C57BL/6;wild type (D4-cre/Ai9 tdTomato);retina;cone photoreceptors;postnatal day 90

238;Enalapril Zantac;9/27/38;F;CAUCASIAN;9/25/03;1/14/05;FALSE;FALSE;FALSE;NO;FALSE;FALSE;1/6/05;4;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;unknown;unknown;unknown;1/6/05;BOTH;BOTH;unknown;unknown;unknown;3/7/05;NEW;ex;1/1/03;5-14;Hypertension Diverticular disease;UC;8-9-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

270;Becotide inhaler;4/30/52;M;CAUCASIAN;1/1/99;8/24/05;FALSE;FALSE;FALSE;unknown;FALSE;FALSE;8/24/05;3;0;0;0;0;0;0;0;FALSE;0;BOTH;unknown;unknown;unknown;unknown;8/24/05;BOTH;unknown;unknown;unknown;unknown;9/14/05;NEW;current;5-14;Asthma;UC;11-15-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

Female (age range 33-49), skin biopsy taken from upper nates 7 hours after nickel exposure

Female (age range 33-49), skin biopsy taken from upper nates 48 hours after nickel exposure

Female (age range 33-49), skin biopsy upper nates. No nickel exposure

Female (age range 33-49), skin biopsy taken from upper nates 96 hours after nickel exposure

TR_N3
Gene expression from the retina of a NeuroD1 cKO mouse at ZT20.

C57BL/6J; NeuroD1flox::Crx-Cre+/-;NeuroD1 cKO;2 months;retina;ZT20

TR_D2
Gene expression from the retina of a NeuroD1 cKO mouse at ZT6.

C57BL/6J; NeuroD1flox::Crx-Cre+/-;NeuroD1 cKO;2 months;retina;ZT6

TR_D3

TR_N1

TR_N2

standardized ratio between standardized sample intrensity vs. Reference pool intensity

Wistar, Sex: male;pooled total RNA from interventricular septum tissue

RNA was isolated using TRIZOL reagent (Gibco-BRL Life Technologies) according to the manufacturers protocol

Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on rat RAE-230A microrray gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

8 wk old BALB/c (or BALB-RAG) mice were sensitized to ovalbumin (or PBS)]on days 1 and 7, and challenged with aerosolized ovalbumin (or PBS) on days 15-21, and samples harvested on day 22

Hunk-deficient animals were crossed to mice harboring an MMTV-c-myc transgene (Leder et al., 1986).  Hunk heterozygous, MMTV-c-myc mice were backcrossed to Hunk heterozygous animals.  MMTV-c-myc female animals of each Hunk genotype were mated twice, then monitored twice weekly for mammary tumors.  Mice possessing tumors with a maximum diameter of 20 mm were sacrificed and organs were examined at necropsy.  Tumor nodules were identified by examination of organs through a Leica Wild MZ8 dissection microscope.

A 129/Sv mouse genomic library (Stratagene, La Jolla, CA) was screened with a Hunk cDNA fragment (nt 1-706) (Gardner et al., 2000b).  The Hunk gene was disrupted by replacement of a 1.1 kb fragment containing the putative promoter and exon 1 of Hunk with a pGKneo cassette flanked by LoxP sites.  25 µg of linearized vector was electroporated into 1x107 E14 ES cells (kindly provided by Marisa Bartolomei, University of Pennsylvania) and selected in 300 µg /ml G418.  Properly target clones, as well as the resulting mice, were screened by Southern hybridization using a 3’ Xho I/Xmn I flanking probe.  Lung protein lysates (7 mg) were subjected to immunoprecipitation and immunoblotting with Hunk-specific C-terminal antisera as previously described (Gardner et al., 2000a).

The data were analyzed with GCRMA using R and quantile normalized

MMTV-c-myc/Hunk WT; Gender: Female; Tissue: Mammary gland tumors; Strain: FVB

MMTV-c-myc/Hunk KO; Gender: Female; Tissue: Mammary gland tumors; Strain: FVB

Stimulations were done with anti-CD3 (1 mg/ml) with or without anti-CD28 (3 mg/ml) in the presence or absence of CsA (1 mg/ml) for 24 hrs. The experiments with anti-CD3- and anti-CD3CD28 stimulations of Wt samples were done at two different occasions, explaining the day 1 and day 2 notes in the sample title.

Gene expression data from mouse CD3+ Wt T-cells with anti-CD3 and anti-CD28 stimulation and CsA-treatment

CD3CD28-stimulated and CsA-treated CD3+ T-cells from Wt C57BL/6 mice

Cells were cultured in RPMI(cancer cell) or DMEM(fibroblast) supplemented with 10% FBS, antibiotics, and glutamine at 37°C in a humidified atmosphere with 5% CO2.

RNA was isolated when culture was subconfluent.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133 plus2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA

Gene expression data from mouse CD3+ Itk knockout T-cells with anti-CD3 and anti-CD28 stimulation

Gene expression data from mouse CD3+ Wt T-cells with anti-CD3 stimulation and CsA-treatment

CD3-stimulated and CsA-treated CD3+ T-cells from Wt C57BL/6 mice

adipose tissue (epididymal);male;Zucker;fatty (fa/fa);Troglitazone

PBMCs from Normal subject
Subject Disease : Normal
Subject Age : 53

Crohn's Disease subject (23 year old caucasian male, SAK_1316577485)

Subject Age : 23

Subject Age : 60

Crohn's Disease subject (38 year old caucasian male, SAK_1316800947)

Subject Age : 38

Crohn's Disease subject (46 year old caucasian female, SAK_1316845653)

Subject Age : 46

Crohn's Disease subject (49 year old caucasian female, SAK_1313179761)

Subject Age : 49

Crohn's Disease subject (31 year old caucasian female, SAK_1313134987)

Csbm/m Mouse_cerebellum_Old_nicotinamide riboside treatment_Replicate-3

Sample name: OLD-CSB_NR-20

C57BL/6;Csbm/m;male;cerebellum;18 months;daily injections of NR (500 mg/kg/d, ip) for one week

Csbm/m Mouse_cerebellum_Old_nicotinamide riboside treatment_Replicate-2

Sample name: OLD-CSB_NR-16

Sample name: OLD-CSB_ctrl-17

C57BL/6;Csbm/m;male;cerebellum;18 months;daily injections of saline for one week

Csbm/m Mouse_cerebellum_Old_nicotinamide riboside treatment_Replicate-4

Sample name: OLD-CSB_NR-23

Sample name: OLD-CSB_ctrl-24

Sample name: OLD-CSB_ctrl-21

Sample name: OLD-WT_ctrl-22

C57BL/6;WT;male;cerebellum;18 months;daily injections of saline for one week

Sample name: OLD-WT_ctrl-19

Wt Mouse_cerebellum_Old_nicotinamide riboside treatment_Replicate-1

Sample name: OLD-Wt_NR-18

C57BL/6;WT;male;cerebellum;18 months;daily injections of NR (500 mg/kg/d, ip) for one week

Sample name: OLD-WT_ctrl-26

Mice carrying the Alk2 conditional allele (Alk2flox/flox) were created by flanking Alk2 exon 7, encoding a critical portion of the kinase domain, with two loxP sites. The Alk2flox/flox mice were bred to mice carrying progesterone receptor-cre knock-in (Pgrcre/+) allele to generate Alk2 flox/flox Pgrcre/+ mice, which were designated as Alk2 cKO. Alk2 flox/flox female mice were used as controls. Mice were genotyped by PCR analyses of genomic tail DNA as described by others. Analysis of DNA recombination in the uterus was performed using DNA isolated from uterine tissue. All mouse lines used in the present study were maintained on a hybrid C57BL/6J and 129S5/SvEvBrd genetic background. Animal handling and surgeries were performed according to the NIH Guide for the Care and Use of Laboratory Animals.

BeadChips are scanned on a HiScan SQ, iScan or BeadArray Reader. Array data were quantile normalized.

Whole uterine tissues were collected from control and Alk2 cKO female mice and stored immediately at -20°C until RNA extraction (according to Illumina protocol).

control mice, whole uterine tissues, mouse lines maintained on a hybrid C57BL/6J and 129S5/SvEvBrd genetic background

Gene expression profile of non-malignant FTE from BRCA1/2-mutation carrier during the luteal phase

Laser-capture microdissected non-malignant FTE from BRCA1/2-mutation carrier

Gene expression profile of non-malignant FTE from control patient during the follicular phase

Laser-capture microdissected non-malignant FTE from normal control patient

Gene expression profile of non-malignant FTE from control patient during the luteal phase

Bone marrow was harvested from the sternum or iliac crest of patients after informed consent. Mononuclear cells were isolated by density gradient centrifugation (LinfoSep, BiomediCs, Madrid, Spain), washed in Hank’s buffered salt solution (HBSS, Lonza Europe, Verviers, Belgium) and seeded at 20,000 cells/cm2 in Dulbecco’s Modified Eagle’s Medium-low glucose (DMEM-LG, Lonza) supplemented with 15% of fetal bovine serum (FBS) (Sigma-Aldrich, Bornem, Belgium), 2 mM of L-glutamine, 50 U/ml of penicillin, and 50 µg/ml of streptomycin (all from Lonza). Cells were incubated at 37°C in a 5% CO2 and 95% humidified atmosphere.

After 48 hours, nonadherent cells were removed by washing and the medium was changed once a week. When subconfluency (80–90%) was achieved, adherent cells were detached with TrypLE Select solution (Lonza) and expanded by replating at a lower density (± 600 cells/cm2).

Image analysis and probe quantification were done with Affymetrix software, which produced raw probe intensity data in the Affymetrix CEL files. Normalization was done with the RMA method, which processed a group of CEL files simultaneously using BRB arrays tools.

Total RNA from each cell culture was extracted in a single step by the TriPure Isolation Reagent (Roche Applied Science, Vilvoorde, Belgium). We performed the reverse transcription reaction with 2 µg RNA using qScript cDNA SuperMix (Quanta Bioscienes, Gaithersburg, MD, USA).

Following fragmentation, 16 µg of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450 according to the Affymetrix protocol (www.affymetrix.com).

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5 µg total RNA (www.affymetrix.com).

bone marrow mesenchymal stromal cells (BM-MSCs);multiple myeloma;IIIa;M;65

bone-marrow mesenchymal stromal cells extracted from myeloma patient

bone marrow mesenchymal stromal cells (BM-MSCs);multiple myeloma;IIIa;F;56

bone marrow derived mast cells;NTAL wild type;C57BL/6;none;none;none

bone marrow derived mast cells;NTAL knock out;C57BL/6;none;none;none

Cells were placed in DMEM supplemented with 0.5% charcoal stripped FBS overnight and then treated with 10 nM dexamethasone (DEX) or vehicle (ethanol; vehicle).  30 hrs later cells were treated with 50 ng/ml IL1β or vehicle.   Cells were harvested 18 hours later for total RNA extraction.

Cells were maintained in DMEM culture medium supplemented with 10% fetal bovine serum

Total RNA was extracted using Trizol according to manufacturer's protocol

Total RNA was labeled using Illumina TotalPrep RNA amplification kit per standard protocol

BMMCs from NTAL WT, NTAL shRNA infected, nonactivated, biological rep1

bone marrow derived mast cells;NTAL wild type;C57BL/6;lentiviral infection - NTAL knock down;pLKO.1/TRCN0000127243;none

BMMCs from NTAL WT, NTAL shRNA infected, nonactivated, biological rep2

BMMCs from NTAL WT, NTAL shRNA infected, nonactivated, biological rep3

BMMCs from NTAL WT, pLKO.1 infected, nonactivated, biological rep1

bone marrow derived mast cells;NTAL wild type;C57BL/6;lentiviral infection;pLKO.1;none

At 4 weeks of age, we injected vehicle (corn oil) i.p. x5 days in Myh11-CreERT2.Tgfbr2f/f Control and Fbn1C1039G/+.Myh11-CreERT2.Tgfbr2f/f Control mice or we injected tamoxifen 1 mg i.p. x5 days for Myh11-CreERT2.Tgfbr2f/f Knockout and Fbn1C1039G/+.Myh11-CreERT2.Tgfbr2f/f Knockout  mice. The animals were euthanized at 6 weeks of age and their ascending aorta was analyzed.

Expression intensities were quantified and compared using Partek Genomics Suite v6.4 (Partek Inc.) with Robust Multi-Array Average for normalization and fold-change calculations. Comparisons between groups were by unpaired Student t-test on log2 transformed data. The results of fold changes and the expression values are shown as anti-logged data.

Total RNA was isolated using RNeasy mini kits(QIAGEN) according to the manufacturer’s protocol.

FBN+/-.TGFBRIIko_12
Gene expression data from fibrillin-1 mutant with Tgfbr4 knockout mice

Fbn1C1039G mutant;conditional disruption of Tgfbr2;ascending aorta;6 weeks

BMMCs from NTAL WT, pLKO.1 infected, nonactivated, biological rep2

BMMCs from NTAL WT, pLKO.1 infected, nonactivated, biological rep3

bone marrow derived mast cells;NTAL wild type;C57BL/6;none;none;2 h 100 ng/ml TNP-BSA

Scanning was done according to the manufacturer's recommendations (Affymetrix). Scanner Model was GeneChip® Scanner 3000 7G. GeneChip® Command Console® 2.0 was used as software.

Raw data were background corrected with RMA and normalized using quantile normalization. All processing was done in R/Bioconductor.

Total RNA was extracted using the RNeasy Mini-Kit from QIAGEN according to the manufacturer's recommendations.

Hybridization was done according to the manufacturer's recommendations (Affymetrix).

Labeling was done according to the manufacturer's recommendations (Affymetrix).

FBN+/-.TGFBRIIko_11
Gene expression data from fibrillin-1 mutant with Tgfbr3 knockout mice

Gene expression data from mouse CD3+ Wt T-cells without stimulation

Gene expression data from mouse CD3+ Itk knockout T-cells without stimulation

No treatments were used.  The only difference in the animals was their genotype, with the mutants being liver-conditional knockouts for Pdss2.

Mutant and control animals were grown in separate cages in the University of Pennsylvania animal facility until time of sacrifice.  Food was removed from the cages 3 hours prior to sacrifice by cervical dislocation without anesthesia.

GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.

Probe-level measurements were normalized, summarized and log2-transformed by dCHIP software using perfect-match-only and invariant-set methods.

Trizol reagent was used according to the manufacturer's instructions to extract total RNA from flash-frozen liver aliquots

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430_2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Revision 5, Affymetrix).

B6.Pdss2loxP/loxP;140-day-old male;40 mg liver used for RNA extraction

B6.Alb/cre,Pdss2loxP/loxP(Liver-conditional knock-out);178-day-old male;40 mg liver used for RNA extraction

B6.Alb/cre,Pdss2loxP/loxP(Liver-conditional knock-out);224-day-old male;40 mg liver used for RNA extraction

B6.Pdss2loxP/loxP;209-day-old male (concurrent control to Alb73);90 mg liver used for RNA extraction

B6.Pdss2loxP/loxP;213-day-old male;40 mg liver used for RNA extraction

B6.Alb/cre,Pdss2loxP/loxP(Liver-conditional knock-out);176-day-old male;70 mg liver used for RNA extraction

female;58 years;pelvis retroperitoneal;4x7x9;myxoid/roundcell liposarcoma;high;G3;metastasis;no;no

female;85 years;lower arm;11x8x4;pleomorphic liposarcoma;high;G3;primary tumor;no;no

male;60 years;thigh;7.5x6x5.5;pleomorphic liposarcoma;high;G3;primary tumor;no;no

female;74 years;thigh;14.5x7.5x9;myxoid/roundcell liposarcoma;high;G3;primary tumor;no;no

Cell culture, EMEM (Sigma, St. Louis, MO) with 10% fetal bovine serum (FBS) (Omega Scientific Inc. Tarzana, CA)

TRI Reagent® according to the manufacturer's instructions, followed by RNeasy columns (Qiagen, Valencia, CA.)

Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

Gene expression data 5-aza-dC plus Trichostatin A  treated HepG2 cells.

A549 cells (lung epithelial cells, a common cell line used in IFN assays)

200 IU of Infergen (Intermune, Inc., Brisbane, CA) + 200 IU IFN-g1b (Actimmune, Intermune Inc)

Pregnant female mice (C57Bl6 genetic background) were euthanized at 14.5 days of gestation (E14.5), embryos were collected and tooth samples (lower incisors, mandibular and maxillary first molars) were microdissected.

The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

CEL files were processed with Affymetrix Expression Console software version 1.3.1.187 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings.

Total RNA was extracted with the RNAeasy micro Kit (Qiagen) from pools of 4 tooth germs to obtain enough RNA for subsequent microarray hybridization.

1.9 μg of cDNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse Gene 1.0 ST arrays (Affymetrix).

Biotinylated single strand cDNA targets were prepared, starting from 150 ng of total RNA, using the Ambion WT Expression Kit (Cat # 4411974) and the Affymetrix GeneChip® WT Terminal Labeling Kit (Cat # 900671) according to Affymetrix recommendations.

To identify and analyze mtDNA mutation-responsive genes, a comparison of cochlea tissues from WT (control) and D257A mice was conducted. We examined changes in gene expression in the cochleae induced by age-related accumulation of mtDNA mutations.

All mice were raised under 12:12 dark/light conditions, and housed in the specific pathogen-free facility at University of Wisconsin-Madison, and provided a nonpurified diet and acidified water ad libitum.

Total RNA was isolated from cochlea tissues using the TriZol Reagent (Invitrogen) according to the manufacturer's instructions.

Hybridization (hybridization oven 640) (Affymetrix), and washing and staining (fluidics station 400) (Affymetrix) were accomplished according to the manufacturer’s instructions.

cDNA synthesis from total RNA (Invitrogen), cRNA amplification and labeling (Enzo BioArray IVT kit) were accomplished according to the manufacturer’s instructions.

PolgD257A/D257A mice;male;9 month-old;cochlea;Kujoth, G.C. et al. (2005) Mitochondrial DNA mutations, oxidative stress, and apoptosis in mammalian aging. Science 309, 481-4.

Polg+/+ mice;male;9 month-old;cochlea;Kujoth, G.C. et al. (2005) Mitochondrial DNA mutations, oxidative stress, and apoptosis in mammalian aging. Science 309, 481-4.

Arrays were scanned on the GeneChip Scanner 3000 (Affymetrix). Image analysis was performed using GCOS 1.3 (Affymetrix).

Hybridization (hybridization oven 640) (Affymetrix), washing, and staining (fluidics station 400) (Affymetrix) were accomplished according to the manufacturer’s instructions.

cDNA synthesis from total RNA (Invitrogen), cRNA amplification and labeling (Enzo BioArray IVT kit) were accomplised according to the manufacture's instructions (Affymetrix).

Wild-type Polg+/+;male;9 months old;cochlea;Kujoth, G.C. et al. (2005) Mitochondrial DNA mutations, oxidative stress, and apoptosis in mammalian aging. Science 309, 481-4.

Arrays were scanned on the GeneChip Scanner 3000 (Affymetrix).
Image analysis was performed using GCOS 1.3 (Affymetrix).

Polg+/+ mice;male;9 months old;cochlea;For additional details about the strain used please refer to the following r;Kujoth, G.C. et al. (2005) Mitochondrial DNA mutations, oxidative stress, and apoptosis in mammalian aging. Science 309, 481-4.

Gene expression profiles for 17 pairs of cancer and non-cancerous tissues from colorectal cancer patients were used.  Five cell lines were treated with 5-aza-2'-deoxycytidine.

The data was normalized by robust multichip analysis (RMA) using Gene Expression Console (Affymetrix)

Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).

Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.

cRNA was prepared using one-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).

Approximately 2x105 cells were plated per well in a 6 well plate. 16-24 hrs later cells were transfected with 1.5 ug shRNA expression construct using FuGENE 6 (Promega) according to the manufacturer’s instructions. Total RNA was extracted from the cells 2.5 days later.

N2A mouse neuroblastoma cells were grown in DMEM supplemented with 10% fetal bovine serum.

Affymetrix CEL files were analysed using the Limma, oligo, and genefilter R Bioconductor packages. Arrays were RMA background corrected, quantile normalised and summary expression values calculated for Refseq and full length mRNAs. Before differential expression analysis, genes changing upon Pou3f3 knockdown were filtered to remove genes showing little variation in expression (variance cut off of 0.2).

Total RNA was isolated using the Qiagen Mini RNeasy kit following the manufacturer’s instructions and RNA integrity assessed on a BioAnalyzer (Agilent Technologies).

Fragmented ssDNA was then labelled and hybridized to the Affymetrix GeneChip Mouse Gene 1.0 ST Array (Affymetrix). Chips were processed on an Affymetrix GeneChip Fluidics Station 450.

200 ng RNA was used to generate labelled sense single stranded DNA (ssDNA) for hybridization with the Ambion WT Expression Kit, the Affymetrix WT Terminal Labelling and Controls Kit and the Affymetrix Hybridization, Wash, and Stain Kit as described by the manufacturer.  Sense ssDNA was fragmented and the distribution of fragment lengths was measured on a BioAnalyzer.

neuro 2A (N2A);neuroblastoma cell line;transiently transfected with Pou3f3 knockdown construct

129P3/J Chronic morphine treated, striatum, biological replicate 1

Caco-2 cells were transfected with either the Sirt1 overexpression construct (pCMV-ENTRY Sirt1) or negative control (pCMV-Neo).  For knockdowns cells were transfected with one of two non-overlapping siRNAs and control samples with a low-GC scrambled siRNA control and cells lysed after 72 hours

Caco-2 cells were maintained  in DMEM medium, 10% Fetal Calf Serum at 37oC, 5% non-essential amino acids

Samples scanned using Illumina iScan array scanner to Illumina protocols

Total RNA was extracted using Trizol followed by Invitrogen PureLink RNA mini kit

750ng of biotinylated cRNA was hybridised to Illumina HT-12 v4 arrays using methods adapted from the Whole-Genome Gene Expression Direct Hybridization Assay Illumina protocol by ServiceXS

Illumina TotalPrep-96 RNA amplification kit was used to generate Biotin labeled cRNA according to manufacturers instructions

PBMC isolated by Ficoll gradient centrifugation from polyaticular course JRA patient
Keywords = Polyarticular course, juvenile rheumatoid arthritis (JRA), peripheral blood mononuclear cells (PBMC)

LOX-1:121301;GFP_oxLDL_6hr:121301;Classification:Good;Gradient Severity:0.03;Distortion Severity:0.03;Defective Area (%):0;Outlier Area (%):0.01;3'/5' Mean:1.64;Background Mean Dev.:1.02;Absent (%):58.02;Absent (%) Dev.:0.18;Scaling Factor:0.73;Scaling Factor Dev.:1.06;GFP;6 hours;Oxidized LDL;121301;HAECT;50 ug/ml;Endothelial;Human:Homo sapiens;GFP_oxLDL_6hr;282295623

LOX-1:121302;GFP_oxLDL_6hr:121302;Classification:Good;Gradient Severity:0.06;Distortion Severity:0.05;Defective Area (%):0;Outlier Area (%):0.01;3'/5' Mean:1.73;Background Mean Dev.:0.4;Absent (%):58.81;Absent (%) Dev.:0.43;Scaling Factor:0.71;Scaling Factor Dev.:0.89;GFP;6 hours;Oxidized LDL;121302;HAECT;50 ug/ml;Endothelial;Human:Homo sapiens;GFP_oxLDL_6hr;282295633

LOX-1:213501;LOX1_Untreated_24hr:213501;Classification:Good;Gradient Severity:0.03;Distortion Severity:0.02;Defective Area (%):0;Outlier Area (%):0.01;3'/5' Mean:1.65;Background Mean Dev.:0.43;Absent (%):59.43;Absent (%) Dev.:0.91;Scaling Factor:0.75;Scaling Factor Dev.:1.18;LOX1;24 hours;(Not applicable);213501;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;LOX1_Untreated_24hr;282295893

LOX-1:113303;GFP_Untreated_6hr:113303;Classification:Good;Gradient Severity:0.03;Distortion Severity:0.02;Defective Area (%):0.01;Outlier Area (%):0.01;3'/5' Mean:1.66;Background Mean Dev.:0.13;Absent (%):58.09;Absent (%) Dev.:0.13;Scaling Factor:0.63;Scaling Factor Dev.:0.14;GFP;6 hours;(Not applicable);113303;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;GFP_Untreated_6hr;282295613

LOX-1:213102;LOX1_0hr:213102;Classification:Good;Gradient Severity:0.04;Distortion Severity:0.07;Defective Area (%):0.01;Outlier Area (%):0;3'/5' Mean:1.58;Background Mean Dev.:1.4;Absent (%):59.09;Absent (%) Dev.:0.65;Scaling Factor:0.6;Scaling Factor Dev.:0.13;LOX1;0 hours;(Not applicable);213102;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;LOX1_0hr;282295453

LOX-1:221301;LOX1_oxLDL_6hr:221301;Classification:Good;Gradient Severity:0.01;Distortion Severity:0.04;Defective Area (%):0;Outlier Area (%):0.01;3'/5' Mean:2.2;Background Mean Dev.:0.45;Absent (%):57.76;Absent (%) Dev.:0.38;Scaling Factor:0.62;Scaling Factor Dev.:0.1;LOX1;6 hours;Oxidized LDL;221301;HAECT;50 ug/ml;Endothelial;Human:Homo sapiens;LOX1_oxLDL_6hr;282295683

LOX-1:113302;GFP_Untreated_6hr:113302;Classification:Medium;Gradient Severity:0.03;Distortion Severity:0.02;Defective Area (%):0;Outlier Area (%):0.01;3'/5' Mean:1.43;Background Mean Dev.:1.03;Absent (%):59.24;Absent (%) Dev.:0.77;Scaling Factor:0.87;Scaling Factor Dev.:2.23;GFP;6 hours;(Not applicable);113302;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;GFP_Untreated_6hr;282295603

LOX-1:221501;LOX1_oxLDL_24hr:221501;Classification:Bad;Gradient Severity:0.05;Distortion Severity:0.03;Defective Area (%):0.02;Outlier Area (%):0.01;3'/5' Mean:1.51;Background Mean Dev.:4.68;Absent (%):57.36;Absent (%) Dev.:0.69;Scaling Factor:0.33;Scaling Factor Dev.:2.44;LOX1;24 hours;Oxidized LDL;221501;HAECT;50 ug/ml;Endothelial;Human:Homo sapiens;LOX1_oxLDL_24hr;282295923

LOX-1:213503;LOX1_Untreated_24hr:213503;Classification:Bad;Gradient Severity:0.04;Distortion Severity:0.08;Defective Area (%):0.03;Outlier Area (%):0.02;3'/5' Mean:1.74;Background Mean Dev.:2.24;Absent (%):61.27;Absent (%) Dev.:2.34;Scaling Factor:1.66;Scaling Factor Dev.:9.07;LOX1;24 hours;(Not applicable);213503;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;LOX1_Untreated_24hr;282295913

Gene expression data from WT mouse mammary gland compared to mice deficient for Caveolin-3

FVB/N genetic background. 4-month old;virgin female mice were used, mice were kept on a 12-hour;light/dark cycle with ad libitum access to chow and water

Alk2 cKO mice, whole uterine tissues, mouse lines maintained on a hybrid C57BL/6J and 129S5/SvEvBrd genetic background

Air
1
12

Air
1
12

Air
1
8

Air
1
8

Raw images were processed using Microarray Suite 5.0 software. For the processing of the microarray data, we used SemiRMA (Bebu et al., 2007).

CG
32 mg
1

CG
32 mg
1

Expression values generated with GCOS affymetrix software using all probe sets scaling factor 1500

Standard Affymetrix hybridization protocols, using five micrograms of target

Used two round Epicentre kit, as per Potter GUDMAP.ORG protocols

strain CD-1 mouse. RV was isolated by laser capture microdissection.

Immune_Peripheral Blood Mononuclear Cells (ficoll)_1

Immune_Peripheral Blood Mononuclear Cells (ficoll)_2

Immune_CD4+_column purified_T-cells_antiCD3, antiCD28-activated

Synovium; chronic arthritis

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D42;2

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D21;2

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D42;P1

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D21;P1

male;non-metastatic prostate cancer;peripheral blood;white blood cells;baseline;2

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D72 (30 days post-EBRT);P1

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D1;2

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D14;2

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D7;2

GeneChips were scanned using an Agilent GeneArray laser scanner. Images were analyzed using Affymetrix MAS 5.0 software.

To compare array data between GeneChips, we scaled the average of the fluorescent intensities of all probes on each array to a constant target intensity of 500

TriTRIzol extraction procedure, followed by a cleanup using QIAGEN RNeasy Mini kit.

10 ug of cRNA was hybridized for 16 hours to an Affymetrix (Santa Clara, CA) mouse 430A GeneChip (5 chips per genotype group), followed by incubations with streptavidin-conjugated phycoerythrin, and then with polyclonal anti-streptavidin antibody coupled to phycoerythrin.

8 ug total RNA was used for cDNA synthesis using a T7-(deoxythymidine)24 primer and Superscript II (Life Technologies, Inc., Gaithersburg, MD). The resulting cDNA was used with the ENZO BioArray High Yield RNA Transcript labeling kit (ENZO, Farmingdale, NY) to synthesize biotin-labeled cRNA. The cRNA was purified on RNeasy spin columns (QIAGEN) and subjected to chemical fragmentation (size range of 35 to 200 bp). Three replicate cRNA targets were made in parallel starting from each RNA pool.

Bacterial sequence-derived probes on the arrays served as external controls for hybridization, whereas the housekeeping genes β-actin and GAPDH served as endogenous controls and for monitoring the quality of the RNA target.

RE1_H18_1930_U133Plus2.0.CEL

RE1_H13_1647_U133Plus2.0.CEL

RE1_H3_1296_U133Plus2.0.CEL

C57BL-6J were given saline.  Lungs were harvested and frozen at 72h.
Lot batch =

The displayed array hybridization values were obtained using the Affymetrix MAS 4.0 software

Analysis of human cancer cell lines depleted of c-MYC via RNA interference (RNAi), or the corresponding control

Mice used were in a mixed background between 129/SvEv and C57BL/6. They were Rp1 knockout mice (Rp1-/-). At P18, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.

Mice used were in a mixed background between 129/SvEv and C57BL/6. They were Rp1 knockout mice (Rp1-/-). At P21, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.

Mice used were in a mixed background between 129/SvEv and C57BL/6. They were Rp1 knockout mice (Rp1-/-). At P14, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.

Mice used were in a mixed background between 129/SvEv and C57BL/6. They were Rp1 knockout mice (Rp1-/-). At P10, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.

Performed according to the manufacturer's (Affymetrix) recommendations

Raw intensities from the CEL files were analyzed using Affymetrix Power Tool (APT, version 1.8.5) to generate robust multi-array average intensity in log2 scale for each probe set. The perfect match intensities for each probe set were corrected for background and quantile-normalized using a robust fit of linear models.

Ambion MessageAmp II-biotin enhanced kit (manufacturer's recommendations)

R version 2.11.1 (x86_64-pc-linux-gnu), affyPLM_1.24.1, preprocessCore_1.10.0, gcrma_2.20.0, affy_1.26.1, Biobase_2.8.0

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430A 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Kyoto rat liver tissue following animal exposure to orotic acid for 3 days

Wistar rat liver tissue following animal exposure to orotic acid for 1 day

Undifferentiated ESCs were plated at on pre-seeded confluent, non-irradiated OP9 stromal cells (day 0) and cultured in αMEM supplemented with 20% FCS (Gibco-Invitrogen). On day 4, 5, and 6 of differentiation “in vitro”, cells were harvested by trypsinization and FACS purified for Flk-1+ cells (98% purity).

Arrays were scanned with an Affymetrix GeneChip Scanner 3000, using the GCOS software from Affymetrix.

Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Gruen) with the Bioretis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the Bioretis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All 3 chips of one group were compared to each 3 chips of any other group, and the following parameters of absolute and comparative analysis were included in the Bioretis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p-value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal I, MI; Decrease, D; Marginal D, MD; No Change, NC), and the p value for that call. Additionally – not calculated with GCOS – t-tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using strict Bonferroni corrected Welch t-tests between 9 SLR values of Experiment group vs. Baseline group and 12 SLR values within both groups (the latter 12 giving a mean SLR value of zero; p-value had to be <= 5.279E-08) or more than 50% of non-parametrically calculated Change calls (Mann-Whitney U test, GCOS) i.e. 5 or more of all 9 Change calls have to be in the same direction. Significantly differentially expressed genes, were filtered using both default parameter sets of filter criteria; these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips and validated with the Affymetrix Latin Square dataset as shown in Menssen et al., 2009. You can find these validation experiments in BioRetis without registering, using the public content and public login. Click on view single results, select any existing Analysis beginning with first 3 letters "SGU" and click on "Next". Click on "Chose an existing parameterset" and select "JRG_Increase" for increased or "JRG_Decrease" for decreased probesets and click on "Fill". At the bottom of the site check the box named "* use Bonferroni correction" and click on "Search only" to get the list of significantly changed increased or decreased probesets, respectively. The Affymetrix Latin Square dataset, consisting of 42 chips in 14 experiments with three replicates each were analyzed in BioRetis with all possible 3 vs. 3 chip comparisons (one direction).

Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including the recommended DNase digest. The amount, purity, and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).

Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.

Gene-expression profiling of three biological replicates was performed at day 6 during the differentiation process of Runx1-/- J1 ESCs (3 samples). Samples were analyzed using mouse Genome 430-2 arrays (Affymetrix).

129-Sv;J1;embryonic stem;6 days;differentiated Flk1+ Runx1-/- ES cells

Gene-expression profiling of three biological replicates was performed at day 6 during the differentiation process of Tal-1-/- J1 ESCs (3 samples). Samples were analyzed using mouse Genome 430-2 arrays (Affymetrix).

129-Sv;J1;embryonic stem;6 days;differentiated Flk1+ Tal-1-/-  ES cells

A549 human lung cancer cells (1X10^5 per T-25 flask in 7 mL complete RPMI 1640 medium) were seeded eights days prior to treatment of non-cycling plateau phase cultures with drug.  At four hours prior to RNA isolation, 1.25uM sapphyrin PCI-2050 (1.25uM final concentration) was added to the culture.  After incubation for four hours, the culture was washed twice with HBSS supplemented with 0.5% BSA and total RNA was isolated.

1.25uM sapphyrin PCI-2050 treated A549 human lung cancer cell cultures replicate C

We used the Affymetrix GeneChip® Scanner 3000 according to the manufacturer's recommended protocols.

We used the RNA Stat-60 reagent (Tel-Test, Inc.) according to the manufacturer's recommended protocols.

We used the Affymetrix Hybridization Oven 640 and GeneChip® Fluidics Station 450 according to the manufacturer's recommended protocols.

We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.

Gene expression data under ER stress from lymphoblastoid cells of twin 1721:1 treated with DMSO.

lymphoblastoid cell line;1721;GM14467;Twin number 1;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1721:1 treated with 500nM thapsigargin.

lymphoblastoid cell line;1721;GM14467;Twin number 1;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1715:1 treated with DMSO.

lymphoblastoid cell line;1715;GM14447;Twin number 1;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1715:1 treated with 500nM thapsigargin.

lymphoblastoid cell line;1715;GM14447;Twin number 1;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1715:2 treated with DMSO.

lymphoblastoid cell line;1715;GM14448;Twin number 2;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1715:2 treated with 500nM thapsigargin.

lymphoblastoid cell line;1715;GM14448;Twin number 2;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1716:1 treated with DMSO.

lymphoblastoid cell line;1716;GM14452;Twin number 1;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1716:1 treated with 500nM thapsigargin.

lymphoblastoid cell line;1716;GM14452;Twin number 1;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1716:2 treated with DMSO.

lymphoblastoid cell line;1716;GM14453;Twin number 2;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1716:2 treated with 500nM thapsigargin.

lymphoblastoid cell line;1716;GM14453;Twin number 2;thapsigargin;500nM;4 hours

Hdh knock-in embryonic stem cells, Q111 line, biological replicate 2

Hdh knock-in embryonic stem cells, Q111 line, biological replicate 1

Hdh knock-in embryonic stem cells, Q111 line, biological replicate 3

The study was performed with aortas isolated from three groups of mice (32-34 weeks of age), i.e. untreated APOE-deficient mice (APOE), APOE-deficient mice treated with captopril (20 mg/kg in drinking water) for 7 months (Capto), and nontransgenic control mice (Cont).

The study was initiated with 4-6 week-old APOE-deficient mice on a C57BL/6J background, and non-transgenic C57BL/6J controls. Mice had free access to food and water, and were fed a standard rodent chow containing 7 % fat and 0.15 % cholesterol (Ain 93-based diet). For atherosclerosis treatment, one subgroup of APOE-deficient mice received captopril in drinking water (20 mg/kg) for 7 months. At an age of 32-34 weeks, aortas were isolated from three study groups (APOE-deficient, captopril-treated APOE-deficient, and nontransgenic control mice), dissected free of fat, and immediately frozen in liquid nitrogen.

The signals were processed using Affymetrix GeneChip Operating Software (GCOS; v.1.4; Affymetrix). To compare samples and experiments, the trimmed mean signal of each array was scaled to a target intensity of 200.

Total aortic RNA was isolated with the RNeasy Midi kit according to the manufacturer`s instructions (Qiagen).

For hybridization, 15 µg of fragmented cRNA were incubated with the chip (Mouse Genome MG430 2.0 Array) in 200 µl of the hybridization solution in a Hybridization Oven 640 (Affymetrix) for 16 h at 45 °C. GeneChips were then washed and stained using the Affymetrix Fluidics Station 450 according to the GeneChip Expression Analysis Technical Manual (Rev. 5).

Biotinylated cRNA was prepared according to the protocol of the manufacturer (Affymetrix; GeneChip Expression Analysis Technical Manual; Rev. 5).

Gene expression data from aortas isolated from non-transgenic C57BL/6J control mice.
Cont-1

Cont-2

Gene expression data of bone marrow-derived macrophages derived from STAT6KO mouse
21_(Mouse430_2).CEL

6;C57Bl/6;STAT6 KO;bone marrow-derived macrophage;Control;Control;10 days

U2-OS human osteosarcoma cells were stably transfected with ERa at low levels. This sample represents EtOH treated cells and was used as a control for the time-course experiment

mice treated with 4-amino tetrahydrobiopterin (50mg/kg every 8 hrs)

female;57 years;thorax;4.9x4x3;pleomorphic liposarcoma;high;G3;local recurrence;no;no

Refer to the protocols on the McGill University and Genome Quebec Innovation Centre website (http://www.genomequebec.mcgill.ca/services/microarray.php?page=tech). An Affymetrix GeneChIP 3000 scanner was used.

The signal intensities shown in the VALUE column are a measure of abundance of transcript and calculated from combined, background adjusted perfect match and mismatched values of the probe set. The raw data is in MAS 5.0 format.

Refer to the protocols on the McGill University and Genome Quebec Innovation Centre website (http://www.genomequebec.mcgill.ca/services/microarray.php?page=tech).

All hybridization were performed at the McGill University and Genome Quebec Innovation Centre. Affymetrix array technology involves the in-situ synthesis of hundreds of thousands of distinct oligonucleotide sequences onto a glass array using photolithography and combinatorial chemistry. Each 25-mer oligonucleotide is represented by millions of copies in a specific area. Each transcriptional sequence is spanned by 11-20 pairs of oligonucleotide probes randomly spaced throughout the array. All sequences designed on the array are selected from GenBank, dbEST and RefSeq. Target RNA is reverse transcribed into cDNA and in-vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization. Hybridized target cRNA is stained with streptavidin phycoerythrin and arrays are scanned using a GeneArray Scanner at an excitation wavelength of 488nm. Light emissions at 570nm are proportional to the bound target at each oligonucleotides position on the GeneChip® array.

Refer to protocols describe on the McGill University and Genome Quebec Innovation Centre website (http://www.genomequebec.mcgill.ca/services/microarray.php?page=tech). An Affymetrix GeneChIP 3000 scanner was used.

Refer to protocols describe on the McGill University and Genome Quebec Innovation Centre website (http://www.genomequebec.mcgill.ca/services/microarray.php?page=tech).

All hybridization were conducted at the McGill University and Genome Quebec Innovation Centre. Affymetrix array technology involves the in-situ synthesis of hundreds of thousands of distinct oligonucleotide sequences onto a glass array using photolithography and combinatorial chemistry. Each 25-mer oligonucleotide is represented by millions of copies in a specific area. Each transcriptional sequence is spanned by 11-20 pairs of oligonucleotide probes randomly spaced throughout the array. All sequences designed on the array are selected from GenBank, dbEST and RefSeq. Target RNA is reverse transcribed into cDNA and in-vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization. Hybridized target cRNA is stained with streptavidin phycoerythrin and arrays are scanned using a GeneArray Scanner at an excitation wavelength of 488nm. Light emissions at 570nm are proportional to the bound target at each oligonucleotides position on the GeneChip® array.

IA, IB, II, IIIA, IIIB, or IV=IIIB;73;female, male:female;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=intestinal type;normal

IA, IB, II, IIIA, IIIB, or IV=IIIB;69;female, male:female;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=IIIB;50;female, male:female;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=IIIB;69;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=IIIB;66;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=mixed type;normal

IA, IB, II, IIIA, IIIB, or IV=IIIB;36;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=IIIB;61;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=IIIB;49;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=IV;68;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=IV;60;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

brain (frontal cortex);healthy control;35 yr;white;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);healthy control;49 yr;white;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);healthy control;44 yr;white;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);healthy control;41 yr;white;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);healthy control;19 yr;white;296.73;17 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);healthy control;42 yr;white;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);healthy control;34 yr;white;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);healthy control;47 yr;white;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

B-Cells from Corielle were incubated at 37oC and 5% CO2 overnight, the day after cells are counted. Cells were expanded in RPMI 1640 with 2mM L-glutamine and 15% FBS following Corielle's lymphoblast line maintenance protocols. 1x10^7 cells were spun down and resuspended in 2 ml Tri-Reagent and frozen overnight at -80oC prior to RNA extraction

Std Tri-Reagent protocol followed by cleanup on RNEasy columns using an on-column DNase step. RNA quality is checked using a Nanodrop and an Agilent Bioanalyzer

129P3/J Chronic morphine treated, striatum, biological replicate 2

G42 cells from Cerebellum, wild type control, biological replicate 1

Gene expression data from G42 GFP labeled Purkinje neurons from the cerebellum (CB), Wild type control.

C57BL6/J;No;10/09/07;73;male;CB (cerebellum);Y/X;G42/-;G42 GFP labeled Purkinje neurons from the cerebellum

10 μg of RNA dissolved in 300 μL of buffer was hybridized to Mouse Genome 430. 2.0 GeneChips (Affymetrix). All samples were prepared with the two-cycle protocol recommended by the manufacturer.

The RNA was amplified, biotin labeled and fragmented using the Gene Chip 3’IVT Express Kit (Affymetrix). Yield of fragmented samples was tested by Nanodrop and RNA size was assessed by Bioanalyzer using the Agilent RNA 6000 Pico kit.

Embryos were removed from the dam and retinas were isolated, then washed in 1X PBS.

The original Onecut1 deficient mice were obtained and cross by us to C57Bl/6 for a few generations. The mice were described in Jacquemin P. et al, 2000 and were from R1 ES cells injected into a "Swiss" strain of mice.
Littermates were allowed to develop normally in utero until age E14, when they were harvested from the pregnant dam.

Amplified RNA was scanned from Affymetrix GeneChip Mouse Genome 430 2.0 arrays at the Iowa State University GeneChip Facility.

Trireagent extraction of total RNA was performed according to the manufacturer's instructions.

Amplified RNA was hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 arrays at the Iowa State University GeneChip Facility.

Total RNA wa amplified, biotinylated, and fragmented using the Ambion MessageAmp III RNA amplification kit according to manufacturer's instructions.

"male subject, 18-45 yrs, whole blood cells 3 h after intravenous endotoxin challenge"

"male subject, 18-45 yrs, whole blood cells 6 h after intravenous endotoxin challenge"

After differentiation, the U937 cells were starved overnight in phenol red free RPMI 1640 media with 0.5% FCS. The cells were then subjected to oxidative stress for 4 hours with the addition of H2O2 (100 uM). The media was then replaced with fresh complete growth media, and then incubated with/without curcumin (1uM) for a further 4hrs or 18 hrs, whereupon the cells were then harvested and total RNA extracted.

The human monocytic cell line (U937) was obtained from the American Type Culture Collection (ATTC, Rockville, MD, USA) and maintained in complete growth media (RPMI 1640 media supplemented with 10% fetal calf serum (FCS), 2 mM L-glutamine, 100 U/ml penicillin and 100 g/ml streptomycin) at +37C in a humidified atmosphere with 5% CO2.  U937 were differentiated into an adherent “macrophage-like” morphology by exposure to  PMA (40 ng/ml) for 4 hours in complete growth media at +37C, then cultured for a further 48hrs.

RNeasy extraction of total RNA was performed according to the manufacturer's instructions (Promega).

differentiated U937 cells, ROS exposed, 1uM curcumin treated, 18h

Following hybridization, arrays were washed and stained in an Affymetrix GeneChip Fluidics Station and scanned with a GeneChip® Scanner 3000 (Affymetrix, Santa Clara, CA).  Quality checks and data analyses were carried out using Affymetrix GeneChip Operating Software (GCOS) and Quality Reporter.

Log-ratios of gene expression data and associated platform p-values were generated in the Rosetta Resolver System (Rosetta Biosoftware, Seattle, WA, version 7.2) for all profiles relative to strain-matched vehicle-treated controls.
For each Affymetrix sequence (or probe set), log-ratio was defined to be the log10 of the intensity ratio of each animal (either treated with vehicle or CMP013) to the mean intensity of that sequence across the five profiles in the corresponding vehicle control group.

Total RNA was isolated from pieces of mouse liver according to the RNeasy extraction procedure (Qiagen, Valencia, CA).  Tissues were homogenized in QIAzol lysis buffer using the GenoGrinder 2000 homogenizer (SPEX SamplePrep, Metuchen, NJ).  Samples were processed on the Qiagen BioRobot Universal system according to the manufacturer’s instructions.  An on-column DNase digestion was performed to remove any residual genomic DNA contamination.  RNA concentration and yield were measured spectrophotometrically using the Nanodrop instrument.  Quality of the nucleic acid samples was evaluated with the RNA 6000 Nano chip kit (Agilent Technologies, Expert software).  Quality of samples was verified with distinct ribosomal 18S & 28S peaks, low baseline, and high RIN values (PXR+/+: 9.3-10; PXR-/-: 8.7-9.6).

For each sample, 10 ug of biotinylated cRNA spiked with hybridization controls (bioB, bioC, bioD and cre) was hybridized to an Affymetrix Mouse 430_2 microarray for 16 h at 45ºC.

Liver RNA from individual mice was profiled separately on the Affymetrix GeneChip® platform without technical replication.  Microarray profiling was performed by Cogenics (Morrisville, NC).  Briefly, 1 g of total RNA was reverse transcribed to double stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit and biotinylated cRNA was generated using the BioArray™ HighYield™ RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY).

bone marrow;CD34+ hematopoietic stem cells (HSC);healthy control

The hybridization was performed for 16 hours at 60 rpm and 45°C in the GeneChip® Hybridization Oven 640 (Affymetrix). Washing and staining of the arrays were done on the Gene Chip® Fluidics Station 400 (Affymetrix) according to the manufacturers recommendation. The antibody signal amplification, washing and staining protocol (Affymetrix) was used to stain the arrays with streptavidin R-phycoerythrin (SAPE). To amplify staining, SAPE solution was added twice with a biotinylated anti-streptavidin antibody (Vector Laboratories, CA) staining step in between.

The human CML lymphoblast K562 cell line (obtained from ATCC), which contains the b3a2 Bcr-Abl translocation, was used in this study.  Cells were grown and maintained in RPMI 1640 medium containing 10% FBS, under standard mammalian cell culture conditions as recommended by the ATCC.

Filter	570
Scanner ID	50206960
Scanner Type	GeneChip Scanner 3000 7G

Used and followed Absolutely RNA Miniprep Kit protocols from Stratagene.

Following fargmentation, 15 microg of cRNA were hybridized for 16 hrs on the GeneChip.  GeneChips were washed and stained in the Fluidics Station 450.

Affymetrix labeling reaction (GeneChip Expression 3' Amplification One-Cycle Target Labeling)

[Sample Info]
Chip Type	HG-U133_Plus_2
Chip Lot	4020537
Operator	administrator
Sample Type	human cell line K562
Description
Project	Gottesfeld_Chou
Comments	041407
Solution Type
Solution Lot
[Fluidics]
Station	1
Module	3
Hybridize Date	Sep 07 2006 12:04PM
[Scanner]
Filter	570
Scan Date	Sep 07 2006 01:30PM

Homo sapiens (human) Morphology: lymphoblast;Organ: bone marrow;chronic myelogenous leukemia (CML);53 years;female;The stemline chromosome number is triploid with the 2S component occurring at 4.2%. Fifteen markers (M1 and M(15)) occurred in nearly all S metaphases. Spontaneous non-specific dicentrics occurred, but rarely. Unstable markers were also rarely seen. The X was disomic, and N9 was nullisomic.

Low_8h_4

Ishikawa;39-year-old parous Japanese female diagnosed with endometrial adenocarcinoma stage 2.;bisphenol A;100 pM;8 hours

Station	1
Module	1
[Scanner]
Filter	570
Scan Date	Sep 07 2006 01:07PM

Low_24h_2

Ishikawa;39-year-old parous Japanese female diagnosed with endometrial adenocarcinoma stage 2.;bisphenol A;100 pM;24 hours

Station	2
Module	4
[Scanner]
Filter	570
Scan Date	Sep 07 2006 12:55PM

Low_8h_3

Low_8h_2

Low_48h_1

Low_24h_4

Mouse frontal cortex was sampled from embryonic day 15 transgenic animals and littermates control using disecction kits.

Mice harboring a Cyfip1 spanning BAC clone (RP24-333C15) were generated in the UCLA transgenic core (http://tmc.ctrl.ucla.edu/tg-core/) by injection into C57BL/6J pronuclei. Transgenic mice were identified by PCR screening of tail derived DNA.

Total RNA was isolated from embryonic day 15 frontal cortex from transgenic animals (n=3) and littermates controls (n=3) using the Qiagen RNeasy Kit. RNA quantity and quality was assessed using a Nanodrop (Nanodrop Technologies) and the Agilent Bioanalyzer (Agilent Technologies), respectively. Total RNA (200ng) was amplified, biotinylated and hybridized on Illumina Mouse ref-8 v2.0 BeadChip arrays, querying the expression of ~25,600 well-annotated Refseq transcripts, as per manufacturer's protocol.

"female subject, 18-45 yrs, whole blood cells 168 h after intravenous endotoxin challenge"

MEFs were grown in DMEM supplemented with 10% FBS, penicillin [100 units/ml], streptomycin [100 µg/ml] and sodium pyruvate [1 mM] prior to treatment.

Raw intensity values were VST transformed and quantile normalised

Total RNA was extracted from cells using an RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.

RNA was hybridised to Mouseref-6 arrays (approx. 47,000 transcripts, Illumina Inc, USA).

The RNA were biotinylated and amplified using an Illumina TotalPrep RNA Amplification Kit (Ambion by Life Technologies).

Skeletal muscle tissue was taken at basal conditions without  prior treatment.

Hybridized arrays were scanned using equipment in the UCSD Medical Center core facility

Probe intensity was sumarized and normalized using Affymetrix Microarray Analysis Suite 5.1. The trimmed mean target intensity of each array was set to 200.

Total RNA from 4 KO and 4 WT animals was extracted using Tri-reagent according to the manufactorer's recommendations. RNA was analyzed by electrophoresis on agarose gel.  The 4 KO and 4 WT samples were combined into 2 KO and 2 WT pools. 100µg were cleaned using QiageneRNA purification kit and analyzed by gel electrophoresis.

Standard Affymetrix hybridization protocol employed by the UCSD Medical Center core facility

Standard Affymetrix biotin labeling protocol employed by the UCSD Medical Center core facility

male;C57BL/6x129;6.5 months;Crhr2+/+;Gastrocnemius and Soleus muscles

male;C57BL/6x129;6.5 months;Crhr2-/-;Gastrocnemius and Soleus muscles

HeLa cells were treated with siRNA directed against firefly luciferase (as described in Mendell et al., Science, 2002; PubMed ID:12228722).  RNA was isolated using Trizol and Qiagen RNeasy kit.

Cell were untreated or treated with 2 uM vemurafenib for 1, 6 or 48 h.

Cells were growth in RPMI growth media supplemented with 10% of fetal bovine serum, 2 mM glutamine, 50 U/ml penicillin and 50 ug/ml streptomycin.

The data were normalised using quantile normalisation with Partek GS Software

Microarray normalisation and calculation of expression measures were performed using Robust Multiarray Average, implemented in the statistical package R provided by Bioconductor (Seattle, WA, USA). The expression values were log 2 transformed to obtain a normal distribution across arrays and samples. Before analysing the expression data we removed Affymetrix control probes, resulting in a total of 12,558 probes.

Total RNA was prepared from muscle cell cultures using RNeasy (Qiagen)

10 µg of fragmented cRNA were hybridised to a U95Av2 GeneChip (Affymetrix) using their standard procedure (45°C, 16-h). Washing and staining was performed in a Fluidics Station 400 (Affymetrix) using the protocol EukGE-WS2v4.

In vitro transcription was performed on 1 µg of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics, USA)

The control subjects had normal glucose tolerance and no family history of diabetes.

~70% confluent keratinocytes treated with 25 ng.ml of EphB2 or EFNA4-Fc conjugates (Sigma)

Standard e.g. as in Banno et al., J Biol Chem 279(31): 32633-32642.

Test compound:  Corn Oil
CAS: 8001-30-07
Delivery Volume:  1 mL/kg

Breifly, fragmented biotin-labeled cRNA was diluted in a hybridization cocktail containing hybridization buffer (100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween 20), 0.5 mg/mL acetylated BSA, 0.1 mg/mL herring sperm DNA, 50 pM of control oligonucleotide B2, and 1.5, 5, 25 and 100 pM of BioB, BioC, BioD and Cre eukaryotic hybridization controls, respectively.  Hybridization cocktails were incubated for 5 min at 99°C followed by incubation for 5 min at 45°C and then injected into the GeneChip® arrays.  Loaded GeneChips® were then incubated in an Affymetrix hybridization oven for 16 hours at 45°C and 60 RPM.  GeneChips® were then washed under a series of non-stringent (buffer A: 0.9 M NaCl,  0.06 M NaH2PO4,  6 mM EDTA, 0.01% Tween-20 at 25°C) and stringent (buffer B: 100 mM MES, 0.1 M NaCl, 0.05% Tween-20 at 50°C) conditions on an Affymetrix fluidics module using the EukGE-WS2v4-450 fluidics script.  GeneChips® were then stained with SAPE solution (100 mM MES, 1 M NaCl, 0.05 % Tween-20, 10 µg/mL streptavidin-phycoerythrin, 2 mg/mL acetylated BSA) and subjected to another series of washes in buffer A.

First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021).  Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol.  Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol.  Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer (200mM Tris acetate - pH = 8.1, 100 mM KOAc, 150 mM MgOAc).

WT and PDPN-deficient embryos were collected from pregnant females between E9.5 and 13.5. MEFs were grown in aMEM with 10% batch-selected fetal calf serum for 7-10 days. MEFs were then purified from any contaminanting endothelial and hematopoietic cells by negative MACS selection with biotinylated anti-CD31 and anti-CD45 antibodies.

Each cDNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis. From http://macf-web.dfci.harvard.edu/

Data were processed using GenePattern (Broad Institute). Data were RMA normalized.

A Qiagen Rneasy kit was used to isolate total RNA, according to the manufacturer's instructions.

Fragmented cDNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control) and hybridized to a microarray chip overnight at 45C. The chips are then washed to remove unhybridized cDNA. Bound cDNA is fluorescently labeled using phycoerythrin-conjugated streptavidin, additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE. From http://macf-web.dfci.harvard.edu/

Single stranded cDNA is synthesised and purified, then fragmented using uracil DNA glycosylase and Apurine/Apyrimidinic Endonuclease I. Fragmented cDNA is end-labeled with a biotinylated nucleotide analogue

Total RNA was extracted from the cell lysate using an RNeasy kit (Qiagen).

KLF4 over-eexpressed Ponesterone-treated samples and untreated controls

aortic biopsy distensible
Keywords = pulse wave velocity, arterial stiffness

Mice on a mixed 129/SvJ and C57BL6/J background were sacrificed and livers frozen.  RNA was isolated using RNeasy, then hybridized to AffyMetrix mouse U74Av2 chip according to manufacturer's protocol.  Data were normalized by AffyMetrix MAS5.0 using defaults.
Keywords = liver cholesterol abc

The brains were immediately removed, and hippocampi rapidly dissected and placed in RNAlater solution (Qiagen, Venlo, The Netherlands) until total RNA extraction.

P300 deficient heterozygous mice were maintained in a C57BL/6J pure background. Mice were group-housed in single-sex cages on a light:dark cycle (12/12 h) with food and water available ad limitum. The wild type mice used as control were, in all cases, littermates of the mutant mice.

GeneSpring GX software (Agilent Technologies Inc) was used. Data were extracting using RMA16 algorithm and values were normalized by the median of all samples. Data are represented as log2.

Total RNA was extracted separately from individual hippocampi using Trizol Reagent (Invitrogen, Carlsbad, CA, USA) per manufacturers instructions followed by a cleanup step using RNeasy RNA purification columns (Qiagen, Valencia, CA, USA). Equal amounts of total RNA from four animals were pooled, processed, and hybridized to Mouse Genome 430 2.0 genechips (Affymetrix, Santa Clara, CA). Three independent biological replicates were prepared for each genotype (wild-type and p300 deficient mice (p300+/-)). Mouse Genome 430 2.0 genechips were hybridized, stained, washed and screened for quality according to the manufacturer's protocol. Microarray data were processed, normalized and statistically analyzed using GeneSpring GX (Agilent Technologies, Santa Clara, CA).

Cell strain 12 of cyclin D1KO 3T3 cells obtained by serial passaging MEFs from E14 embryos, stably infected with MSCV-D1b murine stem cell virus.

Sample from retroviral MSCV-D1b infected cyclin D1 knockout 3T3 cells (line 12).

Gene expression data from cyclin D1 knockout 3T3s (cell line 12) infected with a cyclin D1 splice variant (variant D1b) using Murine Stem Cell Virus (MSCV) system.

U2OS;osteosarcoma cells;nonspecific siRNA (SiNS);dexamethasone (Dex) for 2h

U2OS;osteosarcoma cells;none (non-infected control);dexamethasone (Dex) for 24h

GeneChip Operating Software (GCOS) 1.2
software (Affymetrix, Inc.) using default values (scaling, target signal intensity = 500; normalization, all probe sets; parameters, all set at default values) was used to generate the data.

The study was performed in liver-endothelial cells (LECs) isolated from adult male Wistar rats, undergoing a cirrhosis induction protocol as described previously by our group, and LECs isolated from control Wistar rats, according to the criteria of the Investigation and Ethics Committee of the Hospital Clínic Universitari (Spain).The aim of this study was to evaluate differences in the gene expression pattern between LECs from control and cirrhotic rats. Methods: LECs were isolated from livers by collagenase perfusion, isopycnic centrifugation and incubation of cells with magnetic beads coated with specific antibodies.Total RNA was extracted from LECs with Trizol reagent (Life Technologies, Rockville, MD) after the cell-isolation step described above. RNA quality and concentration were confirmed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). cRNA samples were hybridized to the Rat Expression 230A oligonucleotide microarray (Affymetrix). Microarray samples preparation and processing procedures where performed at the IDIBAPS Genomic Unit (Hospital Clinic Universitari, Barcelona) following the protocol as described in the Affymetrix GeneChip Expression Analysis Manual (Affymetrix, Inc, Santa Clara, CA).

Five strains each of cultured low-passage fibroblasts from keloids and normal scars were thawed from liquid nitrogen, subcultured and triplicate cultures grown to confluency (10 days) under standard culture conditions (daily feeding with Ham’s Nutrient Mixture F10 + 10% FBS) with and without 1.5 micromolar hydrocortisone.

GeneChips were scanned using GeneChip Scanner 3000 7G and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files and to generate gene expression values and ratios of gene expression between the hybridized samples

For statistical analysis, CEL files (raw Affymetrix data) were imported in GeneSpring 7.0 (Agilent Technologies) and transformed by RMA (Robust Multichip Analysis).

Total RNA was isolated using a standard Trizol method with DNase treatment followed by a second Trizol extraction.

Hybridized cRNA was detected using streptavidin coupled to phycoerythrin and visualized using GeneChip Scanner 3000 7G.

Following quality control, the RNA was prepared for microarray analysis using the standard Affymetrix protocol (Affymetrix Inc, Santa Clara, CA).  Briefly, a total of 5 µg of total RNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter.  In vitro transcription from the ds cDNA was then carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides.

Cell cultures were initiated from human biopsy material from normal dermal scars and keloids of adult males and females and frozen at first or second passage, in liquid nitrogen.  Experimental cultures were derived from the first passage of cells thawed from liquid nitrogen.

Primary culture of dermal fibroblasts from keloid, no hydrocortisone treatment

Primary culture of dermal fibroblasts from normal scar, treated with 1.5uM hydrocortisone

Primary culture of dermal fibroblasts from normal scar, no hydrocortisone treatment

in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 8, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 0.07, Units of Dose or Concentration: ppm

nasal epithelium, formaldehyde inhalation exposure, 0.7 ppm, 6 hours per day, 5 days per week, 8 day time point

Rat230_2;15;ul;2.265;1.203;1.85;1:5;8.6;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;144;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.793;0.877;1:5;8.5;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;143;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

in vivo Treatment: Formaldehyde, Treatment Duration: 6, Units of Duration: hrs, Treatment Time: 6, Units of Treatment Time: hrs, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 0.7, Units of Dose or Concentration: ppm

nasal epithelium, formaldehyde inhalation exposure, 0.7 ppm, 6 hour time point

Rat230_2;15;ul;2.04;1.071;1.88;1:5;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;131;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.621;0.822;1.93;1:5;8.4;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;130;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 24, Units of Duration: hrs, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 0, Units of Dose or Concentration: ppm

Sample Type: Cells, Tissue: nasal epithelial cells (level II region), Tissue Harvest Methods: The nose was dissected to isolate the Level II region of both nostrils.  The maxillo turbinate and olfactory epithelium were discarded and the lateral meatus and nasoturbinate were retained for cell isolation.  The dissected nasal sections were rinsed with cold phosphate buffered saline to remove the blood.  After rinsing, a 5 ml buffered mixture of proteases (collagenase, 80 U/ml, Sigma-Aldrich; pronase, 10 mg/ml, Sigma-Aldrich; HEPES, 0.1 M) in Hams F12 medium (Invitrogen, Carlsbad, CA) was added to the nose and incubated at 37°C for 40 minutes to remove the epithelial cell layer.  Following incubation, the mixture was vortexed and the resulting cell suspension was collected in a clean centrifuge tube.  The cell suspension was centrifuged (200 x g, 10 min, 10°C) and the cell pellet was resuspended in 50 ?L PBS and 200 ?L RNAlater (Ambion, Austin, TX).  The epithelial cells acquired consisted primarily of transitional epithelium with some respiratory epithelium., Harvest Time Point: 24, Units of Harvest Time Point: hrs
nasal epithelium, formaldehyde inhalation exposure, air control, 6 hours per day, 24 h time point

Rat230_2;15;ul;1.509;0.793;1.84;1:5;7.9;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;58;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;2.468;1.278;1.88;1:5;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;57;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;2.899;1.476;1.91;1:5;7.5;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;56;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;2.782;1.422;1.91;1:5;8.2;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;54;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 19, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 0, Units of Dose or Concentration: ppm

nasal epithelium, formaldehyde inhalation exposure, air control, 6 hours per day, 5 days per week, 19 day time point

Rat230_2;15;ul;1.808;0.956;1.88;1:5;8.4;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;77;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.748;0.861;2.01;1:5;8.5;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;76;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

At 6 weeks mouse was treated by administration of 5 daily intraperitoneal injections of citrate buffer control (0.05 mol/L; pH 4.5) (Sigma Aldrich).

ApoE-/- RAGE-/-;C57BL/6;Ann Marie Schmidt laboratory, Columbia University;Male;9 weeks;Total aorta from root to bifurcation.;non-diabetic

Aorta from ApoE-/-  RAGE-/- mouse without diabetes sacrificed at 9 weeks.

Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.1 analysis software.

Data for both channels were Lowess-normalized and then log(2) ratio was taken

Microarray experiments were performed using whole-mouse-genome oligoarrays (Mouse430a, Affymetrix). Array data were analyzed using MAYDAY (Version 2.12). Array data were subjected to robust multi-array average (RMA) normalization. Normalized data were used for calculating fold changes of up- and down-regulated genes using Student's test. Only data with a false discovery rate (FDR) adjusted p-value <0.05 and at least 2x differential expression were included in the analysis. Data underwent z-score transformation for display.

four hours upon infection RNA was isolated with the mRNeasy Mini Kit of Qiagen

HepG2 nt and HIF-1-/- cells were infected with S. aureus 8325-4 (MOI: 20) for four hours (5 % CO2, 96 % humidity and 37 °C)

standard affymetrix scanning protocol with affymetrix 3000 7G Scanner

The data were analyzed with GCOS version 1.1.1.052 using Affymetrix default analysis settings and GeneSpring 9.3 software package

Male B6C3F1 mice were purchased from Harlan Sprague-Dawley at 6-7 weeks of age. Mice were housed singly in a pathogen-free facility and provided acidified water ad libitum.

After staining, the gene chips were read at a resolution of 3 μm using a Hewlett Packard GeneArray Scanner (Affymetrix, Santa Clara, CA). The averaged images collected from two scanned images were used for the analysis.

GeneChip Analysis Suite 5.0 was used to analyze the image data. The Affymetrix Mouse Genome U74Av2 chip is derived from selected genes and ESTs. Each gene is represented by the use of 16 perfectly matched and mismatched (MM) control probes. The MM probes acts as specificity controls that allows the direct subtraction of both background and cross-hybridization signals. To determine the quantitative RNA abundance, the average of the differences representing PM minus MM for each gene-specific probe family is calculated, after discarding the maximum, the minimum and any outliers beyond 3 standard deviations. To minimize variability in hybridization, the global scaling method normalizes signals of each chip. The global scaling method is computational technique in which the average signal of all probe sets in one chip is scaled to a target average intensity by multiplying a scaling factor. This scaling factor is multiplied to each probe set signal to give the raw expression.

Total RNA was extracted from frozen tissue using the TRIZOL reagent (Life Technologies, Grand Island, NY) and mRNA was purified from the total RNA with oligo-dT-linked oligotex resin (Qiagen, Valencia, CA). Then, double-stranded cDNA was synthesized from 1ug of mRNA using the SuperScript Choice System (Life Technologies, Grand Island, NY) with an oligo-dT primer containing a T7 RNA polymerase promoter (Genset, La Jolla, CA), purified with phenol-chloroform-isoamyl alcohol, and precipitated with pellet paint co-precipitant (Novagen, Madison, WI). Purified double-stranded cDNA was used to synthesize biotin-labeled cRNA using the BioArray High Yield RNA Transcript Labeling Kit (Enzo, Farmingdale, NY). The biotin-labeled antisense cRNA was then purified with the RNeasy affinity column (Qiagen, Valencia, CA). After purification, biotin-labeled cRNA was fragmented randomly to sizes ranging from 35 to 200 bases.

Total 10ug cRNA was placed in the gene chip. The gene chip I used for this study is the Affymetrix Murine Genome U74Av2 chips (Affymetrix, Santa Clara, CA), which covers 12,422 transcripts. Hybridization was carried out at 45ºC for 16 h with mixing on a rotisserie at 60 rpm. Following hybridization, the hybridization solutions were removed and the gene chips were be installed in a fluidics system for washes and staining.

We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples.

GeneSpring Software (Affymetrix, version 11.5) was used for primary analysis.  Genes were denoted as present if they had a MAS5 present call on 10/40 chips.  The concordance of 3 summarization algorithms were used: MAS5, RMA, and GC-RMA.  Significantly altered genes were determined by a 2x2 ANOVA within GeneSpring on patient group (cerebral palsy or control patients) and muscle (gracilis or semitendinosus) with a False Discovery Rate set at 1%.  This analysis was performed on each of the three summarization algorithms and the overlap of all 3 was used as the significantly different gene set. The RMA and GCRMA in log2 format values are linked to the Series record.

Following fragmentation, 15 ug of cRNA were hybridized for 16-18 hr at 45oC on GeneChip Human Genome U133A Array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2-5 ug total RNA

Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was done across this data set togeteher with all .CEL files from the GSE25168 series by the RMA algorithm using GeneSpring GX11 program. No further adjustments were made to the data in the table.

Total RNA was extracted using RNeasy micro-elute columns (QIAGEN), according to manufacturer's instructions.

2.2 micrograms of cDNA was hybridized for 17 hr to the Affymetrix array as described in the Ovationâ¢ Biotin RNA Amplification and Labeling System manual. GenechipsÂ® were processed using protocol EukGE_WS2v4 450 for GenechipÂ® fluidics station 450.

wildtype;mixed background (Gebuhr TC, Kovalev GI, Bultman S, Godfrey V, Su L, Magnuson T. The role of Brg1, a catalytic subunit of mammalian chromatin-remodeling complexes, in T cell development. J Exp Med. 2003 Dec 15;198(12):1937-49.);P1

Tissue was stored in in buffer RLT (Qiagen) at -80 degrees until processing with an RNEasy kit.

All  samples were harvested fresh from embryos at E17.5 and purified by cell sorting.

Un-normalized summary probe profiles were output from BeadStudio and analysed using the limma package version 3.12.1 (http://www.bioconductor.org) for R 2.15.1 (http://www.r-project.org). Raw intensities were neqc background corrected and normalized with offset 16.

RNA was extracted using QIAGEN RNeasy micro kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

RE1_H12_1628_U133Plus2.0.CEL

RE1_H1_1278_U133Plus2.0.CEL

RE1_H15_1682_U133Plus2.0.CEL

RE1_H8_1389_U133Plus2.0.CEL

RE1_H24_2259_U133Plus2.0.CEL

RE1_H23_2233_U133Plus2.0.CEL

European-American (EA);Female;healthy control;Peripheral blood;CD20-APC;CD20 positive B cells

African-American (AA);Female;healthy control;Peripheral blood;CD20-APC;CD20 positive B cells

European-American (EA);Female;Systemic lupus erythematosus (SLE) patient;Peripheral blood;CD20-APC;CD20 positive B cells

Muscle biopsies were flash frozen in liquid nitrogen and stored at -80°C until usage. Samples were homogenized using an IKA ultra-turrax T8 homogenizer

The data were analyzed with BRB-Array Tools using rma as probeset summarization algoritm

Trizol extraction of total RNA was performed according to the manufacturer's instructions. Tot RNA was further purified using the RNAeasy mini purification kit (QIAGEN) according to the RNA cleanup protocol

Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on HG 133A  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Gene expression data from skeletal muscle tissue of presymptomatic DMD children and age matched controls

Male;12 months;additional patient information found in Series supplementary file

Male;14 months;additional patient information found in Series supplementary file

The data was normalized with RMA (default settings) as implemented in Bioconductor. RMA gives log2 transformed data

Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on Murine Genome U74 Version 2 Set MG-U74A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Male;6 months;additional patient information found in Series supplementary file

Male;7 months;additional patient information found in Series supplementary file

Male;5 months;additional patient information found in Series supplementary file

Male;11 months;additional patient information found in Series supplementary file

Male;8 months;additional patient information found in Series supplementary file

HepG2 cells treated in vitro with fluoroquinolones
Growth Media: Minimal Essential Media with 10%FBS

Primary human hepatocytes incubated in vitro with quinolones
Growth Media:  In Vitro Technologies Hepatocyte Incubation Media (Cat No. Z90009

Primary Human Hepatocyte;Male;In Vitro Technologies;Anoxia;No;2nd technical replicate

HepG2 incubated in vitro with quinolones
Growth Media:  Mimimal Essential Media with 10% FBS

Primary Human Hepatocyte;Female;In Vitro Technologies;Celebral Vascular Accident;Yes;2nd technical replicate

Primary Human Hepatocyte;Male;In Vitro Technologies;Anoxia;No;1st technical replicate

Primary Human Hepatocyte;Female;In Vitro Technologies;Celebral Vascular Accident;Yes;1st technical replicate

GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000

Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U 133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

One-Cycle cDNA synthesis kit and the GeneChip ® IVT labeling kit

An Affymetrix GeneChip Scanner 3000 (Affymetrix Inc., Santa Clara, CA) was used to measure the fluorescent intensity emitted by the labeled target.

Data processing was performed using the Affymetrix GCOS 1.4 software (Affymetrix Inc., Santa Clara, CA). After hybridization and scanning, probe cell intensities were calculated and summarized for the respective probe sets by means of the MAS5 algorithm (Hubbell et al 2002). To compare the expression values of the genes from chip to chip, global scaling was performed, which resulted in the normalization of the trimmed mean of each chip to a target intensity (TGT value) of 500 as detailed in the statistical algorithms description document of Affymetrix (2002). Quality control measures were considered before performing the statistical analysis. These included adequate scaling factors (between 1 and 3 for all samples) and appropriate numbers of present calls calculated by application of a signed-rank call algorithm (Liu et al., 2002). The efficiency of the labeling reaction and the hybridization performance was controlled with the following parameters: Present calls and optimal 3' /5' hybridization ratios (around 1) for the housekeeping genes, for the poly A spike in controls and the prokaryotic control.

Biotin-labeled cRNA samples (15 µg) were fragmented randomly to 35–200 bp at 94°C in Fragmentation Buffer (Affymetrix Inc., P/N 900371, Santa Clara, CA) and were mixed in 300 µl of hybridization buffer containing a hybridization Control cRNA and Control Oligo B2 control (Affymetrix Inc., P/N 900454, Santa Clara, CA), 0.1 mg/ml herring sperm DNA and 0.5 mg/ml acetylated bovine serum albumin in 2-(4-morpholino)-ethane sulfonic acid (MES) buffer, pH 6.7, before hybridization to GeneChip® Mouse Genome 430 2.0 arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 EukGE-WS2v5_450 protocol.

The quality of the isolated RNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies, Delaware, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. Total RNA samples (30 ng) were reverse-transcribed into double-stranded cDNA with Two-Cycle cDNA Synthesis Kit (Affymetrix Inc., P/N 900494, Santa Clara, CA). The double-stranded cDNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA). The purified double-stranded cDNA were in vitro transcribed in presence of biotin-labeled nucleotides using a IVT Labeling Kit (Affymetrix Inc., P/N 900449, Santa Clara, CA). The biotinylated cRNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA) and its quality and quantity was determined using NanoDrop ND 1000 and Bioanalyzer 2100.

Conditional beta cell specific KO mouse model using RIP2-Cre and Vhlh(fl/fl);Herrera PL (2000), Haase VH et al. (2001);male;18 weeks;VhlhKO

Conditional beta cell specific KO mouse model using RIP2-Cre and Vhlh(fl/fl);Herrera PL (2000), Haase VH et al. (2001);female;20 weeks;control

Conditional beta cell specific KO mouse model using RIP2-Cre and Vhlh(fl/fl);Herrera PL (2000), Haase VH et al. (2001);male;18 weeks;control

Conditional beta cell specific KO mouse model using RIP2-Cre and Vhlh(fl/fl);Herrera PL (2000), Haase VH et al. (2001);male;26 weeks;VhlhKO

Conditional beta cell specific KO mouse model using RIP2-Cre and Vhlh(fl/fl);Herrera PL (2000), Haase VH et al. (2001);female;20 weeks;VhlhKO

Gene expression data from motor neurons of the sacral rat spinal cord 60 days post transection

Gene expression data from motor neurons of the sacral rat spinal cord 21 days post transection

This is Nrl-ko-Gfp P10 replicate 1.

This is Nrl-ko-Gfp E16 replicate 3.

This is Nrl-ko-Gfp E16 replicate 2.

This is Nrl-ko-Gfp E16 replicate 1.

This is Nrl-ko-Gfp 4 weeks replicate 4.

This is Nrl-ko-Gfp 4 weeks replicate 3

This is Nrl-ko-Gfp 4 weeks replicate 2

Female C57BL/6 mice were purchased from Charles River Laboratories (Sulzfeld, Germany) at age 4-6 weeks and kept in a pathogen free environment. The microarray experiments were performed in mice 32 - 34 weeks of age. RNA was extracted from the right quadriceps muscle of 5 C57BL/6 mice using TRIzol reagent (Invitrogen, Life Technologies, Carlsbad, USA). Total RNA was purified following the TRIzol standard protocol. Total RNA was treated by deoxyribonuclease I (Invitrogen) and purified using the RNeasy Mini Kit (Qiagen GmbH, Hilden, Germany) according to the manufacture's protocol. RNA integrity was checked by denaturating agarose gel electrophoresis, and only RNA with absorbance ratios 260 nm/280 nm between 1.9 and 2.1 was used. 8 µg RNA were transcribed in double-stranded cDNA by cDNA Synthesis System (Roche Diagnostics GmbH, Mannheim, Germany). cRNA was produced by MEGAscript TM High Yield Transcription Kit (Ambion, Austin, USA) and labelled with biotin-11-CTP and biotin-16-UTP nucleotides (Perkin Elmer Life Sciences, Boston, USA). 5 quardiceps biological replicates were analyzed using standard Affymetrix procedures.
Keywords = Mus musculus,  C57BL/6, skeletal muscle, quardiceps, effect of deleted gene dysferlin

Gene expression data from fetal liver wild type in respect to p38alpha

This is Nrl-ko-Gfp P10 replicate 3.

Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Manual)

RNA was extracted from freshly cultured PMVEC using a Qiagen RNEasy kit

FVB/N;Bmpr2-R899X mutation;pulmonary vascular microendothelial cells (PMVEC)

PMVEC isolated from mice carrying TetO7-Bmpr2-R899X, immortomouse and Rosa26-rtTA transgenes

Primary rib chondroyctes overnight culture in 10 cm dish in 10%FCD-containing DMEM

Total RNA was extracted by SurePrep (Fisher).  Ago2 immunoprecipitation was performed using WAKO's microRNA isolation Kit, mouse Ago2

Primary chondrocytes;Mir140 KO;129sv/C57 mixed background, backcrossed to C57B6 twice, C57B6 dominant

Primary chondrocytes;Wt;Ago2 antibody;129sv/C57 mixed background, backcrossed to C57B6 twice, C57B6 dominant;Wako biochemicals;292-67301;PEK486

Primary chondrocytes;Wt;129sv/C57 mixed background, backcrossed to C57B6 twice, C57B6 dominant

Primary chondrocytes;Mir140 KO;Ago2 antibody;129sv/C57 mixed background, backcrossed to C57B6 twice, C57B6 dominant;Wako biochemicals;292-67301;PEK486

3 min exposure to halothane prior to immediate perfusion with ice cold saline
Keywords = Eckenhoff
Keywords = anesthetics

Gene expression data of IL-4+RSG-treated bone marrow-derived macrophages derived from STAT6KO mouse
24_(Mouse430_2).CEL

6;C57Bl/6;STAT6 KO;bone marrow-derived macrophage;IL-4;Rosiglitazone;10 days

Gene expression data of IL-4-treated bone marrow-derived macrophages derived from STAT6KO mouse
23_(Mouse430_2).CEL

6;C57Bl/6;STAT6 KO;bone marrow-derived macrophage;IL-4;Control;10 days

Cyclophosphamide-treated peripheral blood leukocytes 5 days - Biological Replicate 1 - Technical Replicate 2

Biological replicate 1 of 3. Technical Replicate 2 of 2. Peripheral blood leukocytes,  CTX-treated day 5

Cyclophosphamide-treated peripheral blood leukocytes 5 days - Biological Replicate 1 - Technical Replicate 1

Biological replicate 1 of 3. Technical Replicate 1 of 2. Peripheral blood leukocytes, CTX-treated day 5

Cyclophosphamide-treated peripheral blood leukocytes 5 days - Biological Replicate 2 - Technical Replicate 2

Biological replicate 2 of 3. Technical Replicate 2 of 2. Peripheral blood leukocytes,  CTX-treated day 5

Cyclophosphamide-treated peripheral blood leukocytes 5 days - Biological Replicate 2 - Technical Replicate 1

Biological replicate 2 of 3. Technical Replicate 1 of 2. Peripheral blood leukocytes,  CTX-treated day 5

Cyclophosphamide-treated peripheral blood leukocytes 2 days - Biological Replicate 3 - Technical Replicate 2

Biological replicate 3 of 4. Technical Replicate 2 of 2. Peripheral blood leukocytes,  CTX-treated day 2

Cyclophosphamide-treated peripheral blood leukocytes 2 days - Biological Replicate 3 - Technical Replicate 1

Biological replicate 3 of 4. Technical Replicate 1 of 2. Peripheral blood leukocytes,  CTX-treated day 2

Cyclophosphamide-treated peripheral blood leukocytes 2 days - Biological Replicate 4 - Technical Replicate 2

Biological replicate 4 of 4. Technical Replicate 2 of 2. Peripheral blood leukocytes,  CTX-treated day 2

Cyclophosphamide-treated peripheral blood leukocytes 2 days - Biological Replicate 4 - Technical Replicate 1

Biological replicate 4 of 4. Technical Replicate 1 of 2. Peripheral blood leukocytes,  CTX-treated day 2

liver from a 42 day old male mouse, mutant 391 was dissected out. Total RNA was extracted using an Ambion RNaqueous RNA extraction kit. Targets were produced using modified Affymetrix procedure from 5ug of total RNA. 3 biological replicates were analysed per each group of animals.Sample also known as C1.
Keywords = Mouse, Growth hormone receptor, identification of signalling pathways

liver from a 42 day old male mouse, mutant 391 was dissected out. Total RNA was extracted using an Ambion RNaqueous RNA extraction kit. Targets were produced using modified Affymetrix procedure from 5ug of total RNA. 3 biological replicates were analysed per each group of animals.Sample also known as C2.

liver from a 42 day old male mouse, mutant 391 was dissected out. Total RNA was extracted using an Ambion RNaqueous RNA extraction kit. Targets were produced using modified Affymetrix procedure from 5ug of total RNA. 3 biological replicates were analysed per each group of animals.Sample also known as C3.

liver from a 42 day old male mouse, GHR-/- mouse was dissected out. Total RNA was extracted using an Ambion RNaqueous RNA extraction kit. Targets were produced using modified Affymetrix procedure from 5ug of total RNA. 3 biological replicates were analysed per each group of animals.Sample also known as D1.

Cyclophosphamide-treated peripheral blood leukocytes 5 days - Biological Replicate 3 - Technical Replicate 2

Biological replicate 3 of 3. Technical Replicate 2 of 2. Peripheral blood leukocytes,  CTX-treated day 5

Cyclophosphamide-treated peripheral blood leukocytes 5 days - Biological Replicate 3 - Technical Replicate 1

Biological replicate 3 of 3. Technical Replicate 1 of 2. Peripheral blood leukocytes,  CTX-treated day 5

liver from a 42 day old male mouse, wild type was dissected out. Total RNA was extracted using an Ambion RNaqueous RNA extraction kit. Targets were produced using modified Affymetrix procedure from 5ug of total RNA. 3 biological replicates were analysed per each group of animals.Sample also known as B2.

liver from a 42 day old male mouse, wild type was dissected out. Total RNA was extracted using an Ambion RNaqueous RNA extraction kit. Targets were produced using modified Affymetrix procedure from 5ug of total RNA. 3 biological replicates were analysed per each group of animals.Sample also known as B3.

in vitro Treatment: siLuc (Sense 5'-rCrGUrArCrGrCrGrGrArAUrArCUUrCrGrCTT-3’ Antisense 5’-UrCrGrArArGUrAUUrCrCrGrCrGUrArCrGTT-3’), Treatment Repeat: 1, Units of Treatment Repeat: dose, Treatment Duration: 60, Units of Duration: hrs, Treatment Time: -48, Units of Treatment Time: hrs, Vehicle for Chemical: Lipofectamine`, Amount of Vehicle: 0.44, Route of Exposure: Transfection, Units of Amount of Vehicle: microliter, Dose or Concentration: 3.3, Units of Dose or Concentration: nM

TP082505-32_HG-U133A_2_IMFGN0023: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

Sample Type: Cells, Cell Line: HeLa, ATCC Number: CCL-2, Number of Cells Seeded: 2.20E+05, Cell Type: Cervical Carcinoma, Separation Type: Trypsin, Harvest Time Point: 12, Units of Harvest Time Point: hr

TP082505-31_HG-U133A_2_IMFGN0023: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

in vitro Treatment: siLuc (Sense 5'-rCrGUrArCrGrCrGrGrArAUrArCUUrCrGrCTT-3’ Antisense 5’-UrCrGrArArGUrAUUrCrCrGrCrGUrArCrGTT-3’), Treatment Repeat: 1, Units of Treatment Repeat: dose, Treatment Duration: 52, Units of Duration: hrs, Treatment Time: -48, Units of Treatment Time: hrs, Vehicle for Chemical: Lipofectamine`, Amount of Vehicle: 0.44, Route of Exposure: Transfection, Units of Amount of Vehicle: microliter, Dose or Concentration: 3.3, Units of Dose or Concentration: nM

TP082505-30_HG-U133A_2_IMFGN0023: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

Sample Type: Cells, Cell Line: HeLa, ATCC Number: CCL-2, Number of Cells Seeded: 2.20E+05, Cell Type: Cervical Carcinoma, Separation Type: Trypsin, Harvest Time Point: 4, Units of Harvest Time Point: hr

TP082505-28_HG-U133A_2_IMFGN0023: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

WT1(-KTS) expression was induced for 8 hrs and the expression profile of each time-points was compared to the uninduced sample (0 hr).

U2OS cell line(osteosarcoma;female),Tetracycline-repressible WT1(-KTS) expression, time-course induction of WT1(-KTS) expression.

WT1(-KTS) expression was induced for the uninduced sample (0 hr). This is the control.

U2OS cell line(osteosarcoma;female),Tetracycline-repressible WT1(-KTS) expression, time-course induction of WT1(-KTS) expression

6 mice were fed ad libitum on 1% creatine supplemented pellets for 6 months and 7 mice fed on equicaloric pellets without creatine (Altromin)

Mice were bred and kept at the GSF animal facilities in isolated ventilated cages type II with wood shavings (Altromin, Lage, Germany) as bedding at a temperature of 20 to 24o C, humidity of 50 to 60%, 20 air exchanges per hour and a 12/12-hour light/dark cycle. They were tested for microorganisms in 12-week intervals according to the FELASA Guidelines to the level required for rederived mice

GeneChips were scanned using the Affymetrix GeneChip Scaner 3000.

Genewise tests for significantly regulated transcripts between creatine treated and untreated mice were performed in the statistical programming language R with BioConductor using the dChip and the Robust Multichip Average (RMA) probeset summaries. Data are log-transformed and normalized with a lowess-smoother operating on MA-scale against the mean of the creatine treated group. Transcripts are called significantly regulated if the corresponding p-value of the Welch's t-test is below the 5% FDR significance level.

Total RNA was extracted using the RNeasy kit (Qiagen) according to manufacturer's instructions.

Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 microg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

in vitro Treatment: siLuc (Sense 5'-rCrGUrArCrGrCrGrGrArAUrArCUUrCrGrCTT-3’ Antisense 5’-UrCrGrArArGUrAUUrCrCrGrCrGUrArCrGTT-3’), Treatment Repeat: 1, Units of Treatment Repeat: dose, Treatment Duration: 72, Units of Duration: hrs, Treatment Time: -48, Units of Treatment Time: hrs, Vehicle for Chemical: Lipofectamine`, Amount of Vehicle: 0.44, Route of Exposure: Transfection, Units of Amount of Vehicle: microliter, Dose or Concentration: 3.3, Units of Dose or Concentration: nM

TP082505-34_HG-U133A_2_IMFGN0023: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

Sample Type: Cells, Cell Line: HeLa, ATCC Number: CCL-2, Number of Cells Seeded: 2.20E+05, Cell Type: Cervical Carcinoma, Separation Type: Trypsin, Harvest Time Point: 24, Units of Harvest Time Point: hr

TP082505-33_HG-U133A_2_IMFGN0023: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

the cell culture was grown until the clumps of 0.2-0.4 mm size were formed, upon resuspensions the clumps were easily restored, indicating a healthy culture. The cell clumps were resuspended using a 30-gauge syringe needle, and

Gene expression data from male F344 rats treated with a single dose of 20mg/kg D-Serine for 96 hours

Brain tissue from Fisher 344 male rat, Animal #265, 20mg/kg D-Serine

C57BL/6;male;postnatal day 9;right hippocampus;severe stress + morphine

C57BL/6;male;postnatal day 9;right hippocampus;severe stress + saline vehicle

C57BL/6;male;postnatal day 9;right hippocampus;mild stress + morphine

lung tissue;CD-1;13 weeks + 5 month;2R4F whole mainstream smoke 750 µg/ml, treatment over 5 month, 4x1h exposure per day

Gene expression data from left lung samples from B6.129P2-Il10tmlCgn/J male mice exposed to 0.3 ppm O3  for 24 hours

B6.129P2-Il10tmlCgn/J;Il10-/-;6-8 weeks;Male;Left lung;Jackson Labs, Bar Harbor, ME;24 hours;ozone;0.3 ppm O3;10028-15-6

Study of rat femur fracture healing in older rats (52 weeks old at fracture) at 1 week after fracture.  RNA was pooled from 2 rats for each array.
Keywords = age

At 2 months of age, mice were injected on two sequential days with 50mg/kg/day of Tamoxifen (10mg/ml) dissolved in sunflower seed oil to induce the Cre recombinase. Vehicle injected control mice were injected with sunflower seed oil alone at the same timepoints.

The arrays were washed and stained using Fluidics protocol FS450_0007 on GeneChip Fluidics Station 450. Following wash and stain the GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

The data was analyzed using RMA algorithm using the Expression Console software Version 1.1 default settings.

Following the labeling of sscDNA, 2.5 microgram of sscDNA was used to prepare hybridization cocktail. The cocktail was immediately added to the Affymetrix WT GENE 1.0 ST chip and hybridized using GeneChip Hybridization oven 645 for 17hrs at 45C.

sscDNA were prepared from 450ng of total RNA using the Ambion’s WT expression kit protocol, followed by fragmentation and labeling using the WT Terminal label kit according to the protocol provided by affymetrix. The Affymetrix proprietary DNA labeling reagent covalently linked to biotin was used to label the sscDNA

Cardiac biventricle of vehicle injected PGC-1a-/-bf/f/MerCre mouse (control)

The data were quantile normalized using BeadStudio v3.1 software. Data analysis and quality control were carried out using Partek® software.

Ly-6G+ neutrophils were collected and total RNA was extracted with TRIzol® (Invitrogen) and was purified by RNA micro cleanup Kit (Qiagen).

Biotin-labeled cRNA was hybridized to Illumina Mouse-Ref8 BeadChips (Illumina) following manufacturer's directions.

Biotinylated cRNA was synthesized using an RNA Amplification Kit (Ambion) following manufacturer's directions.

Data processing and analysis were performed using Illumina GenomeStudio v1.5.4  (Gene Expression Module v2009.2)

Total RNA was extracted using Trizol reagent according to manufacturer's instructions

Biotinylated cRNA were prepared with Illumina TotalPrep RNA Amplification Kit (Ambion).

Standard Affymetrix protocol.  The arrays were washed, stained using Fluidics Station (Affymetrix), and then scanned with the GeneChip Scanner (Affymetrix).  Data collection was performed using GeneChip Operating Software (Affymetrix).

Mice were sacrificed by cervical dislocation.  Kidneys were rapidly excised on ice, washed in ice-cold phosphate-buffered saline (PBS), immersed in RNAlater (Ambion) and stored at –20°C.  Total RNA was isolated using TRIzol Reagent (Invitrogen) and cleaned up using an RNeasy minikit with DNase treatment (Qiagen).  The RNA quality and quantity were examined by agarose-gel electrophoresis and a spectrophotometer (GE Healthcare).

Three micrograms of total RNA obtained from each kidney was individually reverse-transcribed, amplified, and labeled using GeneChip One-Cycle Target Labeling and Control Reagent package (Affymetrix) according to the manufacturer’s protocol.

Robust Microarray Analysis (RMA), Bioconductor Suite Version 2.0.0

15~25 ug of total RNA was processed to produce biotinylated cRNA targets.

Clinical information: Sample.ID=648;Tumor.type=D;Size=1.1;Grade=2;Nodes=0/15;ER=Pos;PR=Pos;HER2=Neg;Age=62;DFS=160;Status=non-recur

Clinical information: Sample.ID=651;Tumor.type=D;Size=4.7;Grade=3;Nodes=10/13;ER=Pos;PR=Pos;HER2=Neg;Age=48;DFS=137;Status=recur

C57Bl6;4 weeks;BCR-ABL1 transformed pre-B cells;BCR-ABL1-driven ALL;Bach2 knockout;Imatinib (2uM for 16h)

A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and induced cells, target genes of introduced transcription factor can be identified. This entry corresponds to the RNA isolated from uninduced INS-1 cell line #2 containing hepatocyte nuclear factor-6 (HNF6; onecut1).

total RNA was extracted from Jurkat cells using the RNeasy mini kit (Qiagen, Valencia, CA).

The cRNA products were fragmented to 200 nucleotides or less, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Affymetrix U133 v2 microarrays. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

total RNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.

Peripheral blood mononuclear cells;oligoarticular JIA;GTE6;137min;White;Female

Peripheral blood mononuclear cells;oligoarticular JIA;GTE6;200min;White;Female

Peripheral blood mononuclear cells;oligoarticular JIA;LT6;140min;White;Female

Peripheral blood mononuclear cells;oligoarticular JIA;LT6;100min;White;Male

Peripheral blood mononuclear cells;oligoarticular JIA;GTE6;99min;White;Female

Peripheral blood mononuclear cells;oligoarticular JIA;GTE6;110min;White;Female

Expression profiles generated from the white portion of the gastrocnemicus muscle from AMPK gamma3 knock-out mice

C57BL/6;AMPK gamma3 knock-out;F7;male;white portion of the gastrocnemius muscle;fasted

Peripheral blood mononuclear cells;oligoarticular JIA;LT6;130min;White;Female

Total RNA was isolated from 50 to 100 mg of frozen tissue using the mirVana kit (Applied Biosystems, Foster City, CA). RNA quality control was performed using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

Mice were intranasally infected with exponential phase Streptococcus pyogenes (2-4 x 10^8 CFU per 15 microliters PBS) or 15 ul PBS for 24h (Sham mice)

Mice were housed in Biosafety Level 2 facilities after infection with S. pyogenes

GeneChips were scanned using the Affymetrix Genechip Scanner 3000

Normalization and data filtering was performed by Genesis (GeneLogic, Gaithersburg, MD) using the Affymetrix MAS5 algorithm and the trimmed mean. Data visualization, filtering, and statistical analyses were done by GeneSpring version 7.2 (Agilent Technologies, Carmel, IN).  Genes were excluded if they were flagged “Absent” by GCOS in all samples and were included if they had a normalized mean intensity value > 75 (50% of the chip sensitivity value) in at least one group at 24 h post infection. Using these criteria, only 32% (14,472) of the 45,100 probe sets were considered “detectable”.  The data are presented as the ratio of the mean gene intensity in S. pyogenes-infected mice relative to the mean of time-matched, sham-infected mice.   Genes were defined as differentially transcribed if the average expression level changed at least two-fold compared with those in sham-infected NALTs and were statistically significant by Welch’s t-test, with a p-value < 0.05 and Benjamini and Hochberg multiple testing correction (GeneSpring).

Total RNA was purified using the Qiagen RNeasy kit (Qiagen Inc., Valencia, CA) and on-column DNase digestion.  RNA quality was verified using the Agilent Bioanalyzer and a RNA Nano chip (Agilent Techonologies, Santa Clara, CA) and quantified by Nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE).  Good quality RNA had A260/A280 ratios > 1.8.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

C57BL/6, Gender: female, Age: 6-10 weeks;nasal-associated lymphoid tissue (NALT)

PBMC isolated by Ficoll gradient centrifugation from control
Keywords = Control, peripheral blood mononuclear cell (PBMC)

splenic CD11c+ dendritic cells;C57Bl/6strain: C57Bl/6;WT;tamoxifen

Cells were plated at 20% confluence in low glucose phenol red free medium supplemented with 5% charcoal stripped FBS and glutamine 24h-48h prior to transfection. Treatment with vehicle, OH-Tam (100nM), or OH-Tam (500nM) was begun an additional 24h later. Cells were transfected with control siRNA, ERα siRNA or RARα siRNA in 24 well microplates (2.5pmol/well) or 25cm2 flasks (31.25pmol per flask) using 2μl and 12.5 μl of Dharmafect 1 (Thermo Scientific Dharmacon Inc., Lafayette, CO), respectively, according to the vendor’s protocol. The cell culture medium was not replenished for the duration of the experiment.

Cells were routinely cultured at 37°C and in 5% CO2 in DMEM supplemented with FBS (10%), penicillin (100unit/ml), streptomycin (100μg/ml) and L-glutamine (2mM). Hormone depleted cells were grown in low glucose phenol-red free media supplemented with 5% charcoal-stripped FBS (v/v) and L-glutamine (2mM) for 48 hours before the experiments

Each GeneChip was then washed and stained with Streptavidin–Phycoerythrin conjugate (SAPE; Invitrogen Corp.) using an Affymetrix Fluidics Station 450 and scanned on a Affymetrix GeneChip scanner.

Scanned image files were analyzed using the Gene Chip Operating System Version 1.4 software, and standard thresholding and filtering operations were used.   The data was normalized using house keeping genes. Normalization assumes that for a subset of genes (i.e., housekeeping genes) the ratio of measured expression averaged over the set should be one.

The cRNA was fragmented to 35-200 bases length using Affymetrix protocols and hybridized to HG U133 Plus 2.0 array set at 45ºC for 16 hours in an Affymetrix GeneChip® Hybridization Oven 640.

Isolated total RNA was processed as recommended by Affymetrix, Inc. (Santa Clara, CA). In brief, cDNA was synthesized from the total RNA using the Super-Script Double Stranded cDNA Synthesis kit and T7 Oligo (dT) primers. Using the double stranded cDNA as template, biotin labeled cRNA was generated by in vitro transcription (MEGAscript Labeling Kit) reaction.

Gene expression data from MCF-7cells treated with vehicle and scrambled siRNA
MD40

MCF-7 breast cancer cell line;control (scrambled siRNA);control (vehicle);n/a

Benign or PCa tissues were homogenized using a TissueLyser (Qiagen) at 28 Hz for 5 min.

A biopsy punch was used to select the PCa tissues from the OCT prostate sample blocks.

Total RNA was isolated using Trizol reagent. RNA was quantified by NanoDrop ND-1000 spectrophotometer, and quality was evaluated with Agilent RNA 6000 NanoChip and the 2100 Bioanalyzer, with 28S/18S ratios and RIN determined by 2100 Expert software.

cRNA (15 μg) was fragmented and hybridized to arrays according to the manufacturer's (Ambion® | Life Technologies) protocols.

Biotin-UTP was incorporated during the overnight in vitro transcription step according to the manufacturer's (Ambion® | Life Technologies) protocol.

Gene expression after 6 h in PBS-treated CCRPKO mouse liver
251486838929_1_3

Mice were maintained at all times on a 12-hour light-dark cycle in a specific pathogen-free environment with free access to rodent chow and water

251486838941_1_3

Cell lines were treated with DMSO control or 1 uM PLX4032 for 6h

Selected melanoma cell lines were grown in DMEM supplemented with 10% serum

Array scanning was carried out with the GeneChip Scanner 3000 7G (Affymetrix) according to the manufacturer's instructions

Expression data were normalized, background-corrected, and log2-transformed for parametric analysis. Differentially expressed genes were identified using significance analysis of microarrays (SAM) with the R package 'samr' (FDR<0.05; fold change>2)

Total RNA was extracted using RiboPure Kit (Ambion) according to the manufacturer's instructions

Labeled cDNAs were hybridized to the GeneChip Human Gene 1.0 ST Arrays (Affymetrix) according to the manufacturer's protocol

cDNAs were generated from total RNA and biotinylated according to the standard Affymetrix protocol.

Gene expression data from ICR MEF infected  with pMX-jhdm1b retrovirus

Gene expression after 6 h in phenobarbital-treated CCRPKO mouse liver
251486838941_1_4

251486838940_1_4

in vitro Treatment: H2O2, Treatment Time: 4, Units of Treatment Time: hour, Dose or Concentration: 100, Units of Dose or Concentration: uM

cells_ATCC 16Lu_human lung fibroblasts_JCB_100_4_27_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

JCB_100_4_27_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

Gene expression data from ICR MEF infected  with pMX-Oct4 and pMX-jhdm1b retrovirus

in vitro Treatment: H2O2, Treatment Time: 24, Units of Treatment Time: hour, Dose or Concentration: 100, Units of Dose or Concentration: uM

cells_ATCC 16Lu_human lung fibroblasts_JCB_100_24_45_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

JCB_100_24_45_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

Sample Type: cells, Cell Line: ATCC 16Lu, Cell Type: human lung fibroblasts, Harvest Time Point: 24 hour

cells_ATCC 16Lu_human lung fibroblasts_JCB_100_1_41_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

JCB_100_1_41_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

endometrial stromal cell - Jag1 retrovirus infected1, 3 days post infection

Expression comparison between primary normal human mammary epithelial cell from 50 years old donor and  human breast cancer cell line SKBR3

Expression comparison between primary normal human mammary epithelial cell from 50 years old donor and  human breast cancer cell line BT474

Expression comparison between primary normal human mammary epithelial cell from 50 years old donor and  human breast cancer cell line BT549

Expression comparison between primary normal human mammary epithelial cell from 50 years old donor and  human breast cancer cell line BT20

Expression comparison between primary normal human mammary epithelial cell from 50 years old donor and  human breast cancer cell line MDA_MB_468

Embryos were dissected into ice-cold PBS, followed by limb dissection and immediate placement into Qiazol reagent for RNA extraction.

Embryos were collected at scheduled time points where E0.5 was considered noon on the day a copulatory plug was discovered.

Arrays were scanned using a Gene Chip Scanner3000 scanner enabled for high-resolution scanning according to the manufacturer's instructions.

Gene expression data was processed using Robust Multi-Chip Average (RMA), as implemented in the R statistical package provided by Bioconductor.  RMA data processing Differentially expressed genes were identified using empirical Bayes method implemented in Linear Models for MicroArray (LIMMA) .  Genes were filtered in order to eliminate those with cross-sample variation, using a variation filter estimated on 14 HeLa cell lines and 5 Strategene samples.Pathway enrichment analysis was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) (Dennis et al., 2003; Huang da et al., 2009) and Kyoto Encyclopedia of Genes and Genomes (KEGG) option (Kanehisa et al., 2010). Pathways with EASE score, a modified Fisher Exact p-value less than 0.1 were considered as enriched.Pathway enrichment analysis was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) (Dennis et al., 2003; Huang da et al., 2009) and Kyoto Encyclopedia of Genes and Genomes (KEGG) option (Kanehisa et al., 2010). Pathways with EASE score, a modified Fisher Exact p-value less than 0.1 were considered as enriched.

Total RNA was extracted with Qiazol reagent followed by Qiagen RNEASy mini columns, with a proteinase K digestion step before loading onto the columns, and DNaseI digestion on the column, according to the manufacturer's instructions.

GeneChip Hybridization, Wash and Stain Kit was used according to the manufacturer's instructions.

Total RNA samples were labeled using Affymetrix GeneChip Two-Cycle Target Labeling and Control Reagent Kit (biotin labeling) according to the manufacturer's instructions.

Colonic biopsy was collected during endoscopy from affected area of a patient with Crohn's disease. The standard Affymetrix protocols were followed to prepare target from 5ug of total RNA. The expression profiles generated from normal individuals were compared to that from patients with different types of disease.

disease affected colon of an adult with Crohn's disease (CD). Replicate-2

colonoscopic biopsy from adult with affected colon with Crohn's disease

disease affected colon of an adult with Crohn's disease (CD). Replicate-1

HL-60 cell line infected with scrambled control shRNA, biological rep1
Sample name: HL60_CTRL-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A01_596706.CEL

Mouse ES cells were maintained on irradiated embryonic fibroblast feeder cells and cultured in ES medium (DMEM supplemented with 2 mM L-glutamine, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, 0.1 mM  nonessential amino acids, 50 u/ml Penicillin/Streptomycin, 15% ES cell-qualified FBS, and 1000 u/ml LIF (Millipore)). Cells were passaged twice on 0.1% gelatin-coated dishes to remove feeder cells and then cultured in ES medium on gelatin-coated dishes.

The data were normalized by the  methods Microarray Suite version 5.0 (MAS 5.0)

Trizol extraction of total RNA followed by Qiagen RNeasy mini kit purification was performed according to the manufacturer's instructions.

Sample represents the Neurointermediate lobe of the Pituitary from 5 control animals

Sprague Dawley;Male;10-12 weeks;Neurointermediate lobe of the Pituitary

Sample represents the Neurointermediate lobe of the Pituitary from 5 dehydrated animals (3 Days)

Mice were purchased at 7-8 weeks of age from Charles River laboratory

The raw probe intensities were background subtracted and quartile normalized to adjust for variation that arose from microarray technology and not from biological differences. The normalized probe signals were then summarized into gene-level, during which signals of multiple probes that represent the same gene will be averaged to obtain gene expression level in GenomeStudio™ and exported as a tab-delimited txt file, which was imported into Partek, minimum value shifted to 1.0, and log2 transformed [*gene_level.txt]. Genes that were not expressed in any sample (Non-expressed genes, NEGs, identified by detection P value >= 0.05) were removed from further studies removed to improve the sensitivity of differential gene expression detection
If a gene is expressed in at least one of the 12 samples, the gene was kept for final output; if a gene is not expressed in any sample, it was excluded from subsequent analysis. After this pre-filtering step, 16,410 out of 30,854 genes (53.2%) were kept for DEG detection in Partek.

RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

C57BL/6;male;10 weeks;colistin at 16 mg/kg/day in 2 divided doses;kidney;8324341086;D;PC9-R

C57BL/6;male;10 weeks;0.1% saline twice daily;kidney;8324341086;C;PC5-R

C57BL/6;male;10 weeks;colistin at 16 mg/kg/day in 2 divided doses;kidney;8324341073;B;PC12-R

C57BL/6;male;10 weeks;0.1% saline twice daily;kidney;8324341073;A;PC1-R

C57BL/6;male;10 weeks;colistin at 16 mg/kg/day in 2 divided doses;kidney;8324341073;D;PC13-R

C57BL/6;male;10 weeks;0.1% saline twice daily;kidney;8324341073;C;PC2-R

C57BL/6;male;10 weeks;colistin at 16 mg/kg/day in 2 divided doses;kidney;8324341073;F;PC14-R

C57BL/6;male;10 weeks;0.1% saline twice daily;kidney;8324341073;E;PC3-R

C57BL/6;male;10 weeks;colistin at 16 mg/kg/day in 2 divided doses;kidney;8324341086;B;PC8-R

C57BL/6;male;10 weeks;0.1% saline twice daily;kidney;8324341086;A;PC4-R

Levitiracetam hippocampus 2

Mice were maintained at all times on a 12-hour light-dark cycle in a specific pathogen-free environment with free access to rodent chow and water.

Levitiracetam hippocampus 3

Levitiracetam hippocampus 4

Additional details provided in accompanying manuscript, SLE10-TC

>95% CD3+ T cells negatively isolated with Dynal kit from SLE patient

Levitiracetam hippocampus 5

blast count: 9

Levitiracetam brainstem 5

Levitiracetam brainstem 6

Levitiracetam hippocampus 1

Transgenic mice were produced with microinjection technique with construct of human WT FGF23 behind a 1 alpha col 1 promotor

Subsequent analysis of the gene expression data was carried out in the statistical computing language R using packages available from the Bioconductor project. The raw data was normalized using the GCRMA method.

Gene expression data from kidneys of 8 week FGF23 TG mice and WT littermates

AML blasts from bone marrow;training;wild-type;M0;internal tandem duplication (ITD)

The chips were scanned at 570 nm with 3um resolution in an Affymetrix GeneChip scanner (Hewlett Packard).

The readings from the quantitative scanning were analyzed by the Affymetrix MAS5.0 and normalized using the quantile normalization procedure implemented in robust multiarray analysis (RMA) with GeneSpring software (Silicon Genetics, CA, USA).

RNA was extracted with Trizol reagent (Invitrogen) according to the manufacturer's instructions.

Fragmented cRNA was hybridized to the Affymetrix HG-U133A chip according to the manufacturer's instructions.

Biotinylated cRNA was prepared from 10ug of total RNA according to the standard Affymetrix protocol.

M030-258N
Gene expression data from human normal colonic mucosa sample.

M030-827N

I-c852T
Gene expression data from human colorectal cancer sample.

I-u58T

I-c800T

I-c840T

probe arrays were scanned with the Genechip System confocal scanner (Affymetrix, Santa Clara, CA).

Cells were cultured in Eagle's minimal essential medium (MEM) (Nissui, Tokyo, Japan) supplemented with 1% non-essential amino acid (Invitrogen, Carlsbad, CA), 10% fetal bovine serum and 60 mg/ml kanamycin at 37 ¡C and 5% CO2.

Target preparation and hybridization was performed according to One-Cycle Eukaryotic Target Labeling Assay protocols described in Affymetrix technical manual (Affymetrix, Santa Clara, CA).  Labeled cRNA was fragmented by incubation at 94 ¡C for 35 min in the presence of 40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate.  Ten ug of fragmented cRNA was hybridized to a Human Genome Focus array (Affymetrix, Santa Clara, CA) containing probes for 8795 human genes for 16 h at 45 ¡C.  After hybridization, the microarrays were automatically washed and stained with streptavidin-phycoerythrin by using a fluidics station 450 (Affymetrix, Santa Clara, CA).

blast count: 3

GeneChips were scanned using a high-resolution microarray scanner 3000, and GeneChip Operating Software workstation version 1.3.

The .CEL files were imported into Affymetrix Expression Console software and gene-level data was generated after robust multiarray analysis (RMA) background correction.

RNA was hybridized to GeneChip Mouse Gene 1.0 ST Array (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

Expression profiling of mouse ing2 -/- testis vs WT reveals gene expression differences consistent with spermatogenic arrest and infertility

lung tissue;CD-1_Nrf2 -/-;13 weeks + 5 month;fresh air, treatment over 5 month, 4x1h exposure per day

lung tissue;CD-1_Nrf2 -/-;13 weeks + 5 month;2R4F whole mainstream smoke 750 µg/ml, treatment over 5 month, 2x1h exposure per day

Keap1(flox/+), gender- male, age- 9 weeks, n = 1, # of tissue = 1 tissue: Liver

Background correction and normalization of microarray data was performed using the Robust Multichip Average method implemented in the rma function of R/BioConductor.

RNeasy miniprep columns (Qiagen) were used according to the manufacturer's instructions.

Following fragmentation, 10 ug cRNA were hybridized to the Affymetrix GeneChip Human Genome U133Av2 for 16 hrs.  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNAs were prepared according to the Affymetrix standard labeling protocol.

short access to cocaine, ventral tegmental area, 1 hr/day access to cocaine

Male, Wistar, 1 hr/day access to cocaine, ventral tegmental area

cocaine naive, ventral tegmental area, 0 hrs/day access to cocaine

Male, Wistar, 0 hrs/day access to cocaine, ventral tegmental area

cocaine naive,medial prefrontal cortex, 0 hrs/day access to cocaine

Male, Wistar, 0 hrs/day access to cocaine, medial prefrontal cortex

long access to cocaine, ventral tegmental area, 6 hrs/day access to cocaine

Male, Wistar, 6 hrs/day access to cocaine, ventral tegmental area

Rats were sacrificed 2 weeks after the two-way active avoidance testing and the whole hippocampus were collected and pooled, 3 rats/pool.

Rats were sacrificed 2 weeks after the two-way active avoidance testing and the whole hippocampus were collected.

Individual cell lines were treated with 0.5 ug/mL doxycycline every day for four days to achieve inducible knockdown of ZXDC1/2.  After the first two days of doxycycline treatment, cell lines were treated with either 100 nM PMA or vehicle (0.1% DMSO) and allowed to differentiate for 3 days.

U937 stably transduced with TRIPZ-shRNAmir (Thermo/OpenBiosystems) were cultured in RPMI + 10% FBS, 100 U/mL penicilli, 100 ug/mL streptomycin, and 0.5 ug/mL Puromycin

The data were analyzed with AltAnalyze version 2.02 beta, using RMA for normalization.

Total RNA was extracted via Qiagen Rneasy Micro kit according to the manufacturer's instruction

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array in a GeneChip hybridization oven 640. GeneChips were singly scanned using a Genechip scanner 3000 7G with autoloader. Fluidics and scan functions were controlled by Command Console software ver 1.1 (AGCC).

Biotinylated cRNA were prepared according to the GeneChip 3' IVT Express kit  from 100 ng total RNA (Affymetrix catolog # 901228).

Veh_Veh_1
Gene expression data from cell line treated with vehicle in the absence of doxycycline-inducible knockdown of ZXDC1/2

U937-derived cell line harboring TRIPZ-shRNAmir TetOn cassette (clone ID: V3THS-381738)

LOX-1:113203;GFP_Untreated_2hr:113203;Classification:Good;Gradient Severity:0.04;Distortion Severity:0.02;Defective Area (%):0;Outlier Area (%):0.01;3'/5' Mean:2.09;Background Mean Dev.:0.23;Absent (%):59.1;Absent (%) Dev.:0.66;Scaling Factor:0.68;Scaling Factor Dev.:0.6;GFP;2 hours;(Not applicable);113203;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;GFP_Untreated_2hr;282295493

Cells had been stably tranfected with pcDNA3.1/V5/His-pTOPO vectors containing TFPIalpha or TFPIbeta cDNA, or empty vectors, and selected using puromycin (2mg/ul)

SK-BR-3 cells were grown in RPMI1640 containing phenol red and 2 mM L-glutamine, supplemented with 10% heat inactivated FBS. Cells were cultured at 37 °C in an incubator with a humidified atmosphere and 5% CO2.

Signal intensities were detected by Hewlett Packard Gene Array Scanner 3000 7G and the scanned images were processed using the AGCC.

The RMA algorithm was applied for generation of signal values and normalization using the Partek Genomics Suite software. Probe sets with maximal signal values of less than 5 across all arrays were removed to filter for low and non-expressed genes. For expression comparisons of different groups, profiles were compared using a 1-way ANOVA model.

Total RNA was isolated using the miRVANA miRNA isolation kit, following the manufacturers descriptions for extraction of total RNA

Biotinylated and fragmented single stranded cDNAs were hybridized to the GeneChips. The arrays were washed and stained using FS-450 fluidics station.

Extrats were labeled using the GeneChip HT IVT Labeling Kit, following the manufacturer’s protocol.

SK-BR-3 breast cancer cells stably transfected with empty vector

Embryo was harvested at the designated time point. Total RNA was extracted with the Qiagen RNeasy Plus Mini Kit according to manufacturer's protocol from the embryonic tongue.

Whole genome transcriptome profile of tongue mesenchyme from embryonic day 14.5 mice with a conditional inactivation of Tgfbr2 in the cranial neural crest.

Gene expression data from YFPH YFP labeled neurons from the motor cortex (M1), Mecp2 null

brain, motor cortex, layer 5 thick tufted pyramidal neurons, Mecp2 null

Nasal biopsies were collected and immediately placed in growth medium containing DMEM/Ham F12 supplemented with 10% Fetal Bovine Serum (FBS) and 100 units/mL of penicillin and 100 µg/mL of streptomycin (Invitrogen/Life Technologies). Olfactory ecto-mesenchymal stem cells (OE-MSC) were purified from the lamina propria and cultivated as described before (Delorme et al, 2010; Girard et al, 2011; Nivet et al, 2011). All experiments were performed using OE-MSCs with a low passage number (P1 to P5). When the two cohorts were compared, the same passage number was used. In order to limit biases, stem cells from the 22 individuals were harvested by the same operator, under the same conditions: identical culture medium and level of confluency (100%), equal passaging (P3).

The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE2-v5_10_Apr08 and Grid: 014850_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities. All data were normalized by quantile normalization.

In order to avoid any circadian rhythm-related variations in gene expression, cells were collected at the same time of the day. Total RNA was then isolated using RNeasy Mini kit (Qiagen), according to the manufacturer’s instructions. RNA concentration was determined using a nanodrop 2000 spectrophotometer (Thermo Scientific) and RNA integrity assessed on an Agilent 2100 Bioanalyzer.

Sample hybridization was performed with the Agilent two-color microarray-base analysis (low input quick amp labeling) protocol (Agilent Technologies). Labeled cRNA was purified and fragmented before hybridization on Agilent whole human genome Expression Arrays, containing 45 220 oligonucleotide probes, at 65°C for 17 hours.

Sample amplification and labelling were performed with the Agilent two-color microarray-base analysis (low input quick amp labeling) protocol (Agilent Technologies). Total RNA was reverse transcribed into cDNA using the T7 promoter primer. The reaction intending to synthesize cyanine-3 or cyanine-5 labeled cRNA from cDNA was performed in a solution containing dNTP mix, T7 RNA polymerase and cyanine 3-dCTP and then incubated at 40°C for 2 hours.

comparaison of nasal olfactory stem cells from autistic and control individus

E12.5 fetal liver (FL) cells from GATA-1deltaN mutant embryos were cultured ex vivo in the presence of Tpo for three days. FL-derived megakaryocytes and their progenitors in the culture were separated by BSA density gradient. Megakaryocyte progenitors (“P” population) were further purified by fluorescence-activated cell sorting (FACS) for cells expressing low levels of CD41. Megakaryocytes (“M” population) were further enriched by CD41 antibody coupled with magnetic beads. Total RNA was isolated from either enriched megakaryocyte or progenitor fractions. ~5-15microgram RNA from each sample was submitted to the Dana Farber Cancer Institute Microarray Core Facility for cDNA and cRNA synthesis, labeling, and hybridization with Affymetrix Mouse Genome 430 2.0 chips according to manufacturer’s instructions. All arrays were normalized and analyzed using the dChip program.
Keywords = GATA-1
Keywords = megakaryocyte
Keywords = mouse model

total RNA from biosource CC#8S

Cells were transfected by CaCl2 precipitation, selected with Geniticin and maintained in low Geneticin concentrations.

Cells were grown in DMEM supplemented with fetal calf serum and Glutamax in 5% CO2 in a humified incubator at 37°C.

Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip(r) Scanner 3000 with autolaoader.

Probesets were summarized and probeset-level values normalized with the justRMA() function from the R (version 2.9.0)/Bioconductor package affy (version 2.5) using the CDF environment HuGene-1_0-st-v1.r3.cdf.

Trizol extraction of total RNA followed by a purification step using Qiagen RNeasy Mini Kit was performed according to the manufacturer's instructions.

Arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidics protocol FS450_0007 was used for washing.

RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix.

Human glioma cell line U373 stably transfected with an MAML1-dominant-negative expression vector.

Human glioma cell line U373 stably transfected with an DTX1-myc expression vector.

pre-iPSCs were treated with indicated siRNA for 3 days and then RNA was extracted

CEL files generated were normalized by RMA normalization from the R statistical package

Trizol extraction was carried out according to manufacturer's instructions

Depletion of THOC1 in HeTH-4 cells was induced with doxicycline for 96 h.

The .CEL files were generated using Affymetrix GCOS software and further processed into expression values using Robust Multiarray Average (RMA) method by Irrizarry et al. The following statistical data analysis were performed using the limma package (oneChannelGUI interface) of R/Bioconductor project.

Rneasy mini Kit (Qiagen) of total RNA was performed according to the manufacturer's instruction.

Following fragmentation, 5.5 ug of single-stranded cDNA were hybridized for 16 hr at 45C on GeneChip® Yeast Genome 2.0 Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004.

Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA Labeling Protocol (GeneChip® Whole Transcript Sense Target Labeling Assay Manual, Affymetrix, 2007).

HeTH-4;THOC1-depletion;HeLa cell line with inducible THOC1-depletion, induced

HeTH-4;control;HeLa cell line with inducible THOC1-depletion, non induced

U2-OS human osteosarcoma cells were stably transfected with low levels of ERa. This sample represents E2 10nM treated cells for 48 hours.

Lung tissue and ressected lung taken from smokers
Keywords = Smoking, COPD, lung reduction, airway, molecular screen for spatially restricted transcripts

Gene expression data from BCR-ABL-expressing Hif1a-/- LSCs.

Dulbecco’s Modified Eagle Medium supplemented with 10% (v/v) heat inactivated mycoplasma tested fetal calf serum, 2 mM L-glutamine (6 mM final concentration), 1% (v/v) MEM non-essential amino acids and 50 µg/ml gentamicin. As quercetin in DMEM culture medium was stabilized by 1 mM ascorbate, control cells were exposed to 1 mM ascorbate-only

Caco-2 cells of passage 37 were seeded (1 : 10 split ratio) in triplicate on polycarbonate membrane transwell® inserts (Corning Life Sciences, Cambridge, U.K.), with a membrane diameter of 75 mm (growth area 44 cm2, 0.4 µm pore size) at a density of approx. 40,000 cells/cm2. After 2 days, cell cultures reached confluency, and this time point was considered experimental day 0 and the initial exposure to quercetin. Cells were exposed for a total number of 9 days

Scan protocol with GeneChip® Scanner 3000 7G, according to Affymetrix® GeneChip® Expression Analysis Technical Manual

CEL files were imported in Rosetta Resolver 5.0 (Rosetta Inpharmatics LLC, Seattle, U.S.A.), applying data pre-processing (to estimate and reduce systematic errors) and error modeling (for improvement of accuracy of the present and absent calls for low replicate numbers).

On days 5 and 10 post-confluency, cells were first rinsed with ice cold phosphate buffered saline without calcium or magnesium (InvitrogenTM Life Technologies, Breda, The Netherlands). Subsequently, cells were harvested in 2 x 0.75 ml of ice-cold TRIzol (Life Technologies, Paisley, U.K.), immediately frozen in liquid nitrogen and stored at -80°C for up to 2 months, until RNA isolation according to the TRIzol protocol. Following isolation, total RNA was purified with RNeasy Midi columns (QIAGEN, Westburg, Leusden, The Netherlands), including a DNAse incubation step. Quality of purified total RNA was determined on a UV-VIS spectrofotometer (Shimadzu Benelux, ‘s Hertogenbosch, The Netherlands) by calculation of the A260/A280 ratio (1.7 - 2.0) and confirmed on a Lab-on-a-Chip on the Agilent 2100 bioanalyser (Agilent Technologies, Palo Alto, California, U.S.A.) by determining the 28S/18S ribosomal RNA ratio

Hybridization protocol according to Affymetrix® GeneChip® Expression Analysis Technical Manual

Labeling protocol according to Affymetrix® GeneChip® Expression Analysis Technical Manual

Probe sets with an “absent call” (P ≥ 0.065 for HG-U133A 2.0 GeneChip® arrays) across all 8 arrays (n = 7,285) were considered not to be affected by quercetin treatment and/or incubation time and were therefore excluded from further analyses

The Caco-2 cell line is derived from a male Caucasian with a colon tumor

Lung; Day 24 postnatal

Lung; Day 12 postnatal

NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 7 h. U0126 (20 uM) was added 1 h after stimulation.

NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 12 h.

NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 12 h. U0126 (20 uM) was added 30 min before stimulation.

NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 7 h.

NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 7 h. U0126 (20 uM) was added 30 min before stimulation.

NIH3T3 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% calf serum.To obtain quiescent cells, cells were washed with serum-free DMEM followed by culture for 48 h in DMEM containing 0.1% serum. Serum-starved NIH3T3 cells were stimulated with bFGF (50 ng/ml) for 12 h. U0126 (20 uM) was added 7 h after stimulation.

Mice were euthanized and hearts were rapidly removed and placed in RNAeasy for 48hr at 4C in preparation for RNA extraction.

RNA was extracted using RNeasy Fibrous Tissue kit (Qiagen) according to the manufacturer's instructions.

Hybridization cocktail for a single probe array contained 2.5 ug of fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 7% DMSO, and 1X Hybridization Buffer. GeneChip Mouse Gene 1.0 ST Array (Affymetrix) was hybridized at 45C for 18 hours in the GeneChip Hybridization Oven 640 (Affymetrix).

The Affymetrix Whole Transcript Sense Target Labeling Assay (Affymetrix) is used to create biotin-labeled sense-strand cDNA targets for hybridization to the Gene 1.0 ST Arrays.

Gene expression data from Ppif-/- mouse hearts.
Ppif-/- mice were back-crossed to C57BL/6 from an original Sv129 background. See original description in Baines et al. Nature. 2005; 434:658-662 (PMID 15800627).

C57BL/6,;Male,;between 6-8 weeks,;RM3 (E) 801710 Soya-free powdered diet + 7mg quercetin from B.S & S.,;Colon

C57BL/6,;Male,;between 6-8 weeks,;RM3 (E) 801710 Soya-free powdered diet + 7mg quercetin from B.S & S.,;Ileum

C57BL/6,;Male,;between 6-8 weeks,;RM3 (E) 801710 Soya-free powdered diet from B.S & S.,;Ileum

The data were condensed with MAS 5.0 using the Refiner software from Genedata, Basel,	Switzerland using default settings. The normalization target was set to 500.

Full thickness skin 4 millimeter punch biopsy of lesional skin
RNA was extracted using the Invisorb RNA Kit II (Invitek, Berlin, Germany) according to the manufacturer's instructions.  As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

Following fragmentation, 12 microg of cRNA were hybridized to the Affymetrix HG-U133A chip according to the protocols provided by the manufacturer.

Biotinylated cRNA were prepared from 2 microg total RNA using the BioArray-High-Yield-RNA-Transcript-Labeling-Kit (Enzo, Farmingdale, NY).

Human skin biposy (lesional) from male patient, 56 years old, 16 years of psoriasis, moderate erythema, moderate induration, mild scaling.

R;male;56 years;16 years;30 percent;moderate;moderate (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe);mild (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)

Data were processed using Partek Genomics Suite v6.5. Arrays were preprocessed together with publicly available array data (GSE16190, GSE19902, GSE22499, GSE26451, GSE7179, GSE7879, GSE8590 and GSE9440) using RMA quantile normalization with GC background correction.

Total RNA was extracted using the RNeasy Plus kit (Qiagen). cDNA synthesis and amplification was performed using the Ambion®WT Expression Kit (Ambion).

Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 95° for 5 minutes, then 45° for 5 minutes. • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

Origin of sample: Sciatic nerve pooled from 4 to 7 mice, 60 days old (P60) and carrying the Trembler mutation in the Pmp22 gene.

Origin of sample: Sciatic nerve pooled from 4 to 7 mice, 60 days old (P60) and carrying a Pmp22 transgene (Magyar, J.P., et al. Impaired differentiation of Schwann cells in transgenic mice with increased Pmp22 gene dosage. J. Neurosci. 16:5351-5360 (1996)). RNA extracted with RNeasy kits (Qiagen).

Origin of sample: Sciatic nerve pooled from 4 to 7 mice, 60 days old (P60) and homozygously null for the Pmp22 gene (Adlkofer, K., et al. Hypermyelination nd demyelinating peripheral neuropathy in Pmp22-deficient mice. Nature Genetics 11, 274-280 (1995)).

Origin of sample: Sciatic nerve pooled from 4 to 7 mice, 4 days old (P4) and carrying the Trembler mutation in the Pmp22 gene.

addition of the gamma-secretase inhibitor DAPT (5 uM) and incubation for 48h

RPMI medium 1640 (Invitrogen) supplemented with 10 % FBS, 10 mM HEPES and penicillin-streptomycin (200 U/ml).

standard Affymetrix procedures using a GeneChip Scanner 3000 7G with autoloader

cells were harvested and lysed using Trizol (Invitrogen), with an additional RNA clean-up step using the RNAeasy purification kit (Qiagen).

Affymetrix GeneChip Expression 3’ Amplification One-Cycle Target Labeling kit from about 5ug of total RNA.

MOLT4 cells (a human T-cell acute lymphoblastic leukemia cell line), with a mutation in the NOTCH 1 gene (Weng et al., 2004, Science, 306, 269-271).
Total RNA was harvested from three independent cultures of the MOLT4 cell line before and 48 hours after addition of the gamma-secretase inhibitor DAPT (5 uM).

mutation in the NOTCH 1 gene (Weng et al., 2004, Science, 306, 269-271)

Brown preadipocyte cell lines derived from newborn wildtype littermates of IRS-1 KO mice. Preadipocytes were grown to confluence (day 0) in differentiation medium (Dulbeco’s modified Earle’s medium containing 10% fetal bovine serum supplemented with 20 nM insulin and 1 nM T3). Brown preadipocytes were synchronized by overnight serum starvation. Total RNA was isolated with ULTRASPEC RNA Isolation System (Biotecx Laboratories, Inc., Houston, TX) following the manufacture’s instruction. 28 ug of total RNA were subjected to cDNA and cRNA preparations as previously described. 15 ug of adjusted cRNA were hybridised to Affymetrix U74A-v2 arrays (Santa Clara, CA). Intensity values were quantitated by MAS 5.0 software (Affymetrix). All chips were subjected to global scaling to a target intensity of 1,500 to take into account the inherent differences between the chips and their hybridization efficiencies.
Lot batch = Joslin core 928

Grown for 48 hours in DMEM supplemented with 10% FBS and 1X Penicillin-Streptomycin

Gene expression data from HepG2 cell lines after 18 hours of PCB153 treatment.

Gene expression data from HepG2 cell lines after 6 hours of PCB153 treatment.

MOLT4 cells, a human T-cell acute lymphoblastic leukemia cell line. Contains a mutation in the NOTCH 1 gene (Weng et al., 2004, Science, 306, 269-271).

hsa-mir-30a/30d inhibitor (mir-30a knockdown in OVSAYO), biological rep3

negative control inhibitor (mir-30a knockdown control), biological rep3

negative control inhibitor (mir-30a knockdown control), biological rep1

Whole Blood of Dengue infected patient at convalescent time point

The arrays were scanned using the GeneChip® Scanner 3000. Scanned image files were visually inspected for artifacts and then analyzed, each image being scaled to the same target value for comparison between chips. The GeneChip® Operating Software (GCOS) was used to control the fluidics station and the scanner, to capture probe array data, and to analyze hybridization intensity data. Default parameters provided in the Affymetrix data analysis software package were applied for analysis.

For the comparison analysis, it was ensured that the scale factors for the compared chips did not differ by a factor larger than 3. In this study, with four replicates per group, 16 comparison analyses (4 transgenic versus 4 non-transgenic) were conducted. Comparison ranking analysis was additionally done to study concordance between increase calls (I) or decrease calls (D) for replicates (this is counting the number of I-calls and D-calls out of 16). The unpaired one-sided t-test converting the p-value to a two-sided p-value was used to determine the direction and significance of change in a transcript's expression level (Data Mining Tool, version 3.1). Signal values of each group were used as basis for calculation, with the original p-value cutoff determined to be 0.05. To select up-regulated genes in the c-Myc experiments, the following criteria were applied for the comparison conducted: the average signal value of the treatment had to be higher than 100; 4 P-calls had to be in the 4 treatment arrays; the fold change had to be 2.0 or higher (ratio of average signal values); the result of the t-test had to be an Up-change call (p-value < 0.05) (based on single signal values of 4 replicates); there had to be more than 13 (out of 16) induced calls in the comparison ranking.

Transcriptome analysis was done according to the manufacturer's recommendation (Affymetrix GeneChip® Expression Analysis Technical Manual (Santa Clara, CA)), using the GeneChip® Test Arrays and GeneChip® Mouse Genome 430 2.0. The frozen lung tissues (10-15 mg) were disrupted and homogenized using a rotor-stator homogenizer, and total RNA was isolated from the tissues using the RNeasy total RNA isolation kit (QIAGEN). RNA of individual samples was pooled as described above, and a second cleanup of isolated RNA was done using the RNeasy Mini Kit (QIAGEN). RNA was checked for quantity, purity, and integrity of the 18S and 28S ribosomal bands by capillary electrophoresis using the NanoDrop ND-1000 and the Agilent 2100 Bioanalyzer.

10 µg of biotinylated fragmented cRNA were hybridized onto the GeneChip® Mouse Genome 430 2.0 array according to the manufacturer's recommendation. The hybridization was performed for 16 hours at 60 rpm and 45 °C in the GeneChip® Hybridization Oven 640 (Affymetrix). Washing and staining of the arrays was done on the GeneChip® Fluidics Station 400 (Affymetrix) according to the manufacturer's recommendation. The antibody signal amplification, washing, and staining protocol (Affymetrix) was used to stain the arrays with streptavidin R-phycoerythrin (SAPE; Invitrogen, USA). To amplify staining, SAPE solution was added twice with a biotinylated anti-streptavidin antibody (Vector Laboratories, CA) staining step in between.

8 µg of total RNA were used as starting material to prepare cDNA. Synthesis of double-stranded cDNA was done with the GeneChip® one-cycle cDNA Kit (Affymetrix). The cleanup of double-stranded cDNA was done using the GeneChip® Sample Cleanup module (Affymetrix). 12 µl of cDNA solution were used for in vitro transcription. The in vitro transcription was conducted with the GeneChip® IVT Labeling Kit (Affymetrix). The total amount of the reaction product was purified with the GeneChip® Sample Cleanup module (Affymetrix). Purified cRNA was quantified and checked for quality using the NanoDrop ND-1000 and the Agilent 2100 Bioanalyzer. Purified cRNA was cleaved into fragments of 35-200 bases by metal-induced hydrolysis. The degree of fragmentation and the length distribution of the fragmented biotinylated cRNA were checked by capillary electrophoresis using the Agilent 2100 Bioanalyzer.

c-Myc transgenic;c-Myc transgenic female mice displayed morphological alterations with varying degree of nuclear atypia, such as bronchiolo-adenomas and bronchiolo-adenocarcinomas. Thus, different stages of malignant transformation of alveolar epithelium were observed.

medullary thymic epithelial cells from wild type mice were FACS-sorted by low CD80 expression
Keywords = thymus
Keywords = mTEC
Keywords = promiscuous gene expression

cortical thymic epithelial cells from wild type mice were FACS-sorted
Keywords = cTEC

medullary thymic epithelial cells from AIRE k/o mice were FACS-sorted by high CD80 expression

medullary thymic epithelial cells from AIRE k/o mice were FACS-sorted by low CD80 expression

medullary thymic epithelial cells from wild type mice were FACS-sorted by high CD80 expression

D4_2h_43
Gene expression data from rat tracheal explants exposed to dexamethasone (treatment) at 2hrs.

D3_2h_22

D2_2h_42

D1_2h_27

S3_24h_26
Gene expression data from rat tracheal explants exposed to cigarette smoke (treatment) at 24hrs.

S1_24h_4

D6_2h_46

D5_2h_37

RNA from 1 testis from three 10 day old control (AMHCre) mice. Immediately after removal, testis samples were snap-frozen and stored in liquid nitrogen. Before RNA extraction, testis samples were weighed and homogenized in a Dounce homogenizer. Thereafter RNA was isolated with the QIAGEN RNeasy Kit (Chatsworth, CA) according to the manufacturers instructions, encompassing an on-column DNaseI-treatment of the RNA.

S5_24h_32

S4_24h_20

Data was processed via Partek and normalized using RMA.
meta probe set file: HuGene-1_0-st-v1.r4.mps

Total RNA was isolated from cells using QIAGEN RNeasy Mini Kit with on-column DNaseI digestion.

The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to The Affymetrix Human GeneChip 1.0 ST chips. The chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described by Affymetrix.

Labeling performed using GeneChip WT Terminal Labeling and Controls Kit according to manufacturer's protocol.

Gene expression data from serum-starved shCDK8 HCT116 cells treated with 10% FBS McCoy's 5A for 30 minutes

Pooled splenocytes and mesenteric lymph node cells were stained with anti-CD4-Pacific blue and sorted on the basis of antibody and EGFP fluorescence.  Cultured iTreg cells were sorted on the basis of EGFP fluorescence.  All sorting was done on a FACSAria (Becton-Dickenson). The average purity and viability of the sorted CD4+ populations was 98.96+/–0.14% and 84.31+/–0.68% respectively (n=120). For the treatment experiments, 1 ml of a cell suspension in PBS was injected into the peritoneal cavity of colitis mice that had lost 2.5+/– 5.7% of their initial body weight.

Foxp3EGFP, Foxp3(delta)EGFP on the BALB/c background were generated and screened as described in Haribhai, et.al. (J Immunol 178:2961-2972, 2007). BALB/c Rag1–/– mice and Il10–/– mice were obtained from the Jackson Laboratory.  Il10–/– mice were crossed to Foxp3EGFP mice.  The Animal Resource Committees at the Medical College of Wisconsin approved all animal experiments and moribund mice were sacrificed and analyzed per these protocols.

For all the iTregs, nTregs, and ex-iTreg experiments, two sets of arrays were performed, and the results were averaged. The subset of probe sets whose expression increased or decreased by twofold or more relative to Native (not activated) conventional CD4+T cells (GSE14415) as a common standard was identified and used for further analysis. The data was normalized using the RMA algorithm from the Bioconductor suite. Results represent mean fold change values derived from 2 independent arrays for each cell type and FDR<10% by the Rank Product package from Bioconductor.

Purified total RNA (~50ng) was amplified using the two-cycle cDNA synthesis kit (Affymetrix  900432) and cRNA was synthesized,  labeled,  fragmented and hybridized to the arrays in accordance to standard Affymetrix protocols (Affymetrix,  Santa Clara,  CA)

Gene expression interrogating 45101 transcripts
exiTreg 1 erica mouse 10-5-11_(Mouse430_2).CEL

iTreg 2 erica mouse 10-5-11_(Mouse430_2).CEL

exiTreg 2 erica mouse 10-5-11_(Mouse430_2).CEL

nTreg 1 erica mouse 10-5-11_(Mouse430_2).CEL

iTreg 1 erica mouse 10-5-11_(Mouse430_2).CEL

nTreg 2 erica mouse 10-5-11_(Mouse430_2).CEL

At 21 days of age, mice were weaned onto an enriched diet (9F Sterilizable Rodent Diet 7960, Harlan Teklad, Madison, WI) and were provided a Colyte solution (peg-3350 & electrolytes for oral solution – Schwarz Pharma, Milwaukee, WI) in place of water at half-strength since at full strength it causes adverse effects in non-CF mice. Mice were sacrificed at 23 days.

Data was initially processed with Illumina GenomeStudio software to assess quality control. Raw data was transferred to Integromics Biomarker Discovery for TIBCO Spotfire software (IBD, Madrid, Spain) where data was normalized using Illumina normalization: forcePositive as background correction, log2 as variance stabilization method, and quantile as the normalization method. Wild type group was used as the reference group.

Total RNA was extracted using the RNeasy Midi kit (Qiagen Inc, Valencia, CA. DNase treatment was performed in the column prior to elution. Biotin labeled cRNA was prepared uisng Illumina TotalPrep RNA Amplification kit (Applied Biosystems/Ambion, Austin, TX).

cRNA was hybridized to Beadchips following Illumina's instructions

Gene expression data from YFPH YFP labeled neurons from the motor cortex (M1), wild type control

brain, motor cortex, layer 5 thick tufted pyramidal neurons, wild type

paraventricular nucleus of the hypothalamus, LPS, 10 micrograms, 1 hours

Control (Ovol2flox/+; Ovol1+/- or Ovol2flox/+;K14-Cre, 2 mice/array) and Ovol1 knockout (Ovol1-/-, 2 mice/array) and Ovol1/2 double conditional knockout (Ovol2flox/-;K14-Cre; Ovol1-/-, 2 mice/array)

Trizol extraction of total RNA followed by column purification (Qiagen) was performed according to the manufacturer's instructions.

3.3ug of the labeled, fragmented single-stranded cDNA is hybridized at 45oC with rotation for 17 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix GeneChip 1.0ST array.  The GeneChip arrays were washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 450 (Fluidics protocol FS450_007).

Gene expression data from isolated keratinocytes from skin
Ovol2flox/+; Ovol1+/- or Ovol1-/- or Ovol2flox/-;K14-Cre; Ovol1-/-

Test Compound Concentration:  3 mg/mL

RE1_H19_1935_U133Plus2.0.CEL

48 hrs after lenti-viral infection, 2 microgram/microliter puromycin was added to culture medium for selecting infected cells, and cells were harvested for RNA 72 hrs after puromycin selection. 50 nM TPA was added at the same time with puromycin to induced maturation of the cells.

Cells were grown in 38.5% IMDM + 38.5% RPMI + 20% FCS + %2 Pen/strep + 1% L-Glutamine,

Scanned with GeneChIP scanner 300 7G using the standard protocol.

Expression data were analyzed using R and Bioconductor (http://www.bioconductor.org/).

Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen, catalogue no. 74134).

hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 Arrays (MOE430v2) following standard techniques.

5 microgram RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.

maturation was induced by adding 50 nM (final concentration) 12-O- tetradecanoylphorbol-13-acetate (TPA) to the medium for 3 days

38B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

34B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

35B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

36B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

37B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; not assessable

Gene expression data from G42 GFP labeled neurons from the motor cortex (M1), wild type control

Peripheral blood mononuclear cells;TTF=92min;Race=White;Sex=Female

Peripheral blood mononuclear cells;RF- polyarticular JIA;GTE6;100min;White;Female

MO-B10-WT 9

Peripheral blood mononuclear cells;RF- polyarticular JIA;GTE6;180min;Black/African American;Female

MO-Tg U1
Gene expression data from PBS-injected TG mice brain at 5 d.p.i.

C57BL/6;hsp70 transgenic;brain (right cerebral hemisphere);7 days;PBS control;5

Peripheral blood mononuclear cells;RF- polyarticular JIA;GTE6;165min;White;Female

Gene expression data from G42 GFP labeled neurons from the motor cortex (M1), Mecp2 null

Gene expression data from Klf5-wildtype 6-month mouse dorsal prostate with Pten-null upon PB-Cre4 mediated floxed fragment deletion

MO-B10-WT 3

Scanning is carried out on an Affymetrix Model 7000 scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 7000 scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System. Chip library files specific to each array and necessary for scan interpretation are stored on the computer workstation controlling the scanner and are updated regularly as necessary when updates are made available from Affymetrix. Collected research data is stored on the hard drive of the instrument computer, transferred to a mirrored storage disk and to a raid 5 server operating on the Partners Healthcare network and backed up nightly via the Partners Healthcare Systems IT backup utility.  All systems are CFR21-11 and HIPPA compliant

The GCOS default analysis algorithms and parameters for normalization and transformation were used. There was no scaling done.

Total RNA from flash frozen samples extracted using Trizol (Invitrogen) as per manufacturer's instructions.

Hybridization is carried out according to the Affymetrix GeneChip Manual.  Twnety ug of IVT material is the nominal amount used on the GeneChip arrays.  Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45C overnight.  Preparation of microarrays for scanning is carried out with Affymetrix appropriate was protocols matched to the specific chip type on a Model 450 Fluidics station process.

For each experimental sample, RNA quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100.  Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed.  Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3'-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carreid according to standard Affymetrix protocls using the Affymetrix GeneChip Cleanup Module (Affymetrix Cataolg # 900371). In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried our on a Bio-tek UV Plate Reader.

Expression data from 18h-fasted WT versus KLF15-null mice: heart

Total RNA was isolated from a wild type C57BL/6 mouse treated for 7 days with 4-hydroxytamoxifen (4OHT; Sigma) using Trizol reagent (Gibco BRL). Double stranded cDNA was generated from 10 ug total RNA and used to generate biotinylated cRNA using the Enzo BioArray High Yield Transcription Labelling Kit (Affymetrix). The cRNA was fragmented using the GeneChip Sample Cleanup Module (Affymetrix) and 10 ug were hybridized to GeneChip Mouse Expression Set 430 A oligonucleotide arrays (Affymetrix). Hybridizations were performed according to the manufacturers instructions using an Affymetrix Gene Chip Instrument System. The arrays were scanned on an Affymetrix GeneChip scanner.

Total RNA was isolated from a wild type C57BL/6 mouse treated for 1 day with 4-hydroxytamoxifen (4OHT; Sigma) using Trizol reagent (Gibco BRL). Double stranded cDNA was generated from 10 ug total RNA and used to generate biotinylated cRNA using the Enzo BioArray High Yield Transcription Labelling Kit (Affymetrix). The cRNA was fragmented using the GeneChip Sample Cleanup Module (Affymetrix) and 10 ug were hybridized to GeneChip Mouse Expression Set 430 A oligonucleotide arrays (Affymetrix). Hybridizations were performed according to the manufacturers instructions using an Affymetrix Gene Chip Instrument System. The arrays were scanned on an Affymetrix GeneChip scanner.

total RNA was extracted from liver of one ApoE-/- mouse infected with a control adenovirus expressing GFP

total RNA extracted from one ApoE-/- mouse infected wtih a control adenovirus expressing GFP

Cells were transfected with SDC1-siRNA or a negative control siRNA.

MDA-MB-231 cells were cultured at 37°C in a humidified atmosphere with 5% carbon dioxide.

Data were analysed using GeneSpring GX11.0 with RMA normalisation to median signal intensity.

Fragmented cRNA was hybridised at 45°C for 16 hours to Affymetrix HG U133 Plus 2.0 GeneChips, followed by washing and staining in an Affymetrix FS450 fluidics station.

Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 3.6 µg of total RNA.

Gene expression data from MDA-MB-231 cells transfected with negative control siRNA

Gene expression data from MDA-MB-231 cells transfected with SDC1-siRNA

Expanding hCD34+ cells were seeded in fresh medium 24 hrs post-transduction, and cultured for an additional 24 hrs prior to the start of selection with puromycin.  The empty pLKO.1ps vector and shZBP-89 in the same vector backbone are used.

De-identified cryogenically preserved primary human CD34+  (hCD34+) cells were obtained from the Yale Center of Excellence in Molecular Hematology (New Haven, Connecticut).  They were prepared by magnetically sorting mononuclear samples of G-CSF mobilized peripheral blood from donors.  For erythroid ex vivo differentiation, hCD34+ progenitor stem cells were expanded for 6 days in StemSpan SFEM Medium with 1X CC100 cytokine mix (StemCell Technologies Inc.) and 2% P/S.  On day 6 of expansion, cells were reseeded into erythroid differentiation medium (StemSpan SFEM Medium containing 2% P/S, 20 ng/ml SCF, 1 U/ml Epo, 5 ng/ml IL-3, 2 uM dexamethasone, and 1 uM β-estradiol)

dCHIP program using Affymetrix default analysis settings and global scaling as normalization method

Extraction of total RNA was performed using Qiagen RNeasy Plus Mini Kit according to the manufacturer's instructions.

Erythroid progenitors on day 6 of differentiation;transduced with lentivirus expressing short hairpins against ZBP-89

Mice were treated with either saline or 100mg/kg APAP by IP injection, liver samples harvested eight hours later.

Experimental livers from male mice with a conditional-null allele of txnrd1 disrupted by albCre.

liver cells from txnrd1 liver-null 8wk male mouse 8 challenged with acetaminophen (APAP)_2

The data were imported into FlexArray using RMA preprocessing for analysis.

Ambion RiboPure extraction of total RNA was performed according to the manufacturer's instructions.

Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

One cycle biotinyllated cRNA generated from 1 µg total RNA with Ambion Message Amp-II Biotin Enhanced system.

BALB-c mice were given intratracheal bleomycin (1.5U per kg).  Lungs were harvested and frozen at 14d.
Lot batch =

rat hippocampus (combined dorsal and ventral aspects), young PIO, subject 7

Total RNA was isolated using the TRIzol reagent and following the manufacturer's RNA isolation protocol (Invitrogen, #15596). One milliliter of TRIzol solution was added to each tube containing the frozen tissue block, and the tissue was homogenized by 10 passages through an 18.5 ga syringe needle. After centrifugation, the RNA was precipitated from the aqueous layer, washed, and dissolved in RNase-free water. RNA concentration and integrity were assessed by spectrophotometry and gel electrophoresis. The RNA samples were stored at 80°C.

rat hippocampus (combined dorsal and ventral aspects), young PIO, subject 8

rat hippocampus (combined dorsal and ventral aspects), young PIO, subject 1

rat hippocampus (combined dorsal and ventral aspects), young PIO, subject 2

rat hippocampus (combined dorsal and ventral aspects), young control, subject 7

rat hippocampus (combined dorsal and ventral aspects), young control, subject 8

rat hippocampus (combined dorsal and ventral aspects), young PIO, subject 5

rat hippocampus (combined dorsal and ventral aspects), young PIO, subject 6

rat hippocampus (combined dorsal and ventral aspects), young PIO, subject 3

rat hippocampus (combined dorsal and ventral aspects), young PIO, subject 4

Mouse J1 ES cells were maintained in DMEM (Dulbecco’s modified Eagle’s medium) supplemented with 20% fetal bovine serum (FBS), 2mM of L-glutamine, 100uM of non-essential amino acid, 1% of nucleoside mix (100X stock, Sigma), 100uM of β-mercaptoethanol, 1000U/ml of recombinant leukemia inhibitory factor (LIF, Chemicon) and 50U/ml of penicillin/streptomycin. ES cells were cultured in 0.1% gelatin coated dishes.

Expression data were normalized using a robust multiple array (RMA).

Total RNA was isolated from cultured cells using RNeasy plus mini kit (Qiagen).

A hybridization mixture of the fragmented DNA and probe array control was prepared, followed by hybridization to the probe array during a 16 hour incubation.

cDNA synthesis was performed with qScript cDNA supermix (Qunata), followed by labelling with Cy3.

Briefly, cardiac ventricles were fragmented, digested with ADS buffer containing collagenase (Worthington Biochemical Corp.) and pancreatin (Sigma), and plated in plating medium containing 65% DMEM (Animed), 17% M199 (Animed), 10% Horse Serum (Invitrogen), 5% Fetal Calf Serum (Invitrogen), 2% L-Glutamine (Animed), 1% PS (Invitrogen). After 24h, medium was changed to maintenance medium (86% DMEM, 10% M199, 1% Horse Serum, 2% L-Glutamine, 1% PS).

The fluorescent intensity emitted by the labeled target was measure in Affymetrix GeneChip Scanner 3000 (Affymetrix).

Expression data were RMA background corrected and quantile normalized using the oligo package in R.

5 μg of biotin-labeled cRNA was fragmented randomly to 35-200 bp and hybridized to GeneChip® GeneChip Mouse Genome 430 2.0 Arrays.

airway epithelium, small airways, obtained by bronchoscopy and brushing

B10.PL mice with experimental autoimmune encephalomyelitis (MS model) were treated with either placebo or 200 ng 1,25(OH)2D3. Six hours later, the spinal cords were harvested and mRNA extracted for analysis.  Naive mice served as controls.
Keywords = Experimental autoimmune encephalomyelitis
Keywords = multiple sclerosis
Keywords = 1
Keywords = 25(OH)2D3

Where indicated, animals were fed with CsA (50mg/kg/day) via a gauge

Control and Wnt-1 overexpressing human melanoma cell-lines (A375 and M24met) were injected into the right flank of SCID mice. Primary tumors were removed after a mean tumor volume of 400m3 and RNA was prepared. For Affymetrix chips, 5µg of RNA were reverse transcribed into second strand cDNA. Preparation of cRNA, hybridization to Human Genome U133 Plus 2.0 (Affymetrix) were carried out according to the manufacturer’s protocols (www.affymetrix.com).

SCID mouse-derived samples  were homogenized with RLT lysis buffer using a mixer mill MM200. Total RNA was extracted using the RNeasy Mini Kit (Qiagen).

biotin (GeneChip Expression 3´Amplification One-Cycle Target Labeling and Control Reagents (30Rxn)

A375 melanoma cell-line;wild type;animals were fed with CsA (50mg/kg/day)

A375 melanoma cell-line;Wnt-1 overexpressing;animals were fed with CsA (50mg/kg/day)

The data was analyzed using the RMA and limma methods to assess differential expression [R version 2.15; packages: affy 1.34.0, affyPLM 1.32.0, limma 3.12.1, mouse_4302.db 2.7.1, biomaRt 2.12.0]

total RNA was extracted from cells using miRNeasy kit from Qiagen for RNA extraction

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse 430 2.0 genome arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

Targeted disruption of D-3-Phosphoglycerate dehydrogenase (Phgdh; EC 1.1.1.95) in mice.

Scanning was carried out using Affymetrix® GeneChip® Scanner with GCOS software according to manufactuer's protocol.

Fluorescent data were processed using the Microarray Suite (MAS) 5.0 software (Affymetrix) and then were transferred to GeneSpring 7.0 software (Agilent).

Total RNA from embryo heads was extracted and purified using RNeasy Lipid Tissue kit (Qiagen Inc) according to the manufacturer’s instructions.

Hybridization was carried out for 16 hr at 45 ºC according the Affymetrix GeneChip® Manual.

Labeling was carried out using Affymetrix GeneChip® One-Cycle Target Labeling kit, according to manufactuer's protocol.

E14 (129P2/OlaHsd background), Genotype: Wild (Phgdh+/+), C57BL/6J background, Gestation: 13.5 days, Tissue: head

E14 (129P2/OlaHsd background), Genotype: Knockout (Phgdh-/-), C57BL/6J background, Gestation: 13.5 days, Tissue: head

Lot batch = 2

VILI (40 ml/kg tidal volume, 65 breath/minute, positive expiratory pressure 0 cm H2O, 4 hours)

standard conditions (12h light-dark cycle, 25-27ºC, ~40% humidity)

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) for ABS_Call; Bioconductor GCRMA package for normalization

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse320_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

BALB/c BMDM stimulated overnight with 50 IU/ml IFN-g ans infected with WA(pTTS,pP60)

H20.24hrIGF
MCF-7 cells were plated in 10cm dishes and then switched to SFM on the next day.  Following overnight starvation, cells were treated in triplicate with IGF-I (100ng/mL)  for 24hr.
Reanalysis of GSM183430.

H21.24hrIGF
Reanalysis of GSM183431.

Unimplanted samples were snap-frozen immediately.  Remaining tissue was xenografted into castrated male athymic nude mouse hosts.  Hosts were given 20 IU human chorionic gonadotropin 3x/week for four weeks.  During weeks three and four, hosts were given daily oral gavage of vehicle, 500 mg/kg DBP, or 75 mg/kg abiraterone acetate.

Donor human fetal testis tissue samples originated from spontaneous pregnancy losses, and were donated with full, informed consent.  Hosts were adult male athymic nude mice (Crl:NU(NCr)-Foxn1nu, strain code 490), obtained from Charles River Laboratories (Wilmington, MA, USA) and housed in the Brown University Animal Care Facility under a 12:12 hr light-dark cycle with controlled temperature and humidity.  Mice were given free access to water and Purina Rodent Chow 5001 (Farmer’s Exchange, Framingham, MA, USA).  All animal care protocols were approved by the Brown University Institutional Animal Care and Use Committee.

Microarray data were processed in the R software environment (R Core Team 2012), using the RMA algorithm (R package oligo) (Carvalho and Irizarry 2010) for probe-level summarization and pre-processing with ComBat (Leek et al. 2012) for batch correction.  Gene annotation information was joined to the expression data using the hugene10sttranscriptcluster.db package (Li 2013).

Total RNA was extracted using the Qiagen DNA/RNA AllPrep kit, with on-column DNase digestion using the Qiagen RNase-free DNase set.  RNA was further purified by overnight precipitation at -80C in 3 volumes 70% ethanol, with 0.1 volumes sodium acetate.  RNA was pelleted, washed with 75% ethanol, and reconstituted in RNase-free water.

Hybridization was carried out for 17 h at 45C and 60 rpm.  Arrays were washed and stained on Affymetrix Fluidics Station FS450 using Affymetrix Wash/Stain Reagents and the Affymetrix protocol FS450_0007

5.5. ug cDNA were labelled using the Affymetrix WT terminal labeling kit, according to the manufacturer's instructions.

gene expression data from human fetal testis xenografts or unimplanted samples
21_VEH

testis;20 weeks;castrated male athymic nude mouse hosts;0.3% Tween-20 vehicle

22_ABI

testis;20 weeks;castrated male athymic nude mouse hosts;abiraterone

17_VEH

18_ABI

19_NON

testis;20 weeks;control (unimplanted samples were snap-frozen immediately);N/A

20_NON

13_VEH

testis;22 weeks;castrated male athymic nude mouse hosts;0.3% Tween-20 vehicle

14_ABI

testis;22 weeks;castrated male athymic nude mouse hosts;abiraterone

16_NON

testis;22 weeks;control (unimplanted samples were snap-frozen immediately);N/A

Total RNA was extracted from 1 million cells upon reaching 80% confluence, within passages 2-5 of tissue culture.

Fibroblasts were cultured in IMDM (Iscove's Modified Dulbecco's Medium) supplemented with 4 mM L-glutamine, 10% foetal calf serum, 0.1 mg/ml streptomycin, 100U/ml penicylline (Sigma-Aldrich, St. Louis, MO, USA) at 37°C and 5% CO2.

Cell intensity values and probe detection calls were computed from the raw array data using the Affymetrix GeneChip Operating Software (GCOS). Further data processing was performed in the R computing environment using packages from BioConductor. Robust Multi-Array Average (RMA) normalization was applied. Normalized data were then filtered based on the Affymetrix detection call, so that only probes that had a Present call in at least one of the arrays were retained. Probes with low intensity values (less than 100) in all arrays were also excluded from statistical analysis.

5 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Human Genome U133A 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Total RNA was obtained from approximately 100 mg of rear leg skeletal muscle stored in RNAlater® Qiagen (Valencia, CA) at -80oC using Qiagen RNeasy Maxi kits. Homogenates were made using a Brinkman/Kinetmatica Model PT-2100 polytron (Westbury, NY) for tissue dispersal. Total RNA samples were further processed for poly(A)+ mRNA isolation using Qiagen oligotex mRNA kit.

Approximately 1 ug of mRNA processed to produce biotinylated cRNA targets.

Diabetic Male Wistar rat after 7 days of diabetes induced with streptozotocin and subsequent treatment with oral vanadyl sulfate for 20 days.

Normal Male Wistar rat treated with oral vanadyl sulfate for 28 days.

Peripheral blood mononuclear cells;TTF=140min;Race=White;Sex=Male

Recombinant mouse IFNγ was purchased from Calbiochem (Merck4Biosciences, Germany) and used at concentrations of 100 U/ml. The Listeria monocytogenes EGD strain (kindly provided by Thomas Decker from the MFPL, University of Vienna, Austria) was i.p. injected.

Bone marrow derived macrophages were cultivated as described in PMID 11070173.

Arrays were washed and stained in an Affymetrix GeneChip fluidics station 450, according to the Affymetrix protocols. Arrays were scanned with the GeneChip Scanner GCS3000.

For generation of probe set expression values, CEL files containing probe level data were normalized using the robust multi-chip average (RMA) algorithm (including background correction, quantile normalization across all arrays, median polished summarization based on log transformed expression values) implemented in the Partek Software v.6.5 (Partek Inc, St Louis, MO).

Total RNA was isolated according to the manufacturer's instructions (peqGOLDTriFast, PEQLAB). 100ng of total RNA was used for reverse transcription, cDNA synthesis and purification according to the manufacturer’s instructions (AmbionWT Expression Kit; Life Technologies; Carlsbad, California)

Labeled samples were loaded and hybridized to GeneChip® Mouse Gene 1.0 ST Arrays for 16 hours over night at 45°C according to the manufacturer’s instructions rotating in a hybridization oven.

Fragmentation and labeling was performed using the GeneChip® WT Terminal Label & Controls Kit (Affymetrix, London) according to the manufacturer’s instructions.

C57BL/6N;Stat1 KO (ko);Bone marrow derived macrophages (BMMs);6h IFNg + Listeria monocytogenes (Lis)

C57BL/6N;Stat1 delta beta (db);Bone marrow derived macrophages (BMMs);6h IFNg + Listeria monocytogenes (Lis)

C57BL/6N;Stat1 delta alpha (da);Bone marrow derived macrophages (BMMs);6h IFNg + Listeria monocytogenes (Lis)

Peripheral blood mononuclear cells;TTF=101min;Race=White;Sex=Male

Gene expression data from brain of Npc1+/+ mouse1 of age 60 days

Gene expression data from brain of Npc1+/+ mouse2 of age 60 days

Gene expression data from brain of Npc1-/- mouse1 of age 54 days

Gene expression data from brain of Npc1-/- mouse1 of age 55 days

Gene expression data from brain of Npc1-/- mouse1 of age 59 days

Gene expression data from brain of Npc1-/- mouse1 of age 62 days

Gene expression data from brain of Npc1+/- mouse1 of age 59 days

Neural precursor cells (NPC) were purified from neural rosettes derived from hES cells (Perrier et al, 2004)  by cell sorting using the pan neuronal marker NCAM ( Neural Cell Adhesion molecule or CD56).

Scanning procedures of the Affymetrix GeneChip® Human Genome U133 Plus 2.0 were carried out as described in the Affymetrix technical manual (see manufacturer's web site)

The statistical treatment of the expression data was achieved using the Array Assist 4.1 software (Stratagene). Normalization was performed using the GC-RMA algorithm.

Total RNA was extracted from the cells using the RNeasy Mini kit (Qiagen) according to the manufacturer protocol

Hybridisation, washing and staining procedures of the Affymetrix GeneChip® Human Genome U133 Plus 2.0 were carried out as described in the Affymetrix technical manual (see manufacturer's web site)

100 ng of total RNA was used to generate biotinylated cRNA using the GeneChip® Two-Cycle Target Labeling and Control Reagents from Affymetrix according to the manufactures protocol

Differentiation of hES cells line SA01 towards neural rosettes;Neural precursor phenotype

Neural precursor cells derived from hES cells line SA01, biological replicate  2

Differentiation of hES cells line VUB01 towards neural rosettes;Neural precursor phenotype

Neural precursor cells derived from hES cells line VUB01, biological replicate  2

Neural precursor cells derived from hES cells line VUB01, biological replicate  3

Mesodermal Precursor Cells (MPC) were derived from hES by plating cells on 0,1% Gelatin coated dishes in KO-DMEM medium supplemented with 20% FBS.

Differentiation of hES cells line VUB01 towards MPC-like cells;Mesenchymal stem cells phenotype

Mesodermal Precursor Cells derived from hES cells line VUB01, biological replicate 3

Neural precursor cells derived from hES cells line VUB01, biological replicate  1

training: mice were put into a 30 x 50, 20 cm deep container filled with warm water (35 C) equipped with a floating rotating wheel. Swimming duration was continously increased from 5 minutes to 90 minutes daily (6 times per week) swimming. Mice were stimulated to swim as soon as they began floating to maximize activity in the water.

15 ug of each cRNA sample was hybridized for 16 hours at 45°C to rat expression Affymetrix RAE 230A GeneChip arrays. Following the hybridization arrays were washed and stained with streptavidin-phycoerythrin using a fluidics station in accordance with the Affymetrix protocol.

Mesodermal Precursor Cells derived from hES cells line VUB01, biological replicate 2

Differentiation of hES cells line VUB03_DM1 towards MPC-like cells;Mesenchymal stem cells phenotype

Mesodermal Precursor Cells derived from hES cells line VUB03_DM1, biological replicate 2

Mesodermal Precursor Cells derived from hES cells line VUB03_DM1, biological replicate 3

Control mice were spontaneously breathing room air and received 2microliter/gm PBS in the oropharynx with a pipette.  They were sacrificed 4 hrs later, whole lung removed, homogenized and total RNA isolated.  Labeled cRNA was prepared and hybridized to an Affymetrix GeneChip 430A microarray using Affymetrix protocol.  Microarray was scanned with the GeneChip Scanner and image analysis was performed with Affymetrix MAS 5.0 software.  Background adjustment and quantile normalization of microarray data was performed using RMAExpress.

HepG2;Human hepatocellular liver carcinoma cells;wild type;10 days old tumor spheroids

HepG2;Human hepatocellular liver carcinoma cells;HIF-1α knockdown;10 days old tumor spheroids

Mouse was housed individually in a separate cage under a 12-h light–dark cycle and permitted food and water ad libitum. A period of acclimatization for two weeks was allowed prior to any experimental procedure. Clozapine was added to the animal’s drinking water in a concentration equivalent to the highest human clinical dosage (i.e. 12mg/kg/day for Clozapine) and delivered through light protected bottles. The weight and water consumption was measured weekly and the drug concentration in water was adjusted accordingly .At the end of 4 weeks animal was sacrificed by cervical dislocation and the brain was removed, dissected into left and right hemispheres and cerebellum, flash frozen in liquid nitrogen and stored at -80 C for future use.

GeneChips were scanned using GeneArray Scanner (Agilent Technologies, Foster City, CA).

Normalized expression values were calculated from probe level data (CEL file) using the function of Robust Multi-Array expression measure using sequence information GC-RMA (Wu et al 2004, www.bepress.com/jhubiostat/paper4).Computational steps were implemented in the R-language. GCRMA and it's associated packages were provided by the open source bioconductor project.

Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8-10 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

Gene expression data from the right forebrain of C57BL mouse received Clozapine oral treatment for four weeks.

Forebrain (left hemisphere), Strain: C57BL, Gender: Male, Age: 4weeks, Drug treatment: Atypical antipsychotic Clozapine, Dose: 12mg/kg/day, Route of treatment: Oral treatment-Drug added to drinking water, Period of treatment: 4 weeks, Method of sacrificing: cervical dislocation.

Right brain hemisphere ,C57BL male mouse,Clozapine treated,Orally,4 weeks

GeneChips were scanned using GeneArray Scanner (Agilent Technologies, Foster City, CA)..

Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Gene expression data from the right forebrain of C57BL mouse received Clozapine oral treatment for four weeks..

Mouse was housed individually in a separate cage under a 12-h light–dark cycle and permitted food and water ad libitum. A period of acclimatization for two weeks was allowed prior to any experimental procedure. Haloperidol was added to the animal’s drinking water in a concentration equivalent to the highest human clinical dosage (i.e. 1.6 mg/kg/day) and delivered through light protected bottles. The weight and water consumption was measured weekly and the drug concentration in water was adjusted accordingly .At the end of 4 weeks animal was sacrificed by cervical dislocation and the brain was removed, dissected into left and right hemispheres and cerebellum, flash frozen in liquid nitrogen and stored at -80 C for future use.

Gene expression data from the right forebrain of C57BL mouse received Haloperidol oral treatment four weeks.

Forebrain (left hemisphere), Strain: C57BL, Gender: Male, Age: 4weeks, Drug treatment: Typical antipsychotic Haloperidol, Dose: 1.6mg/kg/day, Route of treatment: Oral treatment-Drug added to drinking Water, Period of treatment: 4 weeks, Method of sacrificing: cervical dislocation.

Right brain hemisphere ,C57BL male mouse,Haloperidol treated,Orally,4 weeks

Gene expression data from the right forebrain of C57BL mouse received Haloperidol oral treatment for four weeks.

Lungs of the hyperresponsive AJ strain of mice 6 hours post aspiration with PBS containing HDM

Lungs of the hyperresponsive AJ strain of mice 6 hours post aspiration with PBS

Lungs of the hyperresponsive AJ strain of mice 24 hours post aspiration with PBS containing HDM

C57BL/6;C-DGCR8 KO (D4-cre/DGCR8 KO/Ai9 tdTomato);retina;cone photoreceptors;postnatal day 30

Cells were grown in the presence or absence of doxycycline for 24 hours for Ls174T-L8 or 72 hours for Ls174T-pTER-β-catenin cells.

Appr. 10 million cells were cultured in RPMI (Invitrogen) containing 5% fetal calf serum at 37 degrees Celsius.

Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.

Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix).

10 µg of labeled cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

Ls174T-L8 cells carry a doxycyclin-inducible dominant-negative Tcf4 transgene. Cells were untreated (con) or trangene expression was induced for 24 hours with doxycycline (dox). Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profiles.

Ls174T-pTER-β-catenin cells carry a doxycyclin-inducible shRNA against β-catenin. Cells were left untreated (con) or shRNA was induced for 72 hours with doxycycline (dox). Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profiles.

Ls174T;intestinal colorectal carcinoma cells;shRNA against β-catenin;72hr

Ls174T;intestinal colorectal carcinoma cells;dominant-negative Tcf4 transgene;24hr

Healthy rats were treated with sodium tunsgtate at a dose of 0.7g/L during one week, and at 2g/L during the next 4-5 weeks without observing any variation in its normoglycemia
Keywords = pancreas regeneration
Keywords = STZ
Keywords = tungstate
Keywords = insulin-like agents
Keywords = beta cell plasticity
Keywords = neogenesis

C57BL/6;wild type (D4-cre/Ai9 tdTomato);retina;cone photoreceptors;postnatal day 60

HCT116 cells were transiently transfected with  siGFP (siControl) or siChe-1 RNA double strand oligos and analyzed 48 hours later.

GeneChips were scanned using the Affimetrix GeneChip Scanner 3000 7G system.

The data were analyzed with Expression Console™ software (v.1.1) (RMA) using Affymetrix default analysis settings and global scaling as normalization method.

Trizol extraction of total RNA was performed according manufacturer's instruction

Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr at 45 °C on Human Gene 1. ST Array. GeneChips were whashed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affimetrix protocol from 6 micrograms of total RNA (Gene Chip Whole Transcript Assay Technical Manual, 2007, Affimetrix)

Affymetrix murine MOE 430 2.0  gene chips were used.GeneChip CEL  files were subjected to  GC-RMA  normalization (get reference) using  the  GeneSpring GX 7.3.1
GeneSpring 7.3.1 (Agilent technologies Inc. Palo Alto, California) was used to normalization, Clustering and filtering.

Total RNA was extracted from the murine spleens using Trizol kit (Invitrogen) and then purified two times using RNeasy columns (Qiagen)

Full Protocol Description: Create a hybridization cocktail for a single probe array that contains  0.067 ug/uL fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 10% DMSO, and 1X Hybridization Buffer.  Heat hybridization cocktail to 99C for 5 minutes, to 45C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 uL of 1X Hybridization Buffer. Incubate at 45C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 uL of the hybridization cocktail. Incubate at 45C for 16 hrs in the Hybridization Oven rotating at 60 rpm.
Fluidics:  Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0004. Arrays were stained with phycoerythrin-conjugated streptavidin [Molecular Probes, Eugene, OR] and hybridization signals were amplified using antibody amplification with goat IgG [Sigma-Aldrich] and anti-streptavidin biotinylated antibody [Vector Laboratories, Burlingame, CA], as described in the Affymetrix GeneChip® Expression Analysis Manual

Samples used for hybridization consisted of non-pooled (NP) RNA extracts from the two genotypic groups namely wild type controls (WT) and Nix knockout animals (Nix-/-). A total of eight hybridization experiments were performed.

RNA extracted from cultured lymphoblastic cell line obtained from normal subject.

RNA extracted from cultured lymphoblastic cell line obtained from FCHL (familial combined hyperlipemia) patient.

Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 20 uM Potassium dichromate for 6h at  37 °C.

Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 10 uM  2,3-Dimethoxy-1,4-naphthoquinone for 6h at 37 °C.

Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 20 uM Mercury (II) chloride for 6h at  37 °C.

Skin biopsies were taken from patients and normal controls from the forearm region, digested with trypsin-EDTA (0.025%) at 37oC for 1 hour in a Petri Dish, trypsin was removed, and 1% collagenase type I in RPMI 1640 was added. The biopsy was cut in small pieces with a sterile scalpel and incubated 3 hrs at 37oC. Then, the tissue was centrifuged at 1200 rpm for 10 minutes at room temperature, the supernatant was discarded and replaced with growth media. We grew skin fibroblasts in DMEM supplemented with 10% Fetal Bovine Serum and L-glutamine, penicillin and streptomycin, in a tissue culture incubator at 5% CO2 and 37oC. We grew the cells until flasks were 50-80% confluent until RNA was prepared.

GeneChips scans were performed by the Mount Sinai School of Medicine Microarray Shared Research Facility on an Affymetrix GeneChip system.

A summarized dataset of the Affymetrix chips was obtained by GC Robust Multi-Chip Average (gcRMA) analysis for the background correction and normalization (Wu et al, 2004). We combined the Affymetrix data to assess consistent differences between the mutant and wild type fibroblasts gene expression and used the following three criteria to find candidate genes: a) the moderated t-statistic is not less than 332 (Gordon 2004); b) the average fold change is no less than two fold increase (or decrease); c) The maximum of the log 2 based signal intensities across the arrays was greater than 3.5, which was approximately twenty percentile of all log 2 based signal intensities. This step was done to filter out genes with extremely low expression levels.

Cells were lysed directly on the culture flask by adding the appropriate amount of RLT solution from the RNeasy kit (Qiagen), as recommended by the manufacturer. RNA was quantified in a Nanodrop system or a Pharmacia spectrophotometer. RNA quality was assessed using the Agilent Bioanalyzer using the RNA Nanoassay.

Gene expression profiles of normal and SS patient fibroblasts were examined by microarray analysis using Affymetrix U133plus2.0 chips. The hybridization steps were performed by the Mount Sinai School of Medicine Microarray Shared Research Facility

Double-stranded cDNA synthesis, in vitro transcription/target labeling, hybridization/control mixture preparation, chip-hybridization, and post-processing procedures were performed using standard protocols from Affymetrix by the Mount Sinai School of Medicine Microarray Shared Research Facility.

1:1 Pool of two control cell lines, one is GM00037, the other is from a normal donor

unaffected sister of Setleis patient in Samples Setleis_05 and _06.

Peripheral blood cells taken from survivors few hours after exposure to trauma.
date: 2001

gastrointestinal stromal tumor;Female;HIGH;KIT mutation detected

Lentiviral pLKO-shRNAs were obtained from Sigma-Aldrich. The tracking numbers of the most effective shRNAs are TRCN0000019894 (YY1), TRCN0000016494 (YY2). To replace the puromycin-resistance gene in pLKO plasmids by neomycin-resistance for combined knockdown, an 827 bp fragment containing neoR gene was amplified from plasmid pCNH with primers 5'-TCA GGA TCC AGG ATC GTT TCG CAT GAT TGA AC-3' and 5'-TCA GGT ACC GAT GCA TGA GTC CCG CTC AGA AGA ACT CG-3', digested by Kpn I and BamH I, and ligated to Kpn I/BamH I-treated pLKO- shRNA plasmids. pLKO-shRNAs were packaged in 293T cells following the manufacturer’s standard protocol (Sigma-Aldrich). Spent medium of 293T cells was collected at 24-hour and 48-hour post-transfection, pooled, and cleared through a 0.45-micron syringe filter. To in-fect, HeLa cells were grown in 6-well culture plates in 2 ml medium and 0.5 ml of lenti-virus-containing medium was added. After 72 hours, cells were selected and maintained in medium containing 2 mg/ml of puromycin. To make combined shRNA transfectants, this process was repeated but selected using 500 mg/ml of Geneticin G418 for dual se-lections. Stable transfectants were split once a week and cells of less than fifteen pas-sages were used in all assays.

HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, and maintained in 37°C incubators with 5% CO2.

Total RNA was prepared by Trizol Reagent (Invitrogen). Ten micrograms of RNA were used to hybridize the Affymetrix U133A2.0 human genome array.

Microarray = Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2

Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)

bone marrow;CD34+ hematopoietic stem cells (HSC);myelodysplastic syndromes (MDS);refractory anemia with excess blasts 2 (RAEB2);del5q plus monosomy7/del7q plus trisomy8 plus other

bone marrow;CD34+ hematopoietic stem cells (HSC);myelodysplastic syndromes (MDS);refractory anemia with excess blasts 1 (RAEB1);del5q

female Spargue-Dawley rats, 9-cis-retinoic-acid, 100 mg/kg diet for 7 days,  tissue: lung

female Spargue-Dawley rats, 9-cis-retinoic-acid, 100 mg/kg diet for 7 days,  tissue: liver

female Spargue-Dawley rats, Targretin, 60 mg/kg BW gavage for 7 days, tissue: mammary gland

female Spargue-Dawley rats, Targretin, 60 mg/kg BW gavage for 7 days, tissue: lung

female Spargue-Dawley rats, Targretin, 60 mg/kg BW gavage for 7 days, tissue: liver

103;None;6/30/65;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;11/9/04;Diarrhoea, now settled, Mum has UC;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

101;Paracetamol;10/5/63;M;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;11/2/04;Weight loss, altered bowel habbit.;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

110;None;3/13/54;M;JEWISH;FALSE;FALSE;FALSE;FALSE;FALSE;12/2/04;Diarrhoea;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;6-2-01;terminal ileum;Uninflamed;total RNA from 10 human cell lines

104;None;1/2/72;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;11/15/04;IBS type symptoms;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;6-2-01;terminal ileum;Uninflamed;total RNA from 10 human cell lines

101;Paracetamol;10/5/63;M;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;11/2/04;Weight loss, altered bowel habbit.;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;6-2-01;terminal ileum;Uninflamed;total RNA from 10 human cell lines

117;Loperamide;3/31/67;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;12/21/04;IBS type symptoms;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;5-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

116;Clomiprimine;1/19/56;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;12/21/04;FH Colon cancer;0;TRUE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;5-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

115;Frusemide, Codine Phosphate;9/14/28;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;12/21/04;Diarrhoea, Also has Prostate Ca;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;5-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

Liver;GPR120 KO;high fat diet HFD;mixed 129/Sv and C57BL/6;mouse 429

Epididymal adipose;GPR120 KO;high fat diet HFD;mixed 129/Sv and C57BL/6;mouse 429

FVB benchmark dataset: 3 month old female mouse
Keywords = cardiac development

Epididymal adipose;GPR120 KO;high fat diet HFD;mixed 129/Sv and C57BL/6;mouse 428

Liver;GPR120 KO;high fat diet HFD;mixed 129/Sv and C57BL/6;mouse 427

Epididymal adipose;GPR120 KO;high fat diet HFD;mixed 129/Sv and C57BL/6;mouse 427

105;None;7/29/84;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;11/15/04;IBS type symptoms;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

104;None;1/2/72;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;11/15/04;IBS type symptoms;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

Hdh knock-in embryonic stem cells, Q20 line, biological replicate 1

6 pairs of littermate male Usp2-KO and WT mice were dissected at the age of 12 weeks at Zeitgeber Time 12, the acrophase of Usp2 expression

Mice were housed for 3 weeks in 12h Light:12h Dark under standard conditions

Gene level normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003).

Total RNA from mice kidney was isolated with the Trizol and phenol chloroform extraction and was purified with RNAqeuous kit. RNA quality and concentration was verified with an Agilent Bioanalyzer 2100

Affymetrix Mouse Gene 1.0 ST arrays were hybridized with 5 micrograms of labeled, amplified cDNA, washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007)

Equal amounts of RNA extracted from 3 mice from the same group were combined as a pool. For all samples, 300 ng of total RNA was used to perform target preparation using the Whole Transcript Sense Target Labeling Protocol procedure (Affymetrix, High Wycombe, UK).

Total RNA was extracted using Qiagen RNeasy midi-kit from bone marrow macrophages in-vitro differentiated using human colony stimulator factor-1 (CSF-1) or from C57BL6/J 17.5 whole embryo.
The cDNA derived from the total RNA was labeled using the amino-alyll indirect labeling with Cy3 mono-reactive dye.

MCF7/BUS cells were inoculated in a plastic dish in DMEM (phenol red-free, 5% stripped fetal calf serum) and cultured for the indicated period (0, 1, or 2 days).

Gene expression data from MCF7 (BUS stock) hormone starved for 2 day2.

Gene expression data from MCF7 (BUS stock) hormone starved for 1 day.

SMhu092

Keywords = macrophages

TNFa-OMe siRNA-B;09/06/16;09/06/29;6;168;2.82;1.157;colon;5% DSS

in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 8, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 6, Units of Dose or Concentration: ppm

nasal epithelium, formaldehyde inhalation exposure, 6 ppm, 6 hours per day, 5 days per week, 8 day time point

Rat230_2;15;ul;1.536;0.766;1.98;1:5;7.8;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;299;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.708;0.892;1.89;1:5;7.8;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;298;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;0.918;0.454;1.99;1:5;7.7;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;301;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;0.977;0.478;1.99;1:5;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;300;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 5, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 6, Units of Dose or Concentration: ppm

nasal epithelium, formaldehyde inhalation exposure, 6 ppm, 6 hours per day, 5 days per week, 5 day time point

Rat230_2;15;ul;1.683;0.839;1.98;1:5;8.1;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;294;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.674;0.969;1.87;1:5;8.2;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;293;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;2.229;1.143;1.93;1:5;7.8;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;297;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.254;0.641;1.98;1:5;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;296;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

in vivo Treatment: Formaldehyde, Treatment Duration: 6, Units of Duration: hrs, Treatment Time: 6, Units of Treatment Time: hrs, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 6, Units of Dose or Concentration: ppm

nasal epithelium, formaldehyde inhalation exposure, 6 ppm, 6 hour time point

Rat230_2;15;ul;1.092;0.567;1.89;1:5;7.7;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;284;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.371;0.727;1.87;1:5;7.7;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;283;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Neural induction was carried out in hESC according to the protocol developed by Chambers et al. (2009).

The data were analyzed with R and Bioconductor packages. Normalization was performed with the RMA package.

Total RNA was extracted with the Rneasy kit (Qiagen) according to the manufacturer's instructions.

The chips were washed, and stained,with Fluidics Station 450 (Affymetrix) and then scanned with the GeneChip Scanner 3000 (Affymetrix) in accordance with the manufacturer's standard protocols.

The scaled values were then analyzed by GeneSpring software (Silicon Genetics, Redwood City, CA). To identify differentially expressed transcripts, pairwise comparison analyses were carried out with Affymetrix GCOS 1.2. Each of the experimental samples (n=3) was compared with each of the reference samples (n=3), resulting in nine pairwise comparisons. This approach based on Mann-Whitney pairwise comparison test allows ranking of the differentially expressed genes as well as calculation of significance (P value <0.05) of each identified change.

Wild-type and Emx2 KO fetuses at E10.5 were frozen in OCT compound without fixation. They were sectioned (30 m), stained with heamatoxylin, and air-dried. Some of them were used for GATA4 immunostaining to locate gonadal primordium. The epithelial cells of the gonadal primordium were obtained by Laser Microdissection System (Leica). The specimens prepared from three individuals of wild-type or Emx2 KO were mixed as one group.

The labeled aRNA was fragmented and hybridized to the GeneChip Mouse Genome 430 2.0 array (Affymetrix) according to the manufacturer’s instructions.

Total RNA was prepared from three groups of wild-type and Emx2 KO specimens, and an aliquot (15 ng) was subjected to two-cycle amplification using MessageAmp™ II aRNA Amplification Kit (Ambion), and thereafter biotin labeling using MessageAmp™ II-Biotin Enhanced Kit (Ambion).

Please see our publication Wilson et al PLoS One 2008, PMID: 18648539

Slides were washed with Gene Expression Wash Buffer 1 and 2 (Agilent Technologies, Santa Clara, CA) followed by Acetonitrile. A final wash in Stabilization and Drying Solution was performed to prevent Cy-5 degradation by ozone. The array was scanned using an Agilent G2505B DNA microarray scanner under extended Dynamic range.

The image files were extracted using the Agilent Feature Extraction software version 9.5.1 applying LOWESS background subtraction and dye-normalization.

Total RNA was isolated separately from five heart samples for each condition using TRIzol reagent (Invitrogen, San Diego, CA) according to the manufacturer's instructions. Total RNA was purified using RNeasy columns (Qiagen, Chatsworth, CA). RNA concentration was measured by spectrophotometry, and RNA integrity assessed with an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA) with 6000 Nano Chips according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to 18S and 28S ribosomal RNA subunits and had a RNA Integrity Number (RIN) greater than six.

cRNA was hybridized to 4×44K whole human genome microarray slides from Agilent (Part G4112F) according to the manufacturer's instructions. The hybridization was carried in a rotating hybridization chamber in the dark at 65°C for 17 h.

Using Low RNA Input Fluorescent Linear Amplification Kits (Agilent Technologies, Santa Clara, CA, USA), cDNA was reverse transcribed from each RNA sample, and cRNA was then transcribed and fluorescently labeled from each cDNA sample. The mouse heart tissue cRNA samples were labeled with Cy5 and the Universal Mouse reference cRNA was labeled with Cy3. The resulting cRNA was purified using an RNeasy kit (Qiagen, Valencia, CA, USA) followed by quantification of the cRNA by spectroscopy using an ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). 825 ng Cy3- and Cy5- labeled and amplified cRNA was mixed and fragmented according to the Agilent technology protocol.

A673 treated with Doxorubicin for 24 hours with concentration of 59.88 nM (EC50), biological rep3

Gene expression data from A673 cell line that has been treated with Doxorubicin for 24 hours with concentration of 59.88 nM (EC50).

A673 cell line that has been treated with Doxorubicin for 24 hours with concentration of 59.88 nM (EC50).

A673 treated with Doxorubicin for 24 hours with concentration of 59.88 nM (EC50), biological rep2

A673 treated with Doxorubicin for 24 hours with concentration of 59.88 nM (EC50), biological rep1

A673 treated with cytarabine (ARA-C) for 5 days with concentration of 0.34 uM (2 x EC50), biological rep2

Gene expression data from A673 cell line that has been treated with cytarabine (ARA-C) for 5 days with concentration of 0.34 uM (2 x EC50).

A673 cell line that has been treated with cytarabine (ARA-C) for 5 days with concentration of 0.34 uM (2 x EC50).

A673 treated with cytarabine (ARA-C) for 5 days with concentration of 0.34 uM (2 x EC50), biological rep1

A673 treated with cytarabine (ARA-C) for 3 days with concentration of 0.34 uM (2 x EC50), biological rep3

A673 treated with cytarabine (ARA-C) for 3 days with concentration of 0.34 uM (2 x EC50), biological rep2

SMhu025

SMhu026

Scanned on an Agilent G2505B scanner.
Images were quantified using Agilent Feature Extraction Software (version A.9.5.3.1).

Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization.
The Sample data tables report Log base2 (rprocessedsignal/gprocessedsignal) - while raw data files report Log base10 Ratios.
Note: all data included, no missing values imputation performed. Controls spots removed.
Refer to raw data files for additional annotation of matrix table rows.

Flash-frozen suprarenal aortic tissue was homogenized for RNA extraction, and isolated using the RNeasy Fibrous Tissue Mini kit (Qiagen) according to the manufacturer's instructions.

Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples in equimolar concentrations were applied to microarrays, enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

For ch 2., 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label.

test;male;ApoE-/-;suprarenal aorta;control (saline);28d;reference

SMhu019

SMhu020

test;male;ApoE-/-;suprarenal aorta;control (saline);14d;reference

test;male;ApoE-/-;suprarenal aorta;control (saline);7d;reference

The data were normalised using quantile normalisation with GeneSpring Gx v 12.0

GeneChip were finally scanned using the GA2500 Affymetrix GeneChip scanner.

Total RNA was extracted using Trizol (Invitrogen-Life Technologies, Paisley, UK). Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA with the Agilent 2100 Bioanalyzer. In order to obtain enough RNA to perform the Affymetrix analysis, 0.6 µg of RNA from CD34+ cells of 5 different normal donors or IM patients were pooled, so as to obtain 3 pools each comprising 3 µg RNA.

The fragmented cRNA was then hybridized to an identical lot of Affymetrix HG-U133A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.

Biotin-labeled labeled cRNA  was purified using RNeasy spin columns (Qiagen, Valencia, CA) and fragmented (20 µg) following the Affymetrix GeneChip protocol. The assessment of cRNA concentration/quality and  fragmentation was performed with the Agilent RNA chips.

The biotin-labeled target synthesis reactions, as well as the Affymetrix HG-U133A GeneChip arrays hybridization, staining, and scanning, were performed using Affymetrix standard protocols (Affymetrix, Santa Clara, CA).

CD34+ hemopoietic progenitors purified from peripheral blood of Idiopathic Myelofibrosis (IM) patients

Mice were first euthanized by cervical dislocation and then eyes were rapidly removed. Neuroretina was obtained and snap frozen for RNA isolation.

8-weeks old db/db diabetic mice and their lean non-diabetic littermates were purchased from Harlan Laboratories.

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0). RMA algorithm was used to normalize the arrays and summarized the probes.

RNA was isolated using the Rneasy Mini Kit (Qiagen, Germany) according to manufacturer`s instructions.

Arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven.

200 ng of total RNA were used to synthesize sense ssDNA with the Ambion WT Expression Kit. Next, ssDNA was fragmented and labelled with a biotinylated compound.

CD34+ hemopoietic progenitors purified from bone marrow of healthy controls

Neuroretina 8-week old db/db mouse: BKS.Cg- + Leprdb/+ Leprdb/OlaHsd

Alpha7 L250T heterozygous mice following nicotine-induced seizures

The data were normalized using average normalization using genome studio software

RNA was extracted using Qiagen Rneasy Mini Prep kit. Quality control was performed with Agilent Bioanalyser.
RNA amplification: Illumina® TotalPrep RNA Amplification Kit, manufactured by Ambion, Inc.

Vc was added to mESC medium at a final concentration of 50 μg/ml. One day after pre-iPSCs were plated onto feeder (D2), media were changed to mESC medium with or without Vc. Vc was continuously added in the Vc treatment group.

MaF pre-iPSCs were cultured on feeder in mESC medium with or without Vc. Media were changed everyday.

Vc was added to mESC medium at a final concentration of 50 μg/ml. At D2 after the 2nd infection, transduced MEFs were changed to mESC medium with or without Vc. Vc was continuously added in the Vc treatment group.

MEFs were cultured in DMEM+10% FBS+NEAA+GlutaMax+penicillin/streptomycin (P/S); after two-rounds of infections, GFP- or SKO-transduced MEFs were cultured in mESC standard medium (DMEM+15% FBS+NEAA+GlutaMax+Sodium pyruvate+P/S+β-mercaptoethanol+1,000U/ml LIF) with or without Vc.

The chips were scanned using the GeneArray scanner (Affymetrix) to produce CEL files.

A rigorous quality control pipeline was developed to prepare the gene expression microarray data for analysis. First, the CEL files were imported into R 2.8.0 using the justRMA function of the Affymetrix library from Bioconductor, which applies background subtraction and quantile normalization. An alternate CDF file (U133Plus2msk.cdf.gz) was used to exclude mis-targeted and nonspecific probes from the microarrays (Zhang et al. 2005), and probesets with less than 7 remaining probes were also excluded. Probesets with more than 50% absent calls were excluded, as calculated using the panp package from Bioconductor. Finally, the ComBat library in R was used to correct for batch effect (Johnson et al. 2007).

Total RNA was collected using the RNeasy Plus Mini Kit (Cat No. 74134) 48 hours after transient transfection of HEK293T cells.

The cRNA probes were then hybridized using standard Affymetrix protocols described in the GeneChip Expression Analysis Technical Manual (Affymetrix P/N 702232).

Samples were then converted to cRNA probes using standard Affymetrix protocols described in the GeneChip Expression Analysis Technical Manual (Affymetrix P/N 702232).

The datasets were pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

B6;wildtype;8 weeks;female;spleen;regulatory T cells (Tregs);CD4+CD25hi;CD19, CD8a, CD11b, CD11c, NK1.1;MoFlo Sorter

B6;Gata1 knockout;8 weeks;female;spleen;regulatory T cells (Tregs);CD4+CD25hi;CD19, CD8a, CD11b, CD11c, NK1.1;MoFlo Sorter

CD-1;20 week;heart left ventricle;dominant negative CREB1 driven by cardiomyocyte-specific myosin heavy chain-? promoter

Normalization according to MAS5.0 algorithm. Only probesets called present in at least one sample were included

Cells were untreated or transfected separately with either pCMV5 vector encoding human PIAS3 or siRNA against STAT3.

Subconfluent A549 cells were seeded in 75-cm2 flasks for 12 h in media supplemented with 10% FBS.

Staining was performed on an Affymetrix fluidics station utilizing streptavidin/phycoerythrin conjugate (Molecular Probes, Invitrogen Life Science), followed by biotinylated antibody to streptavidin (Vector Laboratories, Burlingame, CA) and finally via a second streptavidin/ phycoerythrin conjugate. Stained micro-arrays were scanned on a Hewlett Packard GeneArray Scanner.

Software Expander (version5.1) was used for data processing and analysis including RMA normalization and summarization.

After 48 h of transfection, cells were harvested and total RNA was isolated using an RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.

Labeled cRNA was purified, fragmented and hybridized to human U133A GeneChip micro-arrays (Affymetrix) for 16 h at 45°C.

cDNA was synthesized using SuperScript II Reverse Transcriptase Kit (Invitrogen, Carlsbad, CA) and cRNA was synthesized using the GeneChip IVT Labeling Kit (Affymetrix, Santa Clara, CA) using biotinylated ribonucleotides (Enzo Diagnostics, Farmingdale, NY).

A549;adenocarcinomic human alveolar basal epithelial cells;pCMV5 vector encoding human PIAS3

A549;adenocarcinomic human alveolar basal epithelial cells;siRNA against STAT3

Gene expression data from MigR1 transduced CUTLL1 cells treated with compound E for 3days and washout compund E for 2 hours

Gene expression data from DN-MAML transduced CUTLL1 cells treated with compound E for 3days

Gene expression data from MigR1 transduced CUTLL1 cells treated with compound E for 3days and washout compund E for4 hours

U937 cell line infected with GSK3B Construct 1 shRNA, biological rep2
Sample name: U937_GSK3B_1-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D08_596716.CEL

U937 cell line infected with GSK3B Construct 1 shRNA, biological rep1
Sample name: U937_GSK3B_1-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D03_596708.CEL

MOLM-14 cell line infected with GSK3A Construct 6 shRNA, biological rep1
Sample name: MOLM14_GSK3A_6-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C06_596630.CEL

MOLM-14 cell line infected with GSK3A Construct 5 shRNA, biological rep2
Sample name: MOLM14_GSK3A_5-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C10_596704.CEL

MOLM-14 cell line infected with GSK3A Construct 5 shRNA, biological rep1
Sample name: MOLM14_GSK3A_5-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C05_596604.CEL

MOLM-14 cell line infected with GSK3B Construct 2 shRNA, biological rep2
Sample name: MOLM14_GSK3B_2-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C09_596558.CEL

U937 cell line infected with scrambled control shRNA, biological rep3
Sample name: U937_CTRL-3
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D07_596720.CEL

U937 cell line infected with scrambled control shRNA, biological rep2
Sample name: U937_CTRL-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D02_596628.CEL

U937 cell line infected with scrambled control shRNA, biological rep1
Sample name: U937_CTRL-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D01_596638.CEL

MOLM-14 cell line infected with GSK3A Construct 6 shRNA, biological rep2
Sample name: MOLM14_GSK3A_6-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C11_596726.CEL

GeneChips were scanned using the Affymetrix GeneChip Scanner GSC3000.

Normalization was performed using the RMA method in Gene Chip Operating Software and the obtained data matrix was imported into the TIGR Multi Experiment Viewer for further analysis.

RNA was isolated using the RNeasy isolation kit (Qiagen, Valencia, CA) according to the manufacturers’ instructions. RNA quality was assessed using a Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Gene Chip Human Gene U133 plus 2.0 microarrays. GeneChips were washed and stained in the Affymetrix Fluidics station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Gene Expression Analysis Technical Manual 701021 rev.5).

Gene expression profile of human CD34+ cord blood cells expressing ZMYM2/FGFR1

Human CD34+ cells isolated from umbilical cord blood;ZMYM2/FGFR1;2

L428;Mifepristone + 5-aza-2′-deoxycytidine + Trichostatin A (MAT);5 days

Gene expression profile of human CD34+ cord blood cells expressing BCR/FGFR1

Human CD34+ cells isolated from umbilical cord blood;BCR/FGFR1;1

Gene expression profile of human CD34+ cord blood cells expressing the empty MIG control vector

Human CD34+ cells isolated from umbilical cord blood;MIG control;1

Human CD34+ cord blood cells expressing the empty MIG control vector

Gene expression profile of human CD34+ cord blood cells expressing BCR/ABL1

Human CD34+ cells isolated from umbilical cord blood;BCR/FGFR1;2

Human CD34+ cells isolated from umbilical cord blood;MIG control;2

Enzo BioArray High Yield RNA Transcript Labelling Kit (Affymetrix, Santa Clara, CA, USA and Enzo Diagnostics).

In vitro transcription of template was carried out in the presence of biotinylated UTP and CTP using the Enzo BioArray High Yield RNA Transcript Labelling Kit (Affymetrix, Santa Clara, CA, USA and Enzo Diagnostics).

The data were analyzed with MAS5 using Affymetrix default analysis settings and global scaling as normalization method.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip MOE430A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA were prepared according to the artus ExpressArt mRNA 2-rouind amplification protocol (nano version) from 10 ng total RNA, using the ENZO kit for labelling in the second IVT reaction

RNA was immediately isolated from the cells 17 hours after infection.

Bone marrow collected from femurs and tibias of WT or IFNAR2-/- mice was cultured in petri dishes for 5-6 days in DMEM media supplemented with antibiotics, 1mM non-essential amino acids, 1mM sodium pyruvate, 15% fetal calf serum, and 25% conditioned supernatant from L929 cells (source of M-CSF) in order to differentiate cells to macrophages.  After differentiation, cells were collected by scraping and were replated in tissue culture-treated 6-well plates.  Cells were allowed to adhere overnight, then were infected with a 1:1 MOI of either Toxoplasma or Neospora.  17 hours after infection, RNA was isolated from cells.

The data were quantile normalized without background subtraction using Illumina GenomeStudio V1.8

Cells were lysed by treatement with Buffer RLT (Qiagen) and passage over QiaShredder columns (Qiagen).  Total RNA was isolated using the Qiagen Rneasy Plus kit.

Biotin labeled complementary RNA (cRNA) was made using the Illumina TotalPrep RNA Amplification Kit

Study of rat femur fracture healing in adult rats (26 weeks old at fracture) at 1 week after fracture.  RNA from 2 rats was pooled for each array.  Sample is middle third of femur with external callus, cortical bone and marrow elements.

Study of rat femur fracture healing in adult rats (26 weeks old at fracture) at 3 days after fracture.  RNA from 2 rats was pooled for each array.  Sample is middle third of femur with external callus, cortical bone and marrow elements.

Healthy control;48;Male;N/A;N/A;6.93;23;Left;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 1

Healthy control;40;Male;N/A;N/A;6.67;38;Left;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 1

Healthy control;37;Male;N/A;N/A;6.50;13;Left;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 0

Healthy control;52;Male;N/A;N/A;6.00;28;Left;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 0

Study of rat femur fracture healing in young rats (6 weeks old at fracture) at 1 week after fracture.  RNA from 2 rats was pooled for each array

Healthy control;39;Female;N/A;N/A;6.46;58;Right;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 4

Study of rat femur fracture healing in young rats (6 weeks old at fracture) at 4 weeks after fracture.  RNA from 2 rats was pooled for each array.  Sample is middle third of femur with external callus, cortical bone and marrow elements.

Healthy control;32;Male;N/A;N/A;6.57;13;Right;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 0

Study of rat femur fracture healing in adult rats (26 weeks old at collection) as no fracture control.  RNA from 2 rats was pooled for each array.  Sample is middle third of femur with cortical bone and marrow elements.

Healthy control;55;Male;N/A;N/A;6.70;31;Left;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 1

Equal amounts (7 micro-gram) of RNA were pooled from five animals. This is the first of two independent microarray analyses using this strain of mice.

Equal amounts (7 micro-gram) of RNA were pooled from four animals. This is an independent replicate of sample 1.

Equal amounts (7 micro-gram) of RNA were pooled from four animals. This is the first of two independent microarray experiments using mice of this strain.

Equal amounts (7 micro-gram) of RNA were pooled from five animals. This is the first of two independent microarray experiments using mice of this strain.

C57BL/6 BMDM stimulated overnight with 50 IU/ml IFNg and infected with WA(pYV)

Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and Green PMT is set to 100%).

The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014868_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.

Total RNA was prepared from Gastrocnemius muscles using TRIzol (Life Technologies) following the manufacturer's recommendations.Then a clean-up step and an on-column DNase I treatment were performed using Rneasy Fibrous Tissue Mini Kit (QIAGEN). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction,  55 μl of 2x GEx Hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute at 37°C with GE Wash buffer 2 (Agilent), then dried.

Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

MO-B10-Tg 3

Scanning of the GeneChips was done using the Affymetrix 3000 7G scanner as described by the manufacturer. The Fluidics station and Scanner were controlled using Affymetrix GeneChip Command Console (AGCC).

Hybridization of the GeneChips was carried out in the following the manufacturer’s protocol. Briefly, the fragmented biotin labeled cRNA was mixed with 0.05nM control oligonucleotide B2, 20X Eukaryotic hybridization controls (bioB, bioC, bioD, cre), 0.1 mg/mL herring sperm DNA, 0.5 mg/mL BSA, 2X hybridization buffer (1X 100mM MES/1M NaCl/20mM EDTA/0.01% Tween-20) and 10% DMSO.  The hybridization cocktail was incubated at 99oC for 5 minutes to denature the herring sperm DNA and any secondary structure on the cRNA.  The cocktail was then equilibrated to 45oC for 5 minutes prior to addition to the GeneChip.  Hybridiztion was carried out in the Affymetrix Hybridization Oven 640 at 45oC with rotation at 60rpm for 16 hours.  Following the hybridization step the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 following Fluidics Protocol Mini_euk2v3 as recommended by the manufacturer for this Chip type.  The GeneChips were first washed in a non-stringent wash buffer of 6X SSPE/0.01% Tween-20 followed by stringent wash with 100mM MES/0.1M NaCl/0.01% Tween-20.  The first staining of the GeneChips was done in 2X stain buffer (1X 100mM MES/1M NaCl/0.05% Tween-20), 2mg/mL BSA, and 0.01 mg/mL Streptavidin Phycoerythrin (SAPE).  The GeneChips were washed in non-stringent wash buffer.  A second stain comprised of 2X staining buffer, 2mg/mL BSA, 0.1mg/mL Goat IgG, and 0.003mg/mL of biotinylated antibody was conducted immediately followed by a third stain comprised of the SAPE solution (see above).  Finally, the GeneChips were washed in non-stringent wash buffer prior to scanning.

The labeling of the RNA was done as per the manufacturers instructions (Affymetrix, Santa Clara, CA).  Briefly, One microgram of total RNA was reverse transcribed using an oligo dT-T7 primer under standard conditions.  The resulting first strand cDNA was incubated with RNAse H, E. coli DNA ligase, and E. coli DNA polymerase, dNTPs and buffer to produce second-stranded cDNA.  The cDNA was purified using spin columns following the manufacturer’s instructions (Qiagen).  The purified cDNA was then used in an in vitro transcription assay to produce the target biotin labeled cRNA for hybridization using the 3’ IVT kit from Affymetrix following the manufacturer’s instructions.  The cRNA was purified using a spin column following the kit’s instructions (Qiagen), and fragmented prior to hybridization onto the GeneChips.

tumor tissue from cancer patients;p53 wild type;Microsatellite Stable Stage III Colorectal adenocarcinoma

lung tissue;CD-1_Nrf2 -/-;13 weeks + 5 month;2R4F whole mainstream smoke 750 µg/ml, treatment over 5 month, 4x1h exposure per day

MAT1A_wt15_4
Gene expression data from the wild type used for MAT1A knockout at 15 month.

For Tet1 knockdown (KD), mouse ES cells were infected with lentiviruses expressing both the GFP reporter and short-hairpin RNA (shRNA) specific for Tet1. All analyses were performed using  Tet1-depleted ES cells that were purified on the basis of GFP fluorescence by FACS 8 days after lentiviral transduction. Lentiviruses expressing GFP alone was used as a control. Short-hairpin RNA (shRNA) sequences were cloned into pTY vector under the control of the U6 promoter. To rescue Tet1 knockdown with Nanog, complementary DNA of Nanog was placed downstream of the puromycin-resistant gene and foot-and-mouth disease virus 2A segment.

Mouse E14Tg2A ES cells were maintained on gelatin-coated dishes in Glasgow Minimum Essential medium (GMEM; GIBCO), supplemented with 15% heat-inactivated fetal bovine serum, 55 mM b-mercaptoethanol (GIBCO),        2mM L-glutamine, 0.1mM MEM non-essential amino acid, 5,000 units/ml penicillin/streptomycin and 1,000 units/ml of ESGRO (Chemicon) under feeder-free conditions.

The array was then washed and stained with R-phycoerythrin streptavidin before scanning. Washing, scanning and basic analysis was carried out using Affymetrix GeneChip Microarray Suite 5.0 software.

Raw data (.cel files) were normalized using the RMA method in affy (R/Bioconductor).

For expression microarray analysis comparing control KD, Tet1 KD and Nanog rescued Tet1 KD mouse ES cells, 2 µg of total RNA purified from GFP sorted cells were reverse-transcribed into cDNA with a T7-(dT)24 primer from a custom kit (Life Technologies).

15 ug of fragmented cRNA was then added to a hybridization cocktail (0.05 mg/ml fragmented cRNA, 50 pM control oligonucleotide B2, BioB, BioC, BioD, and cre hybridization controls, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, 100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween 20). 10 ug of cRNA were used for hybridization to Affymetrix GeneChip Mouse Genome 430A 2.0 Array. Hybridization was carried out at 45°C for 16 hours.

Biotinylated cRNA was then generated from the cDNA reaction using the BioArray High Yield RNA Transcript Kit. The cRNA was then fragmented in fragmentation buffer (40 mM Tris-acetate, pH8.1, 100 mM KOAc and 150 mM MgOAc) at 94°C for 35 minutes before microarray hybridization.

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56938
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.67; Parameter Scan Time = 21:02:55; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 12111; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.67; Parameter Scan Time = 21:02:55; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 185716; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.55; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs//56954
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.69; Parameter Scan Time = 20:39:28; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 13123; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.69; Parameter Scan Time = 20:39:28; Parameter PMT Volts = 670; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 186727; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.58; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu:8000/MicroArray/gifs/2004-10/56939.gif
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.58; Parameter Scan Time = 20:13:13; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 12062; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.58; Parameter Scan Time = 20:13:13; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 185667; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.55; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56955
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.54; Parameter Scan Time = 20:26:43; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 13110; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.54; Parameter Scan Time = 20:26:43; Parameter PMT Volts = 670; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 186715; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.59; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

BMDM;C57BL/6;No2 -/-;infected with Neisseria gonorrrhoeae, strain MS11, MOI 10:1 for 3 hrs

lung;;Sporadic IIP;;Nonspecific Interstitial Pneumonia;Stratagene;;740000

EA.hy926 cells were harvested after 24 hours of treatment with mevalonate (500 microM).

HUVECs were harvested after 24 hours of treatment with a combination of atorvastatin (10 microM) and mevalonate (500 microM).

EA.hy926 cells were harvested 24 hours after treatment with a combination of atorvastatin (10 microM) and mevalonate (500 microM).

Array washing and staining as described in chp 6 of above manual using the GeneChip Fluidics station 450 (fluidics script FS450-007). Arrays were scanned on a GeneChip scanner 3000 7G using default scanner settings. Affymetrix GeneChip® Command Console® (AGCC) was used to process all Affymetrix arrays through fluidics and scanning.

Gene level probe set summarisation (signal value), calculation of QC metrics and CHP file generation were performed using GeneChip® Expression Console software using the Robust Multichip Analysis (RMA) algorithm

extraction of total RNA was performed according to the manufacturer's instructions with RNAeasy.

GeneChip Whole Transcript (WT) sense target labeling assay manual, version 4 - starting with 300ng RNA and following the Total RNA labeling protocol to prepare targets for GeneChip gene 1.0 ST Arrays(omitting RiboMinus procedure).

wild type mice TMJ-cartilage
miosge_WT_Tal4_20110623_(MoGene-1_0-st-v1).rma-gene-default.chp
miosge_WT_Tal4_20110623_(MoGene-1_0-st-v1).CEL

Liver; Regeneration 6h

Gene expression data from cochleas of wild type mice at P60.
P60_wildtype_rep2

Mice were used as control or exposed to intratracheal 2% polidocanol 3 days prior to collection (injury).  Mice were culled by pentobarbitol overdose and exsanguinated.  Whole trachea was isolated, excess connective tissue removed, and immediately processed for RNA purification

Total RNA was isolated using the Qiagen RNeasy kit. The integrity of the RNA was confirmed with analysis by the Agilent 2100 bioanalyser using the RNA 6000 LabChip kit.

The arrays were scanned with a probe array scanner (Affymetrix).

Total RNA was extracted from the cells using an RNeasy Total RNA Extraction Kit (Qiagen K. K., Tokyo, Japan). Then, RNA samples were treated with RNase-free DNase.

After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h. The arrays were washed, and stained with streptavidin-phycoerythrin.

5 μg of total RNA was used to synthesize double-strand cDNA with a GeneChip® Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (Affymetrix). Biotin-labeled cRNA was then synthesized from the cDNA using GeneChip® Expression 3’-Amplification Reagents for IVT Labeling (Affymetrix).

HuT-102 cells, a human cutaneous T cell lymphoma, were stably transfected with shRNA expression vectors against human MAP3K7 (TAK1) or firefly luciferase (Luc). HuT-102 cells stably transfected with pSUPER-gfp+neo (firefly luciferase) served as a control. HuT-102 cells stably transfected with pSUPER-gfp+neo (human MAP3K7) were server as shRNA-TAK1. The cells were maintained in media containing 0.5 mg/ml G418. For the experiment, the cells were incubated in media without G418 for 36 h at 37°C.

HuT-102;human cutaneous T cell lymphoma cells;shRNA expression vector against TAK1

HuT-102;human cutaneous T cell lymphoma cells;shRNA expression vector against Luc

Cervical cancer, adenocarcinoma, microdissected, age 46, stage IB2, HPV 16

Cervical cancer, squamous cell carcinoma, microdissected, age 45, stage IB2, HPV negative

plaque type psoriasis;epidermis;74;female;2 y;phototherapy;post-UV

Cervical cancer, squamous cell carcinoma, microdissected, age 35, stage IB1, HPV 18, HPV 45

plaque type psoriasis;epidermis;28;female;> 10y;phototherapy;post-UV

LNCaP cells were maintained in RPMI media supplemented with 10% FBS.

After scanning, the iScan software extracts signal intensities and saves all files for each BeadChip. Raw data is imported to Illumina’s GenomeStudio software V2011.1, Gene Expression module v. 1.9.0. Here the quality of each array and scan is investigated, and text files with both non-normalized and quantile normalized data exported.

Data extraction, quantile normalization and initial quality control of the bead summary raw data were performed using GenomeStudio v2011.1 from Illumina and the Gene Expression module v1.9.0. The data were annotated using the HumanHT-12_V4_0_R2_15002873_B.bgx annotation file from Illumina.

RNA was collected by illustraMiniSpin (GE Healthcare) according to manufacturer’s instructions. Quality control was performed with Agilent Bioanalyser.

Hybridisation of cRNA onto the Illumina HumanHT-12 v.4 Expression BeadChips (Illumina Inc, California, USA) was carried out as per manufacturer's instructions

Labelling was performed with Illumina® TotalPrep™-96 RNA Amplification Kit according to manufacturer's instructions

Male mice were fasted for 6-8 hours and then sacrificed by CO2 inhalation. Upon sacrifice, livers were collected and samples were stored in RNAlater (Qiagen cat. no. 76106) and placed at 4 degrees C for 24 hours before transitioning to -20 degrees C. All samples were disrupted using a rotor-stator homogenizer and RNA extractions were performed using the Qiagen RNeasy Fibrous Tissue kit (Qiagen cat. no. 74704), with on-column DNAase digestion (Qiagen cat. no. 79254). Extracted RNA was quantified using the NanoDrop spectrophotometer and RNA quality was evaluated using the Agilent Bioanalyzer.

Ghrh-KO mice and wild-type controls (on a mixed C57BL6 and 129SV background) were bred in a closed colony, housed under standard conditions (12-hr. light/12-hr. dark cycling and 20-23 degrees C), and fed Lab Diet Formula 5001 (23% protein, 4.5% fat, 6% fiber) (Nestle Purina, St. Louis, MO).

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Genome 430 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Microarrays were scanned using a DNA microarray scanner, Model G2565A (Agilent Technologies).

Data extraction was conducted using Feature Extraction software Version 10.5 (Agilent Technologies). Normalization was performed according to the Agilent Feature Extraction One-Color Protocol. Threshold: 1.0 . Logbase: 2. Technology: Agilent.SingleColor.14850. Normalization: Shift to 75th percentile. Baseline Transformation: median of all samples. FlagSettings: Feature is not Uniform:A. Feature is a population outlier:A. Feature is Saturated:A. Feature is not above background:M. Feature is not positive and significant:M.

RNA was prepared using the Qiagen RNeasy Fibrous Tissue Mini Purification kit with on-column DNase I treatment following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

For each sample, 1.65 ug of Cy3-labeled cRNA was fragmented and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.

Cyanine-3 (Cy3)-labeled cRNA was prepared from 500ng RNA using the Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

mix of 129Sv and C57BL/6;conditional keratinocyte-specific ADAM17 knockout;back skin;10 days

Sample is skeletal muscle from an obese patient undergoing elective abdominal surgery

Sample is skeletal muscle from obese patient undergoing elective abdominal surgery

Sample is skeletal muscle from nonobese patient undergoing elective abdominal surgery

One well of a 6-well dish of E14 cells was treated with purified, control (EGFP) esiRNA (0.33 ng/ul) and Lipofectamine 2000 (Invitrogen) for 72 hr.

This dataset was normalized using robust locally weighted regression (loess) to correct for intensity, spatial and other dye biases (Cleveland 1979, JASA 74(36): 829; Yang et al 2002, NAR 30(4)). This procedure was performed and carried out using the Bioconductor package “marray” (http://www.bioconductor.org). In the context of microarray experiments, loess normalization captures the non-linear dependence of the intensity log-ratio M = log2R-log2G = log2(R/G) on the overall intensity A= (log2R+log2G)/2.

Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 and Cy5 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays (Agilent). Hybridization samples were paired according to group designation and dye swaps were incorporated to correct for any dye bias. Hybridizations were performed for 14 hrs, according to the manufacturers protocol (Agilent).

Total RNA quality was assessed using a Pico Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). RNA was amplified and labeled with Cy3-CTP and Cy5-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol (Agilent).

Mouse embryonic stem cell line E14;Mouse embryonic stem cell line E14

primary unilateral non-metastatic postmenopausal ERα-positive breast tumor;woman;68 years

WT1.CEL (unavailable due to loss from servers)

Estrogen deprived cells were stimulated with 1nM estradiol (Sigma); 100ng/mL FGF10 (Invitrogen); 100ng/mL PD173074 (Sigma-Aldrich)

MCF7 human breast cancer cells were cultured in DMEM supplemented with 10% HI-FCS and antibiotics. Cell synchronisation via estrogen deprivation was carried out for at least 3 days in phenol red-free DMEM (Invitrogen) supplemented with 5% charcoal dextran-treated HI-FBS (Hyclone) and 1% penicillin-streptomycin. All cells were grown at 37oC in 5% CO2. siRNA SMARTpools (Dharmacon) targeting PTTG1 (L-004309) and SPDEF (L-020199) and a control non-targeting pool (D-001810) were transfected into MCF7 cells using Lipofectamine RNAiMAX (Invitrogen). RNA was collected after 72 hours and processed for microarray analysis.

Raw image files were processed and analysed using the Beadarray R package. The data was corrected for spatial artifacts, log (base 2) transformed, and quantile normalised. Note: detection p-values are not available

RNA was extracted using the miRNeasy spin column kit (Qiagen) and quality checked using an RNA 6000 Nano chip on a 2100 Bioanalyser (Agilent). 250ng RNA (RIN>7) was used for cRNA amplification and labelling using the Illumina TotalPrep-96 kit (Ambion 4397949)

Gene expression profile of HT29 cells resistant to Methotrexate.

Muscle biopsy specimen from a patient with dermatomyositis (DM)
Keywords = Inflammatory myopathy, Dermatomyositis, Inclusion body myositis, Polymyositis, MxA, plasmacytoid dendritic cells, Innate immunity, Interferon-alpha

Muscle biopsy specimen from a patient without a neuromuscular disorder (Normal)

Moderate Asthma;Fresh Bronchial Epithelial Cells;female;55.27671

Moderate Asthma;Fresh Bronchial Epithelial Cells;female;24.57534

Moderate Asthma;Fresh Bronchial Epithelial Cells;female;35.01096

Moderate Asthma;Fresh Bronchial Epithelial Cells;female;23.54521

DDR-1-KO mice TMJ-cartilage
miosge_KO_Tal5_20110623_(MoGene-1_0-st-v1).rma-gene-default.chp
miosge_KO_Tal5_20110623_(MoGene-1_0-st-v1).CEL

miosge_WT_Tal3_20110505_(MoGene-1_0-st-v1).rma-gene-default.chp
miosge_WT_Tal3_20110505_(MoGene-1_0-st-v1).CEL

Moderate Asthma;Fresh Bronchial Epithelial Cells;female;20.27123

LKR13 cells were infected with plko.1s vectors carrying an shRNA against GFP.  48 hours after infection, cells were selected with puromycin for 3 days.  RNA was extracted 7 days post-infection.

Microarray data was normalized with Expression Console software (Affymetrix, Santa Clara), using RMA algorithms.

Cell lines derived from Kras-mutant mouse lung cancer model (KrasLA). Tyler Jacks lab (Johnson et al., 2001)

Transduced lineage depleted cord blood cells were grown in liquide culture (M9 media)

RNA was extracted with the Arcturus® Picopure RNA® isolation kit followed by DNase I treatment. Quality control was performed with Agilent Bioanalyser

lineage depleted cord blood cells;liquid culture day 11;BCR-ABL1;Ik6

lineage depleted cord blood cells;liquid culture day 11;control;Ik6

lineage depleted cord blood cells;liquid culture day 11;BCR-ABL1;control

creation of .EXP, .DAT, .CEL, .CHP, .RPT and .TXT files using GeneChip Operating System (GCOS) 1.4.0.036

Total RNA was first isolated using an RNeasy kit (Qiagen Catalog number 74104) according to the manufacturer’s instructions.

A35fluidics protocol EukGE-WS2v4_450 using Affymetrix fluidics Station 450

RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNAs that fall outside of an acceptable range will not be carried forward in the analysis. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The cRNA is purified from the fragmentation reaction using phenol/chloroform extraction and ethanol precipitation.

Gene expression data from LNCaP cell line treated with steroid hormone DHT

BL from WM patient, isolated using Kappa or Lambda-fluorescein isothiocyanate, CD10-PE, CD38-PerCPCy5.5,CD19-PE-Cy7, CD34-APC and CD45-APC-Cy7.

from WM patient, isolated using Kappa or Lambda-fluorescein isothiocyanate, CD10-PE, CD38-PerCPCy5.5,CD19-PE-Cy7, CD34-APC and CD45-APC-Cy7.

tetracycline inducible Ngn3 ESC differentiated for 10 days as EB without doxycycline

tetracycline inducible Ngn3 ESC differentiated for 10 days as EB with doxycycline for 3 days

tetracycline inducible Ngn3 ESC differentiated for 3 days as EB with doxycycline

tetracycline inducible Ngn3 ESC differentiated for 3 days as EB without doxycycline

Approximately 10 mg of snap frozen liver was used to extract >25 ug of total RNA using Ambion's RNAqueous-4PCR RNA exstraction kit.

Approximately 20 µg of total RNA was processed to produce biotinylated cRNA targets.

Wild Type Control for Pit-1 mutant (Snell) resulting in long lived dwarf pheontype

The data were initially analyzed with Afymetrix GCOS software using Affymetrix default analysis settings and global scaling as normalization method. Subsequently, data were imported to GeneSpring v.7.3.1 (Agilent).

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC to GeneChip® Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix).

Gene expression data from the colon of wild-type mice
whole colonic tissue was dissected from mice 6-8 weeks of age

human peripheral blood derived monocytes, no stimulation, biological rep1

Study of rat femur fracture healing in young rats (6 weeks old at fracture).  RNA from two rats were pooled for each microarray.
Lot batch = Sample 01

Monolayers of HUVECs in 9 cm Petri dishes infected with Neisseria meningitidis MC58 delta pilD were washed and collected into Trizol by cell-scraper

Confluent monolayers of HUVECs in 9 cm Petri dishes were infected with Neisseria meningitidis MC58 delta pilD (MOI=10) and cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 4 hours

The data were analyzed with RMA and MAS 5.0 algorithms using Biocondutor 1.7 and default analysis settings.

Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was purified on RNeasy minicolumns (Qiagen) and by NaOAc/ethanol precipitation.

Following fragmentation, cRNA was hybridized for 16 hr at 45C on Affymetrix Human Genome HG-U133A GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station.

Gene expression data from HUVEC infected with Neisseria meningitidis MC58 delta pilD, 4 hours infection

Monolayers of HUVECs in 9 cm Petri dishes infected with Neisseria meningitidis MC58 WT were washed and collected into Trizol by cell-scraper

Confluent monolayers of HUVECs in 9 cm Petri dishes were infected with Neisseria meningitidis MC58 WT (MOI=10) and cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 6 hours

Gene expression data from HUVEC infected with Neisseria meningitidis MC58 WT, 6 hours infection

Confluent monolayers of HUVECs in 9 cm Petri dishes were infected with Neisseria meningitidis MC58 delta pilD (MOI=10) and cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 1 hour

Gene expression data from HUVEC infected with Neisseria meningitidis MC58 delta pilD, 1 hour infection

Confluent monolayers of HUVECs in 9 cm Petri dishes were infected with Neisseria meningitidis MC58 WT (MOI=10) and cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 4 hours

Gene expression data from HUVEC infected with Neisseria meningitidis MC58 WT, 4 hours infection

Confluent monolayers of HUVECs in 9 cm Petri dishes were infected with Neisseria meningitidis MC58 WT (MOI=10) and cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 1 hour

Gene expression data from HUVEC infected with Neisseria meningitidis MC58 WT, 1 hour infection

Neonatal mice and their foster dams were exposed to room-air exposure. Food and water were provided ad libitum. In 24 hr after birth (P1, saccular stage of lung maturation), neonatal mice were placed in cages in a hyperoxia chamber, and were exposed to 100 percent (≥95 percent) O2 (UHP grade, Min. purity 99.994 percent O2 tanks, National Welders, Durham, NC) 23 hr/day continuously for 1, 2, or 3 d with their foster dams. Water and feed were provided ad libitum during the exposure. Neonatal mice and their foster dams assigned to room-air exposure were placed in cages placed on counter top with food and water provided ad libitum for the same exposure duration. The temperature (72±3 degree F) and humidity (50±15 percent) of the chamber were monitored, and mice were exposed to a 12-hr light-dark cycle. The hyperoxia chamber was opened once each morning for 1 hr to replace foster dams and to check animal health (morbidity and mortality) and water and feed.

The chip data was obtained using the GeneChip Command Console Software (AGCC, Version 1.1) and analyzed using Affymetrix GeneChip Operating Software (GCOS) version 1.2. The CEL files for hybridizations were log2-transformed by use of RMA Express (Bioinformatics 2003 19(2):185-193 and Biostatistics 2003 4(2):249-264).The expression value (average difference) for each gene was determined by calculating the average of differences in intensity (perfect match intensity minus mismatch intensity) between its probe pairs.

Total RNA was extracted from lung homogenates of each mouse (n=3 per group) using the Qiagen RNeasy Mini kit (Qiagen, Valencia, CA) and then evaluated by an Agilent 2100 Bioanalyzer analysis (Agilent Technologies, Palo Alto, CA).

The biotinylated RNA (12.5 ug) was fragmented and 10 ug was hybridized to the Affymetrix array for 16 hr at 45◦C in a hybridization oven rotating at 60 rpm using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. The array was stained with streptavidin/phycoerythrin in an Affymetrix Fluidics Station 450 using a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

cDNA was synthesized from RNA using a one-cycle cDNAsynthesis kit. Biotinylated RNA was then synthesized from cDNA using an IVT labeling kit (Affymetrix 3'IVT Expression) after incubating at 37◦C for 16 hr.

Comparisons: Genotype effects on daily hyperoxia/3 day treatment

Comparisons: Genotype effects on daily hyperoxia/2 day treatment

Comparisons: Genotype effects on daily hyperoxia/1 day treatment

Treatment: 1.4 mM HOCl in medium

Cells were infected with retoviral vectors (empty or miR-34a) and selected for 2 weeks in 1 ug/mL puromycin.

HCT116 cells were grown in McCoy's 5A media plus 10% fetal bovine serum plus antibiotics.

GeneChips were scanned using a Hewlett-Packard GeneArray Scanner G2500.

Total RNA was extracted using the Qiagen RNeasy kit according to the manufacturer's instructions.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 Plus 2.0 arrays. GeneChips were washed and stained using the Affymetrix Fluidics Station 400.

Gene expression data from HCT116 cells infected with empty vector.  Described in:
Chang TC, Wentzel EA, Kent OA, Ramachandran K, Mullendore M, Lee KH, Feldmann G, Yamakuchi M, Ferlito M, Lowenstein CJ, Arking DE, Beer MA, Maitra A, and Mendell JT. (2007).  Transactivation of miR-34a by p53 broadly influences gene expression and promotes apoptosis.  Mol Cell, 26: 745-752.

Images were processed using the Affymetrix Microarray Suite 5.0, cel files were normalized with GCRMA and further analyzed using Bioconductir software based on R language

Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.2 ug total RNA (One-Cycle Target Labeling kit).

All lines transfected using HiPerFect (Qiagen) system according to manufacturer's instructions. Silencing constructs consisted of either control #1 siRNA (Ambion) or Silencer Select BAP1. 5 days post transfection cells were harvested for RNA extraction.

Grown in RPMI-1640 (Lonza) supplemented with 10% fetal bovine serum

Data were analyzed using beadarray and limma R packages. Raw data were log2 transformed and quantile normalized. siBAP1 versus siControl contrast was analyzed against the fitted linear model using eBayes functions in limma.

Qiagen RNEasy RNA isolation kit according to manufacturer's instructions.

Illumina TotalPrep RNA Amplification kit (Ambion, AMIL1791). Cleanup with DNA Clean-up and Concentrator 5 columns (zymo research).

(CML) chronic myeloid leukaemia / Granulocyte-Macrophage Progenitors

(CML) chronic myeloid leukaemia / Megacaryocyte-Erythrocyte Progenitors

ACC483 [HPB-ALL];human T-ALL cell line;IKKγ Nemo binding domain (NBD) inhibitory peptide

Liver was obtained from 8 or 9 male, two-month-old, mice for each transgenic model. Three different models were compared, including liver-Cpr-null, Cpr-low, and Cpr-lox (control model), all on mixed C57BL/6 and 129/Sv genetic background. Total RNA was prepared from individual liver samples. Three independent pools of RNA samples were prepared and analyzed for each model. Five micrograms of total RNA were used for the synthesis of biotin-labeled antisense RNA using Ambion's MESSAGEAMP(TM) aRNA Kit.
Keywords = Cytochrome P450
Keywords = NADPH-cytochrome P450 reductase
Keywords = transgenic mice
Keywords = nuclear recetpor

ACC525 [DND41];human T-ALL cell line;IKKγ Nemo binding domain (NBD) inhibitory peptide

KOPT-K;human T-ALL cell line;IKKγ Nemo binding domain (NBD) inhibitory peptide

293T cell infected with RCAS-GFP
Keywords = 293 cell
Keywords = GFP

BioArray High Yield RNA transcript labeling T7 kit (Enzo Life Sciences)

Gender: male Age: 3 weeks Isolation: gradient and handpicking Strain: NOD

Gender: male Age: 3-4.5 weeks Isolation: FACS of CD45-G8.8+Ly51intclassIIhi TECs Strain: NOD

This is from a study of femoral fracture healing in female rats 16 weeks old at fracture to compare intramedullary nailing, screw and plate fixation, and sham surgery.  This sample is from the group receiving sham surgery (no fracture, no plate and no nail) collected 3 days after surgery.  Each sample is a pool of RNA from three rats.  The middle third of the femur was collected with the cortical bone, fracture callus, and marrow elements.

European-American (EA);Female;healthy control;Peripheral blood;CD8-PE;CD8 positive T cells

African-American (AA);Female;healthy control;Peripheral blood;CD8-PE;CD8 positive T cells

SEB-1 sebocytes (p23) were treated in triplicate with 0.1 uM 13-cis RA or vehicle (DMSO) control for 72 hours. Each culture plate was considered an independent sample.

SEB-1 sebocytes were cultured in standard culture medium according to established procedures (Thiboutot et al, 2003).

The arrays were processed on a Gene Chip Fluidics Station 450 and scanned on a Affymetrix GeneChip Scanner (Santa Clara, CA).

The expression values were normalized by using the R-Affy package from Bioconductor version 1.1 to remove background noise and non-biologival variations among arrays. The background noise was removed from the PM probe intensities using the "RMA" method. Normalization was performed using the quantile normalization method (Bolstad et. al., 2003).  To remove the effects of outlier probes and sumerize probe intensities within one probe set to a single expression value, the "Tukey Biweight" method was applied to the background adjusted, normalized PM intensities and not the PM-MM, because it is believed that MM intensities reflect background noise as well as probe-specific signals. Significant gene expression alterations were identified using the computer software: Significance Analysis of Microarrays (Tusher et. al.,2001).

Total RNA was isolated and DNase I treated using the Rneasy Kit (Qiagen, Valencia, CA). RNA was quantified using a spectrophotometer. Approximately 2 micrograms of total RNA from each sample was used to generate double-stranded cDNA using a T7-oligo (dT) primer.

Biotinylated cRNA, produced through in vitro transcription, was fragmented and hybridized to an Affymetrix human U95Av2 microarray.

Gene expression data from SEB-1 cell line with 72hr, ethanol vehicle treatment

sebocytes cultured from M, 55, normal preauricular sebaceous glands and SV-40 immortalized

Testicular germ cell tumor; histological subtype seminoma
Keywords = seminoma
Keywords = testicular germ cell tumor

Where indicated, cells were pretreated with 50 nM Bortezomib for 15 minutes followed by 10 nM 17-  -estradiol for 6 hours.

Cells were grown in phenol-red free DMEM containing 5% charcoal-dextran treated FBS for 48 hours prior to treatment with Bortezomib or estrogen.

The data were analyzed with GCOS (GeneChip Operating Software Version 1.2.0.037) using default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

Total RNA was extracted using the RNeasy Mini Protocol for Isolation of Total RNA from Animal Tissues (Qiagen).

Following fragmentation, 20 ug of cRNA were hybridized for 16 hrs at 45C on Mouse Genome 430 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the Affymetrix Two-Cycle Target Labeling Protocol from 100 ng total RNA (Expression Analysis Technical Manual, November 2004 update, Affymetrix).

Illumina HumanHT-12 V4.0 expression beadchip experiment were performed by the Microarray Centre (University Health Network, Toronto)

The data were normalized using quantile normalization with lumi package in R

Total RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

Lot batch = 5289

Lot batch = 5267

Cell strain 7 of cyclin D1KO 3T3 cells obtained by serial passaging MEFs from E14 embryos, stably infected with MSCV-GFP murine stem cell virus.

Sample from retroviral MSCV-GFP control infected cyclin D1 knockout 3T3 cells (line 7).

Gene expression data from cyclin D1 knockout 3T3s (cell line 7) infected with MSCV-GFP control using Murine Stem Cell Virus (MSCV) system.

Left ventricular myocardium in patients with Cardiac sarcoidosis (28)

Left ventricular myocardium in patients with Cardiac sarcoidosis;myocardium sold commercially

Left ventricular myocardium in patients with Eosinophilic myocarditis (4)

Left ventricular myocardium in patients with Eosinophilic myocarditis;myocardium sold commercially

Left ventricular myocardium in patients with Dilated cardiomyopathty (6)

Left ventricular myocardium in patients with Dilated cardiomyopathty (8)

Left ventricular myocardium in patients with Alcoholic myopathy (10)

Left ventricular myocardium in patients with Alcoholic myopathy;myocardium sold commercially

Left ventricular myocardium in patients with Dilated cardiomyopathty (2)

Left ventricular myocardium in patients with Peripartal cardiomyopathy (25)

Left ventricular myocardium in patients with Peripartal cardiomyopathy;myocardium sold commercially

Left ventricular myocardium in patients with Ischemic cardiomyopathy (26)

Left ventricular myocardium in patients with Ischemic cardiomyopathy;myocardium sold commercially

Left ventricular myocardium in patients with Dilated cardiomyopathty (13)

Left ventricular myocardium in patients with Dilated cardiomyopathty (1)

KJD and SCC25 cells were maintained in SCC Media, consisting of equal parts DMEM (Invitrogen) and Ham’s F12 Nutrient Mix pH 7.1 (Sigma Aldrich), supplemented with 10 μg/mL gentamycin (Pfizer), 1% v/v penicillin/streptomycin/glutamine (Invitrogen), 5% FBS (Bovogen Biologicals) and 0.43 μg/mL hydrocortisone (Sigma Aldrich). Doxorubicin treated cells were treated with 1µM doxorubicin for 48 hours prior to RNA extraction. 3 µg of E2F7b or pcDNA plasmids were transfected into KJD cells prior to RNA extraction. 40nM of E2F7siRNA or GFP control siRNA were transfected into SCC25 cells prior to RNA extraction.

The data were log2 transformed and normalised using robust spline normalisation with lumi R package

RNA was isolated with TRIzol reagent (Life Technologies) and further purified using the RNAeasy mini kit from Qiagen following the manufacturer's protocol. Quality control was performed with Agilent Bioanalyser.

Biotynlated cRNA was prepared with the Illumina TotalPrep RNA Amplification Kit (illumina) for Illumina Arrays

KJD;SV40 virus transformed;epidermal keratinocyte;E2F7b + doxorubicin

KJD;SV40 virus transformed;epidermal keratinocyte;pcDNA3 + doxorubicin

Cells were treated with Lipofectamine2000 (Invitrogen) and LPS (SIGMA).

The data were analyzed with GeneChip Operating Software Ver 1.2.1.001 (GCOS) using Affymetrix default analysis settings.

RNeasy Mini kit (QIAGEN) extraction of total RNA was performed according to the manufacturer's instructions.

Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Human Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5microg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

Gene expression data from OCUBM cells treated without expression vectors.

A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factors can be identified. This entry corresponds to the RNA isolated from uninduced INS-1 cell line #1a containing hepatocyte nuclear factor-1b (HNF1b).
Lot batch =

Small Intestine; proximal jejunum

Large Intestine; Proximal Colon

Small Intestine; ileum sham short bowel resection

Small Intestine; ileum short bowel resection

software package R, version 1.9.1,  libraries gcrma and limma of the Bioconductor Project

Vectors expressing mouse PIK3CA shRNA were purchased from OriGene. Cells were transfected using Lipofectamine-PlusTM (Invitrogen).

Murine lung cancer cells (344SQ) were cultured in RPMI 1640 (Mediatech) with 10% FBS (Sigma-Aldrich).

Gene expression values were processed by Asuragen (Austin, TX) and subjected to quantile normalization.

lung tissue;CD-1_Nrf2 -/-;13 weeks + 5 month + 1 day;2R4F whole mainstream smoke 750 µg/ml, treatment over 5 month + 1 day recovery, 3x1h exposure per day

For each independent experiment, 3x10e4 cells were seeded in triplicate in 24 well-plates  and were transfected with twice 100nM STAT3 siRNA (pool of 4 STAT3 sequences, siGENOME®SMARTpool®, Dharmacon RNAi Technologies, Thermo Fisher Scientific, Lafayette, USA) or Silencer® negative siRNA control (Invitrogen/Life Technologies GmbH, Darmstadt, Germany) using 1µl DharmaFECT (Dharmacon RNAi Technologies, Thermo Fisher Scientific, Lafayette, USA) transfection reagent for OE33 cells or siPORTTM NeoFXTM (Invitrogen/Life Technologies GmbH, Darmstadt, Germany) transfection reagent for OE21 cells.  Cells treated with the STAT3-specific siGENOME®SMARTpool® or the Silencer® negative siRNA control are referred to as “siRNA” and “control” (ctl) treated cells. Effects of siRNA treatments were evaluated for both siRNA and ctl treated cells relative to untreated cells receiving normal medium throughout the experiments.

Esophageal cancer cell lines (OE21, OE33) were obtained from ATCC/LGC Standards (Wesel, Germany) and had been validated before. OE21 and OE33 cells grew adherent and were cultivated in RPMI 1640 medium, supplemented with 10% (v/v) Fetal Calve Serum and 2mM glutamine (all from PAA Laboratories, Pasching, Austria) at 37ºC in a 5% C02 atmosphere.

All arrays were normalized together using quantile normalization algorithm using R Bioconductor packages beadarray and lumi.

For the treatment groups: Mice were injected (by I.P) with 1mg/kg Dexamethasone and the liver was harvested after 6 hours.

All mice used in this study were adrenalectomized to remove endogenous glucocorticoids.

Total RNA was prepared using the Qiagen Rneasy Extraction method, Dnase treated and submitted for quality control and microarray.

US22502532_251486824188_S01_H.tif
US22502532_251486824188_S01_L.tif
Gene expression from untreated knockout liver

US22502532_251486824189_S01_H.tif
US22502532_251486824189_S01_L.tif

US22502532_251486824202_S01_H.tif
US22502532_251486824202_S01_L.tif
Gene expression from Dex-treated knockout liver

Probe level expression values and normalization were calculated using RMAExpress and further analysis was done using dChip

Total RNA extraction was performed with QIAGEN microRNeasy kit according to the manufacturer's instructions.

RNA hybridized to MOE430_2. Chips according to manufacturer manual

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4000 to 7000 cell

lung tissue;CD-1_Nrf2 -/-;13 weeks + 5 month + 13 days;fresh air, treatment over 5 month + 15 days recovery, 4x1h exposure per day

Cells were transiently transfected three consecutive days using HiPerfect with 5nmol scrambled (both Qiagen) or TDP-specific  siRNAs (5’-CAATAGCAATAGACAGTTA-3’) and cultivated for 24h.

HEK293E cells were grown in Dulbecco’s modified Eagle medium (DMEM) (Biochrom) supplemented with 10% fetal bovine serum (PAA) at 37°C under humidified 5% CO2/air

GeneChips were scanned using the Affymetrix GCS3000 gene chip scanner.

The data were analysed using GC-RMA for background correction, normalization and probe summarization using the Bioconductor package gcrma with default values.

RNA  was extracted by using RNeasy Mini Kit (Qiagen) following manufacturers instructions for animal cells.

Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

HEK cells transfected with scrambled siRNA, 24h after transfection

nude mice;iNRAS-475 mouse melanoma cells;Melanoma allograft;AZD6244 MEK inhibitor 100mg/kg for 4 days

P08
JLP_P08_U133_2.CEL

patient8;Systemic lupus erythematosous (SLE);blood;Sorted B cell

P07
JLP_P07_U133_2.CEL

patient7;Systemic lupus erythematosous (SLE);blood;Sorted B cell

P06
JLP_P06_U133_2.CEL

patient6;Systemic lupus erythematosous (SLE);blood;Sorted B cell

P05
JLP_P05_U133_2.CEL

patient5;Systemic lupus erythematosous (SLE);blood;Sorted B cell

P12
JLP_P12_U133_2.CEL

patient12;Systemic lupus erythematosous (SLE);blood;Sorted B cell

P11
JLP_P11_U133_2.CEL

patient11;Systemic lupus erythematosous (SLE);blood;Sorted B cell

P10
JLP_P10_U133_2.CEL

patient10;Systemic lupus erythematosous (SLE);blood;Sorted B cell

P09
JLP_P09_U133_2.CEL

patient9;Systemic lupus erythematosous (SLE);blood;Sorted B cell

P14
JLP_P14_U133_2.CEL

patient14;Systemic lupus erythematosous (SLE);blood;Sorted B cell

P13
JLP_P13_U133_2.CEL

patient13;Systemic lupus erythematosous (SLE);blood;Sorted B cell

SK-MEL-2 cells treated with Ad-E2F-1 at MOI 2 plus doxorubicin (sample 2)

SK-MEL-2 cells treated with Ad-E2F-1 at an MOI of 2 plus doxorubicin 0.1 uM(sample2)

Nrf2 +/+ mice (C57B6/SJL) were crossed with nrf2 -/- mice (C57B6/129SVJ) to generate mice heterozygous for nrf2. Interbreeding these heterozygotes generated the double-knockout mice (nrf2 -/-) as well as the corresponding littermate controls (nrf2 +/+). Mice were housed in plastic cages on a bedding of wood chips and maintained at ~22C, ~60% relative humidity, and a 12 hr light/dark cycle. The animals were fed with mouse diet 5015, which includes 30 IU/g of vitamin A and 35 IU/kg of vitamin E, (LabDiet, Richmond, IN) and drinking water ad libitum. All animal protocols were approved by the Institutional Animal Use and Care Committee at the University of Wisconsin-Madison. Total RNA was extracted from livers and spleens isolated from male and female nrf2 wildtype and knockout mice at 5 months of age (prior to the development of severe autoimmune disease).
Keywords = Nrf2

Nrf2 +/+ mice (C57B6/SJL) were crossed with nrf2 -/- mice (C57B6/129SVJ) to generate mice heterozygous for nrf2.  Interbreeding these heterozygotes generated the double-knockout mice (nrf2 -/-) as well as the corresponding littermate controls (nrf2 +/+).  Mice were housed in plastic cages on a bedding of wood chips and maintained at ~22C, ~60% relative humidity, and a 12 hr light/dark cycle.  The animals were fed with mouse diet 5015, which includes 30 IU/g of vitamin A and 35 IU/kg of vitamin E, (LabDiet, Richmond, IN) and drinking water ad libitum.  All animal protocols were approved by the Institutional Animal Use and Care Committee at the University of Wisconsin-Madison. Total RNA was extracted from livers and spleens isolated from male and female nrf2 wildtype and knockout mice at 5 months of age (prior to the development of severe autoimmune disease).

Gene expression data under ER stress from lymphoblastoid cells of individual GM12892 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12891 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12891 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12875 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12875 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12874 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12874 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12873 treated with DMSO 8 hours.

CCL3-injected C57BL/6, replicate 2

CCL3-injected C57BL/6, replicate 1

Carrier-injected Ccl3-/-, replicate 2

Carrier-injected Ccl3-/-, replicate 1

Gene expression data under ER stress from lymphoblastoid cells of individual GM12892 treated with DMSO 8 hours.

Within 6 hours of collection, blood was processed by density gradient centrifugation using Ficoll-Paque PLUS (GE Healthcare, Sweden).  Residual red blood cells were lysed and washed with phosphate buffered saline (PBS).  The isolated peripheral blood mononuclear cells (PBMC) were stored at -80 oC.

Patients with hepatocellular carcinoma were recruited at diagnosis and patients with chronic hepatitis B were recruited according to the protocol approved by the Institutional Review Board.  Informed consent was obtained from all subjects before blood samples were collected.  A total of 10 ml of blood was collected into BD Vacutainer® Plus K2EDTA tubes (Becton-Dickinson, USA).

The data was analyzed using Partek Genomics Suite version 6.6. CEL files were imported into Partek with GCRMA background correction, quantile normalization and log2 transformation.

Total RNA was extracted from PBMC and WBC using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s protocol.

The final cRNA obtained was hybridized to the GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix, USA).

Five micrograms of total RNA were reverse-transcribed and labeled with biotin.

Gene expression data from PBMC sample of  healthy volunteer
NOR-PBMC-05

NOR-PBMC-04

NOR-PBMC-01

Gene expression data from PBMC sample of  Chronic hepatitis B carriers
CHB-PBMC-12

NOR-PBMC-03

NOR-PBMC-02

Setd2 wt and ko mESCs were cultured on feeder cells in standard ES medium,then trypsinized ES cells were transferred on gelatin-coated cell culture dish, cultured for half an hour, then supernatant ES cells were collected and transferred to new gelatin-coated cell culture dish for 1 passage to maximumly remove feeder cells,two days later, mESCs were collected for microarray analysis.

GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and use Gene Spring Software 11 to normalize data. The trimmed mean target intensity of each array was set to log2.

QIAGEN RNeasy Kit extraction of total RNA was performed according to the manufacturer's instructions.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® mouse genome 430 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

D3;PRMT1 knockdown (siPRMT);4d_old aggregated embrioid bodies;DMSO for 12hr

Pancreases were rapidly dissected after the sacrifice of the animals.

Rkip1 KO and WT mice were derived from the same colony, maintained in a C57BL/6 background.

GeneChips were scanned according to the standard Affymetrix protocol (Affymetrix Genechip Command Console program 3.0.0.1214, scanner GCS 3000-7G)

Raw data was background adjusted, normalized and summarized by Robust Multi-array Analysis (RMA) using the Affy package from Bioconductor on R language.

Total RNA was isolated from whole pancreas using the RNAgents Total RNA Isolation System (Promega, WI, USA)

Following fragmentation, cRNA were hybridized, washed and stained according to the standard Affymetrix protocol.

D3;PRMT1 knockdown (siPRMT);undifferentiated embryonic stem cells

MCF7 cells were transfected with control or cyclin D1 siRNA. Cells were maintained for 48hrs to allow for efficient knock-down. Estradiol or vehicle treated cells were maintained for a further 24 hrs and then processed.

MCF7 cells grown in phenol red free DMEM supplemented with 5% charcoal stripped media

Arrays were inserted into the Affymetrix autoloader carousel and scanned using the GeneChip¬Æ Scanner 3000 with Command Console Software

Raw intensity files from the Affymetrix Human Gene 1.0 ST GeneChip arrays were processed using Affymetrix Expression Console version 1.1.   Gene-level expression measurements were computed using the iterPLIER algorithm on the ‚Äúcore‚Äù probesets and exported

Trizol extraction of RNA was performed as per manufacturer's instructions and purified using Qiagen RNAeasy Mini kit

2.5ug of ST cDNA were hybridized for 18h at 45 degrees on theAffymetrix Gene ChIP Human gene 1.0 ST Array

Biotinylated cDNA were prepared according to standard NuGEN protocol from 50ug total RNA.

Station	1
Module 1

mice were mated and the day on which a vaginal plug was found was designated 0.5.

Pregnant females were killed by cervical dislocation and conceptuses were dissected in PBS. Total RNA were extracted from E12.5 placentas using RNeasy kit (Qiagen). RNA concentration and integrity were tested with an Agilent 2100 Bioanalyzer (Agilent Technologies Inc.).

12,5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450,  protocol EukGE_WS2v5_450

Confluent monolayer of HUVEC was treated with trichostatin A (TSA, 500 nM, Sigma) for 24 hours

Isolation and culture as previously described.
Marsden PA et al.  Molecular cloning and characterization of human endothelial nitric oxide synthase.  FEBS Lett 1992, 307(3):287-293.

See 'Description' above. Data were processed using MAS5.0, RMA and GCRMA.

Total cellular RNA was isolated by guanidinium-isothiocyanate extraction followed by cesium chloride density gradient centrifugation.
Chirgwin JM et al.  Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease.  Biochemistry 1979, 18(24):5294-5299.
Glisin V et al.  Ribonucleic acid isolation by cesium chloride centrifugation.  Biochemistry 1974, 13(12):2633-2637.

Data in the VALUE column were computed using the MAS5.0 algorithm.
Data in the VALUE_RMA column were computed using the RMA algorithm.
Data in the VALUE_GCRMA column were computed using the GCRMA algorithm.

Data were processed using a program that implemented the recommendations of Choe, et al., Genome Biology, 2005 (PMID: 15693945). Background correction was performed as in the Affymetrix MAS 5.0 application. Probe-level normalization was performed using Quantile Normalization as in the RMA method. Perfect Match and Mismatch probes were contrasted as in the Affymetrix MAS 5.0 application. Multiple probes for each probeset were summarized using the median polish method from the RMA method. These summarized metrics where then normalized using LOESS.

Cells were treated with 2.5 uM rosiglitazone (RSG) along with 1 uM AGN193109 (AGN). Ligands or vehicle were added to the cell culture starting from the first day. AGN193109 administration was repeated at day 3.

cRNA was generated from 5 ug of total RNA by using the SuperScript Choice kit (Invitrogen) and the High Yield RNA transcription labeling kit.

Gene expression data from cardiac muscle of two-month-old mouse deficient in Neu5Gc sialic acid and dystrophin.
7 Cmah KO mdx Heart

8 Cmah KO mdx Heart

6 Cmah KO mdx Heart

Cell line SLM2, mutant status WT, condition Treated with Sorafenib 2

RNA from Cell line SLM2, mutant status WT, condition Treated with Sorafenib

Cell line SLM2, mutant status WT, condition Treated with Diclofenac 2

RNA from Cell line SLM2, mutant status WT, condition Treated with Diclofenac

Cell line SLM2, mutant status WT, condition Treated with Sorafenib+Diclofenac 2

RNA from Cell line SLM2, mutant status WT, condition Treated with Sorafenib+Diclofenac

Cell line SLM2, mutant status WT, condition Treated with Sorafenib 1

Cell line SLM2, mutant status WT, condition Treated with Diclofenac 1

Cell line SLM2, mutant status WT, condition Treated with Sorafenib+Diclofenac 1

Cells were treated with 100nM dexametasone (Sigma, Vienna, Austria) or 0.1% ethanol as carrier control.

Cell lines were cultured in RPMI 1640 supplemented with 10% fetal calf serum and 2mM L-glutamine at 37C, 5% carbon-dioxide and saturated humidity. The cells were free of mycoplamsa infection.

Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software.

The raw data was preprocessed in R (version 2.10) using the GCRMA algorithm (Bioconductor's gcrma package).

For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.

20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.

Total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.

GC resistant clone C7H2-R19F2 treated for 6 hours with 100nM dexamethasone (a glucocorticoid).

GC resistant clone C7H2-R19E7 treated for 6 hours with 100nM dexamethasone (a glucocorticoid).

GC sensitive clone C7H2-S2 treated for 6 hours with 0.1% ethanol (carrier control).

GC sensitive clone C7H2-S15 treated for 6 hours with 0.1% ethanol (carrier control).

GC sensitive clone C7H2-S27(ZR) treated for 6 hours with 0.1% ethanol (carrier control).

GC sensitive clone C7H2-S10 treated for 6 hours with 0.1% ethanol (carrier control).

GC resistant clone C7H2-R9C10 treated for 6 hours with 100nM dexamethasone (a glucocorticoid).

GC resistant clone C7H2-R3B5 treated for 6 hours with 100nM dexamethasone (a glucocorticoid).

GC resistant clone C7H2-R10E7 treated for 6 hours with 100nM dexamethasone (a glucocorticoid).

GC resistant clone C7H2-R19E5 treated for 6 hours with 100nM dexamethasone (a glucocorticoid).

ATP was purchased from Sigma-Aldrich (Milan, Italy). Blast cells obtained from 12 AML patients were cultured for 24 h with or without 1 mM ATP.

Primary leukemic cells were obtained from  the peripheral blood (PB) of 12 AML patients at diagnosis, before treatment. Mononuclear cells (MNC) were separated from AML samples, immediately after peripheral blood harvesting by Ficoll-Hypaque centrifugation (Amersham Bioscience, Piscataway, NJ, USA). Blast cells obtained from AML patients were cultured in IMDM + 10%FBS.

GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.

The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

Total RNA from 106 ATP-treated and untreated cells was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.

Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133 Plus2 GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the instrument’s standard FS450_0001 protocol with antibody-mediated signal amplification and GeneChip Hybridization, Wash and Staining Kit.

Biotinylated cRNA were prepared according to the standard One Cycle Affymetrix protocol from 1 ug total RNA (Gene Chip Expression Analysis Technical Manual, 701024 Rev3, Affymetrix). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.

Fifty thousand Lin-Sca1+ infected cells were transplanted into irradiated C57BL6 recipients via intravenous injection. Transplanted animals were monitored for leukemia development by flow cytometry analysis of GFP and CD4/CD8 expression in peripheral blood.

Bone marrow from 8-week old C57BL6 or Sh2b3–/– mice was harvested and lineage depleted using the Mouse Lineage Cell Depletion Kit (Milteny). Lin- progenitor cells were subjected to two rounds of infection with MigR1-ΔE-Notch1 retroviral particles.

Expression values were normalized with GC-RMA using the open-source Bioconductor software (www.bioconductor.org)

RNA isolation from mice tumors was performed in triplicate using the RNeasy Micro kit (QIAGEN) according to manufacturer’s protocol.

hybridized to the Mouse430_2 (Affymetrix) microarray chips according to manufacturer’s protocol

10 ng of RNA from each sample was amplified using the Ovation PicoSL WTA System (NuGen), labeled by the Encore BiotinIL Module (NuGen)

For the establishment of transgenic populations, media was supplemented with Puromycin (Sigma, 80µg/mL) or G418 (Gibco, 100µg/mL). Cultures of 80% confluent cultures were harvested between passages 2 and 4 for microarray analysis.

Control, SOX7 O/E and SOX17 O/E HESC were cultured under standard tissue culture conditions on mitotically inactivated mouse embryo fibroblast feeder layers in Knockout DMEM (Gibco) supplemented with 15% Serum Replacement (Gibco), Glutamax (Invitrogen), penicillin/streptomycin (Gibco), 1 mM non-essential amino acids (Gibco), 0.5mM mercaptoethanol, and 10ug/mL recombinant FGF2 (Peprotech).

MAS 5.0, All GeneChips were scaled to a median intensity setting of 500 and CEL files normalized across all probe sets

15 ug of fragmented cRNA was used to hyb for 17hrs on Affymetrix Human genome U133 Plus 2.0 arrays

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA

Cells were transfected using the Neon system (Life Technologies).  Following the manufacturer’s procedure, 1x10^6 cells were suspended in 100µl suspension solution containing 5 µg siRNA (Dharmacon) or plasmid and pulsed under program 3 for cells

MGHU3 cells were propagated at 37°C in RPMI 1640 (Hyclone; Thermo Scientific, Rockford, IL) supplemented with 10% FBS (Invitrogen).

Arrays were scanned using the GeneChip Scanner 3000 7G and Command Console Software v. 3.2.3.

Data were imported into Partek Genomics Suite Version 6.6 software with the following operations being done to prepare the data for statistical analysis: 1) RMA Background Correction, 2) Quantile Normalization, 3) Log base 2 transformation, and 4) Summary of Probe sets using mean value. Statistical analysis consisted of one-way ANOVA with a single categorical variable, and gene lists were generated for those genes with fold-change magnitude > 2 and p-value with a false discovery rate (FDR) <.05.

Total RNA was processed as recommended by Affymetrix, Inc. Briefly, RNA was isolated using TRIzol (Life Technologies) and passed through RNeasy spin columns (Life Technologies) for further clean up.

2 ug of the labeled, fragmented single-stranded cDNA was then hybridized to probe sets on a Human AffymetrixGeneChip 1.0ST array.

The Ambion WT expression kit (Life Technologies) was used to prepare RNA samples for whole transcriptome microarray analysis per manufacturer's instructions

MGHU3;malignant urothelial cells;FGFR3 Y375C mutation;5ug Control siRNA;100nM PD173074 for 48 hrs

MGHU3;malignant urothelial cells;FGFR3 Y375C mutation;5ug TAK1 siRNA;100nM PD173074 for 48 hrs

MGHU3;malignant urothelial cells;FGFR3 Y375C mutation;5ug Control siRNA

MGHU3;malignant urothelial cells;FGFR3 Y375C mutation;5ug TAK1 siRNA

WM-266 cells transfected with siGENOME siRNA Smartpool Reagent (Dharmacon) for knock-down of Pirin.
siPIR_A

Fibroblasts were grown in 10% FBS DMEM in a 37º incubator with 7% CO2.

Fibroblasts were isolated from mammary gland tissue using a modified protocol for gravity separation.

Gene expression levels were estimated from GeneChip® probe intensities using WEDGE++ algorithm (WPP), an enhanced integrated version of the published RMA, quantile-normalization and background-correction algorithms.

Fibroblasts isolated from mouse mammary glands with Pten deletion in fibroblasts

siPIR_B

siCTR_A

JCRB0033 [CEM];human T-ALL cell line;IKKγ Nemo binding domain (NBD) inhibitory peptide

A549 a pulmonary alveolar epithelial cell line was used in mechanical stretch and parenchymal cell activation experiments. Cells were grown in flexercell plates coated with collagen I, and allowed to grow O/N. Cells were then exposed to TNF alpha 20ng/ml stimulation for 1hr or 4hrs. Two replicates for each time point were performed. This is the second replicate for the 1hr time point. Experiemnt was carried out Jan 31 2003
Keywords = A549 cells RNA
Keywords = mechanical stretch

alveolar epithelial cell line exposed to TNF stimulation 20 ng/ml for 1hr

A549 a pulmonary alveolar epithelial cell line was used in mechanical stretch and parenchymal cell activation experiments. Cells were grown in flexercell plates coated with collagen I, and allowed to grow O/N. Cells were then exposed to cyclic stretch - 20% elongation for 1hr or 4hrs. Two replicates for each time point were performed. This is the second replicate for the 1hr time point. Experiemnt was carried out Jan 31 2003

alveolar epithelial cells exposed to cyclic stretch 20% elongation

A549 a pulmonary alveolar epithelial cell line was used in mechanical stretch and parenchymal cell activation experiments. Cells were grown in flexercell plates coated with collagen I, and allowed to grow O/N. Cells were then treated with LPS 1 mcg/ml for 1hr or 4hrs. Two replicates for each time point were performed. This is the first replicate for the 4hr time point. Experiemnt was carried out Nov 21 2002

alveolar epithelial cell line treated with LPS 1mcg/ml for 4 hr - first replicate

A549 a pulmonary alveolar epithelial cell line was used in mechanical stretch and parenchymal cell activation experiments. Cells were grown in flexercell plates coated with collagen I, and allowed to grow O/N. Cells were then exposed to cyclic stretch - 20% elongation for 1hr or 4hrs. Two replicates for each time point were performed. This is the first replicate for the 4hr time point. Experiemnt was carried out Nov 21 2002

A549 cells exposed to cyclic stretch 20% elongation for a total of 4hrs experiemnt performed on Nov 21 2002

A549 a pulmonary alveolar epithelial cell line was used in mechanical stretch and parenchymal cell activation experiments. Cells were grown in flexercell plates coated with collagen I, and allowed to grow O/N. Cells were then exposed to cyclic stretch - 20% elongation for 1hr or 4hrs. Two replicates for each time point were performed. This is the first replicate for the 1hr time point. Experiemnt was carried out Oct 20th 2002

alveolar epithelial cells exposed to cyclic stretch 20% elongation for 1 hr

A549 a pulmonary alveolar epithelial cell line was used in mechanical stretch and parenchymal cell activation experiments. Cells were grown in flexercell plates coated with collagen I, and allowed to grow O/N. Cells were then treated with LPS 1 mcg/ml for 1hr. Two replicates for each time point were performed. This is the second replicate for the 1hr time point. Experiemnt was carried out Jan 31 2003

A549 an alveolar epithelial cell line was used in mechanical stretch experiments. Cells were grown in flexercell plates coated with collagen I. This sample represent the static control for the 4 hr sample. This is the first replicate. Experiemnt was carried out Nov 20th 2002

A549 a pulmonary alveolar epithelial cell line was used in mechanical stretch and parenchymal cell activation experiments. Cells were grown in flexercell plates coated with collagen I, and allowed to grow O/N. Cells were then treated with LPS 1 mcg/ml for 1hr or 4hrs. Two replicates for each time point were performed. This is the second replicate for the 4hr time point. Experiemnt was carried out Jan 31 2003

A549 a pulmonary alveolar epithelial cell line was used in mechanical stretch and parenchymal cell activation experiments. Cells were grown in flexercell plates coated with collagen I, and allowed to grow O/N. Cells were then treated with LPS 1 mcg/ml for 1hr. Two replicates for each time point were performed. This is the first replicate for the 1hr time point. Experiemnt was carried out Oct 21 2002

Mice heterozygous for dn-p21 littermates were sacrificed at 10 weeks of age. Ventricles were isolated and snap-frozen in liquid nitrogen.  Use 3 month old FVB Females as controls.  [GSM2334, GSM2335, GSM2336]
Read more at http://cardiogenomics.med.harvard.edu/groups/proj1/pages/ras_home.html
Keywords = ras
Keywords = dilated cardiomyopathy

human adipose stem cells were transfected with a control siRNA (siCtrl) or two different siRNA oligos targeting the gene LMO3 (siLMO3_oligo1 or siLMO3_oligo2). 40Hrs later, the transfected human adipose stem cells were induced to differentiate into mature adipocytes with a adipogenic cocktail (FullMix) and RNA isolated at day 0 or day6 after induction of differentiation.

human adipose stem cells were grown in DMEM + FBS (10%) and antibiotics

RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.1

Following fragmentation, 20 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Gene expression data from C57BL/6 strain mouse left ventrical with 60 day LAD ligated heart.

Gene expression data from MRL/MpJ strain mouse left ventrical with 60 day LAD ligated heart.

RNA was extracted from a pool of three thymi taken from four week old nonobese diabetic (NOD) derived NOD.B10 Idd9 R28 congenic mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.

RNA was extracted from a pool of two thymi taken from four week old nonobese diabetic (NOD) derived NOD.B6 Idd3 R450 B10 Idd5 R8 congenic mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.

RNA was extracted from a pool of three thymi taken from four week old C57BL/10 derived B10.NOD H2g7 mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.

RNA was extracted from a pool of three thymi taken from four week old nonobese diabetic (NOD) mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.

Gene expression data from MRL/MpJ strain mouse left ventrical with 30 day LAD ligated heart.

RNA was extracted from a pool of three thymi taken from four week old C57BL/10 derived B10.NOD H2g7 Idd3 congenic mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.

CD-1;lung;20 week;dominant negative CREB1 driven by cardiomyocyte-specific myosin heavy chain-alpha promoter

MDA-MB-231 Breast Cancer Cells Stably Expressing wild-type ERa 1 Hr Treatment Sample B

MDA-MB-231 Breast Cancer Cells Stably Expressing wild-type ERa 1 Hr Treatment of 10 nM E2 Sample B

MDA-MB-231 Breast Cancer Cells Stably Expressing wild-type ERa 1 Hr Treatment Sample A

MDA-MB-231 Breast Cancer Cells Stably Expressing wild-type ERa 1 Hr Treatment of 10 nM E2 Sample A

MDA-MB-231 Breast Cancer Cells Stably Expressing wild-type ERa Control Sample B

MDA-MB-231 Breast Cancer Cells Stably Expressing mutant ERa LQ Sample B

MDA-MB-231 Breast Cancer Cells Stably Expressing Mutant ERa LQ Control Sample B

MDA-MB-231 Breast Cancer Cells Stably Expressing Mutant ERa LQ Control Sample A

MDA-MB-231 Breast Cancer Cells Stably Expressing wild-type ERa 2 Hr Treatment Sample B

MDA-MB-231 Breast Cancer Cells Stably Expressing wild-type ERa 2 Hr Treatment of 10 nM E2 Sample B

MDA-MB-231 Breast Cancer Cells Stably Expressing wild-type ERa 2 Hr Treatment Sample A

MDA-MB-231 Breast Cancer Cells Stably Expressing wild-type ERa 2 Hr Treatment of 10 nM E2 Sample A

hormone-refractory metastatic prostate cancer tissue pool from sample W1,W2,W3 and W4, replicates of WX1

hormone-refractory metastatic prostate cancer tissue pool extraced from sample W1, W2, W3 and W4

Bmi1 transduced embryonic stem cells were cultured on gelatin coated dish in DMEM medium with 15% FSC and leukemia inhibitory factor (LIF).

Bmi1 transduced embryonic stem cells were cultured on gelatin coated dish in DMEM medium with 15% FSC and leukemia inhibitory factor (LIF). Lentivirus containing mouse BMI1 cDNA was used to infect CCE ES cells in the presence of 8 microgram polybrene. Empty vector served as control. After two passages eGFP positive CCE ES cells were sorted by flow cytometry and cells were further grown in culture medium as above.

CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).

Total RNA was extracted using RNeasy Mini kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.

Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 94°C for 35 minutes in Fragmentatin buffer of the compnay.

The nucleus accumbens from a neurologically normal Jpanese male (aged 60 yr).

The specimen was frozen in a deep freezer at autopsy immediately after his death from pneumonia.

glioblastoma cells;H4 cells;STAG2 knock-in post-Cre clone 88-1 (STAG2 corrected)

SFMC isolated by Ficoll gradient centrifugation from JSpA patient
Keywords = Juvenile spondyloarthropahty (JSpA), synovial fluid mononuclear cells (SFMC)

SFMC isolated by Ficoll gradient centrifugation from polyarticular JRA patient
Keywords = Polyarticular course, juvenile rheumatoid arthritis (JRA), synovial fluid mononuclear cells (SFMC)

The data were normalized by log2 transformation, background subtraction and quantile normalization approach with Limma in R (v.2.15.0, 2012-03-30).

Total RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

Biotinylated cRNA were prepared with the Ambion Message Amp kit for Illumina arrays

mixed C57BL/6, FVB, 129 background;BrafV600E::Pten-/-::Pdk+/+, Pdk1 wild-type;tumor

Ctrl_8h_3

Ishikawa;39-year-old parous Japanese female diagnosed with endometrial adenocarcinoma stage 2.;vehicle control;8 hours

Ctrl_8h_2

Mouse Lung AIN Diet 8hr Saline Injection, biological replicate D
AN080306_Sample 64.CEL

Sample 9
293T cells transfected with si-TNIK vs si-control, and induced with Wnt3A medium for 7 hours.

Sample 8
Dye swap of 7. 293T cells transfected with si-TNIK vs si-control, and induced with Wnt3A medium for 4 hours.

Sample 7
293T cells transfected with si-TNIK vs si-control, and induced with Wnt3A medium for 4 hours.

Mouse Lung AIN Diet 5wk Control, biological replicate A
AN080406_Sample 63.CEL

Ctrl_8h_1

Sample 12
Dye swap of 11, biological replicate of 10. 293T cells transfected with si-TNIK vs si-control, and induced with Wnt3A medium for 7 hours.

Sample 11
Biological replicate of 9. 293T cells transfected with si-TNIK vs si-control, and induced with Wnt3A medium for 7 hours.

Sample 10
Dye swap of 9. 293T cells transfected with si-TNIK vs si-control, and induced with Wnt3A medium for 7 hours.

dChip v 1.3 was used for normalization, model-based gene expression estimatation and outlier detection ; Affymetrix Microarray Suite version 5.0 was used to calculate the present call of each transcript

HIV seropositive, CD4 cells decrease over time, sampled at time point 2

GeneChips were scanned using the Genechip scanner 3000 workstation (Affymetrix)

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on  Human Genome U133 Plus 2.0 GeneCHIP.

Gene expression profile of an adrenocortical adenoma  with a S45P  CTNNB1 mutation

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D1;10

male;non-metastatic prostate cancer;peripheral blood;white blood cells;baseline;10

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D42;10

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D21;10

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D14;10

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D7;10

male;non-metastatic prostate cancer;peripheral blood;white blood cells;baseline;11

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D72 (30 days post-EBRT);10

Pool of total RNA from adrenal glands of 62 caucasian subjects aged 15 to 61 years old

Soleus muscles from male BERKO ( estrogen receptor beta knockout)

The slides were then washed and stained using the EukGE-WS2v5 Fluidics protocol on the Genechip® Fluidics Station (Affymetrix) before being scanned on a Genechip® Scanner 3000.

For the initial normalization and analysis steps, data were retrieved on Affymetrix GCOS software. The frequency of positive genes (genes with a flag present) was between 40 and 50% on each slide. After scaling of all probe sets to a value of 100, the range of the reported amplification scales was between 0,8 and 6,7. The signals yielded by the poly-A RNA, hybridization and housekeeping controls (GADPDH 3’/5’ ratio < 2.3 in all the slides) were indicative of the good quality of the amplification and hybridization procedures.

Samples stored at –80°C after overnight incubation in RNALater were used for the microarray hybridizations. Total RNA was extracted from the synovial biopsies using the Nucleospin® RNA II extraction kit (Macherey-Nagel), including DNase treatment of the samples. At least 1 µg total RNA could be extracted from 12 paired samples at T0 and T12 for further processing. RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA nanochips (Agilent technologies Inc).

GeneChip® Human genome U133 Plus 2.0 Arrays (spotted with 1,300,000 oligonucleotides, grouped in 54,675 probe sets informative for about 47,000 transcripts originated from not less than 39,000 genes, Affymetrix UK Ltd, High Wycombe, UK) were hybridized overnight at 45°C in monoplicates with 10 µg cRNA.

Labeling of RNA (cRNA synthesis) was performed according to a standard Affymetrix® procedure (One-Cycle Target Labeling kit, Affymetrix UK Ltd., High Wycombe, UK); briefly total RNA was first reverse transcribed into single-stranded cDNA using a T7-Oligo(dT) Promoter Primer and Superscript II reverse transcriptase. Next, RNase H was added together with E.Coli DNA polymerase I and E. Coli DNA ligase, followed by a short incubation with T4 DNA polymerase in order to achieve synthesis of the second-strand cDNA. The purified double-stranded cDNA served as the template for the in vitro transcription reaction, which was carried overnight in the presence of T7 RNA polymerase and a biotinylated nucleotide analog/ribonucleotide mix. At the end of this procedure, the biotinylated complementary RNA (cRNA) was cleaned, and fragmented by a 35 -minute incubation at 95°C.

twenty patients with ra (17 women and 3 men, average age +/- sem: 52,6+/-3,8 years) were included in the study. All patients met the American College of Rheumatology classification criteria for the diagnosis of RA. All patients had active disease at the time of tissue sampling and were resistant to TNF blockade. They all had erosive changes imaged on conventional x-rays of the hands and/or feet. All of them had a swollen knee at inclusion. Rituximab therapy was administrated at a dose of 1,000 mg IV at baseline (T0) and at week 2, together with 125 mg IV Methylprednisolone. Clinical parameters at baseline (T0) and 12 weeks after the initiation of therapy (T12) was evaluated using DAS(28)-CRP scores and clinical responses were assessed using EULAR response criteria. Synovial biopsies were obtained by needle-arthroscopy of an affected knee from all patients at T0 and T12. For each procedure, 4 to 8 synovial samples were kept overnight at 4°C in a RNA stabilizing solution (RNALater, Ambion, Applied Biosystems, TX, USA) and then stored at –80°C for later RNA extraction. The same amount of tissue was snap-frozen in liquid nitrogen and kept at –80°C for immunostaining experiments on frozen sections. The remaining material was fixed in 10% formaldehyde and paraffin embedded for conventional optical evaluation and immunostaining of selected markers. All the experiments (RNA extraction, histology, immunohistochemistry) were performed on at least 4 biopsies harvested during every procedure in order to correct for variations related to the potential heterogeneous distribution of synovial inflammation. The study was approved by the ethics committee of the Université catholique de Louvain and informed consent was obtained from all patients.

12 weeks of RTX therapy;F;21;synovial knee biopsy;rheumatoid arthritis;EULAR Moderate-responder;synovium

Human synovial biopsies from the knee of a patients with RA prior to (T0) or after (T12) RTX therapy (EULAR Moderate-responder).

baseline;F;21;synovial knee biopsy;rheumatoid arthritis;EULAR Moderate-responder;synovium

12 weeks of RTX therapy;F;68;synovial knee biopsy;rheumatoid arthritis;EULAR Moderate-responder;synovium

baseline;F;68;synovial knee biopsy;rheumatoid arthritis;EULAR Moderate-responder;synovium

12 weeks of RTX therapy;F;47;synovial knee biopsy;rheumatoid arthritis;EULAR Poor-responder;synovium

Human synovial biopsies from the knee of a patients with RA prior to (T0) or after (T12) RTX therapy (EULAR Poor-responder).

baseline;F;47;synovial knee biopsy;rheumatoid arthritis;EULAR Poor-responder;synovium

12 weeks of RTX therapy;M;64;synovial knee biopsy;rheumatoid arthritis;EULAR Poor-responder;synovium

baseline;M;64;synovial knee biopsy;rheumatoid arthritis;EULAR Poor-responder;synovium

12 weeks of RTX therapy;F;59;synovial knee biopsy;rheumatoid arthritis;EULAR Poor-responder;synovium

baseline;F;59;synovial knee biopsy;rheumatoid arthritis;EULAR Poor-responder;synovium

DRG collected from ipsilateral limb after 14 days from sham operated animals

DRG collected from ipsilateral limb after 21 days from sham operated animals

DRG collected from ipsilateral limb after 50 days from sham operated animals

9B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

69B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

68B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

8B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

7B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

B cell fraction was isolated using magnetic beads (B cell isolation kit, Miltenyi). GC B cells (PNAhi/CD95hi) were sorted based on their relative GFP(=MYC) expression in two pools (MYC+, MYC-) for each mouse

8 week old GFPMYC/C57BL6 mouse, Sheep Red Blood Cell (SRBC) immunization, 12 days

Affymetrix GeneChip Scanner 3000 7G, connected to Command Console software.

The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500

Sorted GC B cells. Total RNA isolated using Nucleospin RNA XS kit (Macherey Nagel). cDNA was amplified from 5-20 ng of total RNA using the Ovation RNA amplification kit (NuGEN), following manufacturer's instructions.

3.75 micrograms of fragmented, Biotin-labeled amplified cDNA was hybridized using the Affymetrix HWS kit, Standard Array (49 Format), using NuGEN's Encore Biotin kit instructions. Samples were hybridized for 16 hours. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Encore Biotin Labeling Kit (NuGEN). Biotin labeled and fragmented amplified cDNA was prepared following manufacturer's instructions.

Sample name: GFPMYCneg_10G
Gene expression data from MYC negative GC B cell subpopulation, paired to 9G

Sample name: GFPMYCneg_12G
Gene expression data from MYC negative GC B cell subpopulation, paired to 11G

African-American (AA);Female;Systemic lupus erythematosus (SLE) patient;Peripheral blood;CD8-PE;CD8 positive T cells

control; Gender: female; Age: 60; Tissue: lymphocytes (blood); IT15 CAG repeats: N/A

control; Gender: female; Age: 51; Tissue: lymphocytes (blood); IT15 CAG repeats: N/A

control; Gender: female; Age: 39; Tissue: lymphocytes (blood); IT15 CAG repeats: N/A

control; Gender: female; Age: 30; Tissue: lymphocytes (blood); IT15 CAG repeats: N/A

mRNA extracted from control lung fibroblasts derived from normal periphery of resected tumor. Lung fibroblasts were grown to confluence in DMEM with 10% fetal calf serum. At confluence, lung fibroblasts were serum-deprived overnight, and exposed to 4 ng/ml of activated TGF-ß1 (R&D Systems) in serum-free culture-medium with the addition of 0.1% BSA for 4 hours. At the end of treatment period total RNA was harvested, quantified, and integrity was verified by denaturing gel electrophoresis.

mRNA extracted from control lung fibroblasts derived from normal periphery of resected tumor. Lung fibroblasts were grown to confluence in DMEM with 10% fetal calf serum. At confluence, lung fibroblasts were serum-deprived overnight, and exposed to serum-free culture-medium with the addition of 0.1% BSA for 4 hours. At the end of treatment period total RNA was harvested, quantified, and integrity was verified by denaturing gel electrophoresis.

GeneChips were scanned using the Affymetrix GeneChip Scanner 3007

GeneChips were scanned using the Affymetrix GeneChip Scanner 3006

GeneChips were scanned using the Affymetrix GeneChip Scanner 3005

GeneChips were scanned using the Affymetrix GeneChip Scanner 3004

GeneChips were scanned using the Affymetrix GeneChip Scanner 3011

GeneChips were scanned using the Affymetrix GeneChip Scanner 3010

GeneChips were scanned using the Affymetrix GeneChip Scanner 3009

GeneChips were scanned using the Affymetrix GeneChip Scanner 3008

GeneChips were scanned using the Affymetrix GeneChip Scanner 3013

GeneChips were scanned using the Affymetrix GeneChip Scanner 3012

LKR13 cells were infected with plko.1s vectors carrying one of two shRNAs against Wt1. 48 hours after infection, cells were selected with puromycin for 3 days.  RNA was extracted 7 days post-infection.

MCI-017 was from a premenopausal low BMD woman.

CONTROL_AM0011

MCI-018 was from a premenopausal low BMD woman.

LKR13 cells were infected with plko.1s vectors carrying one of two shRNAs against K-ras. 48 hours after infection, cells were selected with puromycin for 3 days. RNA was extracted 7 days post-infection.

RNA was extracted with Trizol reagent in accordance with the prescribed protocol. Quality control was performed with Agilent Bioanalyser.

Cy3-labeled cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

MCI-002 was from a postmenopausal low BMD woman.

Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Total RNA was further processed to isolate mRNA (see 'Extract protocol').

Gene expression data of HeLa cells

Gene expression data from 12 week old wt mouse liver tissue fed a standard diet
01-WT3

The data were normalised using quantile normalisation with beadarray in R

transfected with Ambion Silencer Select SOX2 siRNA;embryonal carcinoma;NTera-2;40-50

NTera-2 cells transfected with Ambion Silencer Select SOX2 siRNA

transfected with Ambion Silencer Select Negative Control #1;embryonal carcinoma;NTera-2;40-50

NTera-2 cells transfected with Ambion Silencer Select Negative Control #1

Cells were cultured in IMEM supplemented with 5% FBS and 200 ug/ml Geneticin

For .CHP file: MAS5.
For .CEL file and manuscript: Robust Multiple-Array Average (RMA) method from the Bioconductor Project.

Trizol Extraction (Invitrogen), followed by RNeasy Column Cleanup (Qiagen)

To differentiate TS cell FGF4 heparin and feeder conditioned medium were all withdrawn from the media.

TS cells were grown feeder free with 30% feeder conditioned medium, RPMI, FGF4 and heparin as per Tanaka et al , 1998 PMID:9851926

Gene Chips were scanned using the Hewlett-Packard Gene Array Scanner G2500A.

The data were analyzed with Expression Console (Affymetrix) using the quartile normalization and PLIER algorithm

Trizol extraction of total RNA was performed according to the manufacturer's instructions. A second clean up step was done using the RNEasy kit from QIAGEN according to manufactures instructions

Sham operated rat 7 day post-operation
Heart left ventricle and septum
Keywords = 7 day
Keywords = sham

After 72 hrs of starvation, the cells were maintained in complete medium without CdCl2 for 16 hrs.

The cells were grown in Defined Keratinocyte-SFM medium (Invitrogen, Carlsbad, CA) with growth promoting supplement. Cell cultures were maintained at 37°C in a humidified incubator with a 5% CO2 atmosphere.
Before cadmium treatment, the cells were synchronized via starvation by maintaining the cells in medium without supplement for 72 hr.

All steps of data preprocessing including background correction, normalization and expression set summaries were performed using the RMA algorithm. Chip quality was assessed with the affyQCReport package of Bioconductor and one chip (Cd_04hr) was removed from analysis due to poor quality.

Total RNA was extracted from NPrEC cells by using TRIzol reagent (Invitrogen) according to the manufacture’s instruction. The quality of RNA was assessed by the absorbance ratio at 260/280 nm and gel electrophoresis before further analysis.

Immortalized normal prostate epithelial cell line (NPrEC), which showed basal epithelial cell phenotype, was established in our lab (Mobley et al., 2003).

After 72 hrs of starvation, the cells were maintained in complete medium without CdCl2 for 32 hrs.

Keratinocytes were grown in subconfluent condition with the medium composed of 50% complete Keratinocyte-SFM (Life Technologies) and 50% Medium 154 (Life Technologies).

Hereditary gingival fibromatosis(HGF) patient Gingiva replicate2

Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes

Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen)

HGF gingiva tissue removed during surgical procedures and stored in liquid nitrogen immediately

Hereditary gingival fibromatosis (HGF) is a benign disorder manifested by a slowly progressive enlargement of the oral gingival tissues, which results in the teeth being partially or totally engulfed by keratinized gingiva.Affected gingiva tissues were removed from HGF volunteers during surgical procedure.

Cells were serum-starved for 24 h and then treated with 5 ng/mL porcine transforming growth factor beta 1 (TGF-beta, R&D Systems, Minneapolis, MN) for 48 hours.

Panc-1 cells were maintained in RPMI-1640 medium with glutamine, supplemented with 10% FBS, penicillin, and streptomycin and tested for mycoplasma contamination. All tissue culture media and media supplements were purchased from Life Technologies (Gaithersburg, MD).

Total RNA was isolated from the harvested cells using Trizol (Invitrogen) and cleanup performed with an RNeasy kit (Qiagen)

Biotinylated cRNA was prepare from 3-5 ug total RNA using standard Affymetrix protocol

Gene expression data from transforming growth factor beta treated Panc-1 pancreatic cancer cell lines after 48 hours

Gene expression data from untreated Panc-1 pancreatic cancer cell lines

PARP-2 silencing was performed employing shPARP-2 (small hairpin) and scPARP-2 (scrambled) shRNA by lentiviral delivery (Sigma) using 40 MOI lentiviruses coding shRNA sequence against PARP-2.

Arrays were scanned on GeneChip Scanner 7G (Affymetrix). Core software Affymetrix GeneChip Command Console (AGCC).

Microarray data were analyzed by GeneSpring 10 GX software (Agilent BioTechnologies). Affymetrix CEL files were normalized Robust Multichip Analysis (RMA) algorithm and median normalization. Expressed genes were determined by filtering out the lowest 20th percentile of genes based on raw signal intensity. Then genes, which did not show at least 2-fold change difference from the median, were also filtered out, called non-changing genes. Statistical analysis was performed on the list of changing genes using T test, statistically significant difference was considered to p < 0.05 and fold change cut off value was 1.5.

Total RNA was extracted from HepG2 cells using the RNeasy Mini Kit (Qiagen). RNA integrity was checked on Agilent Bioanalyser 2100 (Agilent Technologies), RNA samples with 9.0 RIN value were used in the further experiments. NanoDrop ND-1000 was used to determine RNA concentration.

Samples were hybridized at 45 degrees Celsius for 16 hours and then standard washing protocol was performed using GeneChip Fluidics Station 450. Core software Affymetrix GeneChip Command Console (AGCC).

Global expression pattern was analyzed on Affymetrix GeneChip Human Gene 1.0 ST arrays. Ambion WT Expression Kit (Life Technologies, Hungary) and GeneChip WT Terminal Labeling and Control Kit (Affymetrix) were used for amplifying and labeling 250 ng of total RNA samples. Samples were hybridized at 45 oC for 16 hours and then standard washing protocol was performed using Affymetrix GeneChip Fluidics Station 450, the arrays were scanned on GeneChip Scanner 7G (Affymetrix). RNA labeling and hybridization was processed by UD-GenoMed Medical Genomic Technologies Ltd (Debrecen, Hungary).

male mice (8 wks) were treated with placebo (water only) for 10 weeks (5d per wk). At the end of study subcutaneous fat was harvested for microarray analysis.

Each of the three animal groups was treated with four different ligands for three days by intraperitoneal injection.  The injections were given at 24 hour intervals at 10 am.  Since TCPOBOP is non-metabolized in the mouse, a single injection was given on the 1st day and subsequent corn oil injections were given on days 2 and 3.  6 hours after the last injection on day 3, the mice were sacrificed and their livers harvested for RNA preparation.

Mice were fed normal chow and housed with a 12 hour light/dark cycle.  AH mice were generated and bred to KO mice to generate humanized CAR mice through 2 breeding cycles.

Chips were scanned using an Affymetrix GeneChip Scanner 3000.  Scanning was done as described in the GeneChip Expression Data Analysis Manual, Chapter 2 (701024 Rev 3)

RMA normalization using R version 2.15.0 and affy version 1.34.0

RNA was isolated using Invitrogen Trizol according to a modified version of the manufacturer's instructions.  After the RNA pellet was isolated, a second precipitation was carried out to clean up the RNA. Guanidinium thiocynate/beta-mercaptoethanol was added according to the protocol of Chomczynski & Sachs [1987] plus 100% isopropanol to reprecipitate the RNA which was then resuspended in 100% formamide.  Total RNA was cleaned of contaminating DNA using Qiagen's RNA-ez kit (cat # 741040) according to manufacturer's instructions. References Chomczynski, P., and Sacchi, N. (1987). Single-step method of rna isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162, 156-159.

Hybridization was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1) in a GeneChip Hyb Oven 640.

Labeling was done as described in the Affymetrix GeneChip Expresision Analysis Technical Manual (701047 rev 1).

C57BL/6x129Sv;female;hCAR transgenic in mCAR knockout background;CITCO; 6-(4-chlorophenyl)imidazo[2-1-b][1,3]thiazole-5-carbaldehyde O-(3,4-dichlorobenzyl)oxime

C57BL/6x129Sv;female;hCAR transgenic in mCAR knockout background;corn oil

Gene expression data from male F344 rats treated with a single dose of 5mg/kg D-Serine for 96 hours

Brain tissue from Fisher 344 male rat, Animal #271, 5mg/kg D-Serine

Brain tissue from Fisher 344 male rat, Animal #270, 5mg/kg D-Serine

Brain tissue from Fisher 344 male rat, Animal #269, 5mg/kg D-Serine

Brain tissue from Fisher 344 male rat, Animal #267, 5mg/kg D-Serine

SMhu171

SMhu172

SMhu169

SMhu170

SMhu167

SMhu168

SMhu165

SMhu166

SMhu163

SMhu164

Immature (19/20 days of age) Alpk:APfCD-1 mice were treated with arachis oil (AO) vehicle, 0.4mg/kg 17beta-estradiol (E2), or 250mg/kg genistein (GEN), via a single subcutaneous injection, and sacrificed at 1hr, 2hr, 4hr, 8hr, 24hr, 48hr, 72hr post dose.

RPMI8226 cells were maintained in RPMI-1640 medium supplemented with 10% (v/v) fetal bovine serum and 2 μM L-glutamine in 5% CO2 at 37°C.

Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured according to the manufacturer's instructions.

affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
program-name = Expression Console
program-id = 1.3.1.187

After 72 hours of infection, total RNA was extracted using RNeasy Mini Kit according to the manufacturer's instructions.

The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution is then removed.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1mg of total RNA

Wistar rats were fasted overnight and killed by CO2. A piece of the reight venreal liver lobe was removed and clamp frozen. Total RNA was isolated from the clamp-frozen liver pieces using RNeasyR mini spin columns (Qiagen). The purified RNA was routinely checked for visible signs of degradation in a Bioanalyzer 2100 (Agilent Technologies, Palo Alto, USA), and only high quality RNA was processed.

Approximately 3-5 µg of total RNA was processed to produce biotinylated cRNA targets.

liver sample of Wistar rat fed for 12 weeks with coconut fat diet, after overnight fast

liver sample of Wistar rat fed for 12 weeks with olive oil diet, after overnight fast

liver sample of Wistar rat fed for 12 weeks with lard diet, after overnight fast

liver sample of Wistar rat fed for 12 weeks with standard chow diet, after overnight fast

liver sample of Wistar rat fed for 12 weeks with fish oil diet, after overnight fast

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_3-tu1

CD8 T cells isolated from tumor; transduced with shRNA targeting: Egr2; Sample name: 3-tu1

Cells were transduced with lentivirus in the presence of 8µg/ml hexadimethrine bromide (Sigma) overnight

Cultured in standard condition according to America Type Culture Condition (ATCC) with DMEM supplemented with 10% FBS and 1x penicillin and streptomycin

GeneChips were scanned using the GeneChip Scanner 3000 7G with autoloader

The data were analyzed with Partek Suite version 6.6 using Affymetrix default analysis settings and RMA as normalization method.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in GeneChip® Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (3' IVT PLUS Reagent Kit User Manual, Affymetrix).

Gene expression data from CAPAN2 cells transduced with lentivirus carrying shRNAs targeting LLGL1 transcript

Pancreatic ductal adenocarcinoma;CAPAN2;lentivirus carrying shRNAs targeting LLGL1 transcript

Capan2 cells transduced with lentivirus carrying shRNAs targeting LLGL1 transcript

Rosetta Resolver system for gene expression data analysis (Rosetta Inpharmatics, Inc.)

top2b-/- in 129SvEv (minor 129SvJ) background;;E18.5 embryo;;male;;whole brain

Top2b+/+ in 129SvEv (minor 129SvJ) background;;E18.5 embryo;;male;;whole brain

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_3-tu2

CD8 T cells isolated from tumor; transduced with shRNA targeting: Egr2; Sample name: 3-tu2

Expression analysis of intestinal crypt mRNA of control mice vs. beta-catenin deleted mutant animals (2days of deletion).

intestinal crypt cells isolated by laser capture microdissection

hepatocellular carcinoma from male Fischer344 rat fed choline-deficient, L-amino acid-defined diet for 70 w

HL-60, MOLM-14, and U937 cell lines were transduced in triplicate with a control luciferase-directed shRNA (target sequence CCTAAGGTTAAGTCGCCCTCG), and in duplicate with two SYK-directed shRNAs:  shSYK_1 (clone ID TRCN0000197257,  target sequence  GCAGCAGAACAGACATGTCAA)   and shSYK_2  (clone ID TRCN0000003163 , target sequence  GCAGGCCATCATCAGTCAGAA),  and were then selected with 1 µg/ml puromycin 48 hours post-infection.

HL-60, MOLM-14, and U937 were maintained in RPMI 1640 (Cellgro) supplemented with 1% penicillin-streptomycin and 10% fetal bovine serum (FBS, Sigma-Aldrich) at 37 °C with 5% CO2

Data were extracted from the  CEL files and preprocessed through  the ExpressionFileCreator module implemented  in  GenePattern 3.5.0  software platform (Broad Institute, http://www.broadinstitute.org/cancer/software/genepattern/),  by applying  RMA and the quantile normalization procedures.  The computational analysis of the gene expression data was performed through the Genome Space bioinformatics platform (http://www.genomespace.org).

RNA was extracted using Qiagen Rneasy Mini Kit (74104) at 5 days post infection.

The samples were profiled using the HT U133A Gene Expression Arrays (Affymetrix) at the Broad Institute of MIT and Harvard (Cambridge, MA, USA).

HL-60 cell line, transduced with shSYK_1 and selected with  1 µg/ml puromycin 48 hours post-infection

age	24;gender	male;disease	healthy control;disease phase;previous therapy	no;bcr-abl/G6PDH ratio (%)	n.a.;leukocyte count (/nl)	4.7;hemoglobin (g/dl)	14.2;platelet count (/nl)	192

201;None;4/12/56;M;CAUCASIAN;6/19/03;7/4/03;FALSE;FALSE;FALSE;NO;FALSE;FALSE;9/30/04;1;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;BOTH;BOTH;BOTH;9/30/04;BOTH;HISTOLOGICAL;unknown;unknown;unknown;12/7/04;FAILURE OF THERAPY;ex;1/1/70;1/1/99;25+;None;UC;1-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

211;Predfoam Adcal D3 Alendronate;11/10/44;F;CAUCASIAN;1/1/77;6/7/79;FALSE;FALSE;FALSE;NO;FALSE;FALSE;11/5/04;1;0;0;0;0;0;0;0;FALSE;0;BOTH;unknown;unknown;unknown;unknown;11/5/04;BOTH;unknown;unknown;unknown;unknown;5/31/05;DISEASE IN REMISSION;never;unknown;Coeliac disease 1991;UC;5-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

210;Mesalazine 800mg B, Prednisolone Supps;6/28/56;M;CAUCASIAN;1/1/73;1/10/74;FALSE;TRUE;FALSE;NO;FALSE;FALSE;10/19/04;2;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;BOTH;unknown;unknown;10/14/04;BOTH;unknown;unknown;unknown;unknown;12/9/04;DISEASE IN REMISSION;never;unknown;Scarlet Fever 1964;UC;1-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

208;Prednisolone 25mg/d, Pentaza 1g BD, Fosomax weekly;8/16/85;F;CAUCASIAN;6/1/04;6/25/04;FALSE;FALSE;FALSE;NO;FALSE;FALSE;10/14/04;2;0;17;3;121;8;5;39;FALSE;0;BOTH;BOTH;BOTH;unknown;unknown;11/14/04;BOTH;BOTH;BOTH;unknown;unknown;12/9/04;DISEASE IN REMISSION;never;unknown;None;UC;1-25-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

207;Asacol 800mg BD, Colifoam Enemas Daily;4/29/47;M;CAUCASIAN;3/1/88;8/18/88;FALSE;FALSE;FALSE;NO;FALSE;FALSE;10/14/04;2;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;BOTH;BOTH;BOTH;10/14/04;unknown;unknown;BOTH;BOTH;unknown;12/9/04;DISEASE IN REMISSION;ex;1/10/62;3/15/75;25+;None;UC;1-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

Human HeLa cells were propagated in DMEM medium (GIBCO-BRL) containing 10% fetal bovine serum. 2 X 106 HeLa cells were transiently transfected with in vitro-synthesized nonspecific control siRNA.

Human HeLa cells were transiently transfected with in vitro-synthesized nonspecific control siRNA.

HeLa cells transiently transfected with a nonspecific control siRNA

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_6-sp2

CD8 T cells isolated from spleen; transduced with shRNA targeting: Alk; Sample name: 6-sp2

RNA from prenoplastic mammary gland that is adjacent to erbB2-induced tumor/ part of a 14 genechip exp comparing tumors, preneoplastic neu mammary gland (adjacent neu), and age-matched, wild-type control mammary glands to identify early events of erbB2/neu-induced tumorigenesis
Keywords = transgenic mouse
Keywords = MMTV-neu
Keywords = erbB2
Keywords = HER2
Keywords = mammary tumor
Lot batch = 2001815

preneoplastic MMTV-neu mammary gland that surrounds a MMTV-neu-induced tumor

pooled RNA from mammary glands from 5 control mice/ part of a 14 genechip exp comparing tumors, preneoplastic neu mammary gland (adjacent neu), and age-matched, wild-type control mammary glands to identify early events of erbB2/neu-induced tumorigenesis
Lot batch = 2003877

pooled RNA from mammary glands from 5 mice/ part of a 14 genechip exp comparing tumors, preneoplastic neu mammary gland (adjacent neu), and age-matched, wild-type control mammary glands to identify early events of erbB2/neu-induced tumorigenesis

MMTV-neu mouse mammary tumor set B/ the two tumors in set B were part of a second group of tumors which were used to determine whether there was repeated observation of original changes of gene expression/ part of a 14 genechip exp comparing tumors, preneoplastic neu mammary gland (adjacent neu), and age-matched, wild-type control mammary glands to identify early events of erbB2/neu-induced tumorigenesis

Lot batch = 2006609

Lot batch = 2004907

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_1-tu1

CD8 T cells isolated from tumor; transduced with shRNA targeting: Lacz; Sample name: 1-tu1

Prenatal maternal stress daily during E13–E17, restraining the dams in transparent 250 ml glass cylinders filled up to a height of 5 mm with water, bright light exposure, 3 times daily, for 45 min. per session. Control pregnant females were left undisturbed in their home cages.

heterozygous (+/-) 5-HTT knockout mice ([B6.129(Cg)-Slc6a4tm1Kpl/J] (Bengel, Murphy et al. 1998) were used for breeding. The hippocampi of the offspring were examined.

The tissue was homogenized using 500µl PegGOLD RNAPure (Peglab) and metal beads (3 min., 20Hz in a Tissue Lyser (Qiagen)). After that 100µl chloroform was added and centrifuged (5 min., 4°C, 12.000 x g). The water phase was then mixed with 250µl ethanol and from that point on the the protocol of the RNeasy Mini Kit (Qiagen) was followed

Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on a Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station_450

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (IVT-Express Kit, Technical Manual,  Affymetrix).

Gene expression data from left hippocampus of mice offspring of 5HTT+/- parents at P100, several behavioural tests

skeletal muscle;insulin sensitive;untreated;0.81;112;80;1440;99;57.6;38.9;5702.4

Liver removed from 74-day old male rat fed special diet for 53 days. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 10ug of total RNA.
Keywords = rat, liver, vitamin A deficiency

Liver removed from 74-day old male rat fed special diet for 53 days. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 2ug of total RNA.

skeletal muscle;insulin sensitive;untreated;0.86;161;49;1360;52;39.5;2054

We followed manufacturer's protocol, and used GenePix 4000B.
http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf

CodeLink Expression Analysis v5.0 software (Applied Microarrays, Inc.) was used for quantification.
MicroArray Data Analysis Tool (Filgen, Inc.) was used for Normalization.

We followed manufacturer's protocol.

Rpt3 null;mlc1f-Cre/ Rpt3-floxed;female;6weeks;tibialis anterior

LOX-1:121403;GFP_oxLDL_12hr:121403;Classification:Good;Gradient Severity:0.07;Distortion Severity:0.05;Defective Area (%):0;Outlier Area (%):0;3'/5' Mean:1.65;Background Mean Dev.:1.1;Absent (%):59.3;Absent (%) Dev.:0.81;Scaling Factor:0.64;Scaling Factor Dev.:0.23;GFP;12 hours;Oxidized LDL;121403;HAECT;50 ug/ml;Endothelial;Human:Homo sapiens;GFP_oxLDL_12hr;282295763

LOX-1:121401;GFP_oxLDL_12hr:121401;Classification:Good;Gradient Severity:0.03;Distortion Severity:0.03;Defective Area (%):0;Outlier Area (%):0.01;3'/5' Mean:1.85;Background Mean Dev.:0.54;Absent (%):57.11;Absent (%) Dev.:0.89;Scaling Factor:0.53;Scaling Factor Dev.:0.69;GFP;12 hours;Oxidized LDL;121401;HAECT;50 ug/ml;Endothelial;Human:Homo sapiens;GFP_oxLDL_12hr;282295743

LOX-1:213303;LOX1_Untreated_6hr:213303;Classification:Good;Gradient Severity:0.05;Distortion Severity:0.1;Defective Area (%):0;Outlier Area (%):0.01;3'/5' Mean:1.96;Background Mean Dev.:0.14;Absent (%):57.57;Absent (%) Dev.:0.53;Scaling Factor:0.44;Scaling Factor Dev.:1.44;LOX1;6 hours;(Not applicable);213303;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;LOX1_Untreated_6hr;282295673

LOX-1:221203;LOX1_oxLDL_2hr:221203;Classification:Medium;Gradient Severity:0.11;Distortion Severity:0.06;Defective Area (%):0.01;Outlier Area (%):0;3'/5' Mean:1.66;Background Mean Dev.:0.64;Absent (%):60.01;Absent (%) Dev.:1.36;Scaling Factor:0.72;Scaling Factor Dev.:0.89;LOX1;2 hours;Oxidized LDL;221203;HAECT;50 ug/ml;Endothelial;Human:Homo sapiens;LOX1_oxLDL_2hr;282295583

LOX-1:121502;GFP_oxLDL_24hr:121502;Classification:Good;Gradient Severity:0.07;Distortion Severity:0.03;Defective Area (%):0.04;Outlier Area (%):0.01;3'/5' Mean:1.36;Background Mean Dev.:0.79;Absent (%):58.07;Absent (%) Dev.:0.14;Scaling Factor:0.52;Scaling Factor Dev.:0.75;GFP;24 hours;Oxidized LDL;121502;HAECT;50 ug/ml;Endothelial;Human:Homo sapiens;GFP_oxLDL_24hr;282295873

LOX-1:121402;GFP_oxLDL_12hr:121402;Classification:Good;Gradient Severity:0.02;Distortion Severity:0.01;Defective Area (%):0;Outlier Area (%):0;3'/5' Mean:1.58;Background Mean Dev.:0.11;Absent (%):58.13;Absent (%) Dev.:0.09;Scaling Factor:0.69;Scaling Factor Dev.:0.66;GFP;12 hours;Oxidized LDL;121402;HAECT;50 ug/ml;Endothelial;Human:Homo sapiens;GFP_oxLDL_12hr;282295753

LOX-1:213203;LOX1_Untreated_2hr:213203;Classification:Good;Gradient Severity:0.05;Distortion Severity:0.02;Defective Area (%):0.04;Outlier Area (%):0;3'/5' Mean:1.76;Background Mean Dev.:0.44;Absent (%):57.87;Absent (%) Dev.:0.3;Scaling Factor:0.58;Scaling Factor Dev.:0.29;LOX1;2 hours;(Not applicable);213203;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;LOX1_Untreated_2hr;282295553

LOX-1:121501;GFP_oxLDL_24hr:121501;Classification:Medium;Gradient Severity:0.09;Distortion Severity:0.07;Defective Area (%):0;Outlier Area (%):0;3'/5' Mean:1.58;Background Mean Dev.:2.02;Absent (%):59.77;Absent (%) Dev.:1.17;Scaling Factor:0.61;Scaling Factor Dev.:0.04;GFP;24 hours;Oxidized LDL;121501;HAECT;50 ug/ml;Endothelial;Human:Homo sapiens;GFP_oxLDL_24hr;282295863

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Genome Array.

LOX-1:213101;LOX1_0hr:213101;Classification:Good;Gradient Severity:0.04;Distortion Severity:0.02;Defective Area (%):0.02;Outlier Area (%):0.01;3'/5' Mean:1.53;Background Mean Dev.:1.12;Absent (%):58.17;Absent (%) Dev.:0.07;Scaling Factor:0.51;Scaling Factor Dev.:0.89;LOX1;0 hours;(Not applicable);213101;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;LOX1_0hr;282295443

LOX-1:113102;GFP_0hr:113102;Classification:Medium;Gradient Severity:0.04;Distortion Severity:0.08;Defective Area (%):0;Outlier Area (%):0;3'/5' Mean:1.62;Background Mean Dev.:0.83;Absent (%):60.38;Absent (%) Dev.:1.65;Scaling Factor:0.75;Scaling Factor Dev.:1.2;GFP;0 hours;(Not applicable);113102;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;GFP_0hr;282295423

Alveolar type 2 cells were isolated using an immunoabsorption technique.

Male Spargue Dawley rats were fed the liquid Lieber-DeCarlie diet containg EtOH for 6 wk or an isocaloric control diet without EtOH.

Mouse Genome 430 2.0 GeneChips were scanned using the Affymetrix 3000 scanner/AGCC.

Biotinylation of RNA was completed as described in the Affymetrix user manual.

Sprague Dawley;male;Lieber-DeCarlie diet containg EtOH for 6 wk;Alcohol ingestion;Alveolar type 2 cells

Expression values were generated using the microarray suite (MAS) v5.0 software (Affymetrix, Inc)

Total RNA was isolated as recommended (RNeasy, Qiagen, Valencia, CA), except that tissue was treated with proteinase K (20 mg/ml) for 20 minutes at 55°C.

The resultant biotinylated cRNA was fragmented then hybridized to the GeneChip Mouse Genome 430 2.0 Array (45,000 probe sets used to analyze over 39,000 mouse transcripts and variants from over 34,000 well-characterized mouse genes; Affymetrix, Inc.).  The arrays were washed and stained using the Affymetrix Model 450 Fluidics Station

Five micrograms of total RNA was processed for use on the microarray by using the Affymetrix GeneChip one-cycle target labeling kit (Affymetrix, Inc., Santa Clara, CA) according to the manufacturer’s recommended protocols

mixed genetic backgroud of C57Bl/6 and 129/SvJ;IRF6 null;Embryonic day 17.5

mixed genetic backgroud of C57Bl/6 and 129/SvJ;IRF6 wt;Embryonic day 17.5

Exposures of 24 hours in duration were initiated once flasks were 90 ± 10% confluent using the test chemicals NiCl2, CdCl2, and Na2Cr2O7.

H4-II-E-C3 cells (ATCC, Manassas, VA) were grown in Dulbecco's Modified Eagle's Medium (DMEM; Lonza,Walkersville, MD) containing 10% fetal bovine serum (Invitrogen, Carlsbad, CA) and 10 mL Glutamax (Invitrogen) in T75 flasks incubated at 37 °C with 5% carbon dioxide.

Microarray data was processed for background adjustment, normalization, and summarization using the Robust Multi-Array Averaging method (RMA) using Partek Genomic Suite (GS) software (Version 6.4 Copyright 2009, St. Louis, MO)

Samples were hybridized on the GeneChip Rat Genome 230 2.0 Array using Affymetrix instrumentation according to the manufacturer’s instructions

Mice were given a single dose of 1000 µg/kg TCDD or corn oil vehicle by gavage. TCDD initially was dissolved in ether and added to corn oil; the ether subsequently was evaporated off. TCDD was purchased from the UFA-Oil Institute (Ufa, Russia) and was >99% pure as determined by gas chromatography-mass spectrometry.

Male Ahr–/– mice (10 weeks old) in a C57BL/6J background were obtained from The Jackson Laboratory (Bar Harbor, ME). Wild-type (Ahr+/+) male C57BL/6J mice (15 weeks old) were bred at the National Public Health Institute (Kuopio, Finland) from stock originally obtained from The Jackson Laboratory.

Array data were loaded into the R statistical package (version 2.0.0) using the affy package (version 1.5.8; http://www.bioconductor.org) (Gautier et al., 2004) of the BioConductor open-source project (Gentleman et al., 2004). Data were investigated for spatial and distributional homogeneity, then preprocessed with a sequence-specific version of the RMA algorithm (Irizarry et al., 2003) termed GCRMA, as implemented in BioConductor (version 1.1.3).

Liver was harvested 19 h after treatment, sliced, snap-frozen, and stored in liquid nitrogen until homogenization. Total RNA was extracted using RNeasy kits (QIAGEN, Valencia, CA) according to the manufacturer's instructions. DNase (QIAGEN) was added to the RNeasy elution column as recommended by the manufacturer. RNA yield was quantified by UV spectrophotometry, and RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

CD34 selected cells from G-CSF mobilized PBSC;Unknown Age and Gender

Sample is C57/Bl6 murine liver RNA extract after mock infection with 200ul if PBS at 6 hpi.

C57/BL6 murine Liver RNA- 6 hours post-injection with 200ul PBS (Mock).;Murine Universal RNA (Stratagene, La Jolla, CA) which is a mixture of RNA from 10 control cell lines approximating the expression profile of the majority of murine genes was used.

C57/BL6 murine Liver RNA- 6 hours post-injection with 200ul PBS (Mock);Murine Universal RNA (Stratagene, La Jolla, CA) which is a mixture of RNA from 10 control cell lines approximating the expression profile of the majority of murine genes was used

human immortalized mesenchymal stem cells;control;5 days osteoblast differentiation

human immortalized mesenchymal stem cells;control;2 days osteoblast differentiation

human immortalized mesenchymal stem cells;control;undifferentiated

CD4+CD8+ double positive thymocytes were treated with medium and Dexamethasone (final concentration 1E-07 M) in PBS for 3 hours

CD4+CD8+ double positive thymocytes were plated in 6 well plates  with 3 ml of the  culture  medium at a concentration of 5.0 E+06 cell/ml and kept at 37°C , 5%CO2 in a humidified atmosphere for 3 hours

Thymi from 4 week old C3H/HeN mice were teased in culture medium, CD4+CD8+ double positive (DP) thymocytes were sorted with microbeads Miltenyi Biotech methods and were plated in 6 well plates with 3 ml of the culture medium at a concentration of 5.0E+06 cell/ml together with 1E-07 M Dexamethasone or a corresponding volume of PBS. DP thymocytes were kept at 37°C, 5% CO2 in a humidified atmosphere for 3 hours

CD4+CD8+ double positive (DP) thymocytes 3h Dexamethasone(DEX) (final concentration 1E-07 M) treated

CD4+CD8+ double positive thymocytes were plated in 6 well plates  with 3 ml of the  culture  medium at a concentration of 5.0E+06 cell/ml and kept at 37°C , 5% CO2 in a humidified atmosphere for 3 hours

Gene expression data from  primary HCL cell of  patient E treated with DMSO for 72h
ET43

Gene expression data from  primary HCL cell of  patient E treated with Vemurafenib 1000 nM for 72h
ET44

peripheral blood;primary leukemic cells;patient E;Vemurafenib 1000 nM for 72h

Gene expression data from  primary HCL cell of  patient F treated with DMSO for 48h
ET45

Gene expression data from  primary HCL cell of  patient F treated with Vemurafenib 1000 nM for 48h
ET46

peripheral blood;primary leukemic cells;patient F;Vemurafenib 1000 nM for 48h

Gene expression data from  primary HCL cell of  patient F treated with DMSO for 72h
ET47

Gene expression data from  primary HCL cell of  patient F treated with Vemurafenib 1000 nM for 72h
ET48

peripheral blood;primary leukemic cells;patient F;Vemurafenib 1000 nM for 72h

gastrocnemius-5 months of age-control diet-biological replicate5

allergic asthma, post ICS treatment
not the same patient - same phenotype
DV020808HGA11.CEL

The hybridized arrays were washed, stained and scanned in accordance with the appropriate Nugen and Affymetrix guide lines.

Microarray data in CEL format were analysed using GeneSpring GX11 program. Robust Multi-Array Analysis (RMA) Summarization Algorithm was used for normalisation. Baseline was transformed to Median of all samples. Both 'Raw signal values' and 'Normalized signal values' were exported as text files.

Total RNA was prepared using the Stratagene MicroRNA kit as per manufacturer’s instructions with the exception that DNase treatment was extended to 30 minutes and RNAs were resuspended in RNase-free water.

7 ug of biotin-labeled cell extract was hybridized to Affymetrix Mouse Genome 430_2 GeneChips (representing approximately 39,000 transcripts) for a period of 20 hours. The relative level of hybridization to the GeneChip was assessed using the Affymetrix hybridization controls.

5ng of total RNA in conjunction with the Nugen Ovation V2 amplification system (www.nugeninc.com) was used for preparation of the biotin-labeled cell extract. The efficacy of conversion of total RNA to labeled cDNA was monitored by the inclusion of Affymetrix polyA controls (www.affymetrix.com).

260;asacol 800mg TDS Asprin coproxamol;1/1/54;F;CAUCASIAN;1/1/79;1/1/79;FALSE;TRUE;FALSE;NO;FALSE;FALSE;6/9/05;12;0;0;0;0;0;0;0;TRUE;0;BOTH;unknown;unknown;unknown;unknown;6/9/05;BOTH;BOTH;BOTH;unknown;unknown;8/15/05;DISEASE IN REMISSION;current;5-14;Arthritis Depression Alcohol excess;UC;11-15-01;descending colon;Inflamed;total RNA from 10 human cell lines

260;asacol 800mg TDS Asprin coproxamol;1/1/54;F;CAUCASIAN;1/1/79;1/1/79;FALSE;TRUE;FALSE;NO;FALSE;FALSE;6/9/05;12;0;0;0;0;0;0;0;TRUE;0;BOTH;unknown;unknown;unknown;unknown;6/9/05;BOTH;BOTH;BOTH;unknown;unknown;8/15/05;DISEASE IN REMISSION;current;5-14;Arthritis Depression Alcohol excess;UC;11-15-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

249;Azathioprine 150mg Salazopyrine;1/12/60;M;CAUCASIAN;3/1/90;3/24/90;FALSE;FALSE;FALSE;YES;FALSE;FALSE;4/8/05;3;0;0;0;0;0;0;0;FALSE;0;12;12;12;12;12;11;11;11;12;BOTH;BOTH;BOTH;BOTH;BOTH;4/8/05;BOTH;BOTH;BOTH;BOTH;BOTH;5/30/05;FAILURE OF THERAPY;never;unknown;None;UC;11-15-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

260;asacol 800mg TDS Asprin coproxamol;1/1/54;F;CAUCASIAN;1/1/79;1/1/79;FALSE;TRUE;FALSE;NO;FALSE;FALSE;6/9/05;12;0;0;0;0;0;0;0;TRUE;0;BOTH;unknown;unknown;unknown;unknown;6/9/05;BOTH;BOTH;BOTH;unknown;unknown;8/15/05;DISEASE IN REMISSION;current;5-14;Arthritis Depression Alcohol excess;UC;11-15-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

266;Prednisolone ciproxin mesalazine fosomax Fe SO4;8/12/40;F;CAUCASIAN;1/1/93;1/1/93;FALSE;FALSE;FALSE;NO;FALSE;FALSE;7/22/05;6;700;0;20;93;17;16;23;FALSE;0;0;11;11;11;11;11;11;11;11;BOTH;BOTH;BOTH;BOTH;BOTH;7/22/05;BOTH;BOTH;BOTH;BOTH;BOTH;8/15/05;FAILURE OF THERAPY;never;unknown;COPD-Previous severe pneumonia;UC;11-15-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

262;Asacol 2.4g co-codamol;7/17/43;F;CAUCASIAN;1/1/87;1/1/87;FALSE;FALSE;FALSE;YES;TRUE;FALSE;7/5/05;6;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;unknown;unknown;unknown;7/5/05;BOTH;BOTH;unknown;unknown;unknown;8/15/05;FAILURE OF THERAPY;never;unknown;none;UC;11-15-01;descending colon;Inflamed;total RNA from 10 human cell lines

262;Asacol 2.4g co-codamol;7/17/43;F;CAUCASIAN;1/1/87;1/1/87;FALSE;FALSE;FALSE;YES;TRUE;FALSE;7/5/05;6;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;unknown;unknown;unknown;7/5/05;BOTH;BOTH;unknown;unknown;unknown;8/15/05;FAILURE OF THERAPY;never;unknown;none;UC;11-15-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

Quality control and background normalization were performed using Refiner from Genedata AG (Basel, Switzerland). All arrays were condensed together using the GC-RMA algorithm with quantile normalization composed of 100 bins using Genedata’s Refiner application. Per chip normalization was performed by scaling the median of the genes called present (detection p-value < 0.04) to a value of 500. Per chip normalized data are referred to as “raw” expression values.

20 µg of biotinylated cRNA was fragmented by heating in the presence of Mg2+ (as per Affymetrix’s instructions) and 15 µg of fragmented cRNA was hybridized to Mouse MOE430 v2.0 GeneChips™

cRNA was produced by in vitro transcription (IVT) by T7 RNA polymerase, using the Affymetrix IVT kit as per manufacturer’s instructions.

GCRMA (Wu et al. Journal of the American Statistical Association, 2004 vol 99 page 909)

Y HID_B002

Y HID_B003

Y YOKE_B022

Control Lacrimal Gland ipsilateral to the Experimental Side-7 days after greater superficial petrosal nerve sectioning.

Rats were sacrificed twelve hours after the injection with methylprednisolone

Rats were sacrificed immediately after the injection with methylprednisolone

Rats were sacrificed 15 minutes after the injection with methylprednisolone

Lot batch = Joslin core 1523

signal intensity values for each probe set derived from the Affymetrix Microarray Analysis Suite (v5.0) software; noralized to target value of 150

500 nM tamoxifen ((Z)-4-hydroxytamoxifen) was added to induce recombination as noted

Mouse ES cells were maintained without feeders on gelatinized tissue culture plates in ‘‘knock-out’’ DMEM supplemented with 20% FBS, 2 mM L-glutamine, 100 U/ml Penicillin, 100 lg/ml Streptomycin, 0.14 mM b-mercapto-ethanol, 0.1 mM non-essential amino acids, LIF (1000 U/ml ‘‘ESGRO’’)

GeneChips were scanned using the Affymetrix GeneChip 7G Plus Scanner

The R/Bioconductor Limma open-source software was used to analyze microarray data

ES cells were lysed in QIAGEN Buffer RLT, homogenized using QIAshredder and total RNA was purified using QIAGEN RNeasy Mini spin columns according to manufacturer's instructions

The Affymetrix GeneChip Hybridization, Wash, and Stain Kit was used according to manufacturer's instructions in combination with Molecular Probes Streptavidin R-phycoerythrin conjugate (SAPE)

Biotinylated cRNA was prepared using the Affymetrix GeneChip 3’ IVT Express Kit according to manufacturer's instructions

C57BL/6-129Sv hybrid background;Setdb1 2lox/1lox/Cre;tamoxifen;embryonic stem cell

Gene expression data under ER stress from lymphoblastoid cells of individual GM07055 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM07034 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM07034 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM07022 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM07022 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM07000 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM07000 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM06994 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM07056 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM07055 treated with DMSO 8 hours.

Otic vesicles were directly transferred into 1ml of TRIZOL. The 2B1 cell line was allowed to proliferate at 32oC in the presence of gamma-interferon to a confluency of 70-80% and then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.

Otic vesicles from wild-type and Dlx5-null embryos were microdissected from mouse developmental stages E10 and E10.5 in ice-cold PBS (calcium and magnesium free). These were timed-pregnancies determined by a vaginal plug, and each embryo was staged independently in a litter by the number of somites. Once the vesicles were isolated as cleanly as possible from the embryos, they were placed in 1mg/ml solution of dispase dissolved in PBS (calcium and magnesium free) for 10-15 minutes on ice to facilitate the removal of closely attached mesenchyme. For each stage and genotype two biological replicates were collected, each comprising between 4 and 8 otic vesicles. For the 2B1 cell line, two independent cultures were used for both the empty vector-transfected and the Dlx5- transfected samples. Cells were grown in chick embryo fibroblast medium at 32oC to a confluency of 70-80% in the presence of gamma-interferon, then transfected and shifted to 37oC with no gamma-interferon to induce differentiation for 4 days after which total RNA was isolated.

Analysis was carried out in Expression Console software (Affymetrix) by employing the Robust Multichip Analysis (RMA) algorithm. All normalized (log-base-2) expression values below 5.5 were considered ‘Absent’. For cell line microarray data the cut-off for making ‘Present’ calls was set to 4.8 since this was the expression of Dlx5 in Dlx5-transfected cells.

Fragmentation of cRNA was carried out following the standard Affymetrix procedure, and 10ug of fragmented cRNA from each sample was hybridized to the Mouse Genome 430 2.0 gene chips for 16-18 hours at 45oC.

To synthesize biotin-labeled target (cRNA) for hybridization to Affymetrix arrays, 22ul of the purified cDNA were used as template in in-vitro transcription reactions using the BioArray HighYield RNA Transcript Labeling Kit (ENZO Life Sciences, NY). Besides the template cDNA, all other components were added following the instructions provided by the manufacturer, and reactions were incubated at 37oC for 10 hours on the PCR machine mentioned above under 'extract protocol'. Labeled cRNA was purified using an RNA purification kit (Qiagen) following the manufacturer’s instructions and eluted in 50ul of water.

Gene-expression profiling of three biological replicates was performed at day 4 during the differentiation process of WT J1 ESCs (3 samples). Samples were analyzed using mouse Genome 430-2 arrays (Affymetrix).

129-Sv;J1;embryonic stem;4 days;differentiated Flk1+ WT ES cells

K562 cell line was mock treated.  RNA was extracted using Trizol plus Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA and included suggested level of Affymetrix RNA spike contols.

Gene-expression profiling of three biological replicates was performed at day 6 during the differentiation process of WT J1 ESCs (3 samples). Samples were analyzed using mouse Genome 430-2 arrays (Affymetrix).

129-Sv;J1;embryonic stem;6 days;differentiated Flk1+ WT ES cells

Gene-expression profiling of three biological replicates was performed at day 5 during the differentiation process of WT J1 ESCs (3 samples). Samples were analyzed using mouse Genome 430-2 arrays (Affymetrix).

129-Sv;J1;embryonic stem;5 days;differentiated Flk1+ WT ES cells

2B1 Otic vesicle cell line transiently transfected with an empty vector only containing GFP and differentiated for 4 days at 37oC without gamma-interferon, replicate1

JLI_40

JLI_41

JLI_36

JLI_37

JLI_38

JLI_39

JLI_24

JLI_29

JLI_30

JLI_35

Expression profiles generated from the gastrocnemicus and soleus muscles from wild type control mice for integirn alpha7 transgenic mice

control mouse for integrin alpha7 overexpressing;SJ6/C57BL6 background;wild type;Female;5 week;gastrocnemius and soleus muscle;non-fasted

Wt Mouse_cerebellum_Old_nicotinamide riboside treatment_Replicate-2

Sample name: OLD-Wt_NR-21

Wt Mouse_cerebellum_Old_nicotinamide riboside treatment_Replicate-3

Sample name: OLD-Wt_NR-25

Gene expression data from unstimulated Tregs from a healthy control

MS-2

Csbm/m Mouse_cerebellum_Young_nicotinamide riboside treatment_Replicate-1

Sample name: YOUNG-CSB_NR-1

C57BL/6;Csbm/m;male;cerebellum;4 months;daily injections of NR (500 mg/kg/d, ip) for one week

Csbm/m mouse, cerebellum, young, nicotinamide riboside treatment

Csbm/m Mouse_cerebellum_Young_nicotinamide riboside treatment_Replicate-2

Sample name: YOUNG-CSB_NR-11

C4MKOS1015

C2MKOS413

B1RKOS1306

A5WTS1805

WT C57BL/6 mice, liver, 10-12 weeks old, sacrificed 2 hours after 85% liver resection

B3RKOS1508

Sample name: YOUNG-CSB_ctrl-12

C57BL/6;Csbm/m;male;cerebellum;4 months;daily injections of saline for one week

B5RKOS1710

B4RKOS1609

B6RKOS1911

Sample name: YOUNG-CSB_ctrl-8

Cre expression by the MHCalpha transgene leading to Gata4-flox or Gata6-flox gene deletion during late cardiac development.

Six-ten week old mice were used for all experiments, and were housed under pathogen-free conditions.

Expression values were subjected to RMA normalization using Affymetrix CDF probeset definition and GeneSpringGX v7.3.1.
Relative expression levels for each probeset was calculated in reference to the median of its value in Gata4Flox and Gata6Flox non-CRE control samples. These data are on the Series record.

Harvested hearts were homogenized in Trizol and RNA from homogenates was isolated via ethanol precipitation.

total heart mRNA gene expression as a function of Gata4 or Gata6 knockout

All cells were routinely cultured in DMEM plus 10% FBS (Hyclone). For selection, count cells and plate 5x105/10cm, add 150ug/ml Hygromycin for 2~3days. Repeat the selection one more time.

total RNA from Runx1 knockout mouse embryo, stage E8.5
Keywords = RUNX1, AML1, transcription, knockout, network, mouse

total RNA from wild-type mouse embryo, stage E8.5

Brown preadipocyte cell lines derived from newborn IRS-4 KO mice. Preadipocytes were grown to confluence (day 0) in differentiation medium (Dulbeco’s modified Earle’s medium containing 10% fetal bovine serum supplemented with 20 nM insulin and 1 nM T3). Brown preadipocytes were synchronized by overnight serum starvation. Total RNA was isolated with ULTRASPEC RNA Isolation System (Biotecx Laboratories, Inc., Houston, TX) following the manufacture’s instruction. 28 ug of total RNA were subjected to cDNA and cRNA preparations as previously described. 15 ug of adjusted cRNA were hybridised to Affymetrix U74A-v2 arrays (Santa Clara, CA). Intensity values were quantitated by MAS 5.0 software (Affymetrix). All chips were subjected to global scaling to a target intensity of 1,500 to take into account the inherent differences between the chips and their hybridization efficiencies.
Lot batch = Joslin core 1529

The ligature for aortic banding was sized by tying around a 27 gauge needle. The ligature was placed on the transverse aorta between the brachiocephalic trunk and the left common carotid artery. The identical procedure was used for sham operation, except that the aorta was not manipulated.

An important event in the pathogenesis of heart failure is the development of pathological cardiac hypertrophy. In cultured cardiac cardiomyocytes, the transcription factor Gata4 is required for agonist-induced cardiomyocyte hypertrophy. We hypothesized that in the intact organism Gata4 is an important regulator of postnatal heart function and of the hypertrophic response of the heart to pathological stress. To test
this hypothesis, we studied mice heterozygous for deletion of the second exon of Gata4 (G4D). At baseline, G4D mice had mild systolic and diastolic dysfunction associated with reduced heart weight and decreased cardiomyocyte number. After transverse aortic constriction (TAC), G4D mice developed overt heart failure and eccentric cardiac
hypertrophy, associated with significantly increased fibrosis and cardiomyocyte apoptosis. Inhibition of apoptosis by overexpression of the insulin-like growth factor 1 receptor prevented TAC-induced heart failure in G4D mice. Unlike WT-TAC controls, G4D-TAC cardiomyocytes hypertrophied by increasing in length more than width. Gene expression profiling revealed upregulation of genes associated with apoptosis and
fibrosis, including members of the TGFβ pathway. Our data demonstrate that Gata4 is essential for cardiac function in the postnatal heart. After pressure overload, Gata4 regulates the pattern of cardiomyocyte hypertrophy and protects the heart from loadinduced failure.

This allele contains a deletion of the second coding exon of Gata4, including the start codon and the Nterminal 46% of the coding region. The mice used in this study were all male and on a uniform F1 genetic background resulting from the cross of Gata4WT/Δex2 (abbreviated;G4D) mice, backcrossed for greater than 8 generations into C57BL6/J, to wild-type FVB/N mice. G4D progeny from this cross were present at weaning at the expected Mendelian ratio (104/218, 48%), survived normally to 18 months of age, and had no evidence of structural heart disease (0 out of 15 embryos examined histologically at E15.5-E18.5). Gata4WT/WT littermates (WT) from these crosses were used as controls.

Crohn's Disease subject (41 year old caucasian female, SAK_1277825109)

Crohn's Disease subject (21 year old caucasian male, SAK_1260634232)

Subject Age : 21

Crohn's Disease subject (47 year old caucasian male, SAK_1263137700)

Subject Age : 47

Crohn's Disease subject (56 year old caucasian male, SAK_1260008280)

Crohn's Disease subject (29 year old caucasian female, SAK_1280865117)

Subject Age : 29

in vivo Treatment: MEHP, Treatment Duration: 6, Units of Duration: hours, Treatment Time: 10:10, Units of Treatment Time: am, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.29, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg body weight

KJ_1_6_33_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

Crohn's Disease subject (33 year old caucasian male, SAK_1288174788)

Crohn's Disease subject (64 year old caucasian female, SAK_1260745997)

Subject Age : 64

Levitiracetam brainstem 2

Levitiracetam brainstem 1

Crohn's Disease subject (43 year old black male, SAK_1287548671)

Crohn's Disease subject (47 year old caucasian female, SAK_1280820411)

Phenytoin hippocampus 5

Phenytoin hippocampus 4

Phenytoin hippocampus 3

Phenytoin hippocampus 2

Tissue transferred into RNAlater within 30 minutes of removal, and frozen at -20C

Tissue transferred into RNAlater within 30 minutes of removal, and frozen at -20C.

Total RNA was obtained using the miRNeasy kit (Quiagen) according to the manufacturer’s instructions.

C1_24h_48
Gene expression data from rat tracheal explants exposed to air (control) at 24hrs.

Firstly, ATM-KO and ATM-WT were irradiated at 4.32 Gy, and their cultures were incubated for 72 hours at 37 ºC in a humidified incubator with 5% CO2.

Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides, (Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

The scanned images were analyzed with Feature Extraction Software 11.0 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

RNA was prepared using Trizol (Invitrogene) following the manufacturer's recommendations.  The RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 40°C for 120 minutes in a reaction volume of 100 ml containing 1x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 ug RNA using the Quickamp lebeling kit (Agilent) according to the manufacturer's instructions (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

Filter	570

Protocol	Midi_euk2v3_450
Wash A1 Temperature (C)	30
Number of Wash B Cycles	6
Stain Temperature (C)	35
First Stain Time (seconds)	300
Wash A2 Temperature (C)	30
Second Stain Time (seconds)	300
Third Stain Time (seconds)	300
Wash A3 Temperature (C)	35
Station	1
Module	3
Hybridize Date	Dec 16 2005 11:10AM

Station	1
Module	1
Hybridize Date	Dec 22 2005 11:26AM

Peripheral blood mononuclear cells;TTF=85min;Race=White;Sex=Male

Peripheral blood mononuclear cells;TTF=119min;Race=White;Sex=Male

Peripheral blood mononuclear cells;TTF=105min;Race=White;Sex=Male

Peripheral blood mononuclear cells;TTF=135min;Race=White;Sex=Male

Peripheral blood mononuclear cells;TTF=110min;Race=White;Sex=Male

Peripheral blood mononuclear cells;TTF=125min;Race=White;Sex=Male

Peripheral blood mononuclear cells;TTF=137min;Race=White;Sex=Male

MLL_00261;PBMC;Multilineage dysplasia, acute myeloid leukemia, biallelic

MLL_00230;PBMC;Multilineage dysplasia, acute myeloid leukemia, biallelic

MLL_00255;PBMC;Multilineage dysplasia, acute myeloid leukemia, biallelic

MLL_00252;PBMC;Multilineage dysplasia, acute myeloid leukemia, biallelic

MLL_00248;PBMC;Multilineage dysplasia, acute myeloid leukemia, biallelic

MLL_00235;PBMC;Multilineage dysplasia, acute myeloid leukemia, biallelic

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20585.gif
name: 20585_Infection

Common Reference 2 round amplification 2 ug;Mening UNSTIM WB NP 0a

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20587.gif
name: 20587_Infection

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20584.gif
name: 20584_Infection

Common Reference 2 round amplification 2 ug;Mening UNSTIM WB NP 6b

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20568.gif
name: 20568_Infection

Common Reference 2 round amplification 2 ug;Mening UNSTIM WB NP 12a

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20567.gif
name: 20567_Infection

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20583.gif
name: 20583_Infection

Common Reference 2 round amplification 2 ug;Mening UNSTIM WB NP 6a

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20566.gif
name: 20566_Infection

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20582.gif
name: 20582_Infection

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20588.gif
name: 20588_Infection

Common Reference 2 round amplification 2 ug;Mening UNSTIM WB NP 1a

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20589.gif
name: 20589_Infection

Common Reference 2 round amplification 2 ug;Mening UNSTIM WB NP 1b

The images generated in the scanning were acquired to make the .DAT files, which in turn were converted to probe-intensity coordinated .CEL files, using the GCOS software package (Affymetrix).

Isolation of total RNA was performed using RNeasy spin columns according to the manufacturer's protocol (Qiagen).

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the EukGE-WS2v5 fluidics protocol.

Affymetrix p/n 900493 GeneChip® Expression 3' Amplification One-Cycle Target Labeling and Control Reagents.

non-neoplastic salivary gland;submandibular salivary gland;unknown

liver from a 42 day old male mouse, mutant 569 was dissected out. Total RNA was extracted using an Ambion RNaqueous RNA extraction kit. Targets were produced using modified Affymetrix procedure from 5ug of total RNA. 3 biological replicates were analysed per each group of animals.Sample also known as A3.

Gene expression analysis of the kidney of mouse treated with 7 repeat daily doses of vancomycin at 400 mg/kg administered via the intraperitoneal route (ip)

Kidney from mice treated with 7 daily ip injections of vancomycin at 400 mg/kg

primary unilateral non-metastatic postmenopausal ERα-positive breast tumor;woman;75 years

primary unilateral non-metastatic postmenopausal ERα-positive breast tumor;woman;78 years

primary unilateral non-metastatic postmenopausal ERα-positive breast tumor;woman;79 years

primary unilateral non-metastatic postmenopausal ERα-positive breast tumor;woman;61 years

primary unilateral non-metastatic postmenopausal ERα-positive breast tumor;woman;71 years

Slides were scanned with an Agilent DNA Microarray Scanner model G2539.

Total RNA was extracted from liver tissues using Isogen (Nippon Gene).

1.65 ug of Cy3-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 16 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing.

500 ng of total RNA was amplified and labeled using the Quick Amp Labeling kit (Agilent Technologies) according to the manufacturer's protocol.

Agilent Feature Extraction file: Liver_Keap1 KD_rep3.txt
Gene expression in the liver of  Keap1 KD mice_rep3.

18B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

Agilent Feature Extraction file: Liver_Keap1 KD_rep2.txt
Gene expression in the liver of  Keap1 KD mice_rep2.

S100a10 cells, p11 KO, cortex, TRAP RNA, VEH treated, biological rep2

Gene expression data from the Pre-Frontal contex of naïve FVB/N mice

Gene expression data from the Pre-Frontal contex of naïve AChE-S mice

Gene expression data from the Pre-Frontal contex of MPTP-exposed FVB/N mice

Gene expression data from the Pre-Frontal contex of MPTP-exposed AChE-R mice

Data were analyzed in R and analyzed using variance stabilizing normalization and model based index calculation (MBEI)

Total RNA was extracted from muscle biopsies using the TRIzol protocol including an extra phenol-chloroform step

total RNA was converted to amplified RNA (aRNA) and fragmented using the MessageAmpTM III RNA amplification kit

patients with a mutation (Arg1174Gln) in the tyrosine kinase domain of the insulin receptor gene (INSR);Vastus lateralis muscle;basal state

robust multi-array analysis (RMA) algorithm using BioConductor software

WT and VAChT KD mice were aged to 3 months of age before hearts were excised for RNA extraction.

The data were analyzed with Partek Genomcis Suite using the RMA normalization method

RNA was extracted using the Fatty and Fibrous Tissue RNA Extraction Kit (Bio-rad)

5.5 ug of single stranded cDNA was hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotin end labeled single strand cDNA was prepared according to the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual

non tumorigenic human breast epithelial MCF10A cell line: Vehicle_rep3

non tumorigenic human breast epithelial MCF10A cell line: Vehicle_rep2

non tumorigenic human breast epithelial MCF10A cell line: Vehicle_rep1

Pathohistological and clinical examination of Patient NC08 (27 year-old female) yielded no significant pathological findings.  This patient was considered as a normal control for the purposes of the study.

Pathohistological and clinical examination of Patient NC09 (76 year-old female) yielded no significant pathological findings.  This patient was considered as a normal control for the purposes of the study.

Pathohistological and clinical examination of Patient NC06 (57 year-old female) yielded no significant pathological findings.  This patient was considered as a normal control for the purposes of the study.

Pathohistological and clinical examination of Patient NC07 (84 year-old female) yielded no significant pathological findings.  This patient was considered as a normal control for the purposes of the study.

Pathohistological and clinical examination of Patient CD01 (20 year-old male) yielded to diagnosis of Crohn's disease.
Prior to each hybridization reaction, unused filters were initially washed in 1 X SSC; 0.1% SDS at room temperature for 10 min (X 2) followed by three washes in 0.1 X SSC; 0.1% SDS for 20 min at 80°C.  These washes eliminated the potential problem for unbound or loosely bound probe cDNA from interfering with the hybridization reaction.  Each cDNA filter was pre-wetted with deionized water and placed in a hybridization bottle (3.5 X 25 cm).  The water was completely poured off and the filter was pre-hybridized for 2 hrs at 50°C in a 10 mL of hybridization solution containing 7% SDS, 50% formamide, 5 X SCC, 2% blocking reagent (Roche Diagnostics), 50mM sodium phosphate (pH 7.0) and denatured herring sperm DNA (50microg/microL).  The labeled target was added to the filters in 5 mL of the same preheated solution and hybridization of the filters was performed overnight (24 hrs) at 42°C.  Following overnight hybridization, membranes were removed from the bottles and washed in 1 X SSC/0.1% SDS buffer for 10 min at room temperature followed by two washes for 30 min in 0.2 X SSC/0.1% SDS at 65°C.  Excess moisture was removed by briefly placing the membranes on filter paper (Whatman) and the damp filters were wrapped in commercial grade plastic wrap.  Filters were exposed ~24 hrs to imaging plates (BAS-MS 2325, Fujifilm, Japan) and scanning was carried out at a resolution of 50microns on a FLA-3000G imaging system (Fujifilm, Japan). After hybridization, filters were individually stripped in a boiling solution of 0.5% SDS for 5 min, taken off the heat and agitated for an additional 3 hrs at room temperature and stored damp wrapped in plastic wrap at –20ºC for 7-8 weeks (half-life of 33P is 25.4 days). Prior to re-use, filters were re-scanned as above to ensure that residual radioactivity was negligible.

Pathohistological and clinical examination of Patient CD02 (38 year-old female) yielded to diagnosis of Crohn's disease.

Pathohistological and clinical examination of Patient NC10 (72 year-old male) yielded no significant pathological findings.  This patient was considered as a normal control for the purposes of the study.

Pathohistological and clinical examination of Patient NC11 (41 year-old female) yielded no significant pathological findings.  This patient was considered as a normal control for the purposes of the study.

Pathohistological and clinical examination of Patient CD03 (19 year-old male) yielded to diagnosis of Crohn's disease.

Pathohistological and clinical examination of Patient CD04 (32 year-old female) yielded to diagnosis of Crohn's disease.

10 week Diabetic cavernosal tissue sample, streptozotocin induced
Keywords = penis cavernosum diabetes

10 week Diabetic cavernosal tissue sample
Streptozotocin induced

C57BL/6;Nrf2 KO;Male;9 weeks;kidney;intraperitoneally injected with a single dose of vehicle (saline)

The GCOS default analysis algorithms and parameters for normalization and transformation were used. There was no scaling done. The default values for the analysis and the details on the algorithms can be found in Appendix F in the Affymetrix GCOS Manual.

Flash frozen samples extracted using Trizol (Invitrogen) as per manufacturer's instructions, further purified using Rneasy Micro Kit (Qiagen) as per manufacturer's instructions

Hybridization is carried out according to the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays.  Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station.  Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.

For each experimental sample, RNA quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100. Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371). In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.

Gene expression data from quadriceps skeletal muscle of 4-5 month old, 18h fasted, WT versus KLF15-null female mice

Gene expression data from liver of 4-5 month old, 18h fasted, WT versus KLF15-null female mice

male mice were acclimatized and caged in groups of six or less at our in house facility. Animals were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.

Fluorescent images were captured using gene Array Scanner 2500 and GCOS1.2 software (Affymetrix)

We have used the GeneChip Robust Multi-array Average expression measurements (GC-RMA) as implemented in BioConductor R statistics (www.bioconductor.org). Cell Intensity files (CEL) were used to obtain expression values for all the 22,690 probe sets (transcripts) on each of these

Total RNA was extracted using Trizol (Invtrogen) and further purified using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.

Fragmented labelled cRNA (15µg) was used in 300µl hybridization cocktail containing spiked controls (Affymetrix #900299). An aliquot of 200µl of this hybridization cocktail was used on each chip which was incubated at 45°C for 16 h in the hybridization oven, rotating at 60 rpm. Following hybridization, the arrays were processed using a Genechip Fluidics Station 400 according to recommended protocols (EukGE-WS2v4, Affymetrix) of double-staining and post-hybridisations washes.

8 microgram total RNA was used in Affymetrix one cycle target labelling kit cat. no. 900493

Here we have addressed important question of changes in the global gene expression profile of mdx mouse muscle compared to normal mouse muscle and compared the data with that obtained from the transgenic line (fiona) expressing high level of utrophin on mdx background.

Male wild-type (C57BL/10SnJ) mice were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.

Skeletal muscle tibialis anterior (TA) from Normal wild-type mice

Cells were transfected with control or ETS2-specific siRNA (siRNA from Dharmacon) using Lipofectamine RNAiMAX reagent from Life Technologies according to the manufacturer's instructions.

H441 cells were cultured with DMEM/F12 in a humidified incubator with 5CO2

Gene chips were scanned using the Affymetrix GeneChip Scanner 3000 7G for subsequent generation of raw data (*CEL files)

Raw expression data were normalized and summarized using the Robust Multichip Analysis (RMA) method along with log2 transformation using the integrated BRB-Array Tools software developed by Dr. Richard Simon and the BRB-Array Tools development team.

Total RNA was isolated 48 hours following transfection using the RNeasy Mini Kit from Qiagen according to the manufacturer's instructions.

2.5 ug of fragmented and labeled cDNA, was generated using the Affymetrix GeneChip® WT Terminal Labeling and Controls Kit, were hybridized onto Human Gene 1.0 ST arrays according to the manufacturer’s instructions (Affymetrix). Hybridization cocktails containing samples, control oligonucleotide and eukaryotic hybridization controls in addition to hybridization mixes, DMSO and nuclease-free water were heat denatured at 99oC for 5 minutes, cooled to 45oC for 5 minutes, and finally centrifuged at maximum speed for 1 minute.   After injecting 80 uL of the hybridization cocktails, arrays were incubated for 17 hours in a hybridization oven set to a temperature of 45oC with 60 rpm rotation.   Arrays were washed, stained and processed using Affymetrix GeneChip Fluidics Station 450 systems

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 ug total RNA (Affymetrix).

Time of RNA isolation after siRNA transfection  is 48 hours
Gene expression of H441 cells transfected with siRNA against the ETS2 gene- biological replicate 3

53 healthy male volunteers received 150 mg Q10H2 daily in form of three softgel capsules with each principal meal (a´ 50 mg) for 14 days.

Based on clinical laboratory tests, all study participants fulfilled the following inclusion criteria: 1) no history of gastrointestinal, hepatic, cardiovascular or renal disease; 2) no supplemental vitamin use for > 2 weeks before the start of the study; 3) non- or occasional smoking (< 3 cigarettes/d); and 4) perpetuation of usual nutrition habits.

Fasting blood samples were taken before (T0) and after (T14) supplementation with Q10H2 from all study participants as well as 4 weeks after study completion (T42, washout period) from 9 subjects, respectively.

15 µg of fragmented cRNA was hybridized to a Human Genome U133+ 2.0 Array for 16 hr at 45 °C at 60 rpm. Arrays were washed on GeneChip®  Fluidics station 450 (Affymetrix) and stained with streptavidin-phycoerythrin

Biotinylated cRNA was prepared with the MessageAmp™ II-Biotin Enhanced Kit (Ambion/Applied Biosystems) according to the manufacturer´s instructions.

Cells lysed in RLT with Beta-2-mercaptoethanol, RNA was extracted using RNeasy-Micro kit (QIAGEN, Valencia, CA).

Cerebellum_transgenic nuclear localization signal Htt exon1 142Q S46_3 months_replicate 4

S46 NLS 142Q TG4	F5/12	S46	NLS Htt exon 1 142Q	Mouse	3.5 months	Cerebellum	Female

Cerebellum_transgenic nuclear exclusion signal Htt exon1 142Q A61_8 months_replicate 4

A61 NES 142Q TG4	F5/1	A61	NES Htt exon 1 142Q	Mouse	8 months	Cerebellum	Male

Cerebellum_transgenic nuclear localization signal Htt exon1 142Q S46_3 months_replicate 3

S46 NLS 142Q TG3	F5/10	S46	NLS Htt exon 1 142Q	Mouse	3.5 months	Cerebellum	Female

Cerebellum_transgenic nuclear localization signal Htt exon1 142Q S46_3 months_replicate 1

S46 NLS 142Q TG1	F5/2	S46	NLS Htt exon 1 142Q	Mouse	3.5 months	Cerebellum	Male

Cerebellum_transgenic nuclear exclusion signal Htt exon1 142Q A39_4 months_replicate 1

A39 NES 142Q TG1	F5/51	A39	NES Htt exon 1 142Q	Mouse	4 months	Cerebellum	Female

0.428571429;exon 11;GIST Tumor;Universal Human Reference RNA (Stratagene)

0.25;exon 11;GIST Tumor;Universal Human Reference RNA (Stratagene)

0.2875;exon 11;GIST Tumor;Universal Human Reference RNA (Stratagene)

Gene expression data under ER stress from lymphoblastoid cells of twin 1744:2 treated with DMSO.

lymphoblastoid cell line;1744;GM14536;Twin number 2;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1744:2 treated with 500nM thapsigargin.

lymphoblastoid cell line;1744;GM14536;Twin number 2;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1757:1 treated with DMSO.

lymphoblastoid cell line;1757;GM14583;Twin number 1;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1757:1 treated with 500nM thapsigargin.

lymphoblastoid cell line;1757;GM14583;Twin number 1;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1743:2 treated with DMSO.

lymphoblastoid cell line;1743;GM14533;Twin number 2;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1743:2 treated with 500nM thapsigargin.

lymphoblastoid cell line;1743;GM14533;Twin number 2;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1744:1 treated with DMSO.

lymphoblastoid cell line;1744;GM14535;Twin number 1;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1744:1 treated with 500nM thapsigargin.

lymphoblastoid cell line;1744;GM14535;Twin number 1;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1757:2 treated with DMSO.

lymphoblastoid cell line;1757;GM14584;Twin number 2;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1757:2 treated with 500nM thapsigargin.

lymphoblastoid cell line;1757;GM14584;Twin number 2;thapsigargin;500nM;4 hours

liver from a 42 day old male mouse, mutant 569 wasdissected out. Total RNA was extracted using an Ambion RNaqueous RNA extraction kit. Targets were produced using modified Affymetrix procedure from 5ug of total RNA. 3 biological replicates were analysed per each group of animals.Sample also known as A2.

IMR-32 was cultured for 24 hours in 6 cm plates and transfected with 5.5 μg siRNA using lipofectamin® according to manufacturers’ protocol. RNA was harvested at 0 hours as a control for untreated cells and at 48 hours after transfection with Cyclin D1, CDK4 or GFP siRNA.The siRNA’s used were targeting Cyclin D1 on nucleotide 671 to 691 according to GenBank accession NM_053056, CDK4 on nucleotide 1062 to 1082 according to GenBank accession NM_000075, and a previously designed siRNA directed against GFP was used as negative control (sense sequence GACCCGCGCCGAGGUGAAGTT).

IMR-32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.

Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix

Neuroblastoma were transfected with Cyclin D1, CDK4 and control siRNA. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profil

Normal bladder cell line 2 treated with mock APF#2. Membrane A is used.

Normal bladder cell line 1 treated with mock APF#2. Membrane A is used.

normal bladder cell line 2 treated with APF#1. Membrane B is used

Normal bladder cell line 2 treated with APF#2. Membrane B is used.

Gene expression data from liver after 20 week feeding of western diet containing 0.05% quercetin

male;BALB/c;liver;Western diet containing 0.05% quercetin for 20 weeks

For transfection, cells were plated in 10cm tissue culture dishes. Next day, medium was replaced with fresh growth media without antibiotics. Cells were transfected with NS siRNA(25nM) or Nrf2 siRNA(25nM) using Lipofectamine 2000 transfection reagent. Ninty six hours post transfection, cells were harvested and total RNA was isolated.

A549 cells were cultured in Dulbecco's Modified Eagle Medium with high glucose, 10% FBS and 1% penicillin/ streptomycin

Each array was scanned with the GeneArray scanner (Agilent Technologies, Palo Alto, CA) to obtain image and signal intensities.

Total RNA was isolated using TRIZOL reagent. RNA was further purified using RNeasy kit from Qiagen, quantified. Quality of RNA was evaluated using Bio-analyzer.

Approximately 12.5 g of fragmented cRNA was used in a 250- l hybridization mixture containing herring sperm DNA (0.1 mg/ml; Promega Corp., Madison, WI), plus bacterial and phage cRNA controls (1.5 pmol of BioB, 5 pmol of BioC, 25 pmol of BioD, and 100 pmol of Cre) to serve as internal controls for hybridization efficiency as directed by the manufacturer (Affymetrix). Aliquots (200 l) of the mixture were hybridized onto the array for 18 h at 45°C in a GeneChip Hybridization Oven 640 (Affymetrix)

Briefly, double-stranded cDNA was synthesized from 15 g of total RNA with SuperScript Choice System (Invitrogen) by using oligo(dT)24 primers with a T7 RNA polymerase promoter site added to its 3 end (Genset Corp., La Jolla, CA). The isolated cDNA was then labeled to generate biotinylated cRNA in vitro and amplified using the BioArray T7 RNA polymerase labeling kit (Enzo, Farmingdale, NY).

Gene expression data from A549 cells treated with Transfection reagent alone

Gene expression data from A549 cells transfected with non-targeting NS siRNA (control siRNA)

Human lung adenocarcinoma cells_Non targeting (NS) siRNA transfected

For tumor inoculation, 1 x 10E6 C26 cells in 100 μl RPMI/PS were subcutaneously inoculated in the upper right flank of the mice.  Non-tumor-bearing (NTB) control mice were injected with 100 μl RPMI/PS. Whole gastrocnemius muscle and heart were extracted from separate cohorts of mice, snap-frozen in liquid nitrogen and stored at -80°C until further processing.

C26 carcinoma cells (Amgen Inc., Thousand Oaks, California) were maintained in RPMI/Penicillin Streptomycin PS in a humidified atmosphere with 5% CO2 at 37°C.

Data were collected using the GeneChip operating software (GCOS) v1.4 (Affymetrix, Santa Clara, CA, USA). Probe summarization and quantile normalization of log2 probe intensities using RMA were conducted with the use of Partek® Genomics Suite™ version 6.6 software (Partek, St. Louis, MO, USA) .
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm8.mps

Frozen gastrocnemius and cardiac muscles were homogenized in TRIzol® reagent for the extraction of total RNA according to the manufacturer’s protocol (Invitrogen, Carlsbad, CA, USA).

According to the manufacturer’s protocol, Ambion® WT reagent kit (Life Technologies™, Carlsbad, CA, USA)

250ng of total RNA from each sample were submitted to cDNA synthesis, biotin labeling, cDNA fragmentation, and hybridization with microarray probes using the Ambion® WT reagent kit (Life Technologies™, Carlsbad, CA, USA) according to the manufacturer’s protocol.

RNA of Kidney was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA.  3  biological replicates were analyzed.
Keywords = db/m mice

131;Clear-cell renal cell carcinoma (ccRCC) tumor;Male;51;Clear-cell renal cell carcinoma;T1NxMx;n/a;2;wild type;wild type;mutant

Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 131

209;Normal cortex;Male;63;Clear-cell renal cell carcinoma;wild type;wild type;wild type

131;Normal cortex;Male;51;Clear-cell renal cell carcinoma;wild type;wild type;wild type

233;Normal cortex;Female;79;Clear-cell renal cell carcinoma;wild type;wild type;wild type

233;Clear-cell renal cell carcinoma (ccRCC) tumor;Female;79;Clear-cell renal cell carcinoma;T1N0Mx;n/a;2;wild type;mutant;mutant

Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 233

209;Clear-cell renal cell carcinoma (ccRCC) tumor;Male;63;Clear-cell renal cell carcinoma;T1N0M0;I;2;mutant;wild type;mutant

Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 209

260;Normal cortex;Female;n/a;Clear-cell renal cell carcinoma;wild type;wild type;wild type

260;Clear-cell renal cell carcinoma (ccRCC) tumor;Female;n/a;Clear-cell renal cell carcinoma;T1N0Mx;n/a;2;wild type;wild type;mutant

Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 260

Newborn Snf2h lens-conditional knockout and wildtype mouse whole eyes were enucleated.

Newborn Snf2h lens-conditional knockout and wildtype mouse pups were used.

Total RNA was extracted  using RNeasy micro-elute columns (QIAGEN), according to manufacturer's instructions.

2.2 micrograms  of cDNA was hybridized for 17 hr to the Affymetrix MG_430A_2.0 array as described in the Ovation™ Biotin RNA Amplification and Labeling System manual.   Genechips® were processed using protocol EukGE_WS2v4 450 for Genechip® fluidics station 450.

50 ng total RNA was amplified using the NUGEN Ovation™ Biotin RNA Amplification and Labeling System. Amplified cDNA was fragmented and biotin labeled according to manufacturer's instructions.

Human LIMA artery from patient 2, treatment: bare metal cardiovascular stent

Human LIMA artery from patient 1, treatment: bare metal cardiovascular stent

Human LIMA artery from patient 1, treatment: paclitaxel-eluting stent

Human LIMA artery from patient 2, treatment: paclitaxel-eluting stent

NB168

Medulloblastoma cell line D425;doxycyline inducible shRNA against OTX2;8 hrs;3

NB167

Medulloblastoma cell line D425;doxycyline inducible shRNA against OTX2;0 hrs;3

NB165

Medulloblastoma cell line D425;doxycyline inducible shRNA against OTX2;48 hrs;2

The retroviral vector pLPCX encoding human Nurr1 gene was infected into the PA317 amphotropic packaging cell line. Human NSC lines were infected with a retrovirus encoding human Nurr1 or control. All studies were performed within one week after transduction of retrovirus to avoid shut-down of Nurr1 gene expression in human neural stem cell lines.

Immortalized hNSC lines were maintained and passaged on uncoated culture dishes in DMEM with 10% Fetal bovine serum. All cells transduced with pLPCX or pLPC-Nurr1 were maintained in the same culture condition.

GeneChip 3.0 software (Affymetrix) was used for scanning and for first pass analysis and generation of raw data cell intensity (.cel) files. Data were subsequently submitted to a relational database for quality control assessment to include RNA quality, GeneChip sensitivity, and process quality determinations. Hierarchical clustering was performed and several distinct functional clusters were identified, including a cluster of genes possessed Nurr1-binding elements in promoter region. Hierarchical clustering using hamming distance correlation of the list of differentially expressed genes was conducted using EisenSoftware (Eisen lab, Lawrence Berkeley National Lab).

Total RNA was extracted according to the manufacturer’s protocol (Affymetrix).

Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 701021 Rev 5., Affymetrix).

Whole genome transcriptome profile of murine posterior palatal tissue, collected at E15.5, from mutant mice with a conditional inactivation of Tgfbr2 in epithelial cells.

C57BL/6J;K14-Cre;Tgfbr2 fl/fl;Posterior Palate;E15.5;Not determined

E15.5 K14-Cre;Tgfbr2 fl/fl Conditional Knockout Mutant Mouse Model

BV2 microglial cells were left untreated or were treated for 6h with 100 ng/ml LPS, 20 µM Curcumin, or 100ng/ml LPS + 20 µM Curcumin

BV2 microglial cells were cultured as described recently (Dirscherl et al. J Neuroinflammation. 2010 Jan 14;7:3.)

Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides

The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_105_metrix_Jan09)

Total RNA was extracted using the Qiagen Rneasy kit according to the protocol of the manufacturer

Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Expression Arrays (4x44k) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

Cyanine-3 (Cy3) labeled cRNA was prepared from 100-1000ng of high quality RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

TP_N2

TP_N3

TR_D1

CR_N3

Training of mice in the Morris water maze task was carried out between 10:00 am and 2:00 pm in four trials a day, with each
trial lasting a maximum of 120 sec with a 15-min intertrial interval. The task was performed as previously described (Malleret et al. 1999), with two training phases: 2 d with a visible platform followed by 7 d (spatial phase) with a hidden platform in the training quadrant. Probe trials (60 sec), during which the platform was removed, were performed to assess retention of the previously acquired information. Mice were killed by cervical dislocation and hippocampi were dissected out and immediately frozen in liquid nitrogen.

Housed in groups and according to standard IACUC protocol. Mice received food and water ad libitum and a 12-h light/12-h dark cycle.

Image data were acquired with
a Hewlett-Packard GeneArray scanner. Signal values were generated by using the Affymetrix Microarray Suite 5.0 software.

Hippocampi were homogenized, and total RNA was extracted by using TRIzol (Invitrogen Life Technologies). RNA was precipitated with isopropanol and glycogen, washed in 75% ethanol, and resuspended in RNAse free water (Ambion).

Fragmented amplified RNA was hybridized to Affymetrix Murine Genome U74Av2 arrays (12,486 probe sets). Hybridized arrays
were washed and stained as described in the Affymetrix signal antibody amplification protocol.

According to the GeneChip Expression Analysis Technical Manual (Affymetrix).

M030-230

M030-161C

H-s124T

H-c883T

H-c870T

H-c661T

H-c615T

H-c614T-W

M030-827T

M030-55B

c57bl6 mice were sensitized (DNP-HSA) and challendged intravesically (DNP-OVA). Mice were euthanized 24 hours after OVA.
Keywords = bladder inflammation
Lot batch = 1/3

c57bl6 female mice were challenged with saline.  Mice were euthanized 1 hour after and bladders removed for cDNA array analysis
Lot batch = 2/1

Cells were treated with TGFbeta (R&D systems) and harvested after 48 hours of incubation.

A human HCC cell line, Huh-7, was obtained from the Riken Bioresource Center (Tsukuba, Japan). The cell line was grown in Dulbecco’s modified Eagle medium (American Type Culture Collection) supplemented with 10% heat-inactivated fetal bovine serum at 37C in a 5% CO2 atmosphere.

Raw scan data were normalized using rma() function in Bioconductor's affy package (http://www.bioconductor.org/). For the analysis in the manuscript, the normalized signals were further collapsed into gene symbols by taking median values.

Total RNA was extracted from confluent 10cm culture dish using TRIzol reagent (Invitrogen).

Hepatocellular carcinoma cell lines treated or untreated with TGF-beta.

293T cells stably transfected with 2 shRNA constructs (si1340/si1428) against LEDGF transcript (PSIP1 gene).

Expression values were normalized using the Robust Multichip Average (RMA) methodology.

Both A2AR KO and WT littermate mice received either a single intraperitoneal injection of 20 mg/kg LPS isolated from E. coli (Sigma-Aldrich, St. Louis, MO), or an equal volume of sterile saline vehicle.

A2AR KO mice and WT littermates were obtained from a sub-colony of the original lines generated and characterized by Ledent et al (Nature 388: 674-8, 1997).  Mice were bred and maintained on-site at St. Jude Children’s Research Hospital, with standard laboratory food and water available ad libitum. Animal genotype was confirmed by PCR analysis of tail snips.  All animals originated from the same breeding series.

GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000

Raw expression data were background corrected, normalized and log2 transformed using the Robust Multichip Average (RMA) method in BioConductor/R.

Total RNA was extracted with Trizol reagent, DNase treated, followed by clean-up with QIAGEN RNeasy mini kit in accordance with manufacturers protocols. Quality control was performed with Agilent 2100 BioAnalyzer.

For Trim71 KD, mES cells were treated with a combination of three diffrent siRNAs specific to Trim71 or a non-targeting negative control siRNA and Dharmafect1 according to manufacturers instructions. Cells were harvested 72h post transfection.

Scanning was performed with Affzmetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip Scanner 3000 with autoloader.

Arrays were normalized and probeset-level log2 expression values were calculated using the rma function from the R/Bioconductor (v2.14) package affy.

RNA was extracted using Trizol and further cleaned up using RNeasy Columns.

Affymetrix Gene Chip Arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidiscs protocol FS450_0007 was used for washing.

100ng of extracted total RNA was amplified using the Ambion WT Expression kit (Ambion) and the resulting sense-strand cDNA was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix).

Array scanning and raw data processing were done using
GCOS 1.4 software (Affymetrix)

RNA was isolated and quantified using the Quant-IT RNA Assay Kit (Invitrogen)

Hybridization performed on a Affymetrix FS450/250 Fluidics Station using the FS450_0002 script.

Ambion MessageAmp II aRNA protocol
Two-round amplification and labeling

5 x 10^4 Zfx-flox LSK (Lin-, Sca1+, c-Kit+) cells were sorted directly into Trizol Reagent (Invitrogen) form pooled bone marrow cells from Zfx-flox mice.

5 x 10^4 Zfx-cko LSK (Lin-, Sca1+, c-Kit+) cells were sorted directly into Trizol Reagent (Invitrogen) form pooled bone marrow cells from Zfx-cko mice.

Single-round amplification and labeling

To generate stable knockdown adipocytes, 3T3-F442A pre-adipocytes were infected with shRNA-expressing retrovirus for overnight, followed by a puromycin selection (2ug/ml) for 2 days.

3T3-F442A adipocytes with stable expression of shGFP or shTRPV4 were cultured in DMEM with 10%FBS.  Adipocyte differentiation was induced s by treating confluent cells with 850 nM insulin for 8 days. Rosiglitozone was used for the first two days to faciliate differentiation.

The label, hyb and scan were performed by the Dana-Farber Cancer institute Core facility using affymetrix Gene Chip Mouse Genome 430 2.0 arrays according to established methods.

The data were normalized using the DNA-chip Analyzer (dChip) software.

Total RNA was isolated by TRIzol extraction and purification using QIAGEN Rneasy mini columns according to the manufacturer's instructions.

Following fragmentation, cRNA were hybridized at 45C on Affymetrix mouse genome 430 2.0 arrays.

Peripheral blood was collected during acute exacerbation post glucocorticoid treatment (inhaled salbutamol and ipratropium bromide at 20 min intervals for first hour, and oral prednisolone 1mg/kg) and at convalescence ≥ six weeks later and cryopreserved.

Microarray data were analysed in the open-source statistical software R employing the probe-level model (PLM) algorithm for background subtraction, normalization and summarization of probe set intensities.

Total RNA was extracted from cryopreserved PBMCs using TRIzol followed by RNeasy as according to the manufacturer's instructions. Equal amounts of RNA from 5 subjects were pooled, either at acute exacerbation or convalescent stage, to give a total of 10 pools for analysis.

Following fragmentation, 10 ug of cRNA were hybridized for 16 h at 45°C on Affymetrix U133Plus2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Labeled cRNA were prepared according to the standard Affymetrix protocol from 1 ug of total pooled RNA.

CEL files were normalized using the GC-RMA algorithm as implemented in the Genedata Expressionist Analyst Package.

Total RNA was isolated from testes using TRIzol reagent (Invitrogen #15596-026).

10 µg of purified, fragmented labeled cRNA was hybridized to Affymetrix 430 2.0 microarrays in the Affymetrix 640 hybridization oven according to the manufacturer's instructions as described in the GeneChip Expression Analysis Technical Manual (Affymetrix, 2004).

Labeling was performed by using 5.5 µg of total RNA according to the manufacturer's instructions as described in the GeneChip Expression Analysis Technical Manual (Affymetrix, 2004) with the Affymetrix IVT amplification and labeling kit.

mixed (C57BL6/6J and 129);Dmrt1 flox/flox with SF1-cre;male;testis;postnatal day 28 (P28)

HL-60 cell line, transduced with shSYK_2 and selected with  1 µg/ml puromycin 48 hours post-infection

Left ventricular myocardium in patients with Hypertrophic cardiomyopathy (31)

Left ventricular myocardium in patients with Hypertrophic cardiomyopathy;myocardium sold commercially

Left ventricular myocardium in patients with Dilated cardiomyopathty (29)

Left ventricular myocardium in patients with Dilated cardiomyopathty (14)

Left ventricular myocardium in patients with Dilated cardiomyopathty (34)

mixed (C57BL6/6J and 129);Dmrt1 flox/flox with Dhh-cre;male;testis;postnatal day 28 (P28)

Left ventricular myocardium in patients with Ischemic cardiomyopathy (35)

human peripheral blood derived monocytes, 24 hour LPS stimulation, biological rep1

Left ventricular myocardium in patients with Dilated cardiomyopathty (32)

Sprague-Dawley;spinal cord (ipsilateral dorsal horn);Neonate (P10);7 day post sciatic nerve SNI injury

mixed (C57BL6/6J and 129);Dmrt1 flox/flox with no Cre;male;testis;postnatal day 28 (P28)

See online supplement to Lilly et al., Am J Respir Crit Care Med. 2005 Mar 15;171(6):579-86

Please refer to Lilly et al., Am J Respir Crit Care Med. 2005 Mar 15;171(6):579-86

ALSO NOTE: There is no subject #4 in this series (subject 4 was excluded based on clinical criteria)

Mice were gavaged daily with 100 ul Peptamen including 10 ug/kg body weight lubiprostone for two weeks, as indicated.

All mice were fed from weaning to sacrifice with a liquid diet (Peptamen).

Automated process conducted using the Agilent GeneArray Scanner.
Pixel value = 3um
Wavelength = 570nm

Primary analysis was by GCOS with 'Scaling - All Probe Sets: Target Signal = 500'; 'Normalization – User Defined: Scale Factor = 1' using MAS 5.0.

The entire small intestine was resected into ice cold PBS; the mesentery was trimmed and discarded; the tissue was homogenized in 8 ml Trizol and extracted to isolate total RNA.

GeneChip was prehybridized with Hybridization buffer at 45C 10min.
Denatured Hybridization cocktail was applied to GeneChip.
GeneChip was hybridized 16 hr at 45C in GeneChip Hybridization Oven 640.
Washing and Staining: Automated process using the GeneChip Fluidics Station 400 with the Standard Array Format.

Cells were infected with either mock virus preparation or ZEBOV at a multiplicity of infection (MOI) of 10.

Cells were cultivated in RPMI 1640 (Invitrogen, Carlsbad, CA) containing 20% heat-inactivated human AB serum (Sigma-Aldrich, St. Louis, MO), penicillin (100 U/ml), streptomycin (100 µg/ml), and L-glutamine (2 mM); cells were incubated at 37 ºC in a humidified 5% CO2 environment

The distribution of fluorescent material on the processed array was determined using the Agilent G2500 GeneArray Scanner (Agilent Technologies, Santa Clara, CA). The array image scan was processed using Affymetrix Microarray Suite, version 5.0 (MAS 5.0), which resulted in the generation of raw, probe level data in the CEL file format.

Cell supernatants were removed from the cells 1 h or 6 h post infection, and RNA from cells was purified using the RNeasy Mini Kit (QIAGEN, Valencia, CA) according to the manufacturer's instructions.

The arrays were hybridized in a GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA) for 16 hours at 45°C, followed by washing, staining with streptavidin-phycoerythrin (SAPE; Molecular Probes, Eugene, OR), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs, Burlingame, CA), and a final staining with SAPE. The staining and washing were performed using two GeneChip Fluidic Station 400s (Affymetrix, Santa Clara, CA) running standard Affymetrix fluidics script.

Using 5 µg of total RNA as input, messenger RNA was amplified and labeled in two steps. In the first step, mRNA was converted to double-stranded cDNA using Superscript Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (IDT, Coralville, IA). Double-stranded cDNA was purified by phenol-chloroform-isoamyl alcohol extraction and a standard ethanol precipitation. In the second step, the cDNA was converted to labeled cRNA (the target) using T7 RNA polymerase in the presence of biotinylated UTP and CTP (Enzo, Farmingdale, NY). Unincorporated nucleotides were removed using the RNeasy Mini kit (Qiagen) and was followed by an ethanol precipitation of the labeled target. The target was fragmented to produce a uniform distribution of short cRNAs. 10µg each of fragmented target was combined with hybridization control oligomer (Affymetrix, Santa Clara, CA) and control cRNAs (1.5pM BioB, 5.0pM BioC, 25pM BioD, and 100pM Cre; Affymetrix, Santa Clara, CA), in hybridization buffer and applied to the array.

Mock infected macrophages harvested at 6h post-treatment from donor 3

Ebola-infected macrophages harvested at 6h post-treatment from donor 3

Lot batch = rat 31

Lot batch = rat 28

Lot batch = rat 12

Lot batch = rat 13

Lot batch = rat 10

Standard lentiviral production methods were used in 293FT cells. The shRNA lentivirus was used to infect the cell lines for 2 days, then subjected to 2 days of puromycin selection to ensure a pure population infected cells. RNA was collected at day 4 after infection.

NCI-H1299 and NCI-H2009 were maintained in standard conditions of RPMI media supplemented with 10% FBS

Trizol was used to extract RNA, followed by DNAse treatment in a Qiagen RNA column.

NCI-H2009;lung cancer cells;control hairpins targeting luciferase

Essentially, the cells were cultured for 4-6 weeks in media containing mouse recombinant IL-3 (30 ng/ml) (Peprotech, Rocky Hill, NJ). The cells were maintained at 37 ˚C in a humidified incubator gassed with 95% air and 5% CO2. The purity of the cultures, as assessed by toluidine blue staining and FceRIa and KIT expression, was >99%.

Gene expression data from mouse bone marrow-derived mast cells treated with IL3, rep 1 of 6.

Gene expression data from mouse bone marrow-derived mast cells treated with IL3, rep 2 of 6.

Gene expression data from mouse bone marrow-derived mast cells treated with IL3, rep 3 of 6.

Gene expression data from mouse bone marrow-derived mast cells treated with IL3, rep 4 of 6.

Gene expression data from mouse bone marrow-derived mast cells treated with IL3, rep 5 of 6.

Cells were transfected with oligonucleotides using lipofectamine RNAiMAX

Human epithelial colonic adenocarcinoma, Caco-2, cells were grown in Dulbeco’s Modified Eagle medium, containing 10% (v/v) fetal calf serum; 60 μg/ml gentamycin and 1% (v/v) non essential amino acids (Sigma).

The samples were scanned using the Illumina iScan array scanner.  The samples were scanned using the Illumina iScan array scanner.  The samples were scanned using the Illumina iScan array scanner. There were no deviations from the Illumina protocol.

Data were processed using R/Bioconductor (the lumi package), Raw data were transformed using a Variance Stabilizing Transformation, and normalized with the quantile normalization algorithm. Probes were selected which fulfilled the criteria of Illumina probe detection p-value of <0.01.

Total RNA isolated using Pure Link RNAmini kit [Ambion] following manufacturer’s protocol, RNA integrity checked using Agilent Bioanalyzer.

50 ng of the obtained biotinylated cRNA samples was hybridized onto the Illumina HumanHT-12 v4 as per manufacturer's instructions.

The Illumina TotalPrep-96 RNA Amplification Kit was used to generate Biotin labeled (biotin-16-UTP), amplified cRNA starting from 200ng total RNA.

Dhamracon negative siGENOME Non-Targeting siRNA;Human epithelial colonic adenocarcinoma, Caco-2

siRNA2 (Dhamacon);Human epithelial colonic adenocarcinoma, Caco-2

GeneChips were scanned using the Affymetrix Gene Array Scanner (7G).

All pre-processing and data analyses were performed using R version 2.9 and the Bioconductor packages designed for use with Affymetrix microarray data.

Extraction of total RNA was performed with RNAqueous-4PCR kits (Ambion, Inc., Austin, TX) according to the manufacturer's instructions.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA ( Affymetrix Technical Manual).

lung, upper lobe;surgical biopsy;early idiopathic pulmonary fibrosis (IPF);male;68

lung, upper lobe;explant;advanced idiopathic pulmonary fibrosis (IPF);male;67

lung, lower lobe;explant;advanced idiopathic pulmonary fibrosis (IPF);female;68

lung, lower lobe;explant;advanced idiopathic pulmonary fibrosis (IPF);male;67

lung, upper lobe;explant;advanced idiopathic pulmonary fibrosis (IPF);female;68

Air
1
72

Air
1
72

Male mice from fiona transgenic line (dystrophin-deficient with a transgene expressing high level of full length utrophin) were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction. Biological Replicate 1.

Skeletal muscle tibialis anterior (TA) from fiona transgenic line

Air
1
48

Air
1
48

Air
1
72

.CEL file unavailable for this chip.

Air
1
72

Nervous System; Cerebellum

Nasal; Upper Repiratory Mucosa

Nervous System; Fetal day 18.5 brain

Nervous System; Day 2 postnatal whole brain

Nervous System; Hippocampus

10_Bsl

10_BM

11_BM

10_PC

8_BM

7_PC

8_PC

8_Bsl

11_PC

11_Bsl

GeneChips were scanned using an Affymetrix GeneChip Scanner (Affymetrix).

The data were analyzed with dChip version2006 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to the bottom 10%. of intensity values

Trizol extraction of total RNA was carried out using EZ1 RNA universal tissue kit with BioRobot EZ1 workstation according to the manufacturer's instructions.

Following fragmentation, 5 ug of cRNA were hybridized on Human Genome U133 A_2 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-ws2v5 450.

cells from primary breast cancers were flow sorted to select for CD44+/CD24- cells and compare with the rest of the cells

JLI_43

Ewing family tumor cell-line A673 (transfected with empty vector). Experiment 2.
Lot batch =

Ewing family tumor cell-line A673 (transfected with empty vector). Experiment 1.
Lot batch =

Ewing family tumor cell-line A673 (IL-2 transgenic). Experiment 3.
Lot batch =

Ewing family tumor cell-line A673 (IL-2 transgenic). Experiment 2.
Lot batch =

Ewing family tumor cell-line A673 (IL-2 transgenic). Experiment 1.
Lot batch =

White and grey matter in the distribution on the middle cerebral artery 6 hours after administration of saline (control); second replicate; pooled mRNA from 6 brains.

NCI-H460;human lung large cell carcinoma cells;cisplatin and cigarette smoke extract;2 hours

JLI_45

glioblastoma cells;H4 cells;STAG2 knock-in post-Cre clone 8-3 (STAG2 corrected)

glioblastoma cells;H4 cells;STAG2 knock-in post-Cre clone 8-1 (STAG2 corrected)

Chemiluminescence detection, imaging, auto gridding, and image analysis was done according to Applied Biosystems protocols and the 1700 Chemiluminescent Microarray Analyzer Software v. 1.0.3.

Signal intensities across microarrays were normalized using the quantile-quantile method (www.bioconductor.org).

Tissues were quickly removed and frozen in liquid nitrogen and stored at -80C for subsequent preparation of total RNA. Total RNA was isolated using TRI-Reagent (Molecular Research Center Inc. Cincinnati, Ohio) with modifications to remove DNA using the Qiagen RNAeasy columns and DNaseI Kit (Qiagen, Valencia, CA). RNA was stored at –70C in RNase-free H2O supplemented with the RNase inhibitor Superasin (Ambion, Austin, TX) as per manufacturers directions.  Quality and quantity of RNA was determined using a Agilent Bioanalyzer as per manufacturers procedures (Agilent Technologies, Palo Alto, CA).

Microarray hybridization (using twenty micrograms of fragmented, DIG-labeled cRNA) and processing were performed according to Applied Biosystems protocols.

1 ug of total RNA was used to transcribe DIG-labeled cRNA using Applied Biosystems Chemiluminescent RT-IVT Kit V2.0.

Pooled inguinal fat from 8 C57BL/6J mice with 'high' weight gain after 4 weeks on a high fat diet (D12331;Research Diets, New Brunswick, NJ).  Microarrays were performed in triplicate, H1, H2 and H3.

JLI_44

glioblastoma cells;H4 cells;non-recombinant clone 12 (STAG2 mutant)

glioblastoma cells;H4 cells;non-recombinant clone 10 (STAG2 mutant)

Veh_Veh_3

Dox_PMA_2
Gene expression data from cell line differentiated with PMA in the presence of doxycycline-inducible knockdown of ZXDC1/2

Veh_PMA_3
Gene expression data from cell line differentiated with PMA in the absence of doxycycline-inducible knockdown of ZXDC1/2

Dox_Veh_3
Gene expression data from cell line treated with vehicle in the presence of doxycycline-inducible knockdown of ZXDC1/2

Dox_PMA_3

RNeasy of total RNA was performed according to the manufacturer's instructions (Qiagen). Disrupted by passage through hypedermic needle.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Title: ERRγ Directs and Maintains the Transition to Oxidative Metabolism in the Post-Natal Heart
Abstract: At birth the heart undergoes a critical metabolic switch to transition from a predominant dependence on carbohydrates during fetal life to a greater dependence on postnatal oxidative metabolism.  This remains the principle metabolic state throughout life; although pathologic conditions such as heart failure and cardiac hypertrophy reactivate components of the fetal genetic program to increase carbohydrate utilization. Disruption of the ERRγ gene, which is expressed at high levels in the fetal and postnatal mouse heart, blocks this switch resulting in lactatemia, electrocardiographic (ECG) abnormalities and death during the first week of life. Genomic ChIP-on-chip and expression analysis at E18.5 clearly identifies ERRγ as both a direct and indirect regulator of a nuclear-encoded mitochondrial genetic network that coordinates the postnatal metabolic transition. These findings reveal an unexpected and essential molecular genetic component of the oxidative metabolic gene program in the heart and highlight ERRγ in the study of cardiac hypertrophy and failure.
Key Words: ChIP-on-chip, electrocardiography, fetal gene program, OXPHOS, PGC-1α, sodium current

The image data were compiled into a project using  Beadstudio software gene expression module version 3.2.7.  Quantile normalization was used. The data was exported as txt files using the build-in function of export to GeneSpring GX format. The option of sample probe profile was chosen. Data were subsequently quantile normalized for the analysis.

Total RNA was isolated from tissue specimens using the mirVANA Kit (Ambion, Austin, TX). Transcriptional profiles were generated by the Genomics and Proteomics Core Laboratory at Texas Children's Hospital using Human WG-6 (v3) BeadChip (Illumina, San Diego, CA). Prior to profiling, RNA integrity was determined using the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA).

C57BL/6J;129S5/Brd mixed hybrid;wild type control;uterine;15 days

Sample name: CSB_HFD_2

C57BL/6;Csbm/m;male;cerebellum;1 year;high-fat diet consisting of AIN-93G with 60% of calories from fat (HFD; carbohydrate:protein:fat ratio of 16:23:61) ad libitum for 8 months

WI-38 cells, at 24 h after exposure to DMSO vehicle control, biological rep1

male;grape extract (B);6 months;Isolated peripheral blood mononuclear cells (PBMCs)

Isolated PBMCs from diabetic male patient_Grape extract group_6 months

Sample name: CSB_HFD_4_(5)

Gene expression data under ER stress from lymphoblastoid cells of twin 1705:2 treated with 500nM thapsigargin.

lymphoblastoid cell line;1705;GM14409;Twin number 2;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1705:2 treated with DMSO.

lymphoblastoid cell line;1705;GM14409;Twin number 2;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1706:1 treated with 500nM thapsigargin.

lymphoblastoid cell line;1706;GM14414;Twin number 1;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1706:2 treated with 500nM thapsigargin.

lymphoblastoid cell line;1706;GM14417;Twin number 2;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1706:2 treated with DMSO.

lymphoblastoid cell line;1706;GM14417;Twin number 2;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1710:1 treated with 500nM thapsigargin.

lymphoblastoid cell line;1710;GM14432;Twin number 1;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1710:1 treated with DMSO.

lymphoblastoid cell line;1710;GM14432;Twin number 1;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1710:2 treated with 500nM thapsigargin.

lymphoblastoid cell line;1710;GM14433;Twin number 2;thapsigargin;500nM;4 hours

Sample name: CSB_CR_4

Sample name: CSB_CR_5

Sample name: CSB_HFD_1

B6; gender: mix; age: 0-2d; tissue: rib cartilage; passage #: 4; treatment: untreated; biological replicate: 1

B6; gender: mix; age: 0-2d; tissue: rib cartilage; passage #: 4; treatment: control; biological replicate: 3

Freshly prepared 5A2dC (Sigma; Saint Louis, MO, USA) stock solution was diluted in growth medium to a concentration of 5 μM. A new preparation of the drug in growth medium was added every 24 hours for a total of 72-hour drug exposure. Cells were grown in normal medium following treatment for an additional 24 hours.

treated with 5-aza-2'-deoxycytidine for 72 hours plus 24 hours in normal medium; biological replicate 1

B6; gender: mix; age: 0-2d; tissue: rib cartilage; passage #: 4; treatment: 5-aza-2'-deoxycytidine; biological replicate: 1

treated with 5-aza-2'-deoxycytidine for 72 hours plus 24 hours in normal medium; biological replicate 2

B6; gender: mix; age: 0-2d; tissue: dermis; passage #: 4; treatment: 5-aza-2'-deoxycytidine; biological replicate: 2

treated with 5-aza-2'-deoxycytidine for 72 hours plus 24 hours in normal medium; biological replicate 3

B6; gender: mix; age: 0-2d; tissue: rib cartilage; passage #: 4; treatment: 5-aza-2'-deoxycytidine; biological replicate: 3

Sample name: CSB_HFD_7

For siRNA-mediated downregulation of Lamp3, Hela cells were transfected with LAMP3-specific siRNA (L-004716-01; ON-TARGETplus SMARTpool) or control siRNA (D-001810-01-05; ON-TARGETplus SMARTpool) using Dharmafect 1 transfection reagent (T-2004-01, Dharmacon [Thermo Scientific]; Lafayette, CO) according to the manufacture instructions. Following the initial 24 h transfection, cells were stimulated with IFN-alpha (Roferon-A, Hoffman-LaRoche) at the concentration of 1ng/ml and grown for 24 hr, then split, re-transfected with siRNA, and fresh medium with IFN was added. Cells were incubated for additional 24 or 48 h and collected at 48 hr and 72 hr of initial stimulation with IFN.

AVG_Signal values generated by Bead studio software were imported into BRB Array Tools and median normalized before statistical comparisons

amplification and labeling was performed using Ambion Illumina Total Prep RNA amplification kit

HeLa-LAMP3siRNA-4d;HeLa;LAMP-3 siRNA;4d interferon alpha;interferon alpha

gavage with 0.2 ml vehicle (saturated sucrose);
1st, 3rd and 5th day, once per day

Normalized with MAS5 across the 8 samples in this project; All probe sets included; No log transformation

HeLa-LAMP3siRNA-3d;HeLa;LAMP-3 siRNA;3d interferon alpha;interferon alpha

IA, IB, II, IIIA, IIIB, or IV=IIIB;37;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=IIIB;50;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=IIIA;54;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=IIIA;74;female, male:female;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=IIIA;60;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=IIIA;77;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=II;59;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=II;53;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=II;34;female, male:female;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

brain (frontal cortex);bipolar disorder;44 yr;white;296.74;26 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);bipolar disorder;43 yr;white;296.64;25 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);bipolar disorder;35 yr;white;296.74;14 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);bipolar disorder;38 yr;white;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);bipolar disorder;42 yr;white;296.8;18 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);bipolar disorder;35 yr;white;296.54;19 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);bipolar disorder;44 yr;white;296.53;33 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);bipolar disorder;48 yr;white;296.7;33 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);bipolar disorder;50 yr;white;296.54;25 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);bipolar disorder;56 yr;white;296.54;28 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

ovariectomized mice were allowed to rest for 10-14 days, then injected with 100 ul saline or 250 ng estradiol in 100 ul saline ip. Uterine tissue was collected 2 or 24 hours after injection and frozen in liquid nitrogen

Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters. The Agilent Feature Extraction Software performed error modeling, adjusting for additive and multiplicative noise. The default setting for the protocol we used is polynomial data fit.

frozen uterine tissue was pulverized and each uterus was homogenized in 800 ul of Trizol (Invitrogen) with 250 ug/ml glycogen. Extraction proceeded as descibed in manufacturer's protocol. Following resuspension of RNA pellet, a second preciptation was done with NaAcetate and ethanol. This pellet was then resuspended in depc treated water and cleaned up using the Qiagen RNeasy kit clean up protocol. RNA concentration and A260/280 was checked and quality was evaluated by formaldehyde gel.

gene expression in WT ovariectomized saline vehicle treated uterus

WT;saline control;24h;C57bl6/Jx129;adult (10+ weeks);ovariectomized female;uterus

WT;E2;2h;C57bl6/Jx129;adult (10+ weeks);ovariectomized female;uterus

total RNA of human coronary artery smooth muscle (hcaSMC) cultivated in SMGM-2-MV bulletkit medium were isolated after incubation with nebivolol for 72 hours using Trizol and purified with RNeasy spin columns.

Approximately 7 µg of total RNA was processed to produce biotinylated cRNA targets.

human coronary artery smooth muscle Cells, treated with nebivolol, replicate 2

coronary smooth muscle cells (hcaSMC), treated with nebivolol for 72 hours

Female;67;3.5h;6.1;schizophrenic;superior temporal cortex (Brodmann Area 22, BA22)

breast cancer derived cell line treated with 0.4 uM of Doxorubicin for 12 hours

Male;71;6.5h;6;schizophrenic;superior temporal cortex (Brodmann Area 22, BA22)

Male;44;4h;6.3;schizophrenic;superior temporal cortex (Brodmann Area 22, BA22)

Female;65;3h;6.1;schizophrenic;superior temporal cortex (Brodmann Area 22, BA22)

Male;79;4.5h;6.3;schizophrenic;superior temporal cortex (Brodmann Area 22, BA22)

Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay (biotin)

Mice were treated with either PBS or heart-passaged CVB3 intraperitoneally. Mice were harvested at 90 days post infection and hearts were flash frozen in liquid nitrogen for RNA extraction.

Arrays were transferred to a GCS3000 laser scanner with autoloader and 3G upgrade (Affymetrix) and scanned at an emission wavelength of 570nm at 2.5 um resolution

CEL files were imported and analyzed with the default algorithm workflow RMA-Sketch, which includes RMA background correction, and Sketch-Quantile normalization.
The values recommended by Affymetrix as QC metrics include Positive vs. negative AUC (assessment of sensitivity and specificity), as well as all probeset mean and all probeset relative log expression.

Hearts were homogenized in 2mL TRIzol according to the manufacturer's protocol. PureLink Micro-to-midi Total RNA purification System was used for extraction and purification of RNA

Hybridization cocktails were prepared as recommended for arrays of Mini/169 format using reagents in the Affymetrix Hybridization Wash Stain kit. Hybridization mix and fragmented, labeled ST-sscDNA were incubated at 99oC for 2 min and 45oC for 5 min, and then centrifuged at maximum speed for 5 min prior to pipetting into the GeneChips (Affymetrix Mouse Gene ST 1.0). Hybridization was performed at 45oC for 18 hours at 60RPM in the Affymetrix rotisserie hybridization oven. The signal amplification protocol for washing and staining of eukaryotic targets was performed in an automated fluidies station (Affymetrix FS450) using Affymetrix protocol FS450_0001.

RNAs were processed for hybridization to Affymetrix Mouse Gene ST 1.0 microarrays using the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay, according to manufacturer's recommended protocol. One hundred nanograms of total RNA was amplified.

Gene expression data of female hearts after a 90 day treatment of CVB3

Gene expression data of male hearts after a 90 day treatment of CVB3

Prostate-specific Pten and Lrf deletion anterior prostate tumor 3

GeneChips were scanned using the GeneChip HT Array Plate Scanner

Total RNAs were purified from AP using the RNeasy Mini Kit (Qiagen) and treated with RNase-free DNase set (Qiagen).

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HT MG-430 PM Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

C57BL/6;Pb-Cre4;PtenLoxP/LoxP;LrfLoxP/LoxP;anterior prostate;12 weeks

Prostate-specific Pten and Lrf deletion anterior prostate tumor 2

According to standard Affymetrix protocol (GeneChip® Expression Analysis Technical Manual)

Data extraction and normalization was done using Affymetrix Gene Chip Operating Software (GCOS) version 1.4. The overall intensity value of each GeneChip was scaled to an average value of 200 according to the method of global scaling provided by GCOS. Intensity values between 0 and 30 were set to 30. An unsupervised correlation analysis using all the probe sets expressed above detection level in at least one of the samples was performed with the OmniViz correlation tool (Omniviz, Maynard, MA); this measures correlation patterns by Pearson’s correlation coefficient. We used Robust Multichip Average (RMA) normalization to obtain a list of differentially expressed probe sets, using a fold-change of >1.5 and false discovery rate of 0.01 as criteria. This list was used for cluster analysis by standard hierarchical clustering methods with similarity measured by Euclidean distance, provided by OmniViz software. Potentially relevant biological processes were determined with Ingenuity Pathways Analysis software (Ingenuity, Redwood, CA). Functional annotation was manually curated using the Mouse Genome Informatics Web Site, The Jackson Laboratory (Bar Harbor, ME) (http://www.informatics.jax.org), Online Mendelian Inheritance in Man McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology Information, National Library of Medicine (Bethesda, MD) (http://www.ncbi.nlm.nih.gov/omim/), and the Ensembl genome database at the European Bioinformatics Institute (Hinxton, UK) (http://www.ensembl.org/), July 2007.

Total RNA isolated from single heart stored at -80 degrees Celsius, according to standard Affymetrix protocol (GeneChip® Expression Analysis Technical Manual)

1-cycle target labeling according to standard Affymetrix protocol (GeneChip® Expression Analysis Technical Manual)

vLow_24h_2

vLow_24h_3

vLow_48h_4

vLow_48h_2

Slides were washed and then scanned on an Axon GenePix 4000B scanner

Data was analyzed with CodeLink and GeneSpring software packages

cRNA was fragmented to uniform size.
CodeLink Bioarrays were hybridized with the cRNA target and stained with Cy5-streptavidin

First and second strand cDNA was prepared from the total RNA samples
Biotinylated cRNA target was prepared from the DNA template.

Labelling, hybridisation and data analysis was performed by GenUs Biosystems

Gene expression data from PC3 cells treated with Wee1inhibitorII and 17AAG

Data processed using Robust Multi-Array Averaging (RMA) using software provided by the McGill University and Génome Québec Innovation Centre (http://www.genomequebecplatforms.com/mcgill/home/index.aspx?l=e).

Tissue was stored in RNAlater (Qiagen) at -20oC prior to RNA extraction.  Tissue was homogenized, extracted in Trizol reagent (Sigma), and purified on columns (Qiagen).  RNA integrity was quantified using an Agilent Bioanalyser.

Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45oC on GeneChips according to Affymetrix protocols.

Biotinylated cRNA was prepared according to Affymetrix protocols.

Proximal hindlimb bud tissue (~500um from base of limb bud) pooled from 3 embryos (6 limbs total).

Gene expression data from Deltoid, control, cohort 19, subject 19U

Gene expression data from Biceps, control, cohort 19, subject 19U

Gene expression data from Deltoid, control, cohort 15, subject 15V

Gene expression data from Biceps, control, cohort 15, subject 15V

Gene expression data from Biceps, control, cohort 20, subject 20U

Mouse Lung LRD Diet 5wk 10ppb As Food Exposure, biological replicate D
AN080206_Sample 10 Lung.CEL

Sodium arsenite added to food: 10 ppb, 5wk; Injection: None; Diet: LRD-5001; Sodium arsenite added to drinking water: None

Mouse Lung LRD Diet 5wk Control, biological replicate C
AN080806_Sample 11.CEL

Sodium arsenite added to food: None; Injection: None; Diet: LRD-5001; Sodium arsenite added to drinking water: None

Mouse Lung LRD Diet 5wk Control, biological replicate A
AN080306_Sample 5.CEL

Mouse Lung LRD Diet 5wk Control, biological replicate E
AN080806_Sample 7.CEL

Mouse Lung LRD Diet 5wk 10ppb As Drinking Water Exposure, biological replicate A
AN080906_Sample 8.CEL

Sodium arsenite added to food: None; Injection: None; Diet: LRD-5001; Sodium arsenite added to drinking water: 10 ppb, 5wk

Mouse Lung LRD Diet 5wk 100ppb As Drinking Water Expousre, biological replicate C
AN080206_Sample 9 Lung.CEL

Sodium arsenite added to food: None; Injection: None; Diet: LRD-5001; Sodium arsenite added to drinking water: 100 ppb, 5wk

Clinical information: Sample.ID=25;Tumor.type=D;Size=3.5;Grade=2;Nodes=0/9;ER=Neg;PR=Pos;HER2=Neg;Age=62;DFS=75;Status=recur

Mouse Lung AIN Diet 8hr Saline Injection, biological replicate B
AN080406_Sample 1.CEL

Mouse Lung LRD Diet 5wk 10ppb As Drinking Water Exposure, biological replicate C
AN080806_Sample 3.CEL

Mouse Lung LRD Diet 5wk 10ppb As Food Exposure, biological replicate E
AN080406_Sample 4.CEL

SUM149 cells were transfected with ON-TARGET Plus SMART Pools against TIG1 (NM_002888) and siGENOME Non-Targeting siRNA Pool (control siRNA) at a final concentration of 200 nmol/L by using oligofectamine (Invitrogen) according to the manufacturer’s guidelines.

SUM149 human IBC cells were cultured in Ham’s F-12 medium supplemented with 5% FBS, 5 µg/ml insulin, and 1 µg/ml hydrocortisone.

Using a GeneArray Scanner (Hewlett-Pacrkard, Palo Alto, CA, USA).

The data pre-processing and statistical analysis were performed in R. As part of the standard quality control(QC) analysis, the data were first quantified using the MAS5 algorithm. The Robust Multiarray Analysis (RMA) algorithm that borrows strength across arrays was used to normalize and quantify the data.

Total RNA was extracted and purified using RNeasy mini kit (Qiagen, Inc.) according to the manufacturer’s instructions.

The fragmented cRNA was used for hybridization to the Affymetrix HGU133 chip overnight at 45°C with rotation.

The double-stranded cDNA was transcribed into cRNA in the presence of biotin-labeled ribonucleotides using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Affymetrix) as described by the manufacturer.

SUM149 cells transfected with siGENOME Non-Targeting siRNA Pool (control siRNA)

Gene expression data spleen follicular B in IRF8 conditional KO

Testicular germ cell tumor; histological subtype choriocarcinoma
Keywords = choriocarcinoma
Keywords = nonseminoma

Testicular germ cell tumor; histological subtype yolk sac tumor
Keywords = endodermal sinus tumor
Keywords = yolk sac tumor

Testicular germ cell tumor; histological subtype embryonal carcinoma
Keywords = embryonal carcinoma
Keywords = pluripotency

test;male;ApoE-/-;suprarenal aorta, aneurysm;Ang II;14d;reference

test;male;ApoE-/-;suprarenal aorta, dissected aneurysm;Ang II;7d;reference

test;male;ApoE-/-;suprarenal aorta, non-dissected aneurysm;Ang II;7d;reference

Cells were transfected with Control siRNA or IPMK siRNA and cytoplasmic RNA was harvested 72 hours post-transfection. Some samples were treated with DNA crosslinking reagent mitomycin C (MMC) for 24h prior to harvest

The dataset was filtered before normalization, to remove non-expressed probes to avoid adding noise to the data.

RNA was extracted from cytoplasmic fraction of cells (obtained by digitonin permeabilisation) with QIAGEN RNeasy mini kit according to manufacturers instructions. RNA was treated with RNase free DNase (Qiagen) prior to elution. Quality control was performed with Agilent Bioanalyser.

Biotinylated cRNA was prepared with the Ambion MessageAmp kit for Illumina arrays

rat hippocampus (CA1 region), LowCort, 18 months old, subject 24

rat hippocampus (CA1 region), LowCort, 18 months old, subject 25

rat hippocampus (CA1 region), LowCort, 18 months old, subject 22

rat hippocampus (CA1 region), LowCort, 18 months old, subject 23

rat hippocampus (CA1 region), LowCort, 18 months old, subject 28

rat hippocampus (CA1 region), LowCort, 18 months old, subject 29

rat hippocampus (CA1 region), LowCort, 18 months old, subject 26

rat hippocampus (CA1 region), LowCort, 18 months old, subject 27

Fisher 344;male;18 months;hippocampal CA1 brain;Low-CORT (ADX) + short-term high-dose injected

Trizol extracted total RNA from myometrium tissue. Trizol extracted total RNA from myometrium tissue.

This group received a diet containing 500mg/kg of α- and γ-tocopherol each since the age of 15 months.

agT: 30-month-old a- & g-tocopherol supplemented mouse
Ht: heart
5: sample number

Ht: heart
3: sample number

Ht: heart
4: sample number

Ht: heart
1: sample number

Ht: heart
2: sample number

MDA-MB-231;Breast adenocarcinoma, estrogen receptor-negative;MTDH_WT_KD

5991413017_J
Down's Syndrome;induced pluripotent stem cell;CCL54 C18;rep4

induced pluripotent stem cell;Down's Syndrome;CCL54;male;P55;C18

5991413017_K
Down's Syndrome;induced pluripotent stem cell;CCL54 C18;rep5

5991413017_L
Down's Syndrome;induced pluripotent stem cell;CCL54 C18;rep6

5991413017_F
normal;induced pluripotent stem cell;CRL1502 C32;rep3

5991413017_G
Down's Syndrome;induced pluripotent stem cell;CCL54 C11;rep4

induced pluripotent stem cell;Down's Syndrome;CCL54;male;P55;C11

5991413017_H
Down's Syndrome;induced pluripotent stem cell;CCL54 C11;rep5

5991413017_I
Down's Syndrome;induced pluripotent stem cell;CCL54 C11;rep6

MDA-MB-231;Breast adenocarcinoma, estrogen receptor-negative;MTDH_isoform_KD

Feeder-free wild-type, GSK-3a-/-, Gsk-3b-/-, and Gsk-3 DKO ESCs were grown on gelatin coated plates in high glucose DMEM (GIBCO) supplemented with 15% fetal bovine serum (Hyclone), 1X non-essential amino acids, 1X sodium pyruvate, 2mM L-glutamine, 1X penicillin/streptomycin (GIBCO), 55 mM 2-mercaptoethanol, and 1000 units/ml ESGRO (Millilpore). Media was replenished every other day.

GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)

CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the Background Adjustment Using Sequence Information (gcrma 2.14.1) Package in R version 2.8.0. Data was used to determine differential gene expression by pair-wise comparisons and statistical analysis was performed using both the Linear Models for Microarray Data (limma 2.16.5) and Multiple testing using SAM and Efron's empirical Bayes approaches (siggenes 1.16.0) packages. The genes that were altered two-fold either way with significance at either a 10% FDR or adjusted P value of <= 0.05 were sorted and used for further interpretation of the microarray data.

Cells were collected by addition of 0.25% trypsin EDTA to PBS washed cells and incubated for 1 minute at 37C. Trypsin was inactivated by addition of twice the volume of ESC media. Cells were washed in PBS, and resuspended in TRIzol (Invitrogen), and RNA was isolated following the manufacturer's protocol. RNA was then further purified with the RNeasy RNA cleanup procedure (Qiagen).

Following fragmentation, labeled cRNA was hybridized to the Mouse 430 2.0 array. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).

The Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from total RNA for following manufacturer’s instructions. Briefly, first strand cDNA was synthesized from 25 ng of total RNA using a unique first strand DNA/RNA chimeric primer and reverse transcriptase. Following double strand cDNA generation, amplification of cDNA was achieved by utilizing an isothermal DNA amplification process that involves repeated SPIA™ DNA/RNA primer binding, DNA duplication, strand displacement and RNA cleavage. The amplified SPIA™ cDNA was purified and subjected to a two-step fragmentation and labeling process. The fragmented/biotinylated cDNA content was measured in a ND-1000 spectrophotometer and the quality was analyzed on an RNA 6000 Nano LabChip (Agilent) using Agilent Bioanalyzer 2100.

Muscle RNA from littermate control mice for muscle-specific PPARalpha overexrpessing transgenic mice

Gastrocnemius muscle wild-type mouse - control mouse for PPARalpha overexpressing

Muscle RNA from muscle-specific PPARalpha overexpressing transgenic mouse

Gastrocnemius muscle from transgenic mouse overexpressing PPARalpha

Gastrocnemius muscle wild-type mouse - control mouse for PPARalpha overexpressing -rep 2

Muscle RNA from muscle-specific PPARalpha overexrpessing transgenic mouse

Gastrocnemius muscle for transgenic mouse overexpressing PPARalpha in a skeletal muscle-specific manner

Study of rat femur fracture healing in young rats (6 weeks old at fracture) at 3 days after fracture.  RNA from 2 rats was pooled for each array

Study of rat femur fracture healing in young rats (6 weeks old at fracture) as no fracture control.  RNA from 2 rats was pooled for each array

69 y/o female 46,XX. Not receiving any treatment for RhA at time of marrow

BM CD34 CELLS FROM PATIENT WITH RHEUMATOID ARTHRITIS ON METHROTREXATE

BM CD34 CELLS FROM PATIENT WITH RHEUMATOID ARTHRITIS ON METHOTREXATE

Rat liver, treated with DNP, 15 mg/kg in water per orally, extrated 48 hours after treatment, biological rep5

Rat liver, treated with NMF, 1000 mg/kg in saline i.p., extrated 48 hours after treatment, biological rep1

Comparisons: Hyperoxia effects on wild type/3 day treatment, Genotype effects on daily hyperoxia/3 day treatment

The data were analyzed with the Expression Console application from Affymetrix. We performed MAS5.0 to summarize the data.

Total RNA was extracted from the Z138 MCL cell line stable lentivirally transduced with different shRNA constructs specifically targeting SOX11 (shSOX11.1 and shSOX11.3), and two scramble shRNA constructs (shControl.1 and shControl.2) using TRIZOL. RNA quality and quantity were assessed using the Bioanalyzer 2100 and Nanodrop spectrophotometer.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HU133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol using the 3' IVT Express kit from Affymetrix.

The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).

Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.

Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)

The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).

Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.

Cyclophosphamide-treated bone marrow 5 days - Biological Replicate 5 - Technical Replicate 1

Biological replicate 5 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day 5

Cyclophosphamide-treated bone marrow 5 days - Biological Replicate 5 - Technical Replicate 2

Biological replicate 5 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated bone marrow cells, day 5

Cyclophosphamide-treated bone marrow 5 days - Biological Replicate 2 - Technical Replicate 1

Biological replicate 2 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day 5

Cyclophosphamide-treated bone marrow 5 days - Biological Replicate 2 - Technical Replicate 2

Biological replicate 2 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated bone marrow cells, day 5

Cyclophosphamide-treated bone marrow 5 days - Biological Replicate 1 - Technical Replicate 1

Biological replicate 1 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day 5

Cyclophosphamide-treated bone marrow 5 days - Biological Replicate 1 - Technical Replicate 2

Biological replicate 1 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated bone marrow cells, day 5

Cyclophosphamide-treated bone marrow 5 days - Biological Replicate 4 - Technical Replicate 1

Biological replicate 4 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day 5

Cyclophosphamide-treated bone marrow 5 days - Biological Replicate 4 - Technical Replicate 2

Biological replicate 4 of 5. Technical Replicate 2 of 2.Cyclophosphamide-treated bone marrow cells, day 5

Cyclophosphamide-treated bone marrow 5 days - Biological Replicate 3 - Technical Replicate 1

Biological replicate 3 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day 5

Cyclophosphamide-treated bone marrow 5 days - Biological Replicate 3 - Technical Replicate 2

Biological replicate 3 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated bone marrow cells, day 5

Gene Pattern (Broad Institute) software, Illumina module, Quantile normalization

Illumina® TotalPrep™ RNA Amplification Kit according to protocol

Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14938.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16220.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16205.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/17927.gif

primary unilateral non-metastatic postmenopausal ERα-positive breast tumor;woman;76 years

Cerebellum_transgenic nuclear exclusion signal Htt exon1 142Q A39_10 months_replicate 3

A39 NES 142Q TG7	F2/13	A39	NES Htt exon 1 142Q	Mouse	10 months	Cerebellum	Male

Cerebellum_transgenic nuclear localization signal Htt exon1 18Q x50_16 months_replicate 1

X50 NLS 18Q TG1	F2/34	X50	NLS Htt exon 1 18Q	Mouse	16 months	Cerebellum	Male

Cerebellum_transgenic nuclear localization signal Htt exon1 18Q x50_16 months_replicate 3

X50 NLS 18Q TG3	F2/49	X50	NLS Htt exon 1 18Q	Mouse	16 months	Cerebellum	Male

Cerebellum_transgenic nuclear localization signal Htt exon1 18Q x50_16 months_replicate 2

X50 NLS 18Q TG2	F2/35	X50	NLS Htt exon 1 18Q	Mouse	16 months	Cerebellum	Male

Wistar rat liver tissue following animal exposure to orotic acid for 3 days

Wistar rat liver tissue following animal exposure to orotic acid for 14 days

Kyoto Rat liver tissue following animal exposure to orotic acid for 14 days

Gene expression data from HepG2 cell lines after 24 hours of PCB77 treatment.

HepG2 cell line from ATCC at 8th generation after 24 hours of PCB77 treatment.

C57BL/6J Acute morphine treated, striatum, biological replicate 2

C57BL/6J Acute morphine treated, striatum, biological replicate 3

C57BL/6J Acute morphine treated, striatum, biological replicate 1

129P3/J Acute morphine treated, striatum, biological replicate 3

129P3/J Chronic morphine treated, striatum, biological replicate 3

This sample is also known as 2TA_signal.

This sample is also known as 2TB_signal.

Pathohistological and clinical examination of Patient NC04 (55 year-old male) yielded no significant pathological findings.  This patient was considered as a normal control for the purposes of the study.

Pathohistological and clinical examination of Patient NC05 (46 year-old female) yielded no significant pathological findings.  This patient was considered as a normal control for the purposes of the study.

Pathohistological and clinical examination of Patient NC02 (47 year-old female) yielded no significant pathological findings.  This patient was considered as a normal control for the purposes of the study.

Pathohistological and clinical examination of Patient NC03 (27 year-old male) yielded no significant pathological findings.  This patient was considered as a normal control for the purposes of the study.

Pathohistological and clinical examination of Patient NC01 (44 year-old male) yielded no significant pathological findings.  This patient was considered as a normal control for the purposes of the study.

C57BL/6N;Sta1 Wildtype (wt);Bone marrow derived macrophages (BMMs);none (untreated control)

White adipose tissue was dissected from all 3 genotypes after 16 weeks of high fat diet-feeding. Adipose tissue RNA samples from 3-4 mice per experimental group were used for microarray analysis.

Male wild-type (control) (C57/BL6 background) and ASC-/- and Casp1-/- mice (C57/BL6 background), aged 8-12 weeks at the start of the intervention, were maintained on a high fat diet (45 energy% of fat) for 16 weeks. After the diet intervention, mice were killed and the adipose tissue was removed.

Epidydimal white adipose tissue from Casp1-/- after 16 weeks of high fat diet feeding, replicate 1

Total RNA was prepared from mouse adipose tissue using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

The GeneChip HT MG-430 PM 24 Array Plate consists of 24 single MG-430 PM arrays arranged into standard 96 well plate format. Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations on a GeneTitan Instrument.

All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome HT_MG-430 PM arrays.

Epidydimal white adipose tissue from Casp1-/- after 16 weeks of high fat diet feeding, replicate 2

Epidydimal white adipose tissue from Casp1-/- after 16 weeks of high fat diet feeding, replicate 3

Epidydimal white adipose tissue from WT after 16 weeks of high fat diet feeding, replicate 1

C57BL/6N;Stat1 delta alpha (da);Bone marrow derived macrophages (BMMs);none (untreated control)

PC-3 L+G_1

PC-3 Luteolin_1

PC-3 Gefitinib 1

C57BL/6N;Stat1 delta beta (db);Bone marrow derived macrophages (BMMs);none (untreated control)

C57BL/6N;Stat1 KO (ko);Bone marrow derived macrophages (BMMs);none (untreated control)

mRNA extracted from lung fibroblasts derived from open lung biopsies of a patient (IPF1) with idiopathic pulmonary fibrosis (usual interstitial pneumonia pattern on biopsy). Lung fibroblasts were grown to confluence in DMEM with 10% fetal calf serum. At confluence, lung fibroblasts were serum-deprived overnight, and exposed to serum-free culture-medium with the addition of 0.1% BSA for 4 hours. At the end of treatment period total RNA was harvested, quantified, and integrity was verified by denaturing gel electrophoresis.

lung fibroblasts from a patient with idiopathic pulmonary fibrosis (IPF1)

Gene expression data from PBMC of pooled normal control subjects

Pooled PBMC sample enriched for CD8+ cells from normal control subjects (140CD8)

Gene expression data from pooled PBMC of normal control subjects enriched for CD8+ T cells

Pooled PBMC sample enriched for CD8+ cells from normal control subjects

PBMC from T cell Large granular lymphocyte leukemia patient#1352

PBMC from T cell Large granular lymphocyte leukemia patient#1375

PBMC from T cell Large granular lymphocyte leukemia patient#1233

Phytohemagglutinin-activated PBMCs from normal control subject C (CAcPBMC)

Gene expression data from PBMC of normal control subject C followig PHA+IL2 activation for 10 days

phytohemagglutinin-activated PBMCs from normal control subject C

in vitro Treatment: H2O2, Treatment Time: 8, Units of Treatment Time: hour, Dose or Concentration: 100, Units of Dose or Concentration: uM

cells_ATCC 16Lu_human lung fibroblasts_JCB_100_8_28_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

JCB_100_8_28_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

cells_ATCC 16Lu_human lung fibroblasts_JCB_100_8_43_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

JCB_100_8_43_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

cells_ATCC 16Lu_human lung fibroblasts_JCB_100_4_42_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

JCB_100_4_42_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

cells_ATCC 16Lu_human lung fibroblasts_JCB_100_8_13_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

JCB_100_8_13_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

cells_ATCC 16Lu_human lung fibroblasts_JCB_100_4_12_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

JCB_100_4_12_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

cells_ATCC 16Lu_human lung fibroblasts_JCB_100_24_30_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

JCB_100_24_30_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

cells_ATCC 16Lu_human lung fibroblasts_JCB_100_24_15_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014

JCB_100_24_15_Lung_Fibroblast_H2O2_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

Gene expression data from human colon biopsies; UC patient in remission

Human colon biopsies from UC patient in remission (involved mucosa)

Bleomycin or saline was endotracheally injected into wild type and FIZZ2 knockout mice, then the lungs were purfused with PBS and harvested for total RNA isolation.

Data was analyzed using the limma and affy Bioconductor packages implemented in the R-statistical language. RMA was used to normalize the data and fit log2 transformed expression values.

Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

gene expression profile at day 21 after saline endotracheal injection

gene expression profile at day 21 after bleomycin endotracheal injection

U2-OS human osteosarcoma cells were stably transfected with low levels of ERa. This sample represents E2 10nM treated cells for 4 hours.

U2-OS human osteosarcoma cells were stably transfected with low levels of ERa. This sample represents EtOH treated cells and was used as a control for the time-course experiment

U2-OS human osteosarcoma cells were stably transfected with low levels of ERa. This sample represents E2 10nM treated cells for 24 hours.

U2-OS human osteosarcoma cells were stably transfected with low levels of ERa. This sample represents E2 10nM treated cells for 8 hours.

Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 5.4 mM N-Nitrosodimethylamine for 48h at 37 °C.

Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 10 uM 2,3-Dimethoxy-1,4-naphthoquinone for 6h at 37 °C.

Peripheral blood cells taken from survivors 4 months after exposure to trauma.
date: 2001

pre-treatment expression profiles of a 52 year-old patient with clinical diagnosis of dermatomyositis

Peripheral blood cells taken from survivors 4 month after exposure to trauma.
date: 2002

IA, IB, II, IIIA, IIIB, or IV=IA;73;female, male:male;early gastric cancer or advanced gastric cancer=early gastric cancer;moderately differentiated or poorly differentiated=moderately differentiated;intestinal type, diffuse type, mixed type, or not determined=intestinal type;normal

IA, IB, II, IIIA, IIIB, or IV=IA;60;female, male:male;early gastric cancer or advanced gastric cancer=early gastric cancer;moderately differentiated or poorly differentiated=moderately differentiated;intestinal type, diffuse type, mixed type, or not determined=intestinal type;normal

AML blasts from bone marrow;test;mutated;M2;internal tandem duplication (ITD)

AML blasts from bone marrow;test;mutated;M1;internal tandem duplication (ITD)

AML blasts from bone marrow;training;wild-type;M2;internal tandem duplication (ITD)

AML blasts from bone marrow;training;wild-type;M5a;internal tandem duplication (ITD)

Expression VALUES were generated using RMA (Robust Multi-Array Average expression measure) using R 2.4.0; Absolute Detection (ABS_CALL) was generated using the function mas5calls of the affy package for R.

Mice were sacrificed by CO2 inhalation three days post infection with C. pneumoniae. The lungs were flushed with 10 ml of PBS applied through the right atrium of the heart to remove blood. Immediately thereafter, lungs were transferred to pre-cooled tubes placed in ethanol/dry ice bath and after homogenization, RNA was isolated using Tri-Reagent ® (T9424, Sigma) as described by the manufacturer.

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56915
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.42; Parameter Scan Time = 20:28:40; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 11116; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.42; Parameter Scan Time = 20:28:40; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 184721; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56932
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.12; Parameter Scan Time = 18:30:37; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 11959; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.12; Parameter Scan Time = 18:30:37; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 185564; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.55; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56913
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.36; Parameter Scan Time = 20:04:09; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 11091; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.36; Parameter Scan Time = 20:04:09; Parameter PMT Volts = 650; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 184696; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56914
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.51; Parameter Scan Time = 20:53:31; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 11140; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.51; Parameter Scan Time = 20:53:31; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 184745; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.55; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56930
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.03; Parameter Scan Time = 18:18:18; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 11947; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.03; Parameter Scan Time = 18:18:18; Parameter PMT Volts = 670; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 185552; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.55; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56931
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.48; Parameter Scan Time = 19:47:55; Parameter PMT Volts = 580; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 12036; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.48; Parameter Scan Time = 19:47:55; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 185641; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.55; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-09/55570
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.36; Parameter Scan Time = 18:34:20; Parameter PMT Volts = 550; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 6540; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.36; Parameter Scan Time = 18:34:20; Parameter PMT Volts = 660; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 180081; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.55; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-09/55555
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.78; Parameter Scan Time = 19:22:24; Parameter PMT Volts = 560; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 6587; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.78; Parameter Scan Time = 19:22:24; Parameter PMT Volts = 660; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 180128; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.55; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56910
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.09; Parameter Scan Time = 19:14:40; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 11042; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.45; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.09; Parameter Scan Time = 19:14:40; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 184647; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.55; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56912
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.90; Parameter Scan Time = 18:49:43; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 11018; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.90; Parameter Scan Time = 18:49:43; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 184622; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.55; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Peripheral blood mononuclear cells (PBMC) were isolated by density gradient centrifugation with Ficoll-Hypaque from freshly heparinized blood. The cells were washed in PBS and re-suspended at 1´106 cells/ml in complete medium RPMI-1640 for 48h before harvested for RNA extraction.

GeneChips were then scanned using GeneChip Scanner 3000 7G Plus 2 and Command Console Software (AGCC) version 1.0

Raw gene expression data in the generated CEL files  were then normalized using the GC Robust MultiChip Averaging (GC-RMA) algorithm as implemented in Bioconductor. To identify groups of functionally related genes that were differentially expressed, we conducted gene set analysis using the mixed effects models approach.

Total RNA was extracted from PBMC by RNeasy mini kit and treated with RNase-free DNase set, following manufacturer’s recommendation.

The biotinylated cDNA (5 µg) was fragmented and hybridized to an Affymetrix GeneChip Human Gene 1.0 ST Array

A total of 100ng of total RNA was reverse transcribed to cDNA which was then used as template in an in-vitro transcription reaction followed by fragmentation of the single stranded cDNA and labeling through a terminal deoxy-transferase reaction.  The biotinylated cDNA (5 µg) was fragmented

We transfected cells with MTDH short hairpin RNA  interference constructs provided from ORIGENE (Rockville, MD). Individual cell clones resistant to puromycin were expanded and subjected to screening of the expression of the targeted protein by Western blotting.

These cell lines were cultured in DMEM medium containing 10% fetal bovine serum and 1% penicillin/streptomycin (Gibco BRL)  at 37°C in a humidified atmosphere of 5% CO2 and 95% air.

Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade and data were collected using the using the GeneChip operating software (GCOS) v1.4.

The Partek Genomics Suite was used to perform microarray data analysis and to generate graphics (Partek GS, St. Louis, MO). Affymetrix array raw fluorescence intensity measures of gene expression were normalized and quantified using robust multi-array analysis. To identify genes differentially expressed between groups, we employed an ANOVA between the groups of interest.

mirVana miRNA Isolation Kit (Ambion, Austin, TX) RNA extraction of total RNA was performed according to the manufacturer's instructions.

Biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer (Affymetrix, Inc., Santa Clara, CA), placed onto Affymetrix Human Gene 1.0 ST array (Part No. 901085), and incubated at 45º C for 18 h with 60 rpm rotation in an Affymetrix Model 640 Genechip Hybridization Oven. Following hybridization, the arrays were washed, stained with streptavidin-phycoerythrin (Molecular Probes, Inc., Eugene, OR), signal amplified with antistreptavidin antibody (Vector Laboratories, Inc., Burlingame, CA) using the Affymetrix Model 450 Fluidics Station.

Microarray hybridizations were performed at the University of Iowa DNA Facility. Briefly, 25 nanograms total RNA was converted to SPIA amplified cDNA using the WT-Ovation Pico RNA Amplification System, v1 (NuGEN Technologies, San Carlos, CA, Cat. #3300) according to the manufacturer’s recommended protocol. The amplified SPIA cDNA product was purified through a QIAGEN QIAquick PCR Purification column (QIAGEN Cat #28104) according to modifications from NuGEN. Four ug of SPIA amplified DNA were used to generate ST-cDNA using the WT-Ovation Exon Module v1 (NuGEN Technologies, Cat #2000) and again cleaned up with the Qiagen column as above. Five micrograms of this product were fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module, v2 (NuGEN Technologies, Cat. #4200) per the manufacturer’s recommended protocol.

Gene expression data resulting from the knockdown of MTDH in Hec50co endometrial cancer cells.
1_MTDH-1_4-13-10_s2.CEL

Hec50co endometrial cancer cell line;Loss of p53, loss of hormone receptors ER and PR;Grade 3 endometrioid adenocarcinoma;MTDH knockdown

Hec50co human endometrial cancer cells with MTDH knocked down using ShRNA

lung tissue;CD-1_Nrf2 -/-;13 weeks + 5 month;2R4F whole mainstream smoke 750 µg/ml, treatment over 5 month, 3x1h exposure per day

Region of the left ventricle above the infarction (above the LAD artery)

sham surgery was performed - LAD was not ligated. sample collected after 7d surgery to control for the 7d - IR rats.

Rat underwent sham surgery for LAD occlusion/reperfusion. sample collected 7d after surgery to control for 7d IR.

U2-OS cells were stably transfected with low levels of ERbeta1-530. This sample represents E2 10 nM treated cells for 4 hours.

LAD was ligated for 30 min followed by repefusion. sample collected after 7d of reperfusion.

U2-OS cells were stably transfected with low levels of ERbeta1-530. This sample represents EtOH treated cells and was used as a control for a time-course experiment

LAD was ligated for 30 min followed by repefusion. sample collected after 2d of reperfusion.

Peripheral blood mononuclear cells were isolated from whole blood using BD Vacutainer® CPT™ Cell Preparation Tubes (Becton, Dickinson and Company, NJ, USA) according to the manufacturer's recommendations. Cells were homogenized in TRIzol® (Invitrogen, CA, US) and samples were stored in -80°C until RNA isolation.

The data were GC-RMA normalized and analyzed with GeneSpring 7.3 GX (Agilent Technologies, CA, US). After normalization and data filtering MS_11_REPL2 and MS_12_REPL2 were excluded from analysis.

RNA was extracted with RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array for 16 hours at 45°C and washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 ug total RNA (GeneChip Expression Analysis Technical Manual, 2005-2006, Affymetrix).

Gene expression data from controls representing the general population.

rat hippocampus (CA1 region), IntermediateCort, 18 months old, subject 11

Fisher 344;male;18 months;hippocampal CA1 brain;Intermediate-CORT (ADX)

OA Surgery: ACL transection and partial medial meniscectomy; Exercise protocol: 30 minutes walking on rotating cylinder 3x per week

See Affymetrix GeneChip® Expression Analysis Technical Manual. Used the GeneChip® Scanner 3000 with Workstation.

Raw data gene expression files from Affymetrix GeneChips were imported into GeneSpring, version 7.2, software (Silicon Genetics, Redwood City, CA). GC-robust multichip analysis preprocessing was performed. Raw data transformation set values <0.01 at 0.01, per-chip normalization was set at the 50th percentile, and per-gene normalization was set to the median and to values in control/sham samples. Data sets from sham-operated samples were assigned to the normal treatment group, and thus defined baseline expression for each probe. The remaining data sets (samples from contralateral and ipsilateral joints) were assigned to diseased treatment groups, averaged, and used in subsequent analysis. All data were interpreted using the log-ratio setting. From the starting list of 31,099 probes, 17,597 probes were determined to have a reliable signal, using the GeneSpring 7.2 SG1a-1 signal intensity quality control script. The script was adjusted to require signal intensity above a threshold of 50 in 2 of the 3 conditions. The data were then passed through a parametric Welch one-way analysis of variance (ANOVA) script, with P values less than 0.05 considered significant, which reduced the list to 3,877 probes. Post hoc Bonferroni multiple comparison testing was performed to identify statistically significant changes in expression between sham-operated samples and contralateral samples, and between sham-operated samples and ipsilateral samples, with P values less than 0.05 considered significant.

Tissue dissection and immediate immersion/homogenization in TRIzol. Aqueous phase transferred to QIAgen RNeasy Mini column for RNA prep.

See Affymetrix GeneChip® Expression Analysis Technical Manual. Used the GeneChip® Fluidics Station 450.

Samples underwent 2 rounds of amplification prior to labeling using the Affymetrix GeneChip® Two-Cycle cDNA Synthesis Kit.

Contralateral knee articular cartilage, 4 weeks following OA surgery

Transcriptional 2 Follicular Progenitor (T2-FP) B cells;8-12 weeks;C57/bl6-129sv;KAP1 KO

Transcriptional 2 Follicular Progenitor (T2-FP) B cells;8-12 weeks;C57/bl6-129sv;WT

Gene expression data from HEK293 cells tranfected with with an pCDNA3

Cells transfected with H133W mutant sirtuin 6 and stimulated with TNFa, biological rep2

Cells transfected with H133W mutant sirtuin 6 and stimulated with TNFa, biological rep3

Cells transfected with pCDNA3 and stimulated with TNFa, biological rep2

Gene expression data from HEK293 cells tranfected with with an pCDNA3 and stimulated with TNFa

HEK293 cells tranfected with with an pCDNA3 and stimulated with TNFa

Cells transfected with pCDNA3 and stimulated with TNFa, biological rep3

Cells transfected with pCDNA3 and stimulated with TNFa, biological rep1

Pregnant female mice were euthanized at E8.0/8.5, embryos were collected and tissue samples were quickly dissected, by sectioning with fine tweezers and freezing in liquid nitrogen. Extra-embryonic membranes were used for genotyping of the embryos. The mice used for this study harbor the Raldh2 knockout allele.

Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 3.2.
CEL files were processed with Affymetrix Expression Console software version 1.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings.

Total RNA was extracted with the RNAeasy micro Kit (Qiagen) from individual embryonic samples.

CD1;Raldh2 null mutant; Raldh2 -/-;embryonic brain;Rostral/Anterior;14 somite stage

Gene expression data from liver from 6-8 week old C57BL/6 wildtype mouse

Gene expression data from liver from 6-8 week old C57BL/6 Rap1 knockout mouse

Gene expression data from white adipose tissue from 6-8 week old C57BL/6 wildtype mouse

Grown on 6-well collagen type I coated plates.
Treatment period: 24 hr

400uM Ciprofloxacin treament for human hepatocyte donor A.  Growth media:  In vitro technologies hepatocyte incubation media (cat no. Z90009)

Vehicle:  0.1N KOH added at an equivalent volume as treatment groups

Vehicle treament for human hepatocyte donor B.  Growth media:  In vitro technologies hepatocyte incubation media (cat no. Z90009)

Macrophages were extacted from the peritoneal cavity of wildtype mice (IL-4++) infected with the nematode Brugya Malayi. AAM were extracted and treated for RNA extraction.

Study of rat femur fracture healing in older rats (52 weeks old at fracture) at 2 weeks after fracture.  RNA from two rats were pooled for each sample.

Cells were transfected with either control siRNA (siCtrl) or siRNAs targeting EZH2 (siEZH2), and maintained in androgen-depleted medium for 24 hours, and then treated with either 10 nM 5α-dihydrotestosterone (DHT, for LNCaP cells) or with ethanol only (for abl cells) for another 24 hours before the RNA was extracted.

LNCaP cells were routinely maintained in RPMI-1640 with 10% fetal bovine serum (FBS) plus 1% antibiotics (penicillin and streptomycin). LNCaP-abl (abl) cells were routinely maintained in phenol-red-free RPMI with 10% charcoal-stripped FBS plus 1% antibiotics.

The data is processed by RMA with quantile normalization.
Probes are converted to genes by averaging values of probes mapped to the same gene. Combat is used to remove the batch effect.  The Combat-Matrix.txt files are linked as supplementary files on the Series record.

Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by additional purification using RNeasy Kit (Qiagen, Cat#74104).

Following fragmentation, 15 ug of cRNA were hybridized overnight at 45ºC on Affymetrix human U133 plus 2.0 expression array. The chips were transferred to a fluidics instrument that performs washes and then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE).

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8-15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

Gene expression data from abl cells after transfection with siRNA against EZH2
abl-VEH-siEZH2-0

LNCaP-abl (abl) prostate cancer cells;depleted of EZH2;under hormone depleted conditions

Gene expression data from abl cells after transfection with control siRNA
abl-VEH-siCtrl-0

LNCaP-abl (abl) prostate cancer cells;transfected with control siRNA;under hormone depleted conditions

abl cells transfected with control siRNA under hormone depleted conditions

control;Brain;Ventral midbrain;Postmortem;hypertensive cardiomyopathy

Scanning of microarrays was performed with 5Âµm resolution and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1.1, Agilent Technologies). The probe-level normalized/processed data are included in the LogRatio column of the Agilent Feature Extraction files (ie, normalized log10 Cy5/Cy3 ratios).

Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier. Briefly, samples were homogenized in 1 ml TRIzol, shock frozen and stored at â€“80Â°C. The homogenates were thawed and further processed for total RNA isolation as described by the manufacturer.

After precipitation, purification and quantification, 1.25Âµg labeled samples were mixed and hybridized according to the supplierâ€™s protocol (Agilent Technologies).

Total RNA labeling was performed with the two color Quick Amp Labeling Kit (Agilent Technologies). In brief, mRNA was reverse transcribed and amplified using an oligo-dT-T7-promotor primer and the resulting cRNA was labeled either with Cyanine 3-CTP or Cyanine 5-CTP.

206;Asacol 800mg BD;9/10/59;F;CAUCASIAN;1/1/79;1/1/80;FALSE;FALSE;TRUE;NO;FALSE;FALSE;10/8/04;3;0;0;0;0;0;0;0;FALSE;2;BOTH;unknown;unknown;unknown;unknown;10/8/04;BOTH;unknown;unknown;unknown;unknown;12/9/04;DISEASE IN REMISSION;ex;1/1/94;5-14;None;UC;1-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

203;Asacol 800mg BD, Simvastatin;1/10/35;M;CAUCASIAN;11/1/92;3/23/93;FALSE;FALSE;TRUE;NO;FALSE;FALSE;10/1/04;1;0;14;0;147;6;4;0;FALSE;0;HISTOLOGICAL;HISTOLOGICAL;HISTOLOGICAL;unknown;unknown;10/1/04;BOTH;BOTH;unknown;unknown;unknown;12/9/04;DISEASE IN REMISSION;ex;1/1/50;1/1/57;25+;None;UC;1-25-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

202;Sulphasalazine 3g/d, Folic Acid 5mg/d, HRT, DF118;10/3/50;F;CAUCASIAN;1/1/68;1/1/69;TRUE;TRUE;FALSE;YES;FALSE;FALSE;9/30/04;2;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;BOTH;BOTH;BOTH;9/30/04;unknown;unknown;unknown;unknown;unknown;12/9/04;DISEASE IN REMISSION;never;unknown;Polymyalgia rheumatica;UC;1-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

216;NONE;5/10/36;M;CAUCASIAN;2/19/66;8/20/66;FALSE;FALSE;FALSE;NO;FALSE;FALSE;11/18/04;0;0;0;0;0;0;0;0;FALSE;0;11;11;11;11;11;11;11;11;12;BOTH;BOTH;BOTH;unknown;unknown;11/18/04;unknown;unknown;unknown;unknown;unknown;12/9/04;DISEASE IN REMISSION;never;unknown;NONE;UC;5-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

213;PRED 7MG, ATENOLOL 100MG, ASPRIN 75MG, SIMVASTATI;11/1/43;M;CAUCASIAN;3/1/82;2/2/83;FALSE;FALSE;FALSE;YES;FALSE;FALSE;11/12/04;0;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;unknown;unknown;unknown;11/12/04;COLONOSCOPIC;unknown;unknown;unknown;unknown;12/9/04;DISEASE IN REMISSION;ex;1/1/74;unknown;ISCHEAMIC HEART DISEASE;UC;5-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

Human chondrocytes were isolated by enzymatic digestion. Minced cartilage was digested for 16 hours in a spinner bottle in 10 ml of culture medium containing clostridial collagenase (1 mg per milliliter [150 U per liter]) and deoxyribonuclease I (0.1 mg per milliliter [25,000 U per liter]). . For scaffold culture, 2x106 chondrocytes of passage 2 were per cm2 were seeded in Hyaff-11 and were maintained under serum-free chondotions in presence of TGFbeta 1.

Human chondrocytes obtained from non-weight bearing area of 3 donors undergoing ACT treatment (normal donor) and from biopsies of 3 donors undergoing total knee replacement (OA donors) were expanded by cultivation in DMEM/F12 supplemented with L-ascorbic acid (0.025 mg/ml, gentamicin sulphate (50 mg/l), amphotericin B (250 µg/ml) and L-glutamine (2 mM; Gibco) and 10% human serum for 2 passages,  3D cultured in Hyaff-11 scaffolds for 14 days in DMEM high glucose supplemented with 5.0 µg/ml linoleic acid, insulin-transferrin-selenium-G, 1.0 mg/ml human serum albumin, 10 ng/ml  transforming growth factor beta 1 (TGF-b1), 10-7 M dexamethasone , 14 µg/ml L-ascorbic acid and 1% penicillin-streptomycin

Data were processed with GCOS 1.4 (TGT = 150) and subsequently imported and further analyzed in the BioRetis online database (www.bioretis.de).

Total RNA from chondrocytes cultured in monolayer (passage 2) was isolated applying protocols for animal tissues of the RNeasy Mini Kit (Qiagen, Hilden, Germany). For scaffold cultures, an 8 mm punch was prepared, snap-frozen in liquid nitrogen, and stored at -80°C until further use. Frozen samples were transferred to 1 ml TriReagent (Sigma-Aldrich) and mechanically homogenized. Subsequently, 133 µl 1-Bromo-3-chloro-propane (Sigma-Aldrich) was admixed followed by centrifugation for 45 min at 13000xg. The aqueous phase was collected and nucleic acids were precipitated by addition of an equal volume ice-cold isopropanol. After 30 min incubation the precipitated nucleic acids were pelletized and resolved in 350 µl RLT buffer (Qiagen). Further purification was performed according to protocols for animal tissues of the RNeasy Mini Kit (Qiagen). RNA from each donor was separately handled; no pooling was done at any stage.

50µg/ml of labeled cRNA was hybridized at 45°C for 16h using the Affymetrix GeneChip hybridization oven. Washing and staining was performed on the Affymetrix Fluidics 450 using the EukGE-WS2v5 protocol.

2 µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix)

ND_3_Chon_Med_P2_133P
human chondrocytes cultured in DMEM/F12 supplemented with L-ascorbic acid (0.025 mg/ml, gentamicin sulphate (50 mg/l), amphotericin B (250 µg/ml) and L-glutamine (2 mM; Gibco) and 10% human serum for 2 passages; normal donor group (46-52 years, no pre-existing history of OA, macroscopically healthy cartilage, undergoing ACT treatment)
human chondrocytes isolated from the non-weight bearing area of the knee cartilage of patients undergoing ACT treatment, subcultured up to passage 2 (primary cells = passage 0), monolayer culture from normal donor 3

OA_1_Chon_Med_P2_133P
human chondrocytes cultured in DMEM/F12 supplemented with L-ascorbic acid (0.025 mg/ml, gentamicin sulphate (50 mg/l), amphotericin B (250 µg/ml) and L-glutamine (2 mM; Gibco) and 10% human serum for 2 passages; OA donor group (60-64 years, symptoms of severe OA, undergoing total knee replacement, radiological evidence of OA, OA grade 2-3 according to Ahlbäck, and exhibiting a Mankin score above 3)
human chondrocytes isolated from cartilage biopsies from patients undergoing total knee replacement, subcultured up to passage 2 (primary cells = passage 0), monolayer culture from OA donor 1

ND_1_Chon_Med_P2_133P
human chondrocytes isolated from the non-weight bearing area of the knee cartilage of patients undergoing ACT treatment, subcultured up to passage 2 (primary cells = passage 0), monolayer culture from normal donor 1

ND_2_Chon_Med_P2_133P
human chondrocytes isolated from the non-weight bearing area of the knee cartilage of patients undergoing ACT treatment, subcultured up to passage 2 (primary cells = passage 0), monolayer culture from normal donor 2

ND_1_Chon_CHyaff_D14_133P
human chondrocytes cultured in DMEM/F12 supplemented with L-ascorbic acid (0.025 mg/ml, gentamicin sulphate (50 mg/l), amphotericin B (250 µg/ml) and L-glutamine (2 mM; Gibco) and 10% human serum for 2 passages, 3D culture in Hyaff-11 scaffolds for 14 days maintained in DMEM high glucose supplemented with 5.0 µg/ml linoleic acid, insulin-transferrin-selenium-G, 1.0 mg/ml human serum albumin, 10 ng/ml  transforming growth factor beta 1 (TGF-b1), 10-7 M dexamethasone , 14 µg/ml L-ascorbic acid and 1% penicillin-streptomycin; normal donor group (46-52 years, no pre-existing history of OA, macroscopically healthy cartilage,  undergoing ACT treatment)
human chondrocytes isolated from non-weight bearing area of the knee cartilage of patients undergoing ACT treatment, subcultured up to passage 2 (primary cells = passage 0), seeded onto hyaff-11 scaffold, maintained for 14 days in the presence of TGFbeta 1,  chondrocytes obtained from normal donor 1

human subcultured chondrocytes (passage 2) from normal donors maintained for 14 days in scaffold culture

ND_2_Chon_CHyaff_D14_133P
human chondrocytes isolated from non-weight bearing area of the knee cartilage of patients undergoing ACT treatment, subcultured up to passage 2 (primary cells = passage 0), seeded onto hyaff-11 scaffold, maintained for 14 days in the presence of TGFbeta 1,  chondrocytes obtained from normal donor 2

OA_2_Chon_Med_P2_133P
human chondrocytes cultured in DMEM/F12 supplemented with L-ascorbic acid (0.025 mg/ml, gentamicin sulphate (50 mg/l), amphotericin B (250 µg/ml) and L-glutamine (2 mM; Gibco) and 10% human serum for 2 passages, OA donor group (60-64 years, symptoms of severe OA, undergoing total knee replacement, radiological evidence of OA, OA grade 2-3 according to Ahlbäck, and exhibiting a Mankin score above 3)
human chondrocytes isolated from cartilage biopsies from patients undergoing total knee replacement, subcultured up to passage 2 (primary cells = passage 0), monolayer culture from OA donor 2

OA_3_Chon_Med_P2_133P
human chondrocytes isolated from cartilage biopsies from patients undergoing total knee replacement, subcultured up to passage 2 (primary cells = passage 0), monolayer culture from OA donor 3

ND_3_Chon_CHyaff_D14_133P
human chondrocytes isolated from non-weight bearing area of the knee cartilage of patients undergoing ACT treatment, subcultured up to passage 2 (primary cells = passage 0), seeded onto hyaff-11 scaffold, maintained for 14 days in the presence of TGFbeta 1,  chondrocytes obtained from normal donor 3

OA_1_Chon_CHyaff_D14_133P
human chondrocytes cultured in DMEM/F12 supplemented with L-ascorbic acid (0.025 mg/ml, gentamicin sulphate (50 mg/l), amphotericin B (250 µg/ml) and L-glutamine (2 mM; Gibco) and 10% human serum for 2 passages, 3D culture in Hyaff-11 scaffolds for 14 days maintained in DMEM high glucose supplemented with 5.0 µg/ml linoleic acid, insulin-transferrin-selenium-G, 1.0 mg/ml human serum albumin, 10 ng/ml  transforming growth factor beta 1 (TGF-b1), 10-7 M dexamethasone , 14 µg/ml L-ascorbic acid and 1% penicillin-streptomycin; OA donor group (60-64 years, symptoms of severe OA, undergoing total knee replacement, radiological evidence of OA, OA grade 2-3 according to Ahlbäck, and exhibiting a Mankin score above 3)
human chondrocytes isolated from non-weight bearing area of the knee cartilage of patients undergoing ACT treatment, subcultured up to passage 2 (primary cells = passage 0), seeded onto hyaff-11 scaffold, maintained for 14 days in the presence of TGFbeta 1,  chondrocytes obtained from OA donor 1

human subcultured chondrocytes (passage 2) from OA donors maintained for 14 days in scaffold culture

Gene expression data from mouse bone marrow-derived mast cells treated with IL3, rep 6 of 6.

In-house BALB/c mice; Gender: Male; Age: 4 months old; Tissue: Brain; Treatment: 4 hours post saline ip.

The adult mouse was injected intraperitoneal (ip) with Escherichia coli lipopolysaccharide (LPS, 0.33mg/kg body weight (BW), ~10ug/mouse; serotype O127:B8, Sigma) and was killed 4 hours after injection by CO2 asphyxiation. Brain was removed, separated in half at the longitudinal fissure, frozen in liquid nitrogen and stored at -80C until use.

In-house BALB/c mice; Gender: Male; Age: 4 months old; Tissue: Brain; Treatment: 4 hours post LPS 0.33mg/kg BW ip.

Carrier-injected C57BL/6, replicate 2

GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 7G.

The data were analyzed with RMA Express using the default CDFRME file and settings (Background Adjust - Yes, Normalization - Quantile, Summarization Method - Median Polish, Store Residuals - unchecked).

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Ribavirin was added directly to the media and cells were expoed to drug for 24 hours at a concentration of 100 ug/mL

Cells were grown in 12 well dishes in DMEM, 10% FBS, 1% Antibiotic. 150,000 cells were seeded.

RNA was extracted using the Quiagen RNeasy RNA isolation kit (Valencia, CA)

Expression data was extracted using the GeneChip Operating System v 1.1 (Affymetrix). All GeneChips were scaled to a median intensity setting of 500.

The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides using an In Vitro Transcription kit (Affymetrix). The resultant cRNA product was purified using an RNeasy column (Qiagen) and quantified with a spectrophotometer. The cRNA target (20ug) was incubated at 94ºC for 35 minutes in fragmentation buffer (Tris, MgOAc, KOAc). The fragmented cRNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20, Herring Sperm DNA, Acetylated BSA) containing biotin-labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix). The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes and then injected into a GeneChip cartridge. The GeneChip array was incubated at 42°C for at least 16 hours in a rotating oven at 60 rpm. GeneChips were washed with a series of nonstringent (25°C) and stringent (50°C) solutions containing variable amounts of MES, Tween20 and SSPE. The microarrays were then stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution.

Target was prepared and hybridized according to the Affymetrix Technical Manual. Total RNA (10 ug) was converted into cDNA using Reverse Transcriptase (Invitrogen) and a modified oligo(dT)24 primer that contains T7 promoter sequences (GenSet).

Array normalization, expression value calculation and clustering analysis were performed using DNA-Chip Analyzer (dChip). The Invariant Set Normalization method was used to normalize arrays at probe cell level to make them comparable, and the model-based method was used for probe-selection and computing expression values.

Total RNA was isolated from cells or tissues using Trizol (Invitrogen).

The purified cRNA was fragmented for hybridization and purified by phenol/chloroform extraction and ethanol precipitation. The fragmented cRNA and several biotinylated control oligonucleotides (for quality control) were hybridized to a mouse 430_2 chip overnight at 45C.

cDNA was prepared using a T7 promoter-tailed oligo-dT primer, followed by second strand synthesis. Double-stranded cDNA was used as the template for in vitro transcription (IVT) catalyzed by T7 polymerase and containing biotinylated CTP and UTP. Biotinylated complementary RNA (cRNA) is purified using the RNeasy system (Qiagen).

Subject Age : 44

Subject Age : 28

Subject Race : ASIAN

Subject Age : 39

Subject Age : 40

Wt Mouse_cerebellum_Old_nicotinamide riboside treatment_Replicate-4

Sample name: OLD-Wt_NR-27

Wt Mouse_cerebellum_Old_nicotinamide riboside treatment_Replicate-5

Sample name: OLD-Wt_NR-28

Csbm/m Mouse_cerebellum_Young_nicotinamide riboside treatment_Replicate-3

Sample name: YOUNG-CSB_NR-7

Sample name: YOUNG-CSB_ctrl-2

High;170.4 cm;51.5 kg;17.6;13.88 years;Male;White;196 mg/dl;6.2%

Sense Control siRNA (Ambion);Human epithelial colonic adenocarcinoma, Caco-2

Data analyses were done with the use of MeV (v4.2) (Saeed et al., 2003 Biotechniques 34, 374-378).

Total RNA was extracted with the RNeasy Micro Kit (QIAGEN) according to the manufacturer's instructions.

peripheral CD4+CD25hi cells;Cbfb-flox/flox, Foxp3-ires-Cre;male;5 weeks;purified CD4+CD25hi cells from spleen and lymph nodes

peripheral CD4+CD25hi cells;Cbfb-flox/wt, Foxp3-ires-Cre;male;5 weeks;purified CD4+CD25hi cells from spleen and lymph nodes

peripheral CD4+CD25hi cells;Cbfb-flox/wt, Foxp3-ires-Cre;male;16 weeks;purified CD4+CD25hi cells from spleen and lymph nodes

For individual experiments, murine BMDMs or adherence purified PECs were plated at either 0.5 x 106/mL or 1 x 106/mL in supplemented DMEM medium.  Cells were left unstimulated (as a control) or stimulated with lipopolysaccharide (LPS) from Escherichia coli (0111:B4, 1 μg/mL) for various time-points at 37°C, 5% CO2.  For inhibition studies, BMDMs were pre-treated with the following inhibitors in supplemented DMEM medium for 30 min at 37°C, 5% CO2 prior to stimulation with LPS:  LY-294,002 hydrochloride, 20 μM (Sigma); Rapamycin, 30 nM (Sigma); U0126 ethanolate, 20 μM (Sigma).

BM was harvested from tibiae and femurs of mice by flushing with supplemented DMEM using a 10 mL syringe and 25-gauge needle.  Cells were disaggregated by gentle pipetting and centrifuged at 1200 rpm for 10 min at RT.  The cells were then re-suspended in ACK lysing buffer (Invitrogen) for 30 sec to lyse red blood cells.  Cells were washed in PBS (20-30 mL) and centrifuged again at 1200 rpm for 10 min. Cell pellet was resuspended in supplemented DMEM for cell counting.  Differentiated macrophages were obtained by culturing BM cells on sterile petri dishes at 2 x 106/mL in supplemented DMEM with the addition of macrophage colony-stimulating factor (M-CSF; 10 ng/mL) for 7-10 days at 37°C, 5% CO2.  Cells were adherence purified on day 7-10 by removing media, washing adherent cells with PBS and then harvesting by incubating in 10 mL cell dissociation buffer (Invitrogen) for 15 min at 37°C.  Plates were washed with PBS to collect dislodged cells, and cells were centrifuged at 1200 rpm for 10 min. Cell pellets were resuspended in supplemented DMEM for cell counting.

Expression values were determined with GeneChip Operating Software (GCOS) v1.1.1 software. All data analysis was performed using GeneSpring software GX 11.0. Expression values for each probe were normalized using the Robust Multichip Average (RMA) method.

Total cellular RNA was extracted using an RNeasy Mini kit (Qiagen).

Approximately 10 ug of biotinylated cRNA was hybridized to GeneChip Mouse Genome 430 2.0 arrays (Affymetrix) at 45 degree for 16 hours in accordance with the manufacturer’s protocols

Approximately 10 ug of total RNA was labeled using MessageAmp™ II-Biotin Enhanced Kit (Ambion)

mouse embryonic fibroblasts (MEFs);KSR1 -/-;H-RasV12 and GFP;DBA

gene expression data from 4 weeks old wildtype mouse hind limb skeletal muscle

ID = C502
Stage 1B (DOD)
Total RNA

ID = C512
Stage 2A
Total RNA

ID = C517
Stage 1B
Total RNA

ID = C524
Stage 1B
Total RNA

ID = C494
Stage 1B
Total RNA

ID = C495
Stage 2A (DOD)
Total RNA

ID = C496
Stage 3B (DOD)
Total RNA

ID = C525
Stage 1B
Total RNA

ID = C538
Stage 2A
Total RNA

C3_2h_7

C4_2h_6

Samples from healthy donors were pooled before hybridization.
Then hybridized to Affymetrix HG U95 Av2 GeneChip using Affymetrix fluidics station according to the instructions of the manufacturer

C2_24h_38

C3_24h_12

C4_24h_10

C5_24h_5

C6_24h_8

C1_2h_3

C2_2h_30

C2C12 myoblasts differentiated with 2% horse serum for 5 days.  Treated for 16 hrs with 500 micromolar Palmitate.  RNA collected using Rneasy (Qiagen) protocol.

Grown in DMEM + 20% FBS to confluence.  Then, media is changed to differentiation media (see above).

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse M430A version 2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Gene expression data from Mouse C2C12 Myoblasts differentiated into Myotubes and treated for 16 hrs.

19B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

20B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

22B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

C57BL/6;Nrf2 KO;Male;9 weeks;kidney;intraperitoneally injected with a single dose of cisplatin (15 mg/kg body weight)

According to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA)

Fluorescent signals were detected by the GeneChip Scanner 3000 and recorded and computed by GeneChip Operating Software (GCOS) version 1.4 (Affymetrix)

C57BL/6;WT;Male;9 weeks;kidney;intraperitoneally injected with a single dose of cisplatin (15 mg/kg body weight)

Freshly isolated lymphoma cells were retrovirally transduced by Bcl2 (MSCVpuro) and selected with Puromycin for 48h. These Myc;Bcl2 cells were either left untreated or treated in vitro with 0.05µg/ml Adriamycin for 5 days.

Primary Emu-myc;Suv39h1-/- lymphoma cells were cultivated in B-cell medium (DMEM and IMDM in 1:1 ratio, 10%FBS, 4mM L-glutamine, 25µM beta-mercaptoethanol, 100U/ml penicilin/streptamycin) on gamma-irradiated (20Gy) NIH 3T3 cells as feeder.

The total RNA from untreated or 5 days ADR treated Myc;Bcl2 lymphomas was prepared using an RNeasy Mini kit (QIAGEN, Valencia, California) according to the manufacturer's instructions.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on MOE430 2.0 Arrays (Affymetrix). GeneChips were washed and stained with standard protocols in the Affymetrix Fluidics Station 450.

Biotinylated cRNA was prepared according to the standard Affymetrix protocol (One Cycle Target labeling protocol) from 3 ug total RNA.

Primary lymphoma cells isolated from lymph nodes of Emu-myc; Suv39h1-/- mice with palpable lymphadenopathy.

Emu-myc;Suv39h1-/-;Bcl2;primary lymphoma cells from lymph nodes;none

Primary lymphoma cells, isolated from lymph nodes of Emu-myc,Suv39h1-/- mice and retrovirally transduced by Bcl2, untreated

Emu-myc;Suv39h1-/-;Bcl2;primary lymphoma cells from lymph nodes;Adriamycin (ADR)

Primary lymphoma cells, isolated from lymph nodes of Emu-myc,Suv39h1-/- mice and retrovirally transduced by Bcl2, ADR treated

Peripheral blood mononuclear cells;systemic JIA;GTE6;112min;White;Male

Peripheral blood mononuclear cells;systemic JIA;GTE6;125min;White;Female;94

Peripheral blood mononuclear cells;RF- polyarticular JIA;GTE6;95min;Asian;Female

Peripheral blood mononuclear cells;RF- polyarticular JIA;GTE6;160min;White;Female

Peripheral blood mononuclear cells;RF- polyarticular JIA;LT6;85min;White;Female

Peripheral blood mononuclear cells;TTF=117min;Race=White;Sex=Male

Peripheral blood mononuclear cells;RF- polyarticular JIA;LT6;120min;White;Female

Small intestinal ileal sections were fixed in methacarn and embedded in paraffin.

GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)

The data were RMA-normalized with GeneSpring GX from Agilent technologies (included in sample data table) and further analyzed using differential expression cutoff of 1.33 fold (provided in the final_data.txt).

The Leica LMD6000 Laser Microdissection system was used to capture crypt base epithelial cells and total RNA was extracted using the Arcturus PicoPure RNA isolation kit.

Following fragmentation and labeling, cDNA was hybridized using the GeneChip WT Terminal Labeling and Hybridization kit

Biotinylated cDNA were prepared according to the standard protocol from 100ng total RNA (Ambion WT expression kit)

C57BL/6J;Nod2-/-;8 weeks;small intestine;laser captured Paneth cells

Fourth ventricular choroid plexus from wildtype mice at E13, biological replicate 4

Gene expression data from fourth ventricular choroid plexus of wildtype mice

Fourth ventricular choroid plexus from wildtype mice at E13, biological replicate 2

Fourth ventricular choroid plexus from wildtype mice at E13, biological replicate 3

Fourth ventricular choroid plexus from Otx2ko mice at E13, biological replicate 4

Gene expression data from fourth ventricular choroid plexus of Otx2 k.o. mice

Otx2 deficient mouse strain (Puelles et al., 2003, Nature Neuroscience Vol 6(5))

Fourth ventricular choroid plexus from wildtype mice at E13, biological replicate 1

Lot batch = rat 22

Lot batch = rat 27

Lot batch = rat 24

Lot batch = rat 11

Nanog transgene expression was induced in mice by replacing normal drinking water with 7.5% sucrose solution containing doxycycline (0.2 mg/ml) for 48 h.

Processed Microarrays were scanned on a G2565C DNA microarray scanner (Agilent) and images were analyzed with Agilent Feature Extraction Software (version 10.1.1), which performed feature quantification and additive detrend correction.

Microarray background subtraction was carried out using normexp method. Normalization was performed using quantiles. Differentially expressed genes were obtained by applying linear models with R limma package (Bioconductor project, http://www.bioconductor.org).
Reference: Smyth, G. K. (2005). Limma: linear models for microarray data. In: 'Bioinformatics and Computational Biology Solutions using R and Bioconductor'. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds), Springer, New York, pages 397-420
To account for multiple hypotheses testing, the estimated significance level (p value) was adjusted using Benjamini & Hochberg False Discovery Rate (FDR) correction.

Total cellular RNA was extracted from esophagus using RNeasy Fibrous Tissue Mini Kit (Qiagen), and from liver by combining an initial lysis with Trizol (Invitrogen) with a clean-up with RNeasy Kit (Qiagen). RNA Integrity Numbers (RINs) were in the range 7.3 to 9.5 when assayed on an Agilent 2100 Bioanalyzer

Labeled samples were hybridized to Whole Mouse Genome 4x44K microarrays (Agilent microarray design ID 014868, P/N G4122F)

Total RNA (1 µg) was labeled with the One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) kit (Agilent) following the manufacturer´s instructions. Labeled samples were purified with silica-based RNeasy spin columns (Qiagen)

Sample_ID:n12 // Patient:J-191 // Histology:Normal // Metastasis:NA // p53_mut:NA // E-cadherin_mut:NA // beta-Catenin_mut:NA

Cells were exposed to 10 µM of 2-OH-BDE85 dissolved in 0.1% dimethyl sulfoxide (DMSO) for 24 hours.

AFGE1068-12.CEL

AFGE1068-11.CEL

Embryonic stem cells were reverse transfected with siRNA, 48 hrs post transfection cells were isloated for RNA extraction and hybridization on Affymetrix microarrays

Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using dChip program. No further adjustments were made to the data in the table.

Qiagen RNEasy Plus mini Kit  was used to extract total cellular RNA according to the manufacturer's protocol, and the RNA was amplified and converted into cDNA using the Ovation Amplification v2 and Biotin cDNA Biotin systems

3.75 mcg of biotin-labeled cDNA were hybridized for 16 hrs onto the GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix)

5 ng total RNA was amplified by Nugen Ovation RNA amplification system V2 and the resulting cDNA biotin-labeled using the FL-Ovation™ cDNA Biotin Module V2

Reverse transfection of siRNA with a final concentration of 10 nM was performed in a 24-well plate with 30,000 cells/well by using Lipofectamine RNAiMAX (Invitrogen) according to the manufacturer's instructions. PAX3 siRNA, Ambion ID#215907, sense, GCCGCAUCCUGAGAAGUAAtt, antisense, UUACUUCUCAGGAUGCGGCtg; MITF siRNA, Ambion ID#3816, sense,GGACAAUCACAACCUGAUUtt, antisense, AAUCAGGUUGUGAUUGUCCtt; GL2 luciferase siRNA, Dharmacon Research Inc, target sequence 5'-AACGUACGCGGAAUACUUCGA-3'. Transfection efficiency determined by using the fluorescently labelled luciferase control siRNA was >90%. RNA was isolated from siRNA-treated cells and media-only controls 30 hours post-transfection.

The data was processed with the ExpressionFileCreator module of GenePattern by using the RMA method with quantile normalization and background correction.

Trizol extraction and Qiagen RNeasy column purification according to the manufacturer's instructions.

Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45°C on U133 Plus 2.0 GeneChip arrays. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared from 200 ng total RNA by using an Ambion MessageAmp Premiere kit according to the manufacturer's instructions.

Gene expression data from untreated NZM12 metastatic melanoma cells

skin;NZM12;metastatic melanoma;small intestine;media-only control

Gene expression data from NZM12 metastatic melanoma cells treated with siRNA targeting PAX3

Gene expression data from NZM12 metastatic melanoma cells treated with siRNA targeting MITF

Sample_ID:n09 // Patient:J-128 // Histology:Normal // Metastasis:NA // p53_mut:NA // E-cadherin_mut:NA // beta-Catenin_mut:NA

C2C12 myoblasts were seeded in 100 mm dishes in basal media and incubated for 72 hr at 37°C.  Basal media: Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum, 1% antibiotics and 4 mM L-glutamine.

C2C12 myoblasts were incubated in basal media for 72 hr at 37°C.

The scanned image was converted into numerical values of the signal intensity (Signal) and into categorical expression level measurement (Absolute Call) using the Affymetrix MAS 5.0 software.  The MAS 5.0 statistical algorithm parameters used to attribute the Absoute Calls were set to 0.05 for Alpha 1, 0.065 for Alpha 2 and 0.015 for Tau.  The software scaled the average intensity of all genes of each chip to a target intenisty of 150.

Following fragmentation, 10?g of labeled cRNA were hybridized at 45°C for approximately 16 hr to Gene Chip Mouse Genome 430 2.0 Expression Array (Affymetrix).  The arrays were stained on Gene Chip Fluidics Workstation 450.

Biotinylated cRNA were prepared according to the manufacturer's instructions (Bioarray High yield T7 DNA transcirption kit, ENZO Life Sciences, Inc.)

Gene expression data from undifferentiated C2C12 myoblasts incubated in basal media for 72 hr.

Sample_treatment_protocol_ch1 = C2C12 myoblasts were seeded in 100 mm dishes in basal media and incubated for 72 hr at 37°C.  Basal media: Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum, 1% antibiotics and 4 mM L-glutamine.

C2C12 myoblasts were seeded in 100 mm dishes in pyruvate test media and incubated for 72 hr at 37°C.  Pyruvate test media:  DMEM with no sodium pyruvate supplemented with 10% fetal bovine serum, 1% antibiotics, 4 mM L-glutamine and 50 mM sodium pyruvate.

C2C12 myoblasts were incubated in pyruvate test media for 72 hr at 37°C.

Gene expression data from undifferentiated C2C12 myoblasts incubated in pyruvate test media for 72 hr.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

HepG2 cells treated with 2.5 microMolar 5-aza-dC for 4 days, with medium replaced daily

GeneChips were scanned using the Affymetrix GeneChip? Scanner 3000

E14 (129P2/OlaHsd background),;Wild (Phgdh+/+), C57BL/6J background,;13.5 days,;head

human cellular RNA_primary airway epithelial cells_tracheobronchial _H465_2h_1mM_HG-U133A_2_YCHSUP501

H465_2h_1mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;21.123;2.13

Sample Type: human cellular RNA, Cell Line: primary airway epithelial cells, Cell Type: tracheobronchial

human cellular RNA_primary airway epithelial cells_tracheobronchial _H465_2h_4mM_HG-U133A_2_YCHSUP501

H465_2h_4mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;18.308;2.12

human cellular RNA_primary airway epithelial cells_tracheobronchial _H465_2h_Con_HG-U133A_2_YCHSUP501

H465_2h_Con_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;11.938;2.09

human cellular RNA_primary airway epithelial cells_tracheobronchial _H465_6h_0.4mM_HG-U133A_2_YCHSUP501

H465_6h_0.4mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;23.999;2.12

human cellular RNA_primary airway epithelial cells_tracheobronchial _H421_6h_1mM_HG-U133A_2_YCHSUP501

H421_6h_1mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;26.040;2.11

human cellular RNA_primary airway epithelial cells_tracheobronchial _H421_6h_4mM_HG-U133A_2_YCHSUP501

H421_6h_4mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;23.131;2.11

human cellular RNA_primary airway epithelial cells_tracheobronchial _H421_6h_Con_HG-U133A_2_YCHSUP501

H421_6h_Con_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;27.651;2.11

human cellular RNA_primary airway epithelial cells_tracheobronchial _H465_2h_0.4mM_HG-U133A_2_YCHSUP501

H465_2h_0.4mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;10.008;2.11

human cellular RNA_primary airway epithelial cells_tracheobronchial _H465_6h_1mM_HG-U133A_2_YCHSUP501

H465_6h_1mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;25.920;2.12

Gene expression data from MCF-7 cells, siGL3 treatment 72h, 10 nM E2 for 24h

Oral Squamous cell Epithelium Tissue-Normal;OSCC-2;Floor of Mouth;58;F;T2N0M0;TNM,Tumor-node-metastasis

3496_E_30_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siERK2 treatment 60h, 10 nM E2 for 24h

3499_E_31_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siERK1 treatment 60h, 0.1%EtOH for 24h

3500_E_26_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siERK2 treatment 60h, 0.1%EtOH for 24h

3493_E_29_(HG-U133A_2).CEL

3498_E_35_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siERK1 treatment 60h, 10 nM E2 for 24h

3492_E_32_(HG-U133A_2).CEL

3491_E_34_(HG-U133A_2).CEL

H15.24hrSFM
Reanalysis of GSM183425.

H14.24hrSFM
Reanalysis of GSM183424.

H17.24hrE2
MCF-7 cells were plated in 10cm dishes and then switched to SFM on the next day.  Following overnight starvation, cells were treated in triplicate with E2 (10nM) for 24hr.

H16.24hrE2

H8.3hrIGF
MCF-7 cells were plated in 10cm dishes and then switched to SFM on the next day.  Following overnight starvation, cells were treated in triplicate with IGF-I (100ng/mL)  for 3hr.
Reanalysis of GSM183427.

H7.3hrIGF
Reanalysis of GSM183426.

H13.24hrSFM
Reanalysis of GSM183423.

H9.3hrIGF
Reanalysis of GSM183428.

H19.24hrIGF
Reanalysis of GSM183429.

H18.24hrE2

Keywords = nuclear receptor

3_MTDH-3_4-13-10_s2.CEL

2_MTDH-2_4-13-10_s2.CEL

5_MTDHplus2_4-13-10_s2.CEL

Hec50co endometrial cancer cell line;Loss of p53, loss of hormone receptors ER and PR;Grade 3 endometrioid adenocarcinoma;control

Hec50co human endometrial cancer cells with a control scrambled ShRNA

4_MTDHplus1_4-13-10_s2.CEL

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D72 (30 days post-EBRT);8

Embryos of the appropriate stage were manually selected under the dissecting scope. Four different genotypes of embryos at E11.5 (XY WT, XX WT, XY Cbx2 KO, and XX Cbx2 KO) were frozen in OCT compound (Sakura Finetechnical, Japan) without fixation. They were sectioned to 30 μm slices and stained with hematoxylin.The developing gonadal cells localized by GATA4 immunostaining and morphology were prepared using a Laser Microdissection System (Leica, Germany). The specimens prepared from two or three individuals were combined into one group, and three groups were prepared for each genotype.

Cbx2 KO embryos were generated by heterozygous mice for Cbx2 KO crossing. To stage the embryos accurately, tail somites were counted.

Obtained images files were analysed using Affymetrix data suite system, Expression Console (EC) version 1.1. The data were normalized with the RMA (Robust Multichip Average) normalization method in the R statistical package affy. The expression measure is calculated in log base 2 scale.

RNeasy micro kit (QIAGEN) of total RNA was performed according to the manufacturer's instructions.

Fifteen micrograms of labeled cRNA was fragmented and hybridized to the GeneChip® Mouse Genome 430 2.0 array according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA). GeneChips were washed with R-Phycoerythrin Streptavidin and The GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

Total RNAs (15 ng) prepared from these groups were subjected to two-cycle amplification and biotin labeling using MessageAmp™ II aRNA Amplification and MessageAmp™ II-Biotin Enhanced Kit (Ambion, USA), respectively.

Initiation of sexually dimorphic transcription
Gene expression data from embryonic gonads at E11.5.

kidneys were microdissected on day 15.5, treated with collagenase and trypsin/EDTA followed by FACS to separate GFP-positive TFR1-negative from GFP-negative wildtype cells

The data were analyzed with robust multichip analysis (RMA) using the Affymetrix microarray *.cel image file and GeneTraffic(R) (Silicon Genetics) software

extraction of total RNA using Rneasy mini kit (Qiagen) was performed according to the manufacturer's instructions with on-column DNase digestion.

Following fragmentation, 2.2 ?g biotinylated cDNA were hybridized in duplicate to Mouse Genome 430 2.0 Genechip arrays (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Total RNA (50ng) was amplified and biotin labeled using the Ribo-SPIA isothermal linear amplification kit (Ovation Biotin system; NuGen)

chimeric kidneys from mouse E15.5 embryos derived from blastocysts that were injected with GFP-positive, transferrin receptor (Tfrc)-deleted embryonic stem cells

Gene expression data from endocrine resistant breast cancer cell line LY7

Gene expression data from endocrine resistant breast cancer cell line LY6

Gene expression data from endocrine resistant breast cancer cell line LY3

Gene expression data from endocrine resistant breast cancer cell line LY2

Gene expression data from endocrine resistant breast cancer cell line LY5

Gene expression data from endocrine resistant breast cancer cell line LY4

S-337-N

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;HA1077;6h;1;4421339033

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;Control;12h;1;4421339033

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;HA1077;6h;1;4421339032

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;Control;12h;1;4421339032

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;HA1077;12h;1;4421339032

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;Control;24h;1;4421339032

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;HA1077;24h;1;4421339032

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;Control;2h;1;4421339033

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;HA1077;2h;1;4421339033

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;Control;6h;1;4421339033

LaserPower: 2.61;; 1.35
Temperature: 42.78

LaserPower: 2.55;; 1.34
Temperature: 41.58

LaserPower: 2.62;; 1.35
Temperature: 42.99

LaserPower: 2.56;; 1.34
Temperature: 41.85

LaserPower: 2.64;; 1.31
Temperature: 43.14

LaserPower: 2.62;; 1.33
Temperature: 43.39

LaserPower: 2.58;; 1.32
Temperature: 42.18

LaserPower: 2.65;; 1.3
Temperature: 43.59

LaserPower: 2.59;; 1.3
Temperature: 42.53

LaserPower: 2.54;; 1.6
Temperature: 32.98

Gene expression data from MCF-7 cells, siERK5 treatment 72h, 10 nM E2 for 24h

Gene expression data from MCF-7 cells, siGL3 treatment 72h, 0.1%EtOH for 24h

a time series of ConA injections was administered and  20 mg/kg ConA was injected through the mouse caudal vein at one of 4 time points (0 hr, 1 hr, 3 hr, 6 hr),here is  hepatic gene expression at "0 hr" (rep1)

a time series of ConA injections was administered and  20 mg/kg ConA was injected through the mouse caudal vein at one of 4 time points (0 hr, 1 hr, 3 hr, 6 hr),here is  hepatic gene expression at "0 hr" (rep2)

Primary astrocyte cultures from optic nerve head. Cells were lysed in separate groups in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

Human hepatocellular carcinoma cell line infected with GFP protein (control) 3

HepG2 cells stably expressing HCC-THRA mutant bN treated with vehicle for 6h.

HepG2 cells stably expressing RCCC-THRA mutant 6a treated with 100 nM T3 for 6h.

HepG2 cells stably expressing RCCC-THRA mutant 6a treated with vehicle for 6h.

bone marrow;CD34+ hematopoietic stem cells (HSC);myelodysplastic syndromes (MDS);refractory anemia with ringed sideroblasts (RARS);del5q plus other

female Spargue-Dawley rats, 9-cis-retinoic-acid, 100 mg/kg diet for 7 days,  tissue: mammary gland

Epithelial prostate primary cells from fresh explant from normal tissue, obtained from a cystoprostatectomy of a patient with a bladder carcinoma with no lesions in the prostate

in vivo Treatment: MEHP, Treatment Duration: 1, Units of Duration: hour, Treatment Time: 1:06, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.24, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

KJ_1_1_38_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

Epithelial prostate primary cells from fresh explant of benign hyperplasia

Epithelial prostate primary cells from fresh explant of controlateral normal tissue characterized by the presence of few areas of "PIN" (Prostatic In Situ Neoplasia)

This sample was analyzed as part of aproject aiming to identify PTHrP-responsive genes. Cells were either transfected with siPTHrP or control siRNA (siLuc) and harvested 3 days later for RNA isolation. The RNA of this samples derived from cells treated with siPTHrP (2).

This sample was analyzed as part of aproject aiming to identify PTHrP-responsive genes. Cells were either transfected with siPTHrP or control siRNA (siLuc) and harvested 3 days later for RNA isolation. The RNA of this samples derived from cells treated with siPTHrP (1).

This sample was analyzed as part of aproject aiming to identify PTHrP-responsive genes. Cells were either transfected with siPTHrP or control siRNA (siLuc) and harvested 3 days later for RNA isolation. The RNA of this samples derived from cells treated with siLuc (2).

This sample was analyzed as part of aproject aiming to identify PTHrP-responsive genes. Cells were either transfected with siPTHrP or control siRNA (siLuc) and harvested 3 days later for RNA isolation. The RNA of this samples derived from cells treated with siLuc

neonatal foreskin;primary dermal fibroblasts;shKDM4C construct 3

primary fibroblasts expressing a shRNA construct targeting KDM4C, construct 3, clone 1

neonatal foreskin;primary dermal fibroblasts;shKDM4C construct 2

primary fibroblasts expressing a shRNA construct targeting KDM4C, construct 2, clone 2

RNA was extracted using the Qiagen RNeasy Midi Kit according to manufacturer guidelines

Microarray data were pre-processed using the GC-RMA algorithm in Genespring GX* Expression values were further filtered by retaining only those  probe sets with expression values of at least 50 in at least 25% of all conditions, thus generating a list of 22 091 probe sets. To assess differential gene expression between treatments at both the 6 and 24 hr time points, a Welch ANOVA test with a p-value cut-off of 0.01 and a 5% false discovery rate (FDR) reduced the data to 1158 probe sets. Subsequent 1.5-, 5- and 10-fold change filters produced lists of 162, 21 and 7 probe sets for the 6 hr time point and 399, 53 and 19 probe sets for the 24 hr time point, respectively.
The same data set was normalized in parallel using Robust Multichip Analysis using RMAEXPRESS software v.0.4.1 developed by B. Bolstad, University of California, Berkeley. Background adjustment and quantile normalization parameters were selected for data processing. Logarithmically transformed expression values were used to implement Gene Set Enrichment Analysis (GSEA).

DEX-treated embryonic primary chondrocyte cultures, incubated for 24hr.;Timed-pregnant CD1 mice were purchased from Charles River Laboratories at embryonic day E15.5 mice (E15.5). Dexamethasone was obtained from Calbiochem and reconstituted in Dimethyl sulfoxide (DMSO, vehicle).

DEX-treated embryonic primary chondrocyte cultures, incubated for 24hr.

Gene expression data from male F344 rats treated with a single dose of 50mg/kg D-Serine for 96 hours

Brain tissue from Fisher 344 male rat, Animal #261, 50mg/kg D-Serine

Brain tissue from Fisher 344 male rat, Animal #259, 50mg/kg D-Serine

Brain tissue from Fisher 344 male rat, Animal #258, 50mg/kg D-Serine

Brain tissue from Fisher 344 male rat, Animal #257, 50mg/kg D-Serine

Brain tissue from Fisher 344 male rat, Animal #266, 20mg/kg D-Serine

Brain tissue from Fisher 344 male rat, Animal #263, 20mg/kg D-Serine

Brain tissue from Fisher 344 male rat, Animal #262, 20mg/kg D-Serine

microarray analysis of gene expression after transverse aortic constriction in mice - 3 wks TAC group No.5

HeLa cells were treated in three independent experiments with UPF1 siRNAs or luciferase siRNAs as a negative control. To positively control for the effect of RNAi the efficient depletion of UPF1 was ascertained by immunoblotting. RNA isolated from these cells was analyzed on Affymetrix HG_U133A GeneChips™. The data here correspond to the second control (luciferase siRNA transfection).

HeLa cells were treated in three independent experiments with UPF1 siRNAs or luciferase siRNAs as a negative control. To positively control for the effect of RNAi the efficient depletion of UPF1 was ascertained by immunoblotting. RNA isolated from these cells was analyzed on Affymetrix HG_U133A GeneChips™. The data here correspond to the first control (luciferase siRNA transfection).

HeLa cells were treated in three independent experiments with UPF1 siRNAs or luciferase siRNAs as a negative control. To positively control for the effect of RNAi the efficient depletion of UPF1 was ascertained by immunoblotting. RNA isolated from these cells was analyzed on Affymetrix HG_U133A GeneChips™. The data here correspond to the third control (luciferase siRNA transfection).

HeLa cells were treated in three independent experiments with UPF1 siRNAs or luciferase siRNAs as a negative control. To positively control for the effect of RNAi the efficient depletion of UPF1 was ascertained by immunoblotting. RNA isolated from these cells was analyzed on Affymetrix HG_U133A GeneChips™. The data here correspond to the second experiment (UPF1 siRNA transfection).

HeLa cells were treated in three independent experiments with UPF1 siRNAs or luciferase siRNAs as a negative control. To positively control for the effect of RNAi the efficient depletion of UPF1 was ascertained by immunoblotting. RNA isolated from these cells was analyzed on Affymetrix HG_U133A GeneChips™. The data here correspond to the first experiment (UPF1 siRNA transfection).

In-vivo treatment: Male Rag1 knockout animals at 8 weeks of age were lethally irradiated and reconstituted with 1:1 mixtures of bone marrow cells depleted of mature lineages from 8 week old male Ly5.1- Bach2 knockout and Ly5.1+ wildtype mice. Two months following transfer, Ly5.1- (knockout) and Ly5.1+ (wildtype) CD4 single-positive thymocytes were isolated by FACS from single cell suspensions of thymi from mixed chimeric animals. Total RNA was purified from these cells and global gene expression analysis was performed. Thus we were able to measure Bach2-dependent gene expression in CD4 single-positive thymocytes.

Affymetrix Scanning Protocol; Arrays were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

Affymetrix RMA Data Processing
Calculation Method: Expression summary values were calculated using the Partek Genomic Suite (v.6.6. 6.12.0907) implemented version of RMA (Robust Multichip Average).

Sample Extraction Protocol; Total RNA from sorted cells were isolated using the RNAeasy mini kit (Qiagen).

Affymetrix Hybridization Protocol; Biotinilated cDNA were then hybridized to HumanGene 1.0 ST arrays (Affymetrix) overnight at 450C.

Encore Biotin Module (NuGEN) Labeling; 5.5ug of amplified sscDNA from 12-13ug total amplification were used for fragmentation and biotinilation using Encore(TM) Biotin Module (NuGEN) according to manual.

C57BL/6;male;thymus;CD4 single-positive thymocytes;Bach2 knock out;Ly5.1-

A673 treated with DMSO vehicle control for 3 days, biological rep4

Gene expression data from A673 cell line that has been treated with DMSO vehicle control for 3 days.

A673 cell line that has been treated with DMSO vehicle control for 3 days.

A673 treated with DMSO vehicle control for 3 days, biological rep5

A673 treated with DMSO vehicle control for 24 hours, biological rep5

Gene expression data from A673 cell line that has been treated with DMSO vehicle control for 24 hours.

A673 cell line that has been treated with DMSO vehicle control for 24 hours.

A673 treated with DMSO vehicle control for 24 hours, biological rep6

A673 treated with DMSO vehicle control for 3 days, biological rep1

A673 treated with DMSO vehicle control for 3 days, biological rep2

A673 treated with DMSO vehicle control for 24 hours, biological rep1

A673 treated with DMSO vehicle control for 24 hours, biological rep2

A673 treated with DMSO vehicle control for 24 hours, biological rep3

A673 treated with DMSO vehicle control for 24 hours, biological rep4

Klose RJ, Yan Q, Tothova Z, Yamane K, Erdjument-Bromage H, Tempst P, Gilliland DG, Zhang Y, Kaelin WG. The retinoblastoma binding protein RBP2 is an H3K4 demethylase. Cell (2007)

Analysis name: WK2006060808

Subconfluent RBP2-/- primary mouse embryonic fibroblasts at passage 3.

Analysis name: WK2006060807

Analysis name: WK2006060806

Identification of differentially expressed genes was performed using the Partek Genomic Suite v 6.6beta.  CHP files were generated using Affymetrix Expression Console Software using default settings and the RMA algorithm.

RNA was extracted by the method of Chirgwin et al. Biochemistry18:5294-5299, 1979.

Following labeling, 3.1ug of cDNA were hybridized for17hr @ 45oC on a Genechip Mouse Gene 1.0ST array, then washed and stained according to the standard Affymetrix protocol.

Biotinylated cDNA were prepared according to the WT Terminal Labeling and Hybridization for use with the Ambion WT Expression Kit Manual provided by Affymetrix using 100ng total RNA.

Gene expression data from liver taken from adult mice with a liver specific knockout of RICTOR that were fasted 16hr then given ad libitum access to food for 3 hr.

male;adult;liver;Rictor floxed;fasted 16hr then given ad libitum access to food for 3 hr

Gene expression data from liver taken from control adult mice fasted 16hr then given ad libitum access to food for 3 hr.

male;adult;liver;wild type;fasted 16hr then given ad libitum access to food for 3 hr

Scd1 knock out mice, liver, total RNA processed to biotin-labeled cRNA

Mus musculus (backcrossed to C57BL/6J mice for 5+ generations);Scd1 knock out mouse, chow diet, liver

Scd1-/- on very low fat diet (TD03045 from Harlan Teklad) replicate 1

Scd1-/- on very low fat diet (TD03045 from Harlan Teklad) replicate 2

Mus musculus (backcrossed to C57BL/6J mice for 5+ generations);Scd1 knock out mouse, Harlan Teklad TD03045 diet, liver

Scd1-/- on very low fat diet (TD03045 from Harlan Teklad) replicate 3

Scd1-/- on very low fat diet (TD03045 from Harlan Teklad) replicate 4

Scd1-/- on very low fat diet (TD03045 from Harlan Teklad) replicate 5

Standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual)

TOM-1 leukemia cells were incubated with 10 µM STI571 (Imatinib) for 16 hours. For more information about the cell line, please check: www.dsmz.de

Uterine fibroid tissue carrying wild-type fumarate hydratase gene.

The mice were injected with 5 IU equine chorionic gonadotropin 44 h before oocyte isolation

Average signal intensities for each probe set within arrays were calculated by and exported from Affymetrix’s Expression Console (Version 1.1) software using the RMA method which incorporates convolution background correction, sketch-quantile normalization, and summarization based on a multi-array model fit robustly using the median polish algorithm.

Total RNA was extracted using the Qiagen RNeasy Micro kit according to the manufacturers instructions.

Following fragmentation and labeling , 2ug of cDNA were hybridized for 18 hr at 45C on GeneChip Mouse Gene ST 1.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Fragmented biotinylated cDNA were produced from 1ng total RNA according to the standard protocol using the Ovation Pico WTA System V2 from Nugen for amplification and the Encore Biotin Module from Nugen for fragmentation and labeling.

B6/C3H;Brwd1 mutant;germinal vesicle (GV) stage;oocytes (100 cells)

Ring1B mutant generated by gene targeting (Leeb et al., 2007);ES

MCF-7 cells were transfected with siRNA of either  MTDH-WT or MTDH-isoform (200 pmols) for 24 h.

MCF-7 cells were grown in DMEM  supplemented with 10 % Foetal Bovine Serum, 2mM glutamine and Pen-Strep

The bead-level data were preprocessed using BASH (Cairns et al. (2008) Bioinformatics 24(24):2921-2), a function from the beadarray package (Dunning et al (2007) Bioinformatics 23(16):2183-4) in Bioconductor, and also log base 2 transformed and quantile normalised using the beadarray package.

Total RNA was extracted using the QIAGEN AllPrep kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

Tissue culture for 24 hours,
with DMSO added to the medium at 0,65%

The basal culture medium was Dulbecco’s modified Eagle’s medium (DMEM) containing Glutamax-1 (Gibco BRL, Paisley, Scotland) supplemented with 10% fetal calf serum (FCS; Gibco BRL).

GeneChips were scanned using the
Genechip System confocal scanner (Aligent)

Total RNA was isolated using the RNeasy Mini Kit (Qiagen). Extraction was performed according to the manufacturer's instructions.

Following fragmentation, 16 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Murine Genome U74 Av2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 11 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

Gene expression data from pooled samples of E14 mouse embryo tooth germs

MDA-MB-231 cells transfected with precursor of miR-148b were analyzed 48h after transfection

skeletal muscle;insulin resistant;untreated;0.8;25.2;56.9;1160;64;30.5;42;1952

skeletal muscle;insulin resistant;untreated;0.88;232;60;1770;102;23.5;73.5;2397

C57BL/6;male;ESC-like cells;Prdm14 Knockout;Serum without LIF (day2)

C57BL/6;male;ESCs;No genetic modification;Serum without LIF (day2)

C57BL/6;male;epiblast like cells (EpiLCs);Blimp1-mVenus, Stella-ECFP(BVSC) transgene

C57BL/6;male;ESC-like cells;Prdm14 Knockout, pPyCAG-AGP14 transgene;Serum without LIF (day2)

Rat aortic valve cusps were harvested from adult Sprague-Dawley rats and AVICs were cultured from explants based on published protocols. Briefly, valve leaflets were subjected to collagenase digestion and gently scraped to expose the subendothelial layer. The leaflets were then cut into microscopic pieces (1-2 mm2) and cultured in standard Medium-199 supplemented with 15% FBS, 2 mmol/L glutamine and 100 U/ml penicillin/streptomycin.  Upon reaching 80% confluency, AVICs were passaged using trypsin-EDTA.  AVICs between passage 3 and 8 were used for experiments.  Notch signaling was inhibited using a γ-secretase inhibitor (Sigma Cat. # S2188 or D5942) diluted in DMSO to a concentration of 10 μM. Culture media was changed every 48-72 hours and cells were passaged at each time point of harvest.

CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the RMA algorithm in ArrayAssist 3.4 (Stratagene) and were used to determine differential gene expression by pair-wise comparisons. The genes that were altered by two-fold either ways were sorted and used for further interpretation of the microarray data.

Data were RMA normalized and pairwise comparisons (of averaged signal values) and Student’s t test with Benjamin and Hoschberg adjustment were performed using GeneSifter (VizX Labs, Seattle, WA).  Genes with an average fold-change ≥ 1.5 and an adjusted p value ≤ 0.05 were considered significantly differentially expressed.

Following fragmentation, labeled cRNA was hybridized to the Rat Genome 230 2.0 Array. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).

986
Gene expression data from PTEN+/- IKK2ca/ca (ep) lateral prostate.

C57BL/6;PTEN+/- IKK2ca/ca (epithelium);12 months;lateral prostate

1020

928

we used DNA chip technology to systematically search for genes differentially expressed in early onset CRC. We report a panel of 7 over-expressed genes in the normal appearing colonic mucosa of young patients without dominant family history compared to that of HC that could potentially predict early onset CRC.

human peripheral blood memory B cells (MBCs);LZRS-FOXP1-IRES-YFP;FOXP1 overexpression

RelA (NF-kB subunit) siRNA knocked-down cells, without treatment, replicate A

ATM siRNA knocked-down cells, 4 hrs after NCS treatment, replicate C

RelA (NF-kB subunit) siRNA knocked-down cells, without treatment, replicate C

RelA (NF-kB subunit) siRNA knocked-down cells, without treatment, replicate B

ATM siRNA knocked-down cells, 4 hrs after NCS treatment, replicate B

ATM siRNA knocked-down cells, 4 hrs after NCS treatment, replicate A

RelA (NF-kB subunit) siRNA knocked-down cells, 4 hrs after NCS treatment, replicate B

RelA (NF-kB subunit) siRNA knocked-down cells, 4 hrs after NCS treatment, replicate A

Foxd3 conditional knockout cells treated with Tamoxifen, biological rep2

Foxd3 conditional knockout cells treated with Tamoxifen, biological rep3

06_21_04 TP-1: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

in vitro Treatment: siHSF1_#1 (Sense 5’-rGUrCrGUrCrArArCrArArGrCUrCrAUUrATT-3' Antisense 5’rGrArAUrGrArGrCUUrGUUrGrArCrGrArCTT-3’), Treatment Repeat: 1, Units of Treatment Repeat: dose, Treatment Duration: 52, Units of Duration: hours, Treatment Time: -48, Units of Treatment Time: hrs, Vehicle for Chemical: Lipofectamine 2000, Amount of Vehicle: 0.44, Route of Exposure: transfection, Units of Amount of Vehicle: ul, Dose or Concentration: 3.3, Units of Dose or Concentration: nM

06_21_04 TP-10: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

2-4 month old male Mist1KO mice were injected once hourly for four hours with caerulein and sacrificed at the four hour point following which total RNA was isolated using guanadinium isothiocianate

Approximately 10 µg of total RNA was processed to produce fluoresenctly cRNA targets.

06_21_04 TP-11: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

06_21_04 TP-12: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

Mouse embryonic fibroblasts with an inducible knockout genotype (TetO-Cre, rtTA, Bptf Floxed/Floxed), and control mouse embryonic fibroblasts (rtTA, Bptf Floxed/Floxed) were induced with 10ug/ml doxycycline for 48 hours. Following 48 hour doxycycline induction, the cells were passaged for 8 days to deplete the fibroblasts of residual Bptf protein.

Mouse embryonic fibroblasts were prepared from 12.5 dpc embryos according to standard protocols. Cells were maintained in DMEM supplemented with 10% FBS, 1x Pen/Strep, 1 mM glutamine, 1X NEAA. Cells were grown at 37 C in 5% CO2 and passaged prior to confluence.

BeadChips were scanned using default setting on BeadChip work station.

The data were normalized using quantile normalization with IlluminaGUI in R.

At day 10, total RNA was harvested from cells using Trizol, and further purified using a Qiagen RNeasy minikit.

Labeled RNA was hybridized to BeadChip arrays, washed and detected using standard Illumina protocols.

Total RNA was amplified and labeled with biotinylated nucleotides using Ambion Message Map kit cRNA kit according to standard protocols.

C57/B6x129 mixed background;Bptf KO;12.5 dpc;mouse embryonic fibroblasts

C57/B6x129 mixed background;control;12.5 dpc;mouse embryonic fibroblasts

SMhu108

SMhu105

R1 ESCs were cultured at 37°C and 5% CO2, in ESC media consisting of Dulbecco modified eagle serum (DMEM) supplemented with 15% FBS (North Bio, Lot SF30408), 0.1 mM nonessential amino acids, 1 mM sodium pyruvate, 2 mM L-glutamine (all from Gibco), 1000 U/mL leukemia inhibitory factor (LIF) (ESGRO, from Chemicon, batch 11061065) and 100 µM b-mercaptoethanol (Sigma).  Differentiation media consisted of either ESC media without LIF, or ESC media without LIF and supplemented with 0.1 uM retinoic acid.  Selection media consisted of ESC media supplemented with 150 ug/mL G418 (Gibco).  ESCs were passaged every two days at a ratio of 1:5 by washing with PBS (Gibco), dissociating with 0.05% trypsin (Gibco) for 5 minutes at 37ÃÂ°C and resuspending in ESC media. Media was changed daily.

Cells were seeded at a density of 1x106 per 10 cm Petri dish 24 hours before treatment. Cells were then incubated with 8 ml of regular growth media at 37 ºC for 1 hour. At the end of the 1-hour incubation, the media was removed, cells washed twice in warm PBS, and incubated in drug-free media at 37 ºC for 10 hours.

Cells were grown as a monolayer in RPMI 1640 media containing L-glutamine with 10% FCS, in the absence of antibiotics, in an incubator at 37 ºC with 5% CO2. Cells were passaged twice a week by trypsin/EDTA (0.05% trypsin, 0.7 mM EDTA) treatment. Cells were tested and confirmed to be free of mycoplasma contamination.

Probe arrays were scanned twice at 570 nm using a GeneArray laser scanner (Agilent Technologies, Palo Alto, California, USA) and the fluorescence intensity of the scanned image registered in CEL intensity files.

DNA-Chip Analyser (dChip) software (Li and Wong 2001 PNAS, 98:31) was used to automatically select probes, detect outliers/artefacts, normalise the fluorescence intensity over multiple arrays and calculate model-based expression values from CEL intensity files.

After the 10 hour incubation post-cisplatin treatment, T-RNA was extracted by using TRIzol Reagent (Invitrogen, Paisley, UK), according to the manufacturer’s instructions. All additional reagents used were of molecular biology grade and purchased from Sigma (Poole, UK). Briefly, cells were lysed directly in the culture dish with 1 ml TRIzol Reagent and the resulting cell lysate passed several times through a pipette to achieve homogenisation. The homogenised samples were incubated in microcentrifuge tubes at room temperature for 5 minutes to permit the complete dissociation of nucleoprotein complexes. 200 µl of chloroform were added to each homogenised sample, tubes shaken vigorously by hand for 15 seconds and incubated at room temperature for 2 to 3 minutes. Samples were centrifuged at 12,000 × g for 15 minutes at 4 °C, after which the aqueous phase was transferred to a fresh tube. RNA was precipitated from the aqueous phase by mixing with 0.5 ml isopropyl alcohol. Samples were incubated at room temperature for 10 minutes and centrifuged at 12,000 × g for 10 minutes at 4 °C. Supernatant was removed and RNA pellet washed once with 1 ml of 75% ethanol. Samples were mixed by vortexing and centrifuged at 7,500 × g for 5 minutes at 4 ºC. At the end of the procedure, the RNA pellet was briefly air-dried for 5 to 10 minutes after which RNA was dissolved in an appropriate volume of RNase/DNase-free water, pre-warmed to 60 ºC, by passing the solution a few times through a pipette tip, and incubating for 10 minutes at 55 to 60 ºC. T-RNA concentration was determined by measuring the absorbance of a 1:100 diluted solution at 260 nm in a GeneQuant II RNA/DNA calculator spectrophotometer (Pharmacia Biotech, Cambridge, UK), assuming that if A260 = 1, the content equals 40 µg/ml of RNA. RNA purity was assessed by the ratio A260/A280. T-RNA integrity was investigated in the Agilent 2100 Bioanalyzer, by assessing size distribution of the T-RNA using the Eukaryote Total RNA Nano assay (Agilent Technologies, Palo Alto, California, USA), according to the manufacturer’s specifications.

Fragmented cRNA was added to hybridisation buffer (100 mM 2-Morpholinoethanesulfonic acid (MES), 1 M [Na+], 20 mM EDTA, 0.01% Tween 20) with 0.1 mg/ml herring sperm DNA (Promega, Southampton, UK), 0.5 mg/ml acetylated bovine serum albumin (BSA) (Invitrogen, Paisley, UK). The hybridisation buffer was spiked with 50 pM control oligonucleotide B2 and the eukaryotic cRNA controls bioB, bioC, bioD and cre (1.5, 5, 25 and 100 pM respectively), all controls were from the GeneChip Eukaryotic Hybridisation Control Kit (Affymetrix, Santa Clara, California, USA). The hybridisation mixture was heated to 99 °C for 5 minutes, cooled to 45 °C for 5 minutes and centrifuged at 14,000 × g for 5 minutes to remove any insoluble material from the hybridisation mixture. Each hybridisation mixture containing 10 µg of fragmented biotin-labelled cRNA was hybridised to a pre-wetted (with hybridisation buffer) GeneChip Human Genome Focus (HG-Focus) array (Affymetrix, Santa Clara, California, USA) for 16 hours at 45 °C with permanent rotation at 60 rpm in a Hybridisation Oven 640 (Affymetrix, Santa Clara, California, USA). Probe array washing and staining were performed according to specific Gene Chip protocols (Affymetrix, Santa Clara, California, USA) in the Fluidics Station 400 (Affymetrix, Santa Clara, California, USA). Briefly, HG-Focus arrays were washed in a non-stringent wash buffer containing 6× SSPE (0.9 M NaCl, 0.06 M NaH2PO4, 0.006 M EDTA) (Cambrex, Berkshire, UK) and 0.01% Tween-20 at 25 °C, then with a stringent buffer containing 100 mM MES, 0.1 M [Na+], 0.01% Tween-20 at 50 °C. Following this wash, the probe arrays were stained with a solution containing 10 µg/ml of streptavidin-phycoerythrin (SAPE) conjugate (Invitrogen, Paisley, UK) dissolved in a buffer containing 100 mM MES, 1 M [Na+], 0.05% Tween 20 and 2 mg/ml acetylated BSA (Invitrogen, Paisley, UK). Following staining, the probe arrays were exposed to 3 µg/ml goat biotinylated anti-streptavidin antibody (Vector laboratories, Peterborough, UK) in a buffer as above containing 0.1 mg/ml normal goat IgG (Sigma, Poole, UK) and 2 mg/ml acetylated BSA (Invitrogen, Paisley, UK). Finally, the probe arrays were re-stained with SAPE as described above.

The SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen, Paisley, UK) was used to convert the mRNA in the T-RNA samples into ds-cDNA by reverse transcription with an oligo-dT primer. Initially, first strand cDNA was formed in a reaction containing 15 µg of T-RNA and 100 pmol of T7-oligo (dT) primer (5’ – GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG - (dT)24 – 3’) (Proligo, France). This mixture was incubated at 70 °C for 10 minutes and quickly chilled on ice for 5 minutes, after which the following reagents were added: first strand reaction buffer [50 mM Tris-HCl (pH 8.3) 75 mM KCl, 3 mM MgCl2], 10 mM dithiothreitol (DTT) and 500 µM each dNTP. Tubes were placed at 42 °C for 2 minutes to equilibrate the temperature prior to the addition of Superscript II reverse transcriptase (400 U) and further incubated for 1 hour at 42 °C. The second strand cDNA synthesis was performed by adding, to the solution containing the first strand cDNA, 200 µM each dNTP, 10 U of E. coli DNA ligase, 40 U of E. coli DNA polymerase I, 2 U of E. coli RNase H and second strand reaction buffer [20 mM Tris-HCl (pH 6.9), 90 mM KCl, 4.6 MgCl2, 0.15 mM beta–NAD+, 10 mM (NH4)2SO4]. The reaction was incubated for 2 hours at 16 °C. Following this incubation, 10 U of T4 DNA polymerase were added and incubated for 5 minutes at 16 °C. The reaction was stopped by the addition of 31.25 mM EDTA. The resulting ds-cDNA was extracted against an equal volume of phenol:chloroform:isoamyl alcohol (25:24:1) (Sigma, Poole, UK) using phase lock gels (Eppendorf, Cambridge, UK) and centrifuging at 12,000 × g for 2 minutes. The ds-cDNA was then precipitated from the aqueous phase by the addition of 0.5 volumes of 7.5 M ammonium acetate (Sigma, Poole, UK) and 2.5 volumes of absolute ethanol (Sigma, Poole, UK), using Pellet Paint (Novagen, Nottingham, UK) as a carrier. Pellet was washed in ethanol, dried and resuspended in an appropriate volume of RNase/DNase-free water (Sigma, Poole, UK).
Synthesis of biotin labelled cRNA was performed by in vitro transcription using the BioArray HighYield RNA Transcript Labelling kit (ENZO, Farmingdale, USA), according to the manufacturer’s instructions. Briefly, ds-cDNA synthesised from above was used as template, and T7 RNA polymerase was added to perform the in vitro transcription reaction from the T7 RNA polymerase promoter in the template. Biotin-labelled ribonucleotides (Bio-CTP, Bio-UTP) were included in the reaction along with non-labelled ribonucleotides (ATP, GTP, CTP, UTP) to produce biotin-labelled cRNA molecules. The reaction was incubated at 37 °C for 5 hours. This step was followed by cRNA cleanup with RNeasy Mini columns according to the manufacturer’s specifications (Qiagen, Crawley, UK). Quantification and purity assessment of cRNA was performed in a spectrophotometer by measuring the absorbance at 260 and 280 nm and the adjusted cRNA yield calculated taking into account the carryover of unlabelled T-RNA by the following formula: adjusted cRNA yield = RNAm – (T-RNAi)(y), where RNAm is the amount of cRNA measured after the IVT reaction, T-RNAi is the starting amount of T-RNA and y is the fraction of cDNA used in the IVT reaction. Size distribution of the labelled transcripts was investigated in the Agilent 2100 Bioanalyzer using the Eukaryote Total RNA Nano assay (Agilent Technologies, Palo Alto, California, USA). The appropriate amount of cRNA (13 µg) was fragmented in a buffer containing 40 mM Tris-acetate (pH 8.1), 100 mM KOAc and 30 mM MgOAc for 35 minutes at 94 °C. An aliquot, containing at least 1 µg of cRNA, of each fragmented sample was analysed in a 1% agarose gel electrophoresis to confirm fragmentation efficiency.

Cy-1 cells were maintainted in Dulbecco’s modified minimal essential medium (DMEM) supplemented with 2% fetal bovine serum, 100U/ml penicillin, and 100ug/ml streptomycin in a 37C incubator with 5% CO2

GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 7G.  Raw data files were generated and processed with Affymetrix AGCC software.

The data were analyzed through Bioconductor package, RMA method was used as the background-correction, normalization, and probe summarization method.

RNA was extracted using Qiashredders and Rneasy Mini Kit per manufacturer's protocol

15ug of labeled and fragmented cRNA was hybridized at 45C for 16 hours at 60rpm. GeneChips were then washed and stained on the Affymetrix Fluidics Station 450 according to the manufacturer’s protocol

1ug RNA was used to generate cRNA according to the manufacturer’s protocol in the Affymetrix GeneChip® Expression Analysis Technical Manual

gene expression was measured 24 hours - induction of Cyr61 protein in glioma cells

whole blood;Psoriatic arthritis;Female;1;4.0;69;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Psoriatic arthritis;Female;4;14.0;11;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Psoriatic arthritis;Female;2;37.0;24;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Psoriatic arthritis;Female;1;15.0;32;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Psoriatic arthritis;Male;4;19.0;17;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Psoriatic arthritis;Male;3;13.0;30;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Psoriatic arthritis;Female;4;20.0;19;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Psoriatic arthritis;Female;1;28.0;13;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

The mice were treated once with DMBA, followed by TPA application for 30 wks.

These mice are mixed background of FVB and C57bl6 and the age when they got the papillomas was about 9 months.

Data were extracted using BeadStudio version 3 without any normalization and were then processed after log2 transformation using quantile normalization.

RNA was prepared from papilomas of 2-3 mice (2 for WT and 3 for Knockout) and this was pooled to perform the array.

Technical replicate #3 of ATF2 wildtype. These mice are mixed background of FVB and C57bl6 and the age when they got the papillomas was about 9 months.

RNA was prepared from papilomas of 2-3 mice (2 for WT and 3 for Knockout) and this was pooled to perform the array. Each pooled sample was run in triplicates.   The mice were treated once with DMBA, followed by TPA application for 30 wks.

Technical replicate #1 of ATF2 knockout. These mice are mixed background of FVB and C57bl6 and the age when they got the papillomas was about 9 months.

whole blood;Psoriatic arthritis;Male;3;16.0;25;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Psoriatic arthritis;Female;2;7.0;41;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

CCE ES cells were trypsinized and subjected to embryoid body (EB) assay in bacterial Petri dish. At day 10 EBs were harvested and total RNA was isolated.

CCE ES cells were cultured on gelatin coated dish in DMEM medium with 15% FSC and leukemia inhibitory factor (LIF). Lentivirus containing mouse BMI1 cDNA was used to infect CCE ES cells in the presence of 8 microgram polybrene. Empty vector served as control. After two passages eGFP positive CCE ES cells were sorted by flow cytometry and cells were further grown in culture medium as above. For differentiation CCE ES cells were subjected to EB assay (10 days).

BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).

Embryoid body formation (10 days) of empty vector transduced embryonic stem cells (CCE ES cells).

The data were analyzed with RMA (Gene Pattern's ExpressionFileCreator version 8). Parameters: method   RMA  quantile normalization  yes  background correct  yes  compute present absent calls  no  normalization method  none  value to scale to    clm file    annotate probes  yes The data were analyzed with RMA (Gene Pattern's ExpressionFileCreator version 8). Parameters: method   RMA  quantile normalization  yes  background correct  yes  compute present absent calls  no  normalization method  none  value to scale to    clm file  annotate probes  yes.

Total RNA was isolated using RNeasy (Qiagen) according to the manufacturer's instructions. The Dana Farber Cancer Institute Microarray Core synthesized single-stranded cDNA from the extracted RNA. RNA ws converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis was then carried out.

The double-stranded cDNA was used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) waas purified from the IVT reaction mixture using magnetic particles. The cRNA was quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. The purified cRNA was fragmented in order to facilitate the subsequent hybridization step.

KO - knock-out Treated - 0.5 hrs - repeat 3 - Cy5 - mAdbID:62540

KO - knock-out Treated - 0.5 hrs - repeat 3 - Cy3 - mAdbID:62537

KO - knock-out Treated - 0.5 hrs - repeat 1 - Cy5 - mAdbID:62538

Cells were treated in complete medium with DMSO (control) or 40 uM gamma tocotrienol for 24h

MCF-7 cells were grown in 100 mm dishes in DMEM with 5% FBS at 37oC with 5%CO2

RMA for background adjustment, quantile method for normalization, and a robust multi-array average for summarization

RNA was isolated using trizol following manufacturer's instructions

Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix U133A2 GeneChip Array following manufacturer's instructions.

Gene expression data from MCF-7 cells treated with gamma tocotrienol

Cell populations were infected with pGIPZ shMITF vector or scrambled control and then selected with puromycin for 2 days. Cells were then subjected to 1uM PLX4032 or DMSO control for 24hr and RNA was then harvested.

COLO829 cells were grown in RPMI 1640 medium with 10% FBS and Pen/Strep

Standard scanning protocol for Affymetrix arrays was processed by the Stanford PAN facility

Array data was RMA normalized and differential expression was evaluated with statistical analysis of microarrays (SAM) with an FDR < 0.05 and fold change >= 2

Standard hybridization protocol for Affymetrix arrays was processed by the Stanford PAN facility

Standard labeling protocol for Affymetrix arrays was processed by the Stanford PAN facility

COLO829 melanoma cell line;control;BRAF inhibitor PLX4032 (Vemurafenib)

Gene expression data from left lung samples from C57BL/6 male mice exposed to 0.3 ppm O3  for 24 hours

C57BL/6;Il10+/+;6-8 weeks;Male;Left lung;Jackson Labs, Bar Harbor, ME;24 hours;ozone;0.3 ppm O3;10028-15-6

Gene expression data from left lung samples from B6.129P2-Il10tmlCgn/J male mice exposed to 0 ppm O3  for 24 hours

B6.129P2-Il10tmlCgn/J;Il10-/-;6-8 weeks;Male;Left lung;Jackson Labs, Bar Harbor, ME;24 hours;air;0 ppm O3

Gene expression data from left lung samples from C57BL/6 male mice exposed to 0 ppm O3  for 24 hours

C57BL/6;Il10+/+;6-8 weeks;Male;Left lung;Jackson Labs, Bar Harbor, ME;24 hours;air;0 ppm O3

non tumorigenic human breast epithelial MCF10A cell line: SFN_rep2

non tumorigenic human breast epithelial MCF10A cell line: SFN_rep3

non tumorigenic human breast epithelial MCF10A cell line: NTC siRNA_rep4

non tumorigenic human breast epithelial MCF10A cell line: Keap1 siNA_rep1

Hybridization protocol The Affymetrix GeneChip® Hybridization, Wash, and Stain kit was used according to the protocol supplied with the kit.

Control (GFP overexpressing) LNCaP prostate cancer cell line replicate 2

Control (GFP overexpressing) LNCaP prostate cancer cell line replicate 3

Control (GFP overexpressing) LNCaP prostate cancer cell line replicate 5

FOXA1 overexpressing LNCaP prostate cancer cell line replicate 4

FOXA1 overexpressing LNCaP prostate cancer cell line replicate 5

Arrays were scanned using the Affymetrix® GeneChip® Scanner 3000.

The data were analyzed with whole chip Robust Multi-chip Average (RMA) analysis.

sample collection protocol: The arterial tissues were snap-frozen in liquid nitrogen, and stored at –80 ° C.
Total RNA was isolated using TRIzol (Invitrogen) and cleaned using RNeasy kit (Qiagen) following the manufacturers’ protocol. The integrity of total RNA was confirmed by agarose gel electrophoresis.

Fragmented cRNA were hybridized according to the standard protocol in the GeneChip® Expression Analysis Technical Manual.

Labeled cRNA was synthesized from cDNA using the GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions

Human hepatoma cell line (HepG2) transduced with recombinant Adenovirus expressing GPI-PLD

Gene expression data from Human hepatoma cell line (HepG2) transduced with recombinant Adenovirus expressing GPI-PLD and cultured for 12 hours. Targets were produced using standard Affymetrix procedures from 10ug of total RNA.

Human hepatoma cell line (HepG2), grown for 6 or 12 hours, and then total RNA harvested with Trizol and Qiagen Rneasy kit.

tetracycline inducible Ngn3 ESC differentiated for 3 days without feeder cells or LIF and with doxycycline

Cardiac biventricle of Tamoxifen injected PGC-1a-/-bf/f/MerCre mouse

Mouse embryonic fibroblast derived from MyoD-/-/Myf5-/- animals transduced with retrovirus without ER-MyoD insert in differentiation media for 12hrs

Quadriceps muscle;P.q.1;Pompe;rhGAA;52 Weeks;M;5m;No gains;Increased;Poor Clinical Outcome

Study of rat femur fracture healing in adult rats (26 weeks old at fracture) at 4 weeks after fracture.  RNA from two rats were pooled for each arrray.
Keywords = rat, fracture, age, time, femur

Study of rat femur fracture healing in adult rats (26 weeks old at fracture) at 2 weeks after fracture.  RNA from two rats was pooled for each array.

Study of rat femur fracture healing in older rats (52 weeks old at fracture) with the sample collected at the time of fracture.  RNA from two rats was pooled for each array

Study of rat femur fracture healing in adult rats (26 weeks old at fracture) at 6 weeks after fracture.  RNA from two rats was pooled for each array.

Study of rat femur fracture healing in older rats (52 weeks of age at fracture) at 1 week after fracture.  RNA from two rats was pooled for each array.
Keywords = rat, fracture, femur, age, time

Study of rat femur fracture healing in older rats (52 weeks old at fracture) at 3 days after fracture.  RNA from two rats was pooled for each array.

Study of rat femur fracture healing in older rats (52 weeks of age at fracture) at 4 weeks after fracture.  RNA from two rats was pooled for each array.

Study of rat femur fracture healing in older rats (52 weeks of age at fracture) at 2 weeks after fracture.  RNA from two rats was pooled for each array.

Study of rat femur fracture healing in older rats (52 weeks old at fracture) at 6 weeks after fracture.  RNA from two rats was pooled for each array.

Crushed bones were washed with HBSS until the bone chips were white and endosteal stromal cells were released by digestion for 1 hour at 37°C at 110 rpm with 3 mg/ml type I collagenase (Worthington) dissolved in HBSS. The released endosteal cells were washed with HBSS + 2% FBS, and residual bone material was removed by filtering through a 45 μm filter. Cells were stained with unconjugated rat anti-lineage (B220, CD3, CD4, CD5, CD8, Ter119, Mac-1, Gr-1) antibodies followed by goat anti-rat-Cy5PE or Qdot605 secondary antibodies and directly conjugated CD31-FITC, Sca-1-PB, CD45- Cy7APC and CD51-bio/streptavidin-APC antibodies. Cells were sorted on a FACS ARIAII upon PI exclusion of dead cells. OBCs were single-sorted and directly collected in Trizol.

Control and BA mice were withdrawn from doxycycline at 5 week of age to induce MPN development in BA mice. Five to 6 weeks later, bones were harvested for OBC isolation and RNA extraction

Data was processed using AGCC 3.2.2. Data were GC-RMA normalized and statistically significant differentially expressed genes were determined using Significance Analysis of Microarrays (SAM) (Tusher et al., 2001).

Total RNA was isolated from 500-2300 purified OBCs using the Arcterus PicoPure RNA kit and a modified protocol for Trizol samples according to manufacturers’ instruction. RNA was then amplified using the Nugen Pico WTA kit and amplified products were cleaned using the Qiagen QiaQuick PCR purification kit following Nugen’s protocols.

Biotinylated cRNA were prepared according to the GeneChip Expression Analysis Technical Manual 702232 Rev. 3

Sense-strand cDNA targets were generated using the Nugen WT-Ovation Exon Module, and then fragmented and biotinylated using the Nugen Encore Biotin Module according to manufacturers’ instructions.

Osteoblastic lineage cell;C57BL/6;Scl-tTA::TRE-BCR/ABL;5-6 weeks post doxycylcin withdrawal

BA osteoblastic lineage cells 5-6 weeks post doxycylin withdrawal

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Estradiol + medroxyprogesterone acetate treated. Patient 14.

Endometrium from estradiol- and MPA-treated postmenopausal woman

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Estradiol + medroxyprogesterone acetate treated. Patient 19.

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Estradiol + medroxyprogesterone acetate treated. Patient 9.

short access to cocaine, nucleus accumbens, 1 hr/day access to cocaine

Human glioma cell line U373 stably transfected with an EGFP expression vector.

"female subject, 18-45 yrs, peripheral blood mononuclear cells 6 h after intravenous endotoxin challenge"

Female;78;8h;6.7;control;superior temporal cortex (Brodmann Area 22, BA22)

TH cells from LC, wild type control, young time point, biological replicate 2

TH_LCY_WT_2

C57BL6/J;No;Aug-11;106;male;LC (locus coeruleus);P23;Y/X;TH/-;brain;tyrosine hydroxylase (TH)-positive locus coeruleus (LC) neurons

MCF-7 cells were maintained in DMEM supplemented with 10 percent fetal calf serum, penicillin (100 units/mL), and streptomycin (100 ug/ml)

Each probe array was scanned twice with the GeneArray Scanner, according to the manufacturers procedures (Affymetrix, Santa Clara, CA).

The CEL files for hybridizations of the MCF-7/ADR cells and the MCF-7 cells were log2-transformed by use of RMA Express (Bioinformatics 2003 19(2):185-193 and Biostatistics 2003 4(2):249-264). Microarray data for the expression of 14,500 genes from MCF-7 and MCF-7/ADR were filtered with BRB-ArrayTools (version 3.8.0) (developed by Dr. Richard Simon and BRB-ArrayTools Development Team from the Biometric Research Branch at the National Cancer Institute, NIH, Bethesda, MD). The array data were filtered by use of the exclusion parameters, spot intensities that were less than 10 and genes with a P value for the log-ratio variation that was greater than .01, and a total of 4976 genes were identified for further analysis. These 4976 genes were clustered by use of the Euclidean distance and complete linkage (Supplementary Figure 1, available online). The resulting dendrogram indicated that, for all experimental conditions, the duplicate microarrays form clusters, suggesting that the results were reproducible. A two-sample t test (with random variance model) was used to perform a class comparison and determine the statistically significant genes expressed between the MCF-7 and MCF-7/ADR cells. The univariate test random variance model parameters were a equals 1.68165, b equals 14.3422, and Kolmogorov–Smirnov statistic equals 0.03998. The nominal statistical significance level of each univariate test was .001. The first 419 genes listed were statistically significant at the nominal .001 level in the univariate test with a spot intensity fold change of 10. Genes with a spot intensity fold increase of greater than 10 are shown in Supplementary Table 1 (available online), and genes with spot intensity fold decrease of greater than –10 are shown in Supplementary Table 2 (available online).

RNA was isolated from approximately 1 million MCF-7 and MCF-7/ADR cells grown in two six-well plates. The medium and any detached cells were first removed from the wells, and total RNA was isolated from the cells that remained attached to the culture dish by use of the Qiagen RNeasy kit (Valencia, CA) by the manufacturers protocol. RNA was quantitated by use of a NanoDrop micro-volume spectrophotometer (Thermo Scientific, Wilmington, DE) and then the integrity of the mRNA was verified with an Agilent BioAnalyzer (Santa Clara, CA).

The biotinylated complementary RNA was fragmented for 35 minutes at 94C in fragmentation buffer from the labelling kit (Enzo, Farmingdale, NY) and then hybridized to the Affymetrix GeneChip U133A 2.0 arrays (Santa Clara, CA) for 16 hours at 45C. Each probe array was then washed and stained before being scanned.

Isolated total RNA from the MCF-7 parental cells and MCF-7/ADR cells was used with the GeneChip Sample Cleanup Module to prepare biotinylated eukaryotic complementary RNA to hybridize to the GeneChip expression probe arrays, according to the manufacturers protocol (Qiagen).

DMSO-treated embryonic primary chondrocyte cultures, incubated for 24hr.

DMSO-treated embryonic primary chondrocyte cultures, incubated for 6hr.;Charles River.  Cultures were completed in Frank Beiers laborartory by Veronica Ulici and Claudine James

DMSO-treated embryonic primary chondrocyte cultures, incubated for 6hr.

All mice received a series of 8 injections of tamoxifen starting at 4 months of age to activate Cre recombinase to knock out myostatin in mice with floxed myostatin genes.

Mice were reared under normal conditions with food and water ad libitum.

Scans were done with Affymetrix scanner exactly as recommended by Affymetrix.

background subtraction and normalization were done with the GCRMA method.

Total RNA was extracted into Trizol as recommended by supplier (Invitrogen).

Hybridization, washes, and staining with phycoerythrin-streptavidin (including antibody enhancement step) were carried out as recommended by Affymetrix for eukaryotic expression arrays, using hybridization oven and fluidics station purchased from Affymetrix.

Biotinylated cDNA was prepared with kits from NuGEN as recommended by supplier.

male, 7.5 months old, normal myostatin genes, CAGG-CreER transgene, C57BL/6 background

Male;79;4h;6.2;schizophrenic;superior temporal cortex (Brodmann Area 22, BA22)

Sample is murine liver RNA extract after mock infection with 200ul of PBS at 6 hpi.

C57/BL6 murine Liver RNA- 6 hours post-injection with PBS;Murine Universal RNA (Stratagene, La Jolla, CA) which is a mixture of RNA from 10 control cell lines approximating the expression profile of the majority of murine genes was used.

293T cell infected with RCAS-beta catenin S37A
Keywords = beta-catenin

Female;53;PBMC;Patient 4;BETAFERON;12 month of BETAFERON;multiple sclerosis;NAB+

Female;53;PBMC;Patient 4;BETAFERON;24 month of BETAFERON;multiple sclerosis;NAB+

Female;52;PBMC;Patient 13;baseline;baseline;multiple sclerosis;NAB+

Female;52;PBMC;Patient 13;REBIF;3 month of REBIF;multiple sclerosis;NAB+

Female;53;PBMC;Patient 4;baseline;baseline;multiple sclerosis;NAB+

Female;53;PBMC;Patient 4;BETAFERON;3 month of BETAFERON;multiple sclerosis;NAB+

Female;52;PBMC;Patient 13;REBIF;12 month of REBIF;multiple sclerosis;NAB+

Female;52;PBMC;Patient 13;REBIF;24 month of REBIF;multiple sclerosis;NAB+

Distal and Proximal Large Intestine, 8week old Wild-type mouse 2

The data was extracted from the CEL files using Affymetrix GeneChip Operating Software (1.4) using Affymetrix default analysis settings. Tabulated data (CHP) was generated with global scaing trimmed mean target intensity of 500.

Large Intestine was removed from the mouse, cut longitudinally and rinsed in PBS prior to homogenisation. Tissue was homogenised in 1ml Trizol reagent (Invitrogen) and processed according to manufacturer’s instructions. Precipitated RNA was resuspended in 100ul RNase free water and cleaned using RNeasy Mini columns (Qiagen). RNA was eluted in 40ul elution buffer and the quality confirmed using a Bio-Analyser 2100 (Agilent), only samples with a RNA Integrity score >8 were labelled.

10ug of fragmented biotin labelled cRNA was hybridised to a Mouse Genome 430 2.0 Array GeneChip, according to manufacturer’s instructions. GeneChip was incubated for 16hrs at 45oC in a rotating hybridisation oven at 60rpm. GeneChip was washed using Affymetrix washing script EukGE-WS2v5_450 on a Affymetrix Fluidics Station 450

cRNA was prepared using the Affymetrix One-Cycle Labelling Kit, using 2ug total RNA as starting material.

Distal and Proximal Large Intestine, 8week old Wild-type mouse 3

Winnie mouse is a C57BL/6 strain from a N-ethyl-N-nitrosourea (ENU)-treated C57BL/6 founder line. It carries a unique missense mutation (G9492A, Accession AJ511872) resulting in a cysteine to tyrosine substitution in the D3-domain at the N-terminus of Mucin2 (Muc2).

C57BL/6;Male;8 weeks;Large Intestine (Distal and Proximal);C57BL/6 Winnie G9492A

Distal and Proximal Large Intestine, 8week old Wild-type mouse 1

European-American (EA);Female;Systemic lupus erythematosus (SLE) patient;Peripheral blood;CD14-PerCP;CD14 positive monocytes

Gene expression data from cMet KO, YFP+ muscle stem cells, isolated from hindlimb that was contralateral to an hindlimb were we induced a muscle injury, 2.5 days post injury

C57BL6 mixed FVB;cMetflox/flox;Pax7CreER/+;Rosa26REYFP/+;3-5 months old;BaCl2 muscle injury;hindlimb muscle contralateral to BaCl2 muscle injury;CSC;2.5 days post injury

The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals.
Keywords = human brain aging

Cyclophosphamide-treated spleen 5 days - Biological Replicate 5 - Technical Replicate 2

Biological replicate 5 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated splenocytes, day5

Cyclophosphamide-treated spleen 5 days - Biological Replicate 5 - Technical Replicate 1

Biological replicate 5 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated splenocytes, day5

In vitro activated WT CD8 T cells transduced with Empty retrovirus

In vitro activated Myc-deficient CD8 T cells transduced with Empty retrovirus

In vitro activated Myc-deficient CD8 T cells transduced with AP4-expressing retrovirus

Liver; RegenerationSham 6 hrs

10 male Fischer rats, aged 4 months were trained sequentially on two tasks, SWM and OMT; hippocampal tissue collected 24 hours after a 7 day training/testing sequence

Liver; Regeneration 24 hrs

Cells were exposed to untreated (lo; low calcium; 0.09 mM in base medium) or treated with high calcium (hi; 0.6 mM) for 72 hrs in triplicate.

EPC2-hTERT cells with (n3) or without (scram) N3 knockdown were grown under regular conditions (21% O2, 5% CO2, 95% humidity) at 37°C in serum free medium (Keratinocyte-SFM)(Invitrogen) supplemented with 1 ng/ml epidermal growth factor and 50 µg/ml bovine pituitary extract.

Scanning of Affymetrix chips were performed according manufacturer's instructions

.CEL files (probe level data) were exported from Affymetrix® GeneChip® Operating Software which was also used to calculate detection flags, which were exported in .chp files. Probe level data (.CEL files) were imported with Partek Genomics Suite (v. 6.4, Partek, Inc., St. Louis, MO). The data were normalized and summarized to the probe set level using GC-RMA, yielding log2 intensities for all probe sets on the array. These intensity values were then filtered based on the detection flags, retaining only those probe sets flagged as present in at least 1 of 4 samples for each of the N3 knockdown cell experiments

RNeasy Mini Kit (Qiagen, Inc., Valencia, CA, USA) was used to extract total RNA according to the manufacturer's instructions.

Hybridization of cRNAs to Affymetrix chips were performed according manufacturer's instructions

epithelial cells (keratinocytes);hTERT-immortalized, non-transformed;STR-pGIPZ scramble;Ca 0.09mM, 72 h

Gene expression analysis of the kidney of mouse treated with 7 repeat daily doses of saline, administered via the intravenous route (iv)

RNA probes were labeled according to the supplier’s instructions (Affymetrix, Santa Clara, CA, USA). First strand synthesis was carried out by a T7-(dT)24 primer and SuperScript II Reverse Transcriptase (Gibco BRL Life Technologies) using 10?g of total RNA sample (Qiagen) from c17.2 neural stem cells stably transfected with the orphan nuclear receptor Nurr1 (clone42 and clone 48) or stably transfected with empty puromycin control vector (puro B and puroD)

puroD is a clonal control(puromycin resistant) stable c17.2 neural stem cell line with similar proliferation rate as clone 48 and therefore both were matched for subsequent analysis.

pD  is a clonal control (puromycin resitant) stably-expressing stem cell line

puroB is a clonal control(puromycin resistant) stable c17.2 neural stem cell line with similar proliferation rate as clone 42 and therefore both were matched for subsequent analysis.

pB  is a clonal control (puromycin resitant) stably-expressing stem cell line

clone 48 is a clonal Nurr1 stable c17.2 neural stem cell line with similar proliferation rate as puroD and therefore both were matched for subsequent analysis.

RNA probes were labeled according to the supplier’s instructions (Affymetrix, Santa Clara, CA, USA). First strand synthesis was carried out by a               T7-(dT)24 primer and SuperScript II Reverse Transcriptase (Gibco BRL Life Technologies) using 10?g of total RNA sample (Qiagen) from c17.2 neural stem cells stably transfected with the orphan nuclear receptor Nurr1 (clone42 and clone 48) or stably transfected with empty puromycin control vector (puro B and puroD)

clone 42 is a Nurr1 stable c17.2 neural stem cell line with similar proliferation rate as puroB and therefore both were matched for subsequent analysis.

Total RNA was prepared from CD19-positive splenic B cells isolated from 1-month old ID4+/-TCL1-tg and ID4+/+TCL1-tg mice, using the RNEasy column purification Kit (Qiagen).

Samples were hybridized using Herring sperm DNA, Acetylated BSA (50mg/mL), BioArray Eukaryotic Hybridization Controls (Enzo Life Sciences). Heat 65 degree C for 5 minutes, 99 degree C for 5 minutes, 45 degree C for 5 minutes. Centrifuge top speed for 5 minutes. Hybridize 16 hours at 45 degree C at 60rpm. Fluidics script EukGE-WS2v4_450.

Samples were enzymatically labeled using BioArray HighYield RNA Transcript Labeling kit (Enzo)

F1 littermate of TCL1 (C3H/B6) and ID4+/+ (CD1) mice;ID4+/+TCL1-tg;spleen;CD19+ B;1 month old

F1 littermate of TCL1 (C3H/B6) and ID4+/- (CD1) mice;ID4+/-TCL1-tg;spleen;CD19+ B;1 month old

MCF-7 human breast cancer cells were transfected with 20 nM of siGENOME ctrl (siGL3) or FOXM1 (Thermo Scientific) using Dharmafect1 following the manufacturer’s instructions. After 72 h of transfection, cells were treated with 0.1% control ethanol vehicle or 1 uM TOT for 24h

RNA isolated from spinal cord of human fetus suffering from Lethal Congenital Contracture Syndrome

Effects of SOCS3 on transcriptional response of macrophages to IL-6.
Fetal liver cells from SOCS3+/+ embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages.
Replicate 1 after stimulation for 100 minutes with 10 ng/ml IL-6.

Effects of SOCS3 on the transcriptional response of macrophages to IL-6.
Fetal liver cells from SOCS3+/+ embryos were used to reconstitute irradiated mice. Donor derived cells from the bone marrow  were differentiated to macrophages.

Replicate 1 of unstimulated macrophages.

Keywords = macrophage, SOCS3, IL-6, interferon

Fetal liver cells from SOCS3-/- embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages.
Replicate 1 after stimulation for 400 minutes with 10 ng/ml IL-6.

Replicate 1 unstimulated.

Chips were scanned using an Affymetrix GeneChip Scanner 3000. Chip target intensity was arbitrarily scaled to 100 before rendering CHP files.

Expression values were calculated by RMA express (http://rmaexpress.bmbolstad.com/) using background adjustment and quantile normalization.

Cells were directly sorted into buffer RLT and RNA prepared using RNeasy Micro (Qiagen) according to manufacturer's instructions.

Following fragmentation, 10 microg of cRNA was hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA was prepared according to the standard Affymetrix; Small Sample Labelling Protocol v.2, with the exception that the second round of in vitro transcription (IVT) was performed using Affymetrix GeneChip Expression 3 amplification kit.

The ALK+TCL Sudhl-1 cell line was treated in triplicates with the ALK inhibitor, CEP-14083, or the compound's solvent for 6 h

Cells were cultured at 37 °C and 5% CO2 in RPMI medium 1640, supplemented with 2-mM L-glutamine, 10% heat-inactivated FBS (FBS), 1% penicillin/streptomycin mixture and, where applicable, 200 units of IL-2 (Bender MedSystems)

according to the manufacturer’s instructions as found in GeneChip Expression Analysis Technical Manual, P/N 702232 Rev. 2

Microarray data were normalized using the MAS5 algorithm and analyzed using Partek GS (Partek). Differentially expressed genes were identified using ANOVA

total RNA was isolated using a TRIZOL and Qiagen Rneasy protocols

3ug of input total RNA were amplified and labeled using the Affymetrix 1-cycle kit

SUDHL-1 Cells derived from the a patient with Anaplastic Large Cell Lymphoma;control

Brown preadipocyte cell lines derived from newborn IRS-1 KO mice. Preadipocytes were grown to confluence (day 0) in differentiation medium (Dulbeco’s modified Earle’s medium containing 10% fetal bovine serum supplemented with 20 nM insulin and 1 nM T3). Brown preadipocytes were synchronized by overnight serum starvation. Total RNA was isolated with ULTRASPEC RNA Isolation System (Biotecx Laboratories, Inc., Houston, TX) following the manufacture’s instruction. 28 ug of total RNA were subjected to cDNA and cRNA preparations as previously described. 15 ug of adjusted cRNA were hybridised to Affymetrix U74A-v2 arrays (Santa Clara, CA). Intensity values were quantitated by MAS 5.0 software (Affymetrix). All chips were subjected to global scaling to a target intensity of 1,500 to take into account the inherent differences between the chips and their hybridization efficiencies.
Lot batch = Joslin core 669

Lot batch = Joslin core 678

Lot batch = Joslin core 1525

Lot batch = Joslin core 951

Lot batch = Joslin core 1534

Brown preadipocyte cell lines derived from newborn IRS-2 KO mice. Preadipocytes were grown to confluence (day 0) in differentiation medium (Dulbeco’s modified Earle’s medium containing 10% fetal bovine serum supplemented with 20 nM insulin and 1 nM T3). Brown preadipocytes were synchronized by overnight serum starvation. Total RNA was isolated with ULTRASPEC RNA Isolation System (Biotecx Laboratories, Inc., Houston, TX) following the manufacture’s instruction. 28 ug of total RNA were subjected to cDNA and cRNA preparations as previously described. 15 ug of adjusted cRNA were hybridised to Affymetrix U74A-v2 arrays (Santa Clara, CA). Intensity values were quantitated by MAS 5.0 software (Affymetrix). All chips were subjected to global scaling to a target intensity of 1,500 to take into account the inherent differences between the chips and their hybridization efficiencies.
Lot batch = Joslin core 698

myoblasts grown in media containing human beta-defensin 3 peptide

Mouse was housed individually in a separate cage under a 12-h light–dark cycle and permitted food and water ad libitum. A period of acclimatization for two weeks was allowed prior to any experimental procedure. No treatment was added to the animal’s drinking water .The weight and water consumption was measured weekly. At the end of 12 weeks animal was sacrificed by cervical dislocation and the brain was removed, dissected into left and right hemispheres and cerebellum, flash frozen in liquid nitrogen and stored at -80 C for future use.

Gene expression data from the right forebrain of C57BL mouse received no treatment for twelve weeks.

Forebrain (left hemisphere), Strain: C57BL, Gender: Male, Age: 4weeks, Drug treatment: Untreated-Control, Period of treatment: 12 weeks, Method of sacrificing: cervical dislocation.

Right brain hemisphere ,C57BL male mouse,Un-treated Control,12 weeks

Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Expression Array 430A . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Mouse was housed individually in a separate cage under a 12-h light–dark cycle and permitted food and water ad libitum. A period of acclimatization for two weeks was allowed prior to any experimental procedure. Haloperidol was added to the animal’s drinking water in a concentration equivalent to the highest human clinical dosage (i.e. 1.6 mg/kg/day for Clozapine) and delivered through light protected bottles. The weight and water consumption was measured weekly and the drug concentration in water was adjusted accordingly .At the end of 12 weeks animal was sacrificed by cervical dislocation and the brain was removed, dissected into left and right hemispheres and cerebellum, flash frozen in liquid nitrogen and stored at -80 C for future use.

Gene expression data from the right forebrain of C57BL mouse received Haloperidol oral treatment for twelve weeks.

Forebrain (left hemisphere), Strain: C57BL, Gender: Male, Age: 4weeks, Drug treatment: Typical antipsychotic Haloperidol, Dose: 1.6mg/kg/day, Route of treatment: Oral treatment-Drug added to drinking Water, Period of treatment: 12 weeks, Method of sacrificing: cervical dislocation.

Right brain hemisphere ,C57BL male mouse,Haloperidol treated,Orally,12 weeks

Forebrain (left hemisphere), Strain: C57BL, Gender: Male, Age: 4weeks, Drug treatment: Typical antipsychotic Haloperidol, Dose: 1.6mg/kg/day, Route of treatment: Oral treatment-Drug added to drinking Water, Period of treatment: 12 weeks, Method of sacrificing: cervical dislocation. At the end of the treatment, drug level in the plasma was assessed by Tandem mass Spectrometry LC- MS/MS.

Animal #3149
Rapid progression group
Seven weeks Post infection with SIV MAC251

Animal #3142
Typical progression group
Baseline Uninfected sample

Three weeks Post infection with SIV MAC251

Animal #3176
Rapid Progression group
Baseline Un-Infected sample

Animal #3201
Three weeks Post-Infection with SIV MAC251

Seven weeks Post Infection with SIV MAC251

Seven Weeks Post-Infection with SIV MAC251

DEX-treated embryonic primary chondrocyte cultures, incubated for 6hr.

lung tissue;CD-1;13 weeks + 2 month;fresh air, treatment over 2 month, 4x1h exposure per day

lung tissue;CD-1;13 weeks + 1 day;2R4F whole mainstream smoke 125 µg/ml, treatment over 1 day, 3x1h exposure per day

Oral Squamous cell Epithelium Tissue-Normal;OSCC-14;Floor of mouth;60;F;T4N2bM0;TNM,Tumor-node-metastasis

Oral Squamous cell Epithelium Tissue-Normal;OSCC-18;Floor of Mouth;52;M;T4N2M0;TNM,Tumor-node-metastasis

WT and Kin- S49 T-Lymphoma cells were untreated (0h) or treated with 100uM 8-CPT-cAMP for 2, 6, and 24 h.

Gene expression data from skeletal muscle of two-month-old WT mouse.
66WT Skeletal Muscle

Cell line DM331, mutant status Braf, condition Treated with Sorafenib+Diclofenac 2

RNA from Cell line DM331, mutant status Braf, condition Treated with Sorafenib+Diclofenac

Cell line DM331, mutant status Braf, condition Treated with Sorafenib+Diclofenac 1

Cell line DM331, mutant status Braf, condition Treated with Diclofenac 2

RNA from Cell line DM331, mutant status Braf, condition Treated with Diclofenac

Cell line DM331, mutant status Braf, condition Treated with Sorafenib 2

RNA from Cell line DM331, mutant status Braf, condition Treated with Sorafenib

Cell line VMM39, mutant status Ras, condition Treated with Sorafenib+Diclofenac 2

Cell line DM331, mutant status Braf, condition Treated with Diclofenac 1

Cell line DM331, mutant status Braf, condition Treated with Sorafenib 1

Quadriceps muscle;P.q.1;Pompe;rhGAA;12 Weeks;M;5m;No gains;Increased;Poor Clinical Outcome

gastrocnemius-5 months of age-control diet-biological replicate3

gastrocnemius-5 months of age-control diet-biological replicate2

Gene expression of old mice treated with a low dose of resveratrol

gastrocnemius-5 months of age-control diet-biological replicate1

The data was preprocessed by the Bioconductor lumi package (version 2.6.0). It was vst transformed and quantile normalized.

RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

heart of mouse subjected 2 week to chronic intermittent hypoxia (2A)

heart of female mouse subjected 2 week to chronic intermittent hypoxia

heart of mouse subjected 1 week to chronic intermittent hypoxia (1A)

heart of mouse subjected 2 week to chronic constant hypoxia (2B)

heart of mouse subjected 2 week to chronic intermittent hypoxia (2B)

heart of female mouse subjected 2 week to chronic intermittent hypoxia.

Test Compound Concentration:  10 mg/mL

After MCF-7 cells were grown to 75% to 80% confluence in MEM supplemented with 10% FBS, the cells were serum starved in DMEM/F-12 without phenol red (Invitrogen) and FBS for 24 h.  MCF-7 cells were then treated with vehicle or E2 at a concentration of 10–9 mol/L for 3 and 6 h.  All experiments were performed in triplicate.

MCF-7 cells (American Type Culture Collection) were maintained in MEM (Invitrogen) containing 25 units/mL penicillin, 25 units/mL streptomycin, and 10% fetal bovine serum (FBS) at 37°C and 5% CO2.

GeneChips were scanned using the Hewlett-Packard GeneArray Scanner.

Probe level data was converted to probe set expression values using RMA (Irizarry RA et al., Biostatistics 2003 Apr;4(2):249-64).

Total RNA was extracted from the MCF-7 breast cancer cell line using Tri-Reagent (Sigma) according to the manufacturer's instruction. Total RNA samples were treated with DNase I (Ambion) for 20 min at 37°C according to the product manual.

Following fragmentation, cRNA were hybridized to Human Genome U133Plus2.0 GeneChips. GeneChips were washed and stained in an Affymetrix Fluidics Station.

Sox3 null;R1;Embryonic stem cells differentiated into neural progenitor cells

RNA from 6 different control embryos (+/+ or +/-) were mixed and subdivided into control pool 1 and pool 2.

Agilent Feature Extraction file: Liver_Nrf2 Control_rep3.txt
Gene expression in the liver of  Nrf2 Control mice_rep3.

Agilent Feature Extraction file: Liver_Nrf2 KO_rep1.txt
Gene expression in the liver of  Nrf2 KO mice_rep1.

Agilent Feature Extraction file: Liver_Nrf2 Control_rep1.txt
Gene expression in the liver of  Nrf2 Control mice_rep1.

Agilent Feature Extraction file: Liver_Nrf2 Control_rep2.txt
Gene expression in the liver of  Nrf2 Control mice_rep2.

Agilent Feature Extraction file: Liver_Nrf2 KO_rep2.txt
Gene expression in the liver of  Nrf2 KO mice_rep2.

Agilent Feature Extraction file: Liver_Nrf2 KO_rep3.txt
Gene expression in the liver of  Nrf2 KO mice_rep3.

Mouse Lung AIN Diet 8hr 1mg/kg Dex Injection, biological replicate C
AN080206_Sample 23 Lung.CEL

Sodium arsenite added to food: None; Injection: IP 8hr 1 mg/kg Dexamethasone in saline; Diet: AIN-76A; Sodium arsenite added to drinking water: None

Mouse Lung AIN Diet 8hr 1mg/kg Dex and 1mg/kg As Injection, biological replicate A
AN080206_Sample 21 Lung.CEL

IP 8hr 1 mg/kg sodium arsenite, 1 mg/kg Dexamethasone in saline;AIN-76A

Sodium arsenite added to food: None; Injection: IP 8hr 1 mg/kg sodium arsenite, 1 mg/kg Dexamethasone in saline; Diet: AIN-76A; Sodium arsenite added to drinking water: None

Posterior and anterior second heart field (SHF) tissues were isolated from each embryo and stored in RNAlater RNA stabilization reagent (QIAGEN) at 4 °C.  Non-cardiac tissues were saved for genotyping.  After genotyping, Shh -/-  and Shh +/+ embryos were pooled, homogenized and RNA extracted.

To get the Shh -/- mice, shh +/- female mice on mixed background were superovulated using 5 units each pregnant mare serum gonadotropin (PMS-G) and human chorionic gonadotropin (HCG) administered 48 hours apart.  They were mated to Shh +/- male mice after HCG administration.  Embryos were isolated  at E9.5.

Slides were scanned immediately after washing on the Agilent Technologies Scanner (G2505C US80900103) using one color scan setting for 4x44k array slides (Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014868_D_F_20090416) to obtain median background subtracted mean signal of the spot.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

RNA was extracted from pooled, homogenized SHF tissues using the QIAGEN RNeasy kit following the manufacturer's recommendations.  The protocol includes an on-column DNase treatment.  RNA was quantified using a Nanodrop ND-1000 spectrometer and quality was checked using an agilent bioanalyzer.

1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4112F) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

Cy3 labeled cRNA was created using the agilent quick-amp RNA labeling kit with RNA spike-in, followed by purification using a QIAGEN RNeasy kit.  0.5 ug was used for each sample, and the labeling was validated using a nanodrop spectrometer.

S4PosMns
slide barcode: 251486826534
US80900103_251486826534_S01_GE1_105_Dec08_1_1

C56B/6 and CD-1 mixed;Shh mutant;E9.5;E9.5 embryos;posterior second heart field

HTB-58;male;65 years;Caucasian;squamous cell carcinoma of the lung;anti-Evi1

Mouse Lung AIN Diet 5wk 10ppb As Food Exposure, biological replicate B
AN080406_Sample 12.CEL

HTB-58;male;65 years;Caucasian;squamous cell carcinoma of the lung;control

Vector Control Transfected 3T3 cells treated with A-928605 for 24 h

Data was analyzed using the limma, oligo and affy Bioconductor packages implemented in the R-statistical environment (Affy package v. 1.18 from bioconductor version 2.2).  RMA was used to normalize the data and fit log2 transformed expression values (Affy Expression Console version 1.1.2800.19935).

RNA Stat60 extraction of total RNA was performed according to the manufacturer's instructions.

Following Labeling, 4 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Gene ST 1.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cDNA were prepared according to the Nugen WT-Pico Ovation kit protocol from 10 ng total RNA (WT-Pico Ovation RNA Amplification System Manual, 2007, NuGEN). Subsequently cDNA is made double stranded fragmented and end-labeled following manufacturers standard protocol (NuGEN exon module, encore end-labeling module).

C57BL6/J;Sfrp5 KO (Q27Stop);male;12 weeks;8 wks of high-fat diet;gonadal white adipose tissue (WAT)

C57BL6/J;wild type;male;12 weeks;8 wks of high-fat diet;gonadal white adipose tissue (WAT)

Female C57Bl/6 mice were euthanized by CO2 asphyxiation. For isolation of peritoneal macrophages (PMφ) the abdominal skin was removed, a catheter (24 GA) was inserted into the peritoneal cavity and 10 mL of ice-cold PBS were injected. After massage of the peritoneum, peritoneal fluids were aspirated, centrifuged at 500 g for 5 min, and yielded peritoneal cells (PMφ were resuspended in 0.5-1.5 mL Mφ medium containing DMEM, 10% FCS and MycoZapPlusCL antibiotics (Lonza). Next, cells were seeded in 96-well plates (100 µL of cells/ well) and cultivated at 37°C for 2 h

Data was processed with Affymetrix Expression Console 1.1 software using the RMA algorithm

RNA was extracted using RNeasy mini kit (Qiagen) according to the manufacturer's instructions. Single-strand cDNA was prepared using the Ambion WT Expression kit

5µg of fragmented cRNA was hybridized on a Affymetrix MoGene-1_0-st-v1. GeneChips were washed and stained in an Affymetrix Fluidics Station 450

Nfkbiz-/- peritonial macrophages incubated with 1µg/ml LPS for 4h

Mouse was rendered diabetic at six weeks by administration of 5 daily intraperitoneal injections of streptozotocin, 65 mg/kg in citrate buffer (0.05 mol/L; pH 4.5) (Sigma Aldrich). Serum glucose was measured from tail vein blood using a glucometer. Mice with a glucose concentration greater than 250 mg/ml were considered diabetic. All nondiabetic mice had a glucose concentration well below 200 mg/ml. Beginning at age 9 weeks, certain diabetic and nondiabetic mice were euthanized. Serum glucose was measured again before euthanization. Total Aortic segments from root to bifurcation) were snap-frozen for further analysis. Aortic roots were embedded into OCT (Tissue-Tek) and further sectioned for histological and immuohistochemical analysis.

NCI-H460;human lung large cell carcinoma cells;cigarette smoke extract;24 hours

NCI-H460;human lung large cell carcinoma cells;radiation;24 hours

NCI-H460;human lung large cell carcinoma cells;radiation and nicotine;24 hours

We used MCK-Cre transgenic mice for the selective expression of Cre protein in muscle tissues as shown previously. Crossbreeding of homozygous MnSOD flox mice
(flox/flox, f/f) with MCK-Cre transgenic mice gave rise to heart/muscle-specific MnSOD-deficient mice (del/del, d/d).

OrganismPart:Muscle;StrainOrLine:C57BL6/129SV; Anterior tibialis removed from 3-month old muscle glycogen synthase WT or knockout mouse. RNA was extracted using GibcoBRL TRIzol Reagent and a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA.
Sample_series_id: GSE2198

NCI-H460;human lung large cell carcinoma cells;radiation and cigarette smoke extract;24 hours

GeneChip Scanner 3000 7G was used for scanning.  Affymetrix GeneChip Command Console software (AGCC 3.2) was used for image processing

total RNA was extracted using the miRNeasy Mini Kit (Qiagen) per manufacturer's instruction

HIV seropositive drug naïve group, viral load medium

HIV seropositive drug naïve group, viral load high

Sample_ID:t18 // Patient:J-209 // Histology:Intestinal // Metastasis:- // p53_mut:+ // E-cadherin_mut:+ // beta-Catenin_mut:+

Sample_ID:t19 // Patient:J-222 // Histology:Intestinal // Metastasis:+ // p53_mut:- // E-cadherin_mut:+ // beta-Catenin_mut:-

Sample_ID:t14 // Patient:J-256 // Histology:Intestinal // Metastasis:- // p53_mut:++ // E-cadherin_mut:+ // beta-Catenin_mut:-

Sample_ID:t15 // Patient:J-264 // Histology:Intestinal // Metastasis:- // p53_mut:+ // E-cadherin_mut:+ // beta-Catenin_mut:++

Sample_ID:t16 // Patient:J-277 // Histology:Intestinal // Metastasis:- // p53_mut:++ // E-cadherin_mut:+ // beta-Catenin_mut:++

Sample_ID:t17 // Patient:J-166 // Histology:Intestinal // Metastasis:+ // p53_mut:- // E-cadherin_mut:+ // beta-Catenin_mut:+

Sample_ID:t10 // Patient:J-163 // Histology:Intestinal // Metastasis:+ // p53_mut:+ // E-cadherin_mut:+ // beta-Catenin_mut:-

Sample_ID:t11 // Patient:J-175 // Histology:Intestinal // Metastasis:+ // p53_mut:+ // E-cadherin_mut:+ // beta-Catenin_mut:-

Sample_ID:t12 // Patient:J-191 // Histology:Intestinal // Metastasis:- // p53_mut:++ // E-cadherin_mut:+ // beta-Catenin_mut:-

Sample_ID:t13 // Patient:J-194 // Histology:Intestinal // Metastasis:+ // p53_mut:- // E-cadherin_mut:+ // beta-Catenin_mut:-

The α- and γ-tocopherol-supplemented group was fed with a diet containing 500mg/kg of α- and γ-tocopherol each since the middle age (15 months).

The GeneChip Operating Software (GCOS) version 1.2 was used to analyze the image data. GCOS determines the presence of mRNA in samples and computes the signals of probe sets using the differences and ratios between PM and MM signals. Signals in each image are normalized to minimize an overall variability in hybridization intensities by a global scaling method.

Total 10ug cRNA was placed in the gene chip. The gene chip I used for this study is the Affymetrix MOE 430 2.0 arrays (Affymetrix, Santa Clara, CA). The Affymetrix MOE 430 2.0 array has 45,037 probe sets. Hybridization was carried out at 45ºC for 16 h with mixing on a rotisserie at 60 rpm. Following hybridization, the hybridization solutions were removed and the gene chips were be installed in a fluidics system for washes and staining.

Br: brain(neocortex)

Type II cells were isolated by instilling and incubating lung with Dispase II for 45 munutes.lungs were teased and cells were incubated on IgG coated plates for an hour to remove lung macrophases. The non adherent cells were further incubated on petridishes for two hours for fibroblast adherence.  The non adherent cells were cultured on fibronectin/collagen coated plates in the presense of keratinocyte growth factor for five days.

Data extraction was processed by Affy GeneChip® Operating Software v1.3 (Affymetrix).  Global scaling was equal to 500.  Normalization factor was equal to 1.  Analysis of differentially expressed transcripts was accomplished using a pairwise comparative analysis (Affy Data Mining Tool v3.1; Affymetrix).  3 sets B6 18/26 months x 3 sets B6 2 months comparison (1.5 fold cutoff (FC), Mann-Whitney test < 0.05, 6 out of 9 comparisons). Also, ABS |FC - FC SEM| >= 1.5

Trizol extraction of total RNA was performed followed by RNA clean up using Qiagen Rneasy kit according to the manufacturers' instructions.

Following fragmentation, 1 200 ul of hybridization cocktail containing 5 ug of fragmented cRNA placed on chip - Hybridized for 18 hours in GeneChip Hybridization Oven 640 - Washed and stained using 2 strepavidin stains and one antibody stain on GeneChip Fluidics Station 400 for 1.5 hours (GeneChip Expression Analysis Technical Manul- Affymetrix)

Healthy control;48;Male;N/A;N/A;6.86;31;Right;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 0

wildtype litter mate to the mice that have the overexpression of tgf beta

HL60 cells were treated with dimethylsulfoxide (DMSO; final concentration 0.1%) and incubated for 5 days

Hl60 cells were treated with 1µM tretinoin in dimethylsulfoxide (DMSO; final concentration 0.1%) for 5 days

RNA was isolated from HUVEC (passage 3) after stimulation with  2 ng/ml TNF for 5 h.

RNA was isolated from unstimulated HUVEC (passage 3) cultured for 5 h.

mRNA extracted from lung fibroblasts derived from open lung biopsies of a patient (IPF1) with idiopathic pulmonary fibrosis (usual interstitial pneumonia pattern on biopsy). Lung fibroblasts were grown to confluence in DMEM with 10% fetal calf serum. At confluence, lung fibroblasts were serum-deprived overnight, and exposed to 4 ng/ml of activated TGF-ß1 (R&D Systems)in serum-free culture-medium with the addition of 0.1% BSA for 4 hours. At the end of treatment period total RNA was harvested, quantified, and integrity was verified by denaturing gel electrophoresis.

lung fibroblasts from a patient (IPF1) with idiopathic pulmonary fibrosis

mRNA extracted from lung fibroblasts derived from open lung biopsies of a patient (IPF2) with idiopathic pulmonary fibrosis (usual interstitial pneumonia pattern on biopsy). Lung fibroblasts were grown to confluence in DMEM with 10% fetal calf serum. At confluence, lung fibroblasts were serum-deprived overnight, and exposed to serum-free culture-medium with the addition of 0.1% BSA for 4 hours. At the end of treatment period total RNA was harvested, quantified, and integrity was verified by denaturing gel electrophoresis.

lung fibroblasts from a patient (IPF2) with idiopathic pulmonary fibrosis

mRNA extracted from lung fibroblasts derived from open lung biopsies of a patient (IPF2) with idiopathic pulmonary fibrosis (usual interstitial pneumonia pattern on biopsy). Lung fibroblasts were grown to confluence in DMEM with 10% fetal calf serum. At confluence, lung fibroblasts were serum-deprived overnight, and exposed to 4 ng/ml of activated TGF-ß1 (R&D Systems) in serum-free culture-medium with the addition of 0.1% BSA for 4 hours. At the end of treatment period total RNA was harvested, quantified, and integrity was verified by denaturing gel electrophoresis.

Animal #3214
Slow progression group

Animal #3204

Animal #3206

Animal #3213
Three weeks post -infection with SIV MAC251

Animl #3213
Seven weeks Post-Infection with SIV MAC251

control;male;66;n/a;Porto;Hypertension, hypercholesterolemia;ever smoker, ever drinker

Wild-type and PPAR(alpha)-null mice were given four daily gavage doses of DEHP (1150 mg/kg/bw/day) in corn oil or corn oil alone.

Food (LabDiet 5001, PMI Nutrition International, St. Louis, MO) and municipal tap water were provided ad libitum.  Animal facilities were controlled for temperature (20°C–24°C) and relative humidity (40%–60%) and kept under a 12-h light-dark cycle.

The fluorescence intensities were measured with Affymetrix GeneChip scanner 3000 with 7G upgrade

The intensity data files (.cel files) were loaded to Rosetta Resolver (Rosetta Biosoftware, Seattle, WA) for analysis.

Total RNA was isolated and purified from mouse livers according to the mirVana™ miRNA isolation kit (Ambion, Austin, TX)    The integrity of each RNA sample was determined using an Agilent 2100 Bioanalyzer (Agilent, Foster City, CA), and RNA quantity was determined using a Nanodrop ND-1000 (Thermo Fisher Scientific, Wilmington, DE).

Total RNA (300 ng per sample) was labeled using the Affymetrix GeneChip WT cDNA Synthesis and Amplification kit protocol.

PPAR(alpha)-null mice (129S4/SvJae-Pparatm1Gonz/J, stock #003580) and wild-type mice (129S1/SvlmJ, stock #002448) were originally purchased from The Jackson Laboratory (Bar Harbor, ME) and maintained as an inbred colony on the 129/Sv background
gene expression data from wildtype mouse liver treated with DEHP

gene expression data from PPAR(alpha)-null mouse liver

gene expression data from PPAR(alpha)-null mouse liver treated with DEHP

transcripts expression data from Igf1 -/- mouse vestibular organ at E18.5

vestibular organ;hybrid Mf1 with 129/sv background;E18.5;Igf1 -/-

11-KO2

10-KO1

Gene expression data from 12 week old SIRT3KO mouse liver tissue fed a standard diet
05-KO4

04-KO1

03-WT5

02-WT4

Gene expression data from 12 week old wt mouse liver tissue fed a high-fat diet
09-WT3

08-WT2

07-WT1

06-KO5

Starting with the rat insulinoma cell line INS-1, clones were generated that contain a FRT site for site specific integration of specific genes (INS-1 Flp-In T-REx). In addition, the clones contain the tetracycline repressor allowing tetracycline (tet) induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factor can be identified. This entry corresponds to the RNA isolated from the INS-1 cell line #1-1.2
Keywords = Flp-In T-Rex

Starting with the rat insulinoma cell line INS-1, clones were generated that contain a FRT site for site specific integration of specific genes (INS-1 Flp-In T-REx). In addition, the clones contain the tetracycline repressor allowing tetracycline (tet) induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factor can be identified. This entry corresponds to the RNA isolated from the INS-1 cell line #1-1.16

Starting with the rat insulinoma cell line INS-1, clones were generated that contain a FRT site for site specific integration of specific genes (INS-1 Flp-In T-REx). In addition, the clones contain the tetracycline repressor allowing tetracycline (tet) induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factor can be identified. This entry corresponds to the RNA isolated from the INS-1 cell line #5-3.14

Starting with the rat insulinoma cell line INS-1, clones were generated that contain a FRT site for site specific integration of specific genes (INS-1 Flp-In T-REx). In addition, the clones contain the tetracycline repressor allowing tetracycline (tet) induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factor can be identified. This entry corresponds to the RNA isolated from the INS-1 cell line #5-3.19

Starting with the rat insulinoma cell line INS-1, clones were generated that contain a FRT site for site specific integration of specific genes. In addition, the clones contain the tetracycline repressor allowing tetracycline (tet) induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factor can be identified. This entry corresponds to the RNA isolated from the parental INS-1 cell line.
Keywords = insulinoma

ImaGene feature extraction (Biodiscovery Ltd, Marina del Rey, CA, USA) was used to record spot intensities. The signal mean was taken to represent the actual spot intensity, after subtraction of the mean background values. All spot were log2 transformed and intensities lower than 10, typical for the empty spots, were classified as missing. Next for each micro-array, the spot intensities were Z score normalized (Cheadle C, et al. J Mol Diagn  2003;5:73-81), while missing values (some 6% overall) were handled so as to minimize their effect on statistics. Specifically, such values were set equal to the mean of the micro-array distribution after Z score normalization, thus equal to zero. So for each micro-array, Z scores were computed for each green labeled spot intensity according to(2log(G) - mu) / sigma, where mu is the mean and sigma the standard deviation of all 2log(G) of the micro-array. Likewise the Z score was computed for each red labeled spot intensity and the result subtract from the ‘green’ Z score for each spot on the micro-array. These differences were then again Z score normalized to obtain the so called Z ratio for each spot.This information will soon be available in a publication.

lymphoblastoid cell line from T3.02, one out of seven of insensitive group, 50*10e6 cells;Pooled RNA from a number of lymphoblastoid cell lines (with and without bleo treatment) and head and neck cancer cell lines.

lymphoblastoid cell line from R, one out of seven of sensitive group, 50*10e6 cells;Pooled RNA from a number of lymphoblastoid cell lines (with and without bleo treatment) and head and neck cancer cell lines.

lymphoblastoid cell line from P910, one out of seven of sensitive group, 50*10e6 cells;Pooled RNA from a number of lymphoblastoid cell lines (with and without bleo treatment) and head and neck cancer cell lines.

lymphoblastoid cell line from F23.05, one out of seven of insensitive group, 50*10e6 cells;Pooled RNA from a number of lymphoblastoid cell lines (with and without bleo treatment) and head and neck cancer cell lines.

lymphoblastoid cell line from F16.01, one out of seven of insensitive group, 50*10e6 cells;Pooled RNA from a number of lymphoblastoid cell lines (with and without bleo treatment) and head and neck cancer cell lines.

Replicate_4
6816115033_B

Replicate_3
6816115033_C

Naïve CD8+ T cells were stimulated with plate-bound anti-CD3 (4 mg/ml, clone 2C11, BD Pharmingen) and anti-CD28 (4 mg/ml, clone 37.51, BD Pharmingen) in the presence of recombinant human IL-2 (100 U/ml, R&D Systems) for 3 days to generate in vitro effector CD8+ T cells.

Primary P14 TCR transgenic CD8+ T cells were isolated from wild-type or BATF-/- mice using CD8 negative selection magnetic-activated cell sorting (MACS) and cultured in RPMI 1640 supplemented with 10% fetal bovine serum, 10mM HEPES, 50 U/ml of Penicillin, 50 mg/ml of Streptomycin, and 50 mM b-mercaptoethanol.

The arrays were scanned on the GeneChip Scanner 3000 7G using AGCC (Affymetrix Gene Command Console) for the image proccessing.

The data were processed using GenePattern (RMA) and custom scripts (differential expression, collapsing probes to genes, etc).

RNA extraction was performed using the RNeasy Mini kit (Qiagen).  Concentrations of total RNA were determined using a Nanodrop spectrophotometer (Wilmington, DE).  RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies, Santa Clara, CA).

The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution is then removed.  The chips are transferred to a Fludics Station 450 that performs washes and staining with Affymetrix Hybe/Wash/Stain (cat # 900720) to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out.  The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.  The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using magnetic particles. The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements.  The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.

C57Bl/6;BATF-/- P14 TCR transgenic C57Bl/6;Day 3 in vitro effector CD8+ T cells

C57Bl/6;BATF-/- P14 TCR transgenic C57Bl/6;Day 0 Naïve CD8+ T cells

C57Bl/6;P14 TCR transgenic C57Bl/6;Day 3 in vitro effector CD8+ T cells

A pool of two pure subsets of peripheral blood CD4+ T cells (CD19- CD3+ CD4+ CD8- CD16- CD56-), stringently sorted by flow cytometry, from two age and gender matched stage IV (American Joint Committee on Cancer) melanoma patients.;Pooled RNA from the total peripheral lymphocyte fraction from 20 healthy donors, used as a common reference.

A pool of two pure subsets of peripheral blood CD8+ T cells (CD19- CD3+ CD4- CD8+ CD16- CD56-), stringently sorted by flow cytometry, from two age and gender matched healthy donors.;Pooled RNA from the total peripheral lymphocyte fraction from 20 healthy donors, used as a common reference.

Control and mutant mice were injected i.p. with 1mg of tamoxifen for 3 days for the SRF deletion.

GeneChips were scanned using the Affymetrix GeneChip 3000 Scanner.

The raw data were analyzed with GeneChip Operationg Software version 1.4 (GCOS) and statistical analyses were carried out with the BioConductor suite.

total RNA extraction using Rneasy Fibrous tissue kit (Qiagen), according to the manufacturer's instructions.

Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip450 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Aorta;SRF-flex2neo;SRF-flex2neo littermates (control);4 month-old

The scanned images were analyzed using the GeneChip operating software version 1.4 (Affymetrix 690036) with Microarray Suite version 5.0 (MAS 5.0). Affymetrix default analysis settings and global scaling was used as normalization method. The trimmed mean target intensity of each array was set to 500.

RNA for microarray analysis was isolated with TRIzol reagent (Life Technologies, Rockville, MD, USA)  according to the manufacturer’s instructions. RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (GeneChip Expression Wash, Stain and Scan User Manual For Cartridge Arrays, P/N 702731 Rev. 2)

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChipR 3’ IVT Express Kit User Manual, P/N 702646 Rev. 1).

Injection of ketamine/xylazine (300mg/kg; 40mg/kg) before sacrifice.

Specifically bound probe was detected by incubating the arrays with SAPE (Molecular Probes) and scanning the chips with a Hewlett-Packard GeneArray scanner (Affymetrix). A second scan was performed after signal enhancement with biotinylated anti-streptavidin antibody (Vector Laboratories).

The scanned images were analyzed using the GeneChip Analysis Suite 3.3 (Affymetrix) to identify genes differentially expressed among the RNA samples. Data were normalized using the RMA algorithm.

The hybridization mixture was prepared by mixing 15 ug biotinylated probe with control oligonucleotide B2 (final concentration 50 pM; Affymetrix), herring sperm DNA (final concentration 0.1 mg/ml; Research Genetics), acetylated bovine serum albumin (final concentration 0.5 mg/ml; Gibco BRL Life Technologies) in a final volume of 300 ml of 13 MES hybridization buffer (100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween-20; all reagents from Sigma). The hybridization mixture was denatured for 10 minutes at 99 C, incubated for 5 minutes at 45 C, and spun for 5 minutes in a benchtop microcentrifuge. The microarray was warmed to room temperature and prehybridized in hybridization buffer for 10–20 minutes at 45 C. The prehybridization solution was removed and 150 ml of the hybridization mix was added to the array. The array and probe fragments were incubated at 45 C overnight (16–20 hours). After hybridization, nonspecifically bound probe was removed by washing with the GeneChip Fluidics station 400 (Affymetrix). In total, 10 low-stringency washes (63 SSPE, 0.01% Tween-20, 0.005% Antifoam) and 4 high-stringency washes (100 mM MES, 0.1 M NaCl, 0.01% Tween-20, 50 C) were performed (all reagents from Sigma).

Monitor the effect of Hnf1alpha loss in the mouse jejunum epithelium.

migratory cells only found in diseased OA tissue with stem cell characteristics

SMhu114

SMhu113

SMhu116

SMhu115

SMhu118

SMhu117

Sample data was processed using GCOS 1.3.0 (Affymetrix default settings) and normalized using GCRMA (R Bioconductor, gcrma package).

RNA extracted using RNEasy (Qiagen) according to the manufacturers guidelines

Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133 2.0 Plus Array (Affymetrix GeneChipHybridization Oven 640). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2008, Affymetrix).

corresponds to sample Hu1 in table 1
Gene expression data from whole biopsies, primary mucosal tissue

corresponds to sample Hu3 in table 1

SMhu091

corresponds to sample Hu5 in table 1

corresponds to sample Hu6 in table 1

corresponds to sample Hu7 in table 1

corresponds to sample Hu8 in table 1

corresponds to sample Hu9 in table 1

SMhu086

SMhu085b

SMhu085

SMhu090

SMhu089

SMhu088

SMhu087

Human skin biopsies were obtained from patients before isotretinoin and after 1-week isotretinoin treatment. Biospies were flash frozen and stored at -80C until RNA isolation

The expression values were normalized by using the R-Affy package from Bioconductor version 1.1 to remove background noise and non-biologival variations among arrays. The background noise was removed from the PM probe intensities using the "RMA" method. Normalization was performed using the quantile normalization method (Bolstad et. al., 2003).  To remove the effects of outlier probes and sumerize probe intensities within one probe set to a single expression value, the "medianpolish" method was applied to the background adjusted, normalized PM intensities and not the PM-MM, because it is believed that MM intensities reflect background noise as well as probe-specific signals. Significant gene expression alterations were identified using the computer software: Significance Analysis of Microarrays (Tusher et. al.,2001).

Biopsies were sectioned using a cryostat to facilitate tissue homogenization. Total RNA was isolated and DNase I treated using the Rneasy Fibrous Tissue Kit (Qiagen, Valencia, CA). RNA was ethanol precipitated and quantified using a spectrophotometer. Approximately 2 micrograms of total RNA from each sample was used to generate double-stranded cDNA using a T7-oligo (dT) primer.

Biotinylated cRNA, produced through in vitro transcription, was fragmented and hybridized to an Affymetrix human U133A 2.0 microarray

Subjects included males and females ages 14 to 40 years who were scheduled by their dermatologist to receive treatment with 13-cis RA (isotretinoin, brand not noted) for severe acne.  All aspects of the patients’ treatment with 13-cis RA apart from the skin biopsies were standard of care and were not part of this research.  Exclusion criteria included patients with underlying medical conditions requiring treatment with systemic medications that might interfere with the gene array analysis.

Gene expression data from SEB-1 cell line with 72hr, 0.1uM 13-cis retinoic acid treatment

sebocyte cell line, SV-40 immortalized, 13-cis retinoic acid treated

mixed 129Sv/C57BL6;Col1a1+/+;Rosa26rtTA/+;male;8 months;esophagus

mixed 129Sv/C57BL6;Col1a1tetO-Nanog/+;Rosa26rtTA/+;male;8 months;esophagus

Rat230_2;15;ul;1.15;0.539;2.03;1:5;7.8;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;217;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;2.03;1.028;1.96;1:5;7.4;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;218;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.652;0.857;1.92;1:5;7.9;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;215;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;2.042;1.079;1.95;1:5;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;216;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 24, Units of Duration: hrs, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 2, Units of Dose or Concentration: ppm

nasal epithelium, formaldehyde inhalation exposure, 2 ppm, 6 hrs per day, 24 h time point

Rat230_2;15;ul;1.607;0.846;1.83;1:5;8.3;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;213;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;2.172;1.137;1.87;1:5;8.5;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;214;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.377;0.716;1.86;1:5;8.1;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;211;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.124;0.574;1.86;1:5;8.3;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;212;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;0.898;0.49;1.84;1:5;7.2;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;209;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.749;0.86;1:5;8.3;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;220;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

hESC H1 cells were targeted with AAV-based vectors to knock out B2M gene, clone 1
Sample name: B2MKOc1

Total RNA was isolated from whole brains using TRI REAGENT (Sigma-Aldrich, St. Louis, MO) according to the manufacturer’s instructions, and further purified on a Qiagen RNeasy mini kit (Qiagen Sciences, Germantown, MD).

Affymetrix murine expression U430 2.0 chips were scanned using an Affymetrix GeneChip Scanner 3000® and images interpreted and monitored using GCOS version 1.2.

Data from all CEL files was normalized together using R and Bioconductor packages (open source program; http://www.bioconductor.org <http://www.bioconductor.org/>) and statistically analyzed for significant differences (false discovery rate of 0.1) as follows. Briefly, normalization was done by the robust multichip average method (RMA; Irizarry et al. 2003) with the affy package

Total RNA was extracted from heart tissue with Trizol reagent (Life Technologies) and purified with the RNEasy Kit (Qiagen Inc., Valencia, CA).

GeneChip Hybridization Oven 640® (Affymetrix, Santa Clara, CA). Washing and staining was performed using an Affymetrix GeneChip Fluidics Station 650

Affymetrix GeneChip® One-Cycle Target Labeling and Control Kit as described in the Affymetrix Eukaryotic RNA One-cycle cDNA Synthesis and Labeling manual using an MJ Research DNA Engine Tetrad 2 thermocycler® (Bio-Rad Laboratories, Hercules, CA)

Rat underwent sham surgery for LAD occlusion/reperfusion. sample collected 2d after surgery to control for 2d IR.

Oct4-Gip ES cells (60,000 cells in 2ml media) were reverse transfected in 6 well plates with 800ng esiRNAs, 2ul lipofectamine (Invitrogen) and 200ul Opti-MEM (Invitrogen). 72 hours after transfection, RNA was extracted as described above. In total, 6 arrays including 3 replicates of control (Luc) and 3 replicates of experiment (Panct1 knockdown) were processed and hybridized on the Mouse 430 version 2 Array (Affymetrix).

ES cells (E14TG2a, R1/E, Oct4-Gip34) were cultured in Dulbecco’s Modified Eagle Medium (Invitrogen) supplemented with 4.5 g/l D Glucose and pyruvate, 10% fetal bovine Serum (Pan Sera), 30 uM 2-mercaptoethanol, 0.6X NEAA (Invitrogen), 300 units of Penicillin/Streptomycin (Invitrogen) and 8ng LIF (prepared in-house). Media was changed every day and ES cells were detached by treatment with Trypsin-EDTA (Invitrogen) and split every 2 days.

Arrays were washed and stained with streptavidin-phycoerythrin in the Affymetrix Fluidics Station 400 and further scanned using the AFFYMETRIX GeneChip Scanner 3000 7G.

The image data were analyzed with GCOS 1.4 using Affymetrix default analysis settings. Arrays have been quantile-normalize using the RMA algorithm.

Total RNA from ES cells was extracted using RNeasy Mini Kit (QIAGEN) with DNAse I treatment. 1.5 ug of total RNA was reverse transcribed using Superscript III Reverse Transcriptase (Invitrogen) and a 1:1 mix of oligo(dT)12-18 primer (Invitrogen) and Random Hexamers (Applied Biosystems) according to manufacturer’s instructions. cDNA was diluted 1:5 in water and qPCR was performed with the SYBR Green qPCR kit (Abgene) on an MX P3000 qPCR machine (Stratagene).  Dilution curves for primer efficiency were plotted and products were run on gel and sequence verified for the lncRNAs obtained as screen hits. For all qPCR measurements, Beta-2-microglobulin or GAPDH mRNA were used as housekeeping markers and all measurements were normalized to these controls.

After fragmenting of the cRNA for target preparation using the standard Affymetrix protocol 15 µg fragmented cRNA was hybridized for 16 h at 45 °C to Mouse Genome 430 v. 2 array.

Biotinylated cRNA was synthesized with Perkin-Elmer's nucleotide analogs using the MEGAScript T7 kit (Ambion).

Gene expression data from Oct4-Gip ES cells 72h after Luc-esiRNA (negative control) treatment.

Cells were transfected using RNAiMax and harvested 48 hours after transfection

RNA was extraction with the miRVana kit for total RNA, followed by Dnase I treatment (Ambion) all per kit instructions

Gene expression profile of an adrenocortical adenoma  with wild-type CTNNB1 gene

bone marrow;CD34+ hematopoietic stem cells (HSC);myelodysplastic syndromes (MDS);refractory anemia with ringed sideroblasts (RARS);del5q

Control fetal heart (vehicle treated with corn oil on gd14.5 via oral gavage, collected on gd17.5)

T3 fetal heart (treated on gd 14.5 via oral gavage, collected on gd17.5)

T1.5 fetal heart (treated on gd14.5 via oral gavage, collected on gd 17.5)

T3 fetal heart (treated on gd14.5 via oral gavage, collected on gd17.5)

T1.5 fetal heart (treated on gd14.5 via oral gavage, collected on gd17.5)

Gene expression profile of  an adrenocortical adenoma  with a  S37C  CTNNB1 mutation

Healthy control;35;Female;N/A;N/A;6.6;23;Right;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 1;0 (no use) to 6 (heavy use)): 0

Healthy control;44;Female;N/A;N/A;6.3;25;Right;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 1

Healthy control;52;Male;N/A;N/A;6.5;8;Left;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 1

Bipolar disorder;30;Male;7;23;5.8;56;Right;0;No;No;No;Yes;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 1

Bipolar disorder;50;Female;34;16;6.1;18;Left;12000;No;No;No;No;0 (no use) to 5 (heavy use)): 5;0 (no use) to 6 (heavy use)): 3

Bipolar disorder;37;Female;14;23;6.5;29;Right;1200;Yes;No;Yes;Yes;0 (no use) to 5 (heavy use)): 4;0 (no use) to 6 (heavy use)): 6

Healthy control;52;Male;N/A;N/A;6.5;28;Left;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 2

Healthy control;58;Male;N/A;N/A;6.0;27;Left;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 1

Healthy control;52;Male;N/A;N/A;6.2;22;Right;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 3

Healthy control;53;Male;N/A;N/A;6.2;28;Left;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 2;0 (no use) to 6 (heavy use)): 2

"Peripheral blood mononuclear cells were isolated 0, 30 min, 6 h, 24 h, and 7 day after saline challenge (control) using cell preparation tubes (Vacutainer® CPT). The PBMC layer was lysed with RLT buffer, homogenized, and then stored at –80°C. Total RNA was extracted as per RNeasy‚ Midi protocol (Qiagen). Double stranded cDNA was synthesized from total RNA (5 to 20 µg) using 7-d(T)24  primer and SuperScript‰ Double-Stranded cDNA Synthesis Kit and purified by phase lock gel-phenol/chloroform extraction followed by ethanol precipitation. Biotin-labeled cRNA was prepared by in vitro transcription using HighYield‰ RNA Transcript Labeling Kit followed by fragmentation with 5X fragmentation buffer.  Fragmented cRNA (10 µg) was hybridized to Affymetrix Hu95Av2 oligonucleotide probe arrays for 16 h at 45?C.  After removal of hybridization fluid, the arrays were washed, stained with streptavidin phycoerythrin (SAPE), and signal amplified by anti-streptavidin antibody using Affymetrix Fluidics Station 400.  Probe set signals were measured using Agilent GeneArray Scanner (Affymetrix‚, Santa Clara, CA)."

"male subject, 18-45 yrs, peripheral blood mononuclear cells 168 h after intravenous saline challenge"

"male subject, 18-45 yrs, peripheral blood mononuclear cells 24 h after intravenous saline challenge"

MMTV-neu mouse mammary tumor/ part of a 14 genechip exp comparing tumors, preneoplastic neu mammary gland (adjacent neu), and age-matched, wild-type control mammary glands to identify early events of erbB2/neu-induced tumorigenesis

MMTV-neu mouse mammary tumor, part of a 14 genechip exp comparing tumors, preneoplastic neu mammary gland (adjacent neu), and age-matched, wild-type control mammary glands to identify early events of erbB2/neu-induced tumorigenesis
Lot batch = 2004097

"male subject, 18-45 yrs, peripheral blood mononuclear cells 6 h after intravenous saline challenge"

"male subject, 18-45 yrs, peripheral blood mononuclear cells 30 minutes after intravenous saline challenge"

Progenitors were isolated from 13.5 day mouse fetal livers and grown into megakaryocytes in differentiation media. Megakaryocytes were isolated on a BSA gradient and RNA isolated.

"male subject, 18-45 yrs, peripheral blood mononuclear cells prior to (baseline - 0 h) intravenous saline challenge"

pancreas from 3 week old BDC2.5/NOD mouse.  RNA was extracted by GITC method. Targets were produced using standard Affymetrix procedures from about 10ug of total RNA.  RNA was isolated twice from 6 animals each and pooled.
Pancreas
Keywords = BDC2.5/NOD, pancreas

Neonatal (P0) whole brain mRNA from 39,Xm (XmO) C57BL/6J x C3H/Paf

Amplified total RNA from microdissected tumor cells from mastectomy specimen from postmenopausal patient with invasive ductal carcinoma (IDC)

tumor tissue from mastectomy specimen from postmenopausal patient with invasive ductal carcinoma (IDC)

LOX-1:121202;GFP_oxLDL_2hr:121202;Classification:Medium;Gradient Severity:0.04;Distortion Severity:0.02;Defective Area (%):0;Outlier Area (%):0.01;3'/5' Mean:2.74;Background Mean Dev.:0.6;Absent (%):58.51;Absent (%) Dev.:0.2;Scaling Factor:0.72;Scaling Factor Dev.:0.95;GFP;2 hours;Oxidized LDL;121202;HAECT;50 ug/ml;Endothelial;Human:Homo sapiens;GFP_oxLDL_2hr;282295513

LOX-1:221303;LOX1_oxLDL_6hr:221303;Classification:Medium;Gradient Severity:0.06;Distortion Severity:0.03;Defective Area (%):0;Outlier Area (%):0.01;3'/5' Mean:1.51;Background Mean Dev.:0.77;Absent (%):59.52;Absent (%) Dev.:0.98;Scaling Factor:0.87;Scaling Factor Dev.:2.24;LOX1;6 hours;Oxidized LDL;221303;HAECT;50 ug/ml;Endothelial;Human:Homo sapiens;LOX1_oxLDL_6hr;282295703

LOX-1:121303;GFP_oxLDL_6hr:121303;Classification:Good;Gradient Severity:0.02;Distortion Severity:0.04;Defective Area (%):0.01;Outlier Area (%):0.01;3'/5' Mean:1.62;Background Mean Dev.:1.42;Absent (%):57.76;Absent (%) Dev.:0.38;Scaling Factor:0.45;Scaling Factor Dev.:1.43;GFP;6 hours;Oxidized LDL;121303;HAECT;50 ug/ml;Endothelial;Human:Homo sapiens;GFP_oxLDL_6hr;282295643

LOX-1:221403;LOX1_oxLDL_12hr:221403;Classification:Good;Gradient Severity:0.03;Distortion Severity:0.01;Defective Area (%):0;Outlier Area (%):0.01;3'/5' Mean:1.62;Background Mean Dev.:0.18;Absent (%):58.56;Absent (%) Dev.:0.24;Scaling Factor:0.68;Scaling Factor Dev.:0.56;LOX1;12 hours;Oxidized LDL;221403;HAECT;50 ug/ml;Endothelial;Human:Homo sapiens;LOX1_oxLDL_12hr;282295823

LOX-1:113103;GFP_0hr:113103;Classification:Good;Gradient Severity:0.04;Distortion Severity:0.04;Defective Area (%):0;Outlier Area (%):0.01;3'/5' Mean:1.66;Background Mean Dev.:0.49;Absent (%):58.03;Absent (%) Dev.:0.17;Scaling Factor:0.63;Scaling Factor Dev.:0.13;GFP;0 hours;(Not applicable);113103;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;GFP_0hr;282295433

The LRRK2 mutant knockin H9 hESC derived NSC were mock treated or treated with 3µM LRRK2-IN-1 for 5 days.

Lot batch = EEG011

Standard Affymetrix Protocal

Lot batch = EEG069

Lot batch = EEG075

Lot batch = EEG070

Gene expression data from C57BL/6 strain mouse left ventrical with 30 day LAD ligated heart.

GeneChips were scanned using the Affymetrix Genechip Scanner 3000.

The data were analyzed with Genespring 7.3.1 (Agilent) using RMA normalization, then normalized to median of the non-transgenic mice.

Trizol (Invitrogen, Carlsbad, CA).
Quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Palo Alto, CA).

Following fragmentation, cRNA were hybridized on the Affymetrix MOE430 plus 2.0 GeneChip array according to the standard Affymetrix protocol.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microgram total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

heart from AC5 transgenic mice at 90 days of age. The alpha-myosin heavy chain promoter was utilized to direct expression of the human AC5 cDNAs to cardiac myocytes.

C: control diet
30: 30-month-old

5x106 CLL cells were treated with 0.1 μM CDKI-73, 10 μM fludarabine or the two drugs in combination for 4h.

Primary CLL cells were cultured in RPMI supplemented with 10% fetal bovine serum (FBS), penicillin (50 U/ml), streptomycin (50 µg/ml) and recombinant human IL-4 (R and D Systems, Abingdon, UK) (5 ng/ml).

The data were analyzed with MADRAS bespoke software using Affymetrix default analysis settings and global scaling as normalization method.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC on Affymetrix U133 2.0 Gene Chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

5: 5-month-old

Vehicle (DMSO) or T3 ( 1 mg/kg body weigh) were administrated daily by oral gavage for 3 days

Unmodified microarray data obtained from GenomeStudio (Illumina) was background-subtracted and quantile-normalized using the lumi package within R

RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided within the kit. RNA quality was assessed with an Agilent Bioanalyzer.

The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450, followed by scanning on a GeneChip Scanner 3000. The results were quantified and analyzed using GCOS 1.1.1 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity = 500; Normalization, All Probe Sets; Parameters, all set at default values).

Isolated total RNA samples were processed as recommended by Affymetrix, Inc. (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetric, Inc., Santa Clara, CA). In brief, total RNA was initially isolated using TRIzol Reagent (Gibco BRL Life Technologies, Rockville, MD), and passed through an RNeasy spin column (Qiagen, Chatsworth, CA) for further clean up. Eluted total RNAs were quantified with a portion of the recovered total RNA adjusted to a final concentration of 1 ug/ul. All starting total RNA samples were quality assessed prior to beginning target preparation/processing steps by running out a small amount of each sample (typically 25-250 ng/well) onto a RNA Lab-On-A-Chip (Caliper Technologies Corp., Mountain View, CA) that was evaluated on an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix Mouse Genome 430 2.0 array.

Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+ mRNA  present in the isolated total RNA (10 ug total RNA starting material each sample reaction) using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen Corp., Carlsbad, CA ) and poly (T)-nucleotide primers that contained a sequence recognized by T7 RNA polymerase. A portion of the resulting ds cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction (IVT), using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics, Inc., Farmingdale, NY).  15ug of the resulting biotin-tagged cRNA was fragmented to strands of 35-200 bases in length following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).

Get1, grainyhead epithelial transactivator 1. Also known as grainyhead-like 3 (Grhl3)

Embryonic stem cells were cultured at 37oC under standard conditions maintaining the undifferentiated state, i.e., KO-DME supplemented with LIF. 5% CO2/21% O2.

The raw data have been normalized together using the RMA algorithm (developed and described by R. A. Irizarry (2003)) in the statistical package R (http://www.r-project.org/).

Total RNA was purified using the Qiagen miRNeasy kit (cat. No. 217004) according to the manufacturer's instructions.

Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45oC on a GeneChip Mouse Genome Array 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA (3_ivt_express_kit_manual, 2009, Affymetrix).

C10-2
Whole genome gene expression data from Alkbh1-/- C57BL/6 mouse embryonic stem cells.

C57BL/6;Alkbh1-/-;embryonic stem cells;day 0, undifferentiated;8

C10-3

C3-3
Whole genome gene expression data from wild type C57BL/6 mouse embryonic stem cells.

C57BL/6;wild type;embryonic stem cells;day 0, undifferentiated;8

C10-1

A SIT_B098

Y HID_B039

Dorsal Telencephalon of WT or cKO (Emx2Cre) E14.5 embryos were dissected and dissolved in Trizol immediately until RNA extraction is performed.

The data were analyzed with Expression Console Software using Affymetrix default analysis settings and global scaling as normalization method.

Following fragmentation, 10ug  cRNA were hybridized for 16 hr at 45C on GeneChip Mus Musculus Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

A VIS _B067

Y VIS _B065

A VIS _B069

A VIS _B068

A HID I_B008

A VIS _B096

A VIS _B033

Y VIS _B030

238;Enalapril Zantac;9/27/38;F;CAUCASIAN;9/25/03;1/14/05;FALSE;FALSE;FALSE;NO;FALSE;FALSE;1/6/05;4;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;unknown;unknown;unknown;1/6/05;BOTH;BOTH;unknown;unknown;unknown;3/7/05;NEW;ex;1/1/03;5-14;Hypertension Diverticular disease;UC;8-9-01;descending colon;Inflamed;total RNA from 10 human cell lines

205;Pentaza 3g/d;6/8/79;M;CAUCASIAN;10/1/03;8/30/04;FALSE;TRUE;FALSE;NO;FALSE;FALSE;10/8/04;4;0;15;19;110;5;3;43;FALSE;0;BOTH;BOTH;BOTH;unknown;unknown;10/8/04;BOTH;BOTH;BOTH;unknown;unknown;12/9/04;NEW;ex;1/1/85;3/1/03;15-24;None;UC;8-9-01;descending colon;Inflamed;total RNA from 10 human cell lines

243;Atenolol Pravastatin Asprin Adalat BFZ Balsalizide;2/17/25;F;CAUCASIAN;8/1/04;3/29/05;FALSE;FALSE;FALSE;NO;FALSE;FALSE;3/29/05;5;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;BOTH;BOTH;BOTH;3/29/05;BOTH;BOTH;BOTH;BOTH;BOTH;6/1/05;NEW;never;unknown;IHD Deaf;UC;8-9-01;descending colon;Inflamed;total RNA from 10 human cell lines

245;Pentaza 1g BD;11/4/67;F;CAUCASIAN;11/4/04;3/16/05;FALSE;FALSE;FALSE;NO;FALSE;FALSE;3/16/05;3;0;0;0;0;0;0;0;TRUE;0;BOTH;unknown;unknown;unknown;unknown;3/16/05;BOTH;unknown;unknown;unknown;unknown;6/3/05;NEW;never;unknown;Asthma;UC;8-9-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

201;None;4/12/56;M;CAUCASIAN;6/19/03;7/4/03;FALSE;FALSE;FALSE;NO;FALSE;FALSE;9/30/04;1;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;BOTH;BOTH;BOTH;9/30/04;BOTH;HISTOLOGICAL;unknown;unknown;unknown;12/7/04;FAILURE OF THERAPY;ex;1/1/70;1/1/99;25+;None;UC;1-25-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

Chips were scanned using an Agilent Gene Array scanner 2000 driven by Affymetrix MicroArray Suite 5.0.  The scanner PMT was set to the later, wide dynamic range setting.

Preparation of Hybridization cocktails: The standard hybridization cocktail volume was 300 ul. 150 ul of 2X hybridization buffer was added (final concentrations : 100mM MES, 1M [Na+], 20mM EDTA, 0.01% Tween 20) Herring sperm and acetylated BSA were added to a final concentration of 0.1 and 0.5mg/ml respectively. The amount of fragmentation reaction containing 15ug of cRNA was added to the cocktail and the remaining volume was made up with molecular biology grade water.

Double-stranded cDNA was made from the pooled RNA samples using the Superscript Double Stranded cDNA Synthesis kit (Invitrogen, Carlsbad, CA; cat# 11917-010) and an oligo-dT primer coupled to the T7 RNA polymerase promoter. Biotin-labeled cRNA was generated with the Enzo BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA; cat# 900182) and purified using the Qiagen RNEasy kit (cat# 74104).

Thoracic mammary glands were collected from three virgin wild type F1 CF-1/FVB mice at 16 weeks of age; RNA was pooled before synthesis of cDNA. This and two other distinct wild type samples were compared to mammary glands from 16 week old LH-overexpressing mice.

Thoracic mammary glands were collected from three virgin wild type F1 CF-1/FVB mice at 16 weeks of age; RNA was pooled before synthesis of cDNA.

Thoracic mammary glands were collected from three virgin F1 CF-1/FVB LH-overexpressing (transgenic) mice at 16 weeks of age; RNA was pooled before synthesis of cDNA. This and two other distinct transgenic samples were compared to mammary glands from 16 week old wild type mice.

Thoracic mammary glands were collected from three virgin F1 CF-1/FVB LH-overexpressing (transgenic) mice at 16 weeks of age; RNA was pooled before synthesis of cDNA

Thoracic mammary glands were collected from three virgin F1 CF-1/FVB LH-overexpressing (transgenic) mice at 16 weeks of age and pooled before synthesis of cDNA. This and two other distinct transgenic samples were compared to mammary glands from 16 week old wild type mice.

thoracic mammary glands were collected from three virgin F1 CF-1/FVB LH-overexpressing (transgenic) mice at 16 weeks of age and pooled before synthesis of cDNA

Thoracic mammary glands were collected from three virgin F1 CF-1/FVB LH-overexpressing (transgenic) mice at 16 weeks of age; RNA was pooled before synthesis of cDNA. Data from this and two other distinct transgenic samples were compared to mammary glands from 16 week old wild type mice.

thoracic mammary glands were collected from three virgin F1 CF-1/FVB LH-overexpressing (transgenic) mice at 16 weeks of age; RNA was pooled before synthesis of cDNA

Total RNA was prepared using TRIzol reagent from the pancreas one 57 day old male mouse.  The genotype was gastrin+/-, CFTR+/+ on 95% black6, 5% 129Sv background.  Mice were fed Peptamen from age 10 days to prevent intestinal obstruction.
Keywords = Cystic fibrosis

1 ug of tetracycline was treated to stabel cell-lines which overexressing WT and mutant TRPM7 channel for 72 hours

Stabel cell-lines were grown in in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum and an antibiotic, 5 ug/mL blasticidin (Invitrogen). Cells were cultured in a humidified atmosphere of 5% CO2 at 37 °C.

After hybridization, the arrays were washed in a GeneChip Fluidics Station 450 with a non-stringent wash buffer at 25°C followed by a stringent wash buffer at 50°C. After washing, the arrays were stained with a streptavidin-phycoerythrin complex. After staining, intensities were determined with a GeneChip scanner 3000 (Affymetrix), controlled by GCOS Affymetrix software.

Fragmented cRNA was hybridized to the Human Genome UI133 Plus 2.0 Array (Affymetrix) at 45°C for 16 h according to the Affymetrix standard protocol.

5 ug of total RNA from each cell-lines was used for labeling. Probe synthesis from total RNA samples, hybridization, detection, and scanning were performed according to standard protocols from Affymetrix, Inc..

Gene expression data from HEK cells expressing WT TRPM7 channel
WT tet3

Gene expression data from HEK cells non-expressing mutant TRPM7 channel
Mutant no1

Mutant no2

Mutant no3

Gene expression data from HEK cells expressing mutant TRPM7 channel
Mutant tet1

Mutant tet3

Gene expression data under ER stress from lymphoblastoid cells of individual GM12145 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12146 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12057 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12144 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12144 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12145 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12044 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12056 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12056 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12057 treated with 4 ug/ml tunicamycin 8 hours.

RNA-STAT extraction of total RNA was performed according to the manufacturer's instructions.

For MPH treatment, LCL culture medium was supplemented with 30 ng/µl MPH, corresponding to the maximum recommended concentration in human blood.

LCLs were generated from the EDTA-blood of ADHD patients and unaffected controls according to the Leucosep-protocol (Greiner Bio-One) Ficoll-Paque PLUS and transformed with Eppstein-Barr virus (EBV). LCLs were cultured in RPMI1640 medium (Gibco) supplemented with 15% fetal bovine serum (FBS) and 2 mM L-glutamine at 37 °C and 5% CO2.

Microarrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix).

Data were preprocessed in the R v3.0.1 environment with Bioconductor packages affy and vsn; VSN normalization and RMA probeset summary were performed with the vsnrma command using default parameter settings.

Total RNA was isolated with the RNeasy Protect Cell kit (Qiagen) according to the  manufacturer's protocol.

200µl hybridization mix prepared from labeled cRNA fragments was hybridized for 16h at 45°C to GeneChip Human Genome U133 Plus 2.0 arrays. Microarrays were washed and stained in the Affymetrix Fluidics Station 450 using script FS450_0001.

100ng of total RNA were amplified and labeled with the IVT Express Kit (Affymetrix); all steps were performed according to the manufacturers' protocols.

ADHD;untreated;EBV-transformed lymphoblastoid cell lines;LCLs from 7 ADHD patients

in vitro Treatment: siLuc (Sense 5\'-rCrGUrArCrGrCrGrGrArAUrArCUUrCrGrCTT-3’ Antisense 5’-UrCrGrArArGUrAUUrCrCrGrCrGUrArCrGTT-3’), Treatment Repeat: 1, Units of Treatment Repeat: exposure, Treatment Duration: 52, Units of Duration: hrs, Treatment Time: -48, Units of Treatment Time: hrs, Vehicle for Chemical: Lipofectamine 2000, Amount of Vehicle: 0.44, Route of Exposure: transfection, Units of Amount of Vehicle: ul, Dose or Concentration: 3.3, Units of Dose or Concentration: nM
Treatment_2: in vitro Treatment: Heat, 43ºC, Treatment Repeat: 1, Units of Treatment Repeat: exposure, Treatment Duration: 1.5, Units of Duration: hrs, Treatment Time: 0, Units of Treatment Time: hrs, Route of Exposure: convection, Dose or Concentration: 43, Units of Dose or Concentration: degree Celcius

TP090705_29_HG-U133A_2_IMFGN0023: This is a repeat of one sample, that was masked in the orginial array (completed 8/31/05). These samples are from the 6_22_05 experiment, they are the siLUC samples

Sample Type: Cells, Cell Line: HeLa, ATCC Number: CCL-2, Number of Cells Seeded: 2.20E+05, Cell Type: Cervical carcinoma, Separation Type: trypsin, Harvest Time Point: 4, Units of Harvest Time Point: hr

in vitro Treatment: siLuc (Sense 5'-rCrGUrArCrGrCrGrGrArAUrArCUUrCrGrCTT-3’ Antisense 5’-UrCrGrArArGUrAUUrCrCrGrCrGUrArCrGTT-3’), Treatment Repeat: 1, Units of Treatment Repeat: dose, Treatment Duration: 48.5, Units of Duration: hrs, Treatment Time: -48, Units of Treatment Time: hrs, Vehicle for Chemical: Lipofectamine 2000, Amount of Vehicle: 0.44, Route of Exposure: Transfection, Units of Amount of Vehicle: microliter, Dose or Concentration: 3.3, Units of Dose or Concentration: nM
Treatment_2: in vitro Treatment: Heat, 43ºC, Treatment Repeat: 1, Units of Treatment Repeat: exposure, Treatment Duration: 0.5, Units of Duration: hrs, Treatment Time: 0, Units of Treatment Time: hrs, Route of Exposure: Convection, Dose or Concentration: 43, Units of Dose or Concentration: degrees Celcius

TP082505_24_HG-U133A_2_IMFGN0023: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

Sample Type: Cells, Cell Line: HeLa, ATCC Number: CCL2, Number of Cells Seeded: 2.20E+05, Cell Type: Cervical Carcinoma, Separation Type: Trypsin, Harvest Time Point: 0.5, Units of Harvest Time Point: hr

TP082505_23_HG-U133A_2_IMFGN0023: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

in vitro Treatment: siLuc (Sense 5'-rCrGUrArCrGrCrGrGrArAUrArCUUrCrGrCTT-3’ Antisense 5’-UrCrGrArArGUrAUUrCrCrGrCrGUrArCrGTT-3’), Treatment Repeat: 1, Units of Treatment Repeat: dose, Treatment Duration: 48, Units of Duration: hrs, Treatment Time: -48, Units of Treatment Time: hrs, Vehicle for Chemical: Lipofectamine 2000, Amount of Vehicle: 0.44, Route of Exposure: Transfection, Units of Amount of Vehicle: microliter, Dose or Concentration: 3.3, Units of Dose or Concentration: nM
Treatment_2: in vitro Treatment: Heat, 43ºC, Treatment Repeat: 1, Units of Treatment Repeat: exposure, Treatment Duration: 0, Units of Duration: hrs, Treatment Time: 0, Units of Treatment Time: hrs, Route of Exposure: Convection, Dose or Concentration: 43, Units of Dose or Concentration: degrees Celcius

TP082505_21_HG-U133A_2_IMFGN0023: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

Sample Type: Cells, Cell Line: HeLa, ATCC Number: CCL2, Number of Cells Seeded: 2.20E+05, Cell Type: Cervical Carcinoma, Separation Type: Trypsin, Harvest Time Point: 0, Units of Harvest Time Point: hr

TP082505_20_HG-U133A_2_IMFGN0023: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

TP082505-36_HG-U133A_2_IMFGN0023: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

TP082505-35_HG-U133A_2_IMFGN0023: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

C57BL/6;male;10 weeks;0.1% saline twice daily;kidney;8324341086;E;PC7-R

C57BL/6;male;10 weeks;colistin at 16 mg/kg/day in 2 divided doses;kidney;8324341086;F;PC11-R

unaffected;untreated;EBV-transformed lymphoblastoid cell lines;LCLs from 6 unaffected controls

ADHD;MPH;EBV-transformed lymphoblastoid cell lines;LCLs from 7 ADHD patients

FVB;transformed by c-myc gene;Primary prostate epithelial cell culture, oncogene-transduced

cells were grown in Dulbecco’s modified Eagle’s medium supplemented with 10% (v/v) foetal calf serum at 37°C in a humidified CO2 (5%) incubator

see Affymetrix GeneChip Expression Analysis Manual and Microarray Analysis Suite 5.0 Software. Affymetrix. Reference 701001rev2. 2001.
parameters settings: alpha 1 = 0.05, alpha 2 = 0.065, tau = 0.15

RNA was isolated using Trizol 7 days after infection. RNA was further prepared by passage over an RNeasy column. cDNA synthesis, biotinylation of cRNA and hybridization to mouse Genechip 430_2containing was performed according to the manufacturer’s instructions (Affymetrix, Santa Clara).

DP (CD4+/8+) cells from Notch1-IC over-expressing peripheral tumor (thymoma) Replicate 2

Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was done by the RMA algorithm using Agilent GeneSpring GX10 program.

10 mcg of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

100 ng total RNA converted to cRNA using Affymetrix GeneChip® 3' IVT cDNA Synthesis and in vitro transcription kit resulting into biotin-labeled cRNA, fragmented prior to hybridization (Affymetrix Expression Analysis Technical Manual, as described).

Gene expression data from DP (CD4+/8+) cells from Notch1-IC over-expressing peripheral tumor (thymoma) Replicate 2

T-ALL;DP (CD4+/8+) cells from Notch1-IC over-expressing peripheral tumor (thymoma);WT C57/BLACK6;DP (CD4+/8+) cells

DP (CD4+/8+) cells from Notch1-IC over-expressing peripheral tumor (thymoma)

Gene expression data from DP (CD4+/8+) cells from Normal Thymus Replicate 2

WT;DP (CD4+/8+) cells from Notch1-IC over-expressing peripheral tumor (thymoma);WT C57/BLACK6;DP (CD4+/8+) cells

DP (CD4+/8+) cells from Notch1-IC over-expressing peripheral tumor (thymoma) Replicate 1

Gene expression data from DP (CD4+/8+) cells from Notch1-IC over-expressing peripheral tumor (thymoma) Replicate 1

Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was done by the RMA algorithm using Agilent GeneSpring GX10 program. N

Gene expression data from DP (CD4+/8+) cells from Normal Thymus Replicate 1

Subject Age : 30

Subject Age : 45

Subject Age : 55

Ulcerative Colitis (55 year old caucasian female, SAK_1319013894)

Ulcerative Colitis (37 year old caucasian female, SAK_1286609838)

Subject Age : 37

Ulcerative Colitis (49 year old caucasian female, SAK_1286431014)

Ulcerative Colitis (25 year old caucasian female, SAK_1286453367)

Subject Age : 25

Levitiracetam frontal cortex 3

Levitiracetam frontal cortex 4

Levitiracetam frontal cortex 1

Levitiracetam frontal cortex 2

Control hippocampus 6

Control hippocampus 7

Control hippocampus 4

Control hippocampus 5

Levitiracetam frontal cortex 5

Levitiracetam frontal cortex 6

Treatment: 0.35 mM HOCl in mediu

Treatment: 0.35 mM HOCl in medium

Treatment: 0.14 mM HOCl in medium

GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) and GCOS software

The data were analyzed with R/Bioconductor. Data were normalized with RMA.

Total RNA was extracted with Trizol followed by RNAeasy columns (Qiagen) according to the manufacturer's instructions.

Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array, according to Affymetrix protocol.

Strip Arrays were scanned using the Affymetrix Gene Atlas system.

Data was analyzed using the limma and affy Bioconductor packages implemented in the R-statistical environment version 2.15.1. RMA was used to normalize the data and fit log2 transformed expression values.

Following fragmentation, 7.5 ug of aRNA were hybridized for 16 hr at 45C on MG-430 PM Strip Arrays using the Affymetrix Gene Atlas system (software version 1.0.4.267).

Biotinylated aRNA were prepared according to the Affymetrix GeneChip 3' IVT Express kit protocol from 250 ng total RNA (Affymetrix GeneChip 3' IVT Express kit Instruction Manual, P/N 702646 Rev. 5).

Gene expression data from wild type liver, pool 2
Wild type and Neuregulin 4 (Nrg4) knockout mice were fed high-fat diet starting at 3 months of age for eight weeks.

C57BL/6;liver;wild type;high-fat diet fed starting at 3 months of age for eight weeks.

Gene expression data from wild type liver, pool 1

Gene expression data from Nrg4 knockout liver, pool 1

C57BL/6;liver;Nrg4 knockout;high-fat diet fed starting at 3 months of age for eight weeks.

Gene expression data from wild type liver, pool 3

Gene expression data from Nrg4 knockout liver, pool 3

Gene expression data from Nrg4 knockout liver, pool 2

paraventricular nucleus of the hypothalamus, restraint stress, 1 hours

Discordant twin pair 1 (Unsffected pateint of MZ twin pair DCE1)

Discordant twin pair 2 (Unaffected pateint of MZ twin pair DCE2)

Discordant twin pair 3 (Unaffected pateint of MZ twin pair DCE3)

TP37;DCE5.1;Juvenile Absence Epilepsy + Febrile Seizures;-13;27;30;FEMALE;Epilim

C57Bl6;Gata4_S105A_homozygous mutant;9 weeks old;whole heart ventricle

Testicular intratubular germ cell neoplasia (alias carcinoma in situ or intratubular malignant germ cells), adjacent to a germ cell tumor
Keywords = carcinoma in situ
Keywords = intratubular germ cell neoplasia
Keywords = intratubular malignant germ cells

0.5 mg/kg/ml Isoproterenol treatment, 1 hour time point,  biological rep 3

CHIPEXP_NAME: 230_2_050531tpj_35h

0.5 mg/kg/ml Isoproterenol treatment, 1 hour time point,  biological rep 2

CHIPEXP_NAME: 230_2_050531tpj_34h

0.5 mg/kg/ml Isoproterenol treatment, 1 hour time point,  biological rep 1

CHIPEXP_NAME: 230_2_050531tpj_33h

CHIPEXP_NAME: 230_2_050531tpj_6h

CHIPEXP_NAME: 230_2_050531tpj_5h

CHIPEXP_NAME: 230_2_050531tpj_4h

skeletal muscle;mixed background (C57Bl/6 and 129);Yin Yang 1 (YY1) knockout;6 months

Keratinocytes were grown in Gibco SFM medium in subconfluent conditions to maintain the progenitor state

Pre-treatments with cycloheximide (10 microg/ml, Sigma) or vehicle DMSO (0.1%) were initiated 1 h before hormonal treatment with 17{beta}-estradiol (E2, 25 nM, Sigma) or vehicle (0.1% ethanol) for 24h.

MCF-7 breast carcinoma cells were maintained in {alpha}-minimal Eagle’s medium ({alpha}-MEM) (Wisent, St-Bruno, QC, Canada) supplemented with 10% fetal bovine serum (FBS) (Sigma-Aldrich, Oakville, On, Canada). Three days before experiments, cells were switched to phenol red-free Dulbecco’s modified Eagle’s medium (DMEM) (Wisent) containing 10% charcoal-treated FBS, 1% sodium pyruvate (Wisent), 1% penicillin/streptomycin (Wisent) and 1% L-glutamine (Wisent). Cells were seeded in 10 cm plates at a density such that near-confluency is obtained at the end of the treatment. The day before hormonal stimulation, the medium was changed to phenol red-free DMEM supplemented with 0,5% charcoal-treated FBS.

After completion of hormonal treatments, medium was completely removed and cells were collected in 1 ml of TRI-Reagent (Sigma). Total RNA was extracted as recommended by the manufacturer and further purified with RNeasy MinElute Cleanup Kit (QIAgen, Mississauga, On, Canada).

Amplified total RNA from microdissected normal ductal cells from mastectomy specimen from postmenopausal patient with invasive ductal carcinoma (IDC)

normal tissue from mastectomy specimen from postmenopausal patient with invasive ductal carcinoma (IDC)

Amplified total RNA from microdissected normal lobular cells from mastectomy specimen from postmenopausal patient with invasive ductal carcinoma (IDC)

Gene expression data from cochleas of wild type mice at P3.
P3_wildtype_rep2

P3_wildtype_rep3

P3_wildtype_rep1

Human GFAP-negative lamina cribrosa cells were generated from optic nerve head tissue. They were treated for 24 hours with vehicle (4mM HCl/1% BSA).  RNA extraced using Qiagen RNeasy mini collumns. *.Cel file normalised using Robust multichip average (RMA). Cell cultures from human donor A. Experiment conducted in duplicate (separate passages).

Human GFAP-negative lamina cribrosa cells were generated from optic nerve head tissue. They were treated for 24 hours with TGFB1 (10ng/ml).  RNA extraced using Qiagen RNeasy mini collumns. *.Cel file normalised using Robust multichip average (RMA). Cell cultures from human donor A. Experiment conducted in duplicate (separate passages).

Cells were transfected with pCMV-TARBP2 and pCMV-GFP using TransIT regaent (Mirus) per manufacturer guidelines.

Non-normalized values indicate the average probe hybridization signal.
Final processed values are logFC of average normalized signals in pCMV-TARBP2 relative to pCMV-GFP.

Keywords = spleen

This is a study of the change in gene expression in mouse kidney after feeding control or low phosphate diet to normal or Hyp mice for 3 days.  RNA from 3 mice were pooled for each microarray.

Study of change in gene expression in mouse kidney after feeding control or low phosphate diet to normal or Hyp mice for 3 days.  RNA from 3 mice is pooled for each sample.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12155 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12156 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12156 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12234 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12146 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12154 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12154 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12155 treated with 4 ug/ml tunicamycin 8 hours.

Peripheral blood mononuclear cells;oligoarticular JIA;GTE6;165min;Asian;Male

Center code: 2

Keywords = penis
Keywords = cavernosum
Keywords = erectile dysfunction

Cells were in serum-free RPMI-1640.  siRNA was diluted to 20nM in Optimem with Oligofectamine.  Cells were treated with siRNA for 24 hours prior to replenishing 10% FBS and allowing for cell growth for 48 hours.

RPMI-1640 media plus 10% FBS and 1% penicillin-streptomycin antibiotics.  Grown at 37 degrees C with 5% CO2.

Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

RWPE-PCAT1 cells transfected with non-targeting siRNA, RNA was harvested after 48 hours, replicate #1

RWPE-1-PCAT-1 (CRL-11609);< 20 cell passages from derivation;RWPE-1-LacZ;< 20 cell passages from derivation

Du145-PCAT1 cells transfected with non-targeting siRNA, RNA was harvested after 48 hours, replicate #1

Du145-PCAT1 (HTB-81);< 20 cell passages from derivation;Du145-LacZ;< 20 cell passages from derivation

breast cancer derived cell line treated with 0.3 mM of 5-Fluorouracil for 24 hours

immortalized human mammary epithelial cell line treated with 0.2 uM of Doxorubicin for 12 hours

14 days after ovariectomy, mice were injected subcutaneously with
progesterone dissolved in sesame oil (Sigma; 0.2mg/0.1mL/mouse),
followed by sacrifice and removal of uterine horns at 6 hours after
injection.  8 uterine horns from 4 mice were pooled to form one
sample.  Total RNA preparation, cRNA labeling and hybridization were
performed according to recommendations by Affymetrix.

of the Hoxa-10 gene (GenBank # NM_008263) present (wildtype).  These
mice were littermates of Hoxa-10-/- mice used in parallel
experiments.  14 days after ovariectomy, mice were injected

subcutaneously with sesame oil (Sigma; 0.1mL/mouse), followed by
sacrifice and removal of uterine horns at 6 hours after injection.
8 uterine horns from 4 mice were pooled to form one sample.  Total
RNA preparation, cRNA labeling and hybridization were performed
according to recommendations by Affymetrix.

-0.094736842;exon 11;GIST Tumor;Universal Human Reference RNA (Stratagene)

0.291666667;exon 11;GIST Tumor;Universal Human Reference RNA (Stratagene)

0.272727273;wildtype;GIST Tumor;Universal Human Reference RNA (Stratagene)

-0.213114754;exon 9;GIST Tumor;Universal Human Reference RNA (Stratagene)

n/a;exon 9;GIST Tumor;Universal Human Reference RNA (Stratagene)

0.177419355;exon 11;GIST Tumor;Universal Human Reference RNA (Stratagene)

Mouse ES cells were routinely maintained on gelatin-coated plates in the ESGRO complete plus clonal grade medium (Millipore). For siRNA transfection experiments, passage 20-35 cells were cultured in M15 medium: DMEM (Invitrogen) supplemented with 15% FBS (vol/vol), 10 mM 2-mercaptoethanol, 0.1 mM nonessential amino acids (Invitrogen), 1× EmbryoMax nucleosides (Millipore), and 1U per ml of ESGRO mLIF (Millipore)

Arrays were scanned in an Affymetrix Scanner 3000 and data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1).

Data was processed by performing background correction, quantile normalization, and calculation of expression set summaries using the Robust Multichip Average (RMA) protocol (Irizarry et al. (2003); Biostatistics 4: pages 249-264) as implemented in the affy packge from Bioconductor (http://www.bioconductor.org).  Log-scale data was further normalized by 1) setting the per-sample median to 6.5 and 2) subtracting the per-gene median.

One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol, performing the IVT reaction for 16 hours. 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to Affymetrix 430 2.0 array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

Labeling was performed using Affymetrix's IVT labeling kit following manufacturer's directions.

Gene expression data of HSC cells from MSI2-inducible mouse rep1

Gene expression data of HSC cells from MSI2-inducible mouse rep2

Portions of the livers were rapidly snap-frozen in liquid nitrogen and stored at -70°C until analysis.

Adult male wild-type mice and PXR-KO mice were maintained on standard laboratory chow and were allowed food and water ad libitum.

male;resveratrol-enriched grape extract (C);12 months;Isolated peripheral blood mononuclear cells (PBMCs)

Isolated PBMCs from diabetic male patient_RES-enriched Grape extract_12 months

With approval from the institutional review board, peripheral blood mononuclear cells were isolated from human peripheral blood using Histopaque (Sigma, St.Louis, MO) followed by negative isolation with magnetic beads (Stem cell, Vancouver, Canada). Monocyte purity was 96.2 ± 0.2 % as assessed by CD14 expression. After red blood cell lysis and several wash steps with 1 mM EDTA, monocytes were essentially free from platelet contamination as demonstrated by virtual absence of CD41 positivity in flow cytometry (data not shown). Monocytes were cultured in macrophage serum-free medium (Gibco, Carlsbard, CA) supplemented with Nutridoma SP (Roche, Indianapolis, IN) and penicillin/streptomycin (Sigma, St. Louis, MO) for six days in the presence of 100 ng/ml rhMCSF (Peprotech, Rocky Hill, NJ) or 1 µM rhCXCL4 (Peprotech). The concentration of 1 µM rhCXCL4 was chosen because this concentration was previously demonstrated to be sufficient to induce macrophage differentiation from monocytes (13). Furthermore, our own preliminary experiments confirmed that after six days, this concentration induced expression of typical macrophage markers like CD11b or CD68 to a similar extent as MCSF (Fig. 1 and data not shown).

Signal intensity values were obtained from the Affymetrix MicroArray Suite software (MAS 5.0).

Microarray gene expression intensities were normalized to ensure that all chips have the same interquartile ranges (IQR). In addition, they were log-transformed with base 2, which transforms the right-skewed distribution closer to a normal distribution. For statistical analysis, an open source statistical software package R (www.r-project.org) was used, which includes the local pooled error (LPE) test for differential expression discovery under two conditions, the heterogeneous error model (HEM) for differential expression discovery under multiple conditions, hierarchical clustering and heat-map analysis, and self-organizing maps (SOM), especially the last two widely used in microarray data analysis. The annotation information available from the Affymetrix web site (www.affymetrix.com) was used to identify the genes represented on the HG-U133A chip for the various classes of genes analyze. We eliminated nonexpressed (within 2 SD from zero in all conditions) and housekeeping genes [not significantly regulated with false discovery rate (FDR) <0.05]. We analyzed the regulated genes in two approaches; candidate gene analysis using LPE, HEM, and heat-map analysis, and unbiased analysis of all regulated genes without prior knowledge such using hierarchical clustering analysis.

For each condition RNA was isolated from macrophages derived from two donors using columns including a DNAse-step followed by reverse transcription (all reagents from Qiagen, Valencia, CA).

Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16178.gif

Myoblast Cell Line Stably Transfected with Galgt2 Differentiated rep1

Gene expression data from C2CT myotubes - C2C12 myoblasts stably transfected with Galgt2

Mouse Myoblast Cell Line Stably Transfected with Galgt2, Differentiated

T cells were precipitated untouched from 4 ml peripheral blood mononuclear cells, washed in PBS + 2mM EDTA, lysed in TriZol

Cryostat sections of vulvar biopsies were homogenized by sonography and RNA was isolated using Trizol (Invitrogen, Life Technologies, Philadelphia, PA, USA). 1 ?g of total RNA was used to prepare antisense biotinylated RNA (www.affymetrix.com). The level and quality of cRNA was measured on the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA) and only intact RNA was used. The cRNA was fragmented with the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA, USA). Hybridization to Affymetrix U133plus2 GeneChips (54,614 probe sets, representing approximately 47,000 transcripts), staining, washing, and scanning procedures were carried out as described (Affymetrix, Santa Clara).

Scanning procedures were carried out as described  by Affymetrix, Santa Clara.

The data were analyzed with MRAExpress using Affymetrix default settings and were normalized according to the quantile method (Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003;19:185-93). After normalization, the intensity values below 30 were set at 30.T

Trizol extraction of total RNA was performed according to the manufacturer's instructions (Affymetrix, Santa Clara, CA, USA)

Hybridization to Affymetrix U133plus2 GeneChips , staining and  washing were carried out as described (Affymetrix, Santa Clara).

Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14942.gif

The data were normalized using quantile normalisation with IlluminaGUI in R and log2 transformed

RNA was extracted with Trizol reagent, followed by DNase I treatment (Amersam Biosciences) in accordance with the prescribed protocol provided by the manufacturer

Biotinylated cRNA were prepared with the Ambion Illumina® TotalPrepTM RNA Amplification Kit

Human skin biposy (lesional) from male patient, 40 years old, 19 years of psoriasis, moderate erythema, moderate induration, moderate scaling.

G;male;40 years;19 years;12 percent;moderate;moderate (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe);moderate (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)

Full thickness skin 5 millimeter punch biopsy of uninvolved skin

Human skin biposy (uninvolved) from male patient, 40 years old, 19 years of psoriasis, clear erythema, clear induration, clear scaling.

G;male;40 years;19 years;12 percent;clear;clear (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe);clear (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)

Human skin biposy (lesional) from male patient, 61 years old, 21 years of psoriasis, mild erythema, moderate induration, mild scaling.

D;male;61 years;21 years;12 percent;mild;moderate (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe);mild (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)

Human skin biposy (uninvolved) from male patient, 61 years old, 21 years of psoriasis, clear erythema, clear induration, clear scaling.

D;male;61 years;21 years;12 percent;clear;clear (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe);clear (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)

Human skin biposy (lesional) from male patient, 32 years old, 17 years of psoriasis, moderate erythema, severe induration, moderate scaling.

C;male;32 years;17 years;8 percent;moderate;severe (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe);moderate (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)

Human skin biposy (uninvolved) from male patient, 32 years old, 17 years of psoriasis, clear erythema, clear induration, clear scaling.

C;male;32 years;17 years;8 percent;clear;clear (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe);clear (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)

Human skin biposy (lesional) from male patient, 47 years old, 28 years of psoriasis, moderate erythema, mild induration, moderate scaling.

F;male;47 years;28 years;15 percent;moderate;mild (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe);moderate (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)

Human skin biposy (uninvolved) from male patient, 47 years old, 28 years of psoriasis, clear erythema, clear induration, clear scaling.

F;male;47 years;28 years;15 percent;clear;clear (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe);clear (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)

Human skin biposy (lesional) from male patient, 51 years old, 24 years of psoriasis, mild erythema, mild induration, mild scaling.

E;male;51 years;24 years;8 percent;mild;mild (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe);mild (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)

Human skin biposy (uninvolved) from male patient, 51 years old, 24 years of psoriasis, clear erythema, clear induration, clear scaling.

E;male;51 years;24 years;8 percent;clear;clear (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe);clear (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)

219;Sulphasalazine 1.2g Colifoam;1/5/43;F;CAUCASIAN;1/1/81;1/1/81;FALSE;FALSE;FALSE;NO;FALSE;FALSE;12/7/04;1;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;unknown;unknown;unknown;12/7/04;BOTH;BOTH;unknown;unknown;unknown;3/7/05;DISEASE IN REMISSION;never;unknown;None;UC;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

220;Asacol 800mg BFZ 2.5mg Metformin Simvastatin;6/28/48;M;CAUCASIAN;1/10/95;3/25/95;FALSE;FALSE;FALSE;NO;FALSE;FALSE;12/10/04;0;0;0;0;0;0;0;0;TRUE;0;BOTH;BOTH;BOTH;BOTH;BOTH;12/10/04;BOTH;BOTH;BOTH;BOTH;BOTH;3/7/05;DISEASE IN REMISSION;ex;1/1/90;5-14;Type 2 DM.;UC;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

225;Asacol;5/30/76;F;CAUCASIAN;1/1/03;6/2/03;FALSE;FALSE;FALSE;NO;FALSE;FALSE;1/6/05;3;0;0;0;0;0;0;0;TRUE;0;BOTH;unknown;unknown;unknown;unknown;1/6/05;BOTH;unknown;unknown;unknown;unknown;3/7/05;DISEASE IN REMISSION;ex;1/1/99;5-14;None;UC;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

224;Salazopyrin BFZ Losartan Thyroxine Doxazosin;2/21/38;F;CAUCASIAN;1/1/77;1/1/77;FALSE;FALSE;FALSE;NO;FALSE;FALSE;1/6/05;1;0;0;0;0;0;0;0;FALSE;0;12;12;12;12;12;11;12;11;11;BOTH;unknown;unknown;unknown;unknown;1/6/05;BOTH;BOTH;unknown;unknown;unknown;3/4/05;DISEASE IN REMISSION;never;unknown;Hypertension Hashimoto's Thyroditis;UC;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

228;None;11/22/48;F;CAUCASIAN;1/1/80;1/1/82;FALSE;FALSE;FALSE;YES;TRUE;FALSE;1/14/05;2;0;0;0;0;0;0;0;FALSE;0;12;12;12;12;12;11;11;11;11;BOTH;BOTH;unknown;unknown;unknown;1/6/05;BOTH;BOTH;unknown;unknown;unknown;3/4/05;DISEASE IN REMISSION;never;unknown;Migraines;UC;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

rat hippocampus (combined dorsal and ventral aspects), young control, subject 3

rat hippocampus (combined dorsal and ventral aspects), young control, subject 2

241;Asacol 800mg bd Azathioprine 100mg;6/25/62;F;CAUCASIAN;11/1/90;11/11/91;FALSE;FALSE;FALSE;YES;FALSE;FALSE;2/10/05;2;0;0;0;0;0;0;0;FALSE;0;22;22;22;22;22;11;11;11;11;BOTH;BOTH;BOTH;BOTH;BOTH;3/10/05;BOTH;BOTH;BOTH;BOTH;BOTH;5/30/05;FAILURE OF THERAPY;never;unknown;None;UC;8-9-01;ascending colon;Inflamed;total RNA from 10 human cell lines

241;Asacol 800mg bd Azathioprine 100mg;6/25/62;F;CAUCASIAN;11/1/90;11/11/91;FALSE;FALSE;FALSE;YES;FALSE;FALSE;2/10/05;2;0;0;0;0;0;0;0;FALSE;0;22;22;22;22;22;11;11;11;11;BOTH;BOTH;BOTH;BOTH;BOTH;3/10/05;BOTH;BOTH;BOTH;BOTH;BOTH;5/30/05;FAILURE OF THERAPY;never;unknown;None;UC;8-9-01;descending colon;Inflamed;total RNA from 10 human cell lines

241;Asacol 800mg bd Azathioprine 100mg;6/25/62;F;CAUCASIAN;11/1/90;11/11/91;FALSE;FALSE;FALSE;YES;FALSE;FALSE;2/10/05;2;0;0;0;0;0;0;0;FALSE;0;22;22;22;22;22;11;11;11;11;BOTH;BOTH;BOTH;BOTH;BOTH;3/10/05;BOTH;BOTH;BOTH;BOTH;BOTH;5/30/05;FAILURE OF THERAPY;never;unknown;None;UC;8-9-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

rat hippocampus (combined dorsal and ventral aspects), young control, subject 6

rat hippocampus (combined dorsal and ventral aspects), young control, subject 5

mcad -/-;Male;BL6/SV129 mixed;50-60 days of age;12 hrs fasted;vehicle;liver

Gene expression data from mouse CD8+ Wt T-cells without stimulation

wild type;Male;BL6/SV129 mixed;50-60 days of age;12 hrs fasted;LPS;liver

Briefly, E13 cortices were electroporated with the constructs for overexpression and knockdown including GFP as transfection control. 24h after transfection GFP positive cells were isolated by FACS.

RMA probeset summary with standard settings of the Affymetrix Expression Console software (v.1.2) including median polish and Sketch-Quantile normalisation.

Embryonic cerebral cortex, Trnp1 knockdown, biological replicate 1

Gene expression data from embryonic cerebral cortex, Trnp1 knockdown

mixed C57BL/6, FVB, 129 background;BrafV600E::Pten-/-::Pdk1-/-, Pdk1 knock out;tumor

LC-MA9
Gene expression data from resected non-tumor liver tissue

C57BL/6 mice were bred with mice heterozygous for Nf1.  Their male pups were euthanized at P32 and  brains quickly dissected and flash-frozen.  Their livers were also removed and frozen for the purpose of genotyping.  Hippocampi from two wild-type mice were pooled and RNA extracted for expression profiling.
Lot batch =

C57BL/6 mice were bred with mice heterozygous for Nf1.  Their male pups were euthanized at P32 and  brains quickly dissected and flash-frozen.  Their livers were also removed and frozen for the purpose of genotyping.  Hippocampi from two NF+/- mice were pooled and RNA extracted for expression profiling.
Lot batch =

C57BL/6 mice were bred with mice heterozygous for Nf1.  Their male pups were euthanized at P18 and  brains quickly dissected and flash-frozen.  Their livers were also removed and frozen for the purpose of genotyping.  Hippocampi from two NF+/- mice were pooled and RNA extracted for expression profiling.
Lot batch =

C57BL/6 mice were bred with mice heterozygous for Nf1.  Their male pups were euthanized at P28 and  brains quickly dissected and flash-frozen.  Their livers were also removed and frozen for the purpose of genotyping.  Hippocampi from two wild-type mice were pooled and RNA extracted for expression profiling.
Lot batch =

RNA was extracted from lung tissue using a Trizol protocol.  The RNA of 3-5 mice was pooled and one RNA sample of the pool analysed.  Targets were produced using standard Affymetrix procedures from about 10ug of total RNA.

Keywords = mouse, lung, bleomycin, strain differences

whole right lung, 3 weeks after a bleomycin dose of 100mg/kg, given by osmotic minipump.

whole right lung, 3 weeks after a bleomycin dose of 80mg/kg, given by osmotic minipump.

Cells were transfected with mock(background) and harvested for preparation of RNA after 44 hours.

TIG3 diploid fibroblasts were were grown in DMEM media supplemented with 10% (v/v) fetal calf serum. Cells were transfected with mock(background) and harvested for preparation of RNA after 44 hours.

The Identification of gene expression changes in human embryonic fibroblast cells, background. Sample A

Images were scanned using an Affymetrix GeneArray Scanner, using default parameters. The resulting images were analysed using Microarray Suite version 5 (MASv5), Affymetrix cat# 690018.

Hybridization procedures and parameters:
Hybridization mix for target dilution (100 mM MES, 1 M [Na +], 20 mM EDTA, 0.01% Tween 20) was prepared as indicated by Affymetrix, including pre-mixed biotin-labeled control oligo B2 and bioB, bioC, bioD and cre controls (Affymetrix cat# 900299) at a final concentration of 50 pM, 1.5 pM, 5 pM, 25 pM and 100 pM respectively. Targets were diluted in hybridization buffer at a concentration of 150µg/ml and denatured at 99°C prior to introduction into the GeneChip cartridge. Three copies of the complete GeneChip HG-U133 set (HG-U133A, HG-U133B) were then hybridized with each biotin-labeled target.
Hybridizations were performed for 14-16 hours at 45°C in a rotisserie oven. GeneChip cartridges were washed and stained in the Affymetrix fluidics station following the EukGE-WS2 standard protocol (including Antibody Amplification):
1.	Wash 10 cycles of 2 mixes/cycle with Wash Buffer A (6X SSPE, 0.01% Tween 20) at 25°C
2.	Wash 4 cycles of 15 mixes/cycle with Wash Buffer B (100 mM MES, 0.1 M [Na+], 0.01% Tween 20) at 50°C
3.	Stain the probe array for 10 minutes in SAPE solution (10 µg/mL SAPE in 100 mM MES, 1 M [Na +], 0.05% Tween 20, 2 mg/mL BSA) at 25°C
4.	Wash 10 cycles of 4 mixes/cycle with Wash Buffer A at 25°C
5.	Stain the probe array for 10 minutes in antibody solution (Normal Goat IgG 0.1 mg/mL,
6.	Biotinylated antibody 3 µg/mL, 100 mM MES, 1 M [Na +], 0.05% Tween 20, 2 mg/mL BSA) at 25°C
7.	Stain the probe array for 10 minutes in SAPE solution at 25°C
8.	Final Wash 15 cycles of 4 mixes/cycle with Wash Buffer A at 30°C

TIG3  diploid lung embryonic fibroblasts were transfected with siRNA oligos specific for MOCK. After 44 hours expression analysis was performed.

Cyclophosphamide-treated bone marrow 2 days - Biological Replicate 5 - Technical Replicate 1

Biological replicate 5 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day 2

The Identification of gene expression changes in human embryonic fibroblast cells, background. Sample B

TIG3  diploid lung embryonic fibroblasts were untreated (MOCK). After 44 hours expression analysis was performed.

The data were normalised using quantile normalisation in R; quantile normalization in natural scale

MYC positive B-cell;MycEGFP (a Myc reporter allele, in which a MYC-EGFP fusion protein (MYCEGFP) is expressed from the endogenous Myc locus);C57/Bl6

MYC negative B-cell;MycEGFP (a Myc reporter allele, in which a MYC-EGFP fusion protein (MYCEGFP) is expressed from the endogenous Myc locus);C57/Bl6

Tregs were stimulated with anti-CD3 nd anti-CD28 for 16 hours prior to RNA extraction

The data were analyzed with Partek Genomics Suite to produce RMA

Labeled DNA were hybridized for 17 hr at 45C on Mouse Gene 1.0 St Genechips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated DNA were prepared according to the Affymetrix standard WT protocol using 100ng of total RNA (not pretreated with Ribominus (Invitrogen))

Islet isolation was accomplished from 8 weeks-old mice by 100 mg of collagenase digestion (211U/mg) followed by purification through a Histopaque gradient. Islet perifusion was carried out by placing 30 islets into a perifusion chamber (Milipore) as describe previously (Gao N 2007).

Pancreas-specific knock-out animals were generated by breeding mice harbouring a floxed Ppar-beta (PPARbetafl/fl) to mice expressing the Cre transgene under the control of the Pdx1 promoter (Pdx1Cre).

Total RNA from islets or pancreas was extracted by using guanidine thiocyanate (Sigma) according to the manufacturer’s recommendation.  RNA quality and quantity was assessed by NanoDrop®ND-1000 spectrophotometer and Aligent 2100 bio-analyzer.

Affymetrix Mouse Genome 430 2.0 arrays were hybridized with 11 microgramme of labeled, amplified cRNA , washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol EukGeWS2v5_450)

The synthesis of cRNA was performed using the MessageAmp™ II-Biotin Enhanced Single Round aRNA Amplification kits according to the manufacturers' protocols (Ambion, Austin, TX). Labeling, hybridization and scanning of the samples were performed as described by Affymetrix (www.affymetrix.com).

A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factors can be identified. This entry corresponds to the RNA isolated from tet-induced INS-1 cell line #4a containing MODY5 mutant A263insGG of hepatocyte nuclear factor-1b (HNF1b).

A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factors can be identified. This entry corresponds to the RNA isolated from uninduced INS-1 cell line #4a containing MODY5 mutant A263insGG of hepatocyte nuclear factor-1b (HNF1b).

CD1;Raldh2 null mutant; Raldh2 -/-;embryonic brain;posterior;4 somite stage

CD1;wild type; Raldh2 +/+;embryonic brain;posterior;4 somite stage

Fluorescent images were captured using gene Array scanner 3000 7G and Affymetrix GeneChip Command Console, v 3.1 software (Affymetrix).

Raw data were processed using Partek Genomics Suite v. 6.5 to generate RMA normalised intensities. Differential expression was assessed using One-way or Two-way ANOVA in the Partek software dependent of if the samples were paired or not.

RNA extraction was performed with PAXgene Blood RNA kit according to manufactors instructions, and RNA quality assesed with Bioanalyzer

Fragmented and labeled DNA (2500ng) was used in 100 µl hybridization cocktail containing control oligonucleotide B2 (50pM) and hybridization controls (Affymetrix #900454), of which 80 µl was hybridised to each chip for 17h in the hybridization oven at 45ºC and rotating at 60rpm. Arrays were processed using Genechip Fluidics Station 450 according to recommended protocols (FS450_007) of double-staining and post-hybridization washes using GeneChip hybridization, wash and stain kit (Affymetrix #900720).

Isolated total RNA was used with GeneChip WT cDNA synthesis and amplification kit (Affymetrix#900672) to produce fragmented single-stranded DNA, which was labeled using terminal labeling kit (Affymetrix#900670) to generate biotin-labeled sense targeted DNA probes.

Rat liver, treated with ANIT, 125 mg/kg in corn oil per orally, extrated 48 hours after treatment, biological rep1

LP50 cells were infected with AR shRNA lentivirus or non-target control lentivirus; 12h after infection the cells were grown in hormone-free media to deplete androgen. The cells were then treated for 6h with either vehicle or R1881 (1nM) and harvested to obtain total RNA.

Cells were routinely cultured at 37°C and in 5% CO2 in RPMI 1640 medium supplemented with FBS (10%), penicillin (100units/mL).  streptomycin (100 mg/mL), L-glutamine (2mM), and sodium pyruvate (1mM). To obtain hormone depletion, cells were grown in the same medium except with 10% Dextran charcoal-stripped FBS and transferrin (20 μg/mL),

Gene expression data from late passage LP50 cells treated with vehicle and AR shRNA

Cells were transduced with EF1a-control, OE-NANOG, OE-OCT4 or OE-SOX2 lentivirus in the presence of polybrene.

35;Adenocarcinoma of breast, ductal;G3;IIA;T2;N0 (i-);1;0;65;0;0

67;Adenocarcinoma of breast, ductal;G3;IIA;T2;N0 (i+);1;1;17;0;0

42;Adenocarcinoma of breast, ductal;G3;IIA;T2;N0 (i-);0;0;26;1;0

MAT1A_wt_8_5
Gene expression data from the wild type used for MAT1A knockout at 8 month.

MAT1A_wt_8_4

MAT1A_wt_8_3

MAT1A_wt_8_2

MAT1A_wt_8_1

MAT1A_8_5
Gene expression data from MAT1A knockout at 8 month, when the tissue has been histopathologically determined to be non-alcoholic steatohepatitis.

C57B6SJL;MAT1A knockout;8 months;liver;non-alcoholic steatohepatitis

Mouse liver, MAT1A knockout, non-alcoholic steatohepatitis, 8 months

The distribution of fluorescent material on the processed array is determined using the Agilent GeneArray laser scanner (Affymetrix). Image inspection is performed manually immediately following each scan.

*Array hybridization and processing. *Labeled target is fragmented at 95^o C in the presence of high magnesium concentration. The fragmented material is combined with biotinylated hybridization control oligomer and biotinylated control cRNAs for BioB, BioC, BioD and CreX (Affymetrix) in hybridization buffer. Ten mg of target is hybridized with the GeneChip /(insert array name) /array (Affymetrix) overnight, followed by washing, staining with streptavidin-phycoerythrin (Molecular Probes), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs), and a final staining step on the Fluidics Station 400 (Affymetrix).

*Data analysis. *The array image scan is processed with Affymetrix Microarray Suite, version 5.0 (MAS 5.0) software. The GeneChip expression arrays contain control probe sets for both spiked and endogenous RNA transcripts (e.g., BioB, BioC, BioD, CreX and species-specific actin and GAPDH). Following image processing and absolute analysis of the array pattern with MAS, six values are examined to assess overall assay performance: background, noise, average Signal, % Present, ratio of Signal values for probe sets representing the 5' and 3' ends of actin and GAPDH transcripts, and total Signal for probe sets for BioC, BioD and CreX. Assays demonstrating poor or marginal performance are flagged.
An MAS 5.0 absolute expression analysis was performed for each GeneChip genome array hybridization. Following the initial analysis, the absolute analyses were rerun using global scaling to an average target intensity of */350/*. The scaling allows for the direct comparison of hybridization values from the different targets analyzed in this project (and with any additional GeneChip sample assays you run using the same array type). For each analysis, scaled or unscaled, the parameters a_1 and a_2 are set to 0.1 and 0.15 respectively. These parameters set the point at which a probeset is called present(P), marginal(M), or undetectable(A). This call is based on the Detection p-value of the probeset.

liver RNA, ATP 7B KO mouse (first described Hum. Mol. Genet. (1999) 8:1665-1671)

After differentiation by cell culture at air-liquid interface, the cellular monolayer was treated on apical side with 15 μM DMNQ (2, 3-dimethoxy-1, 4-naphtoquinone) for a 24 hours period

Cultured in an air-liquid condition, cells were coated on collagen plastic dishes with serum-free bronchial epithelial cell growth medium with supplements (BEGM, Cambrex)

10 μg of the resulting cRNA were then loaded on each chip and scanned with a Genechip Scanner 3000 workstation

For each hybridized chips, the probe intensity levels were extracted by the Affymetrix® Scanner 3000 7G and the data analyzed by the Microarray Analysis Suite (version 5.0) algorithm. Expression data files were generated for each chip to generate a CEL file

RNAs were purified with the RNeasy Mini Kit (Qiagen, Valencia, CA)

Washing and staining with streptavidin-phycoerythrin (Invitrogen, Carlsbad, CA)

The probes were labelled with biotin and fragmented using Affymetrix’s reagents following standard protocol

Gene expression data from CF cell line cultivated on Air-liquid Interface with 24 hours of DMNQ treatment

Gene expression data from normal cell line cultivated on Air-liquid Interface

Gene expression data from normal CF cell line cultivated on Air-liquid Interface

Gene expression data from normalCF cell line cultivated on Air-liquid Interface

Gene expression data from normal CF cell line cultivated on Air-liquid Interface with 24 hours of DMNQ treatment

Gene expression data from normal cell line cultivated on Air-liquid Interface with 24 hours of DMNQ treatment

Identified as an outlier and removed from further analysis

wt_on_15_11

Cells were transfected with either a non-targeting control (shControl) or BAP1 RNA interference (shBAP1) plasmid using Lipofectamine 2000 and were  selected with puromycin containing medium. Then, the cells were synchronized at the G1/S border using a thymidine double block protocol.

U2OS osteosarcoma cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum and penicillin/streptomycin.

Probe arrays have been scanned using the Affymetrix® GeneChip® Scanner 3000.

Gene expression levels from shControl and shRNAs were subjected to comparative analysis using the expression analysis software Flex Array V1.1 (Michal Blazejczyk, Mathieu Miron, Robert Nadon (2007), Genome Quebec, Montreal, Canada, URL http://genomequebec.mcgill.ca/FlexArray). Data were normalized with Robust Multi-Array Average (RMA) and the algorithm EB (Wright and Simon) was used for statistical analysis.

RNA was prepared using Trizol reagent (Invitrogen) and the RNeasy kit (QIAGEN) according to the manufacturer's instructions.

The hybridizations to Human genome Hu133 plus 2.0 arrays (Affymetrix) were conducted following the One-Cycle target Labeling Protocol of the GeneChip ® Expression Analysis Technical Manual from Affymetrix (Genome Québec Innovation Centre, Montréal, Canada).

The generation of cDNA and biotinylated cRNA were conducted following the One-Cycle target Labeling Protocol of the GeneChip ® Expression Analysis Technical Manual from Affymetrix (Genome Québec Innovation Centre, Montréal, Canada).

U2OS osteosarcoma cell line transfected with an shControl construct

U2OS osteosarcoma cell line transfected with shBAP1 #1 construct

E14 ES cells were maintained on mouse embryo fibroblast (MEF) feeder cell layers in Dulbecco-modified Eagle medium containing 14% KnockOut Serum Replacement (Invirtogen), 1% fetal bovine serum, 100 units/ml LIF, 0.1 mM nonessential amino acids, 1 mM sodium pyruvate, 2 mM L-glutamine, and 100 μM 2-mercaptoethanol.

GeneChips were scanned using the AFFYMETRIX GeneChip Scanner GCS3000.

The data were analyzed by RMA using GeneSpring software with the default settings.

Total RNA was extracted using Fast pure RNA kit (TAKARA) according to the manufacturer's instructions.

Mouse Genome 430 2.0 Array GeneChips were hybridized with 15 ug of fragmented aRNA. The hybridization, staining, and washing were carried out using the Affymetrix GeneChip Hybridization Wash and Stain Kit (P/N 900720) following the manufacturer’s protocols. The arrays were hybridized for 16 hr at 45C using an Affymetrix Hybridization Oven 640 (P/N 800139). FS450_0001 protocol was used for staining and washing the GeneChips using the Affymetrix Fluidics Station 450 (P/N 00-0079).

HEK293-cells transiently transfected with pIRES2-EGFP, 48 h post transfection, first of two independent transfections

HEK293-cells transiently transfected with pIRES2-EGFP, 48h post transfection, second of two independent transfections

HEK293-cells transiently transfected with EWS-FLI1 type I, 48h post transfection, second of two independent transfections

CG
32 mg
12

CG
32 mg
12

CG
32 mg
8

CG
32 mg
8

RNA was extracted using the Qiagen RNeasy Midi Kit according to the manufacturers guidelines

Total cellular RNA from IFNb-treated (2500 units/ml for 5 h) MEFs was extracted with TRIzol reagent (Invitrogen) according to the manufacturer's instructions.

Total RNA from MDA-MB-231 cells infected with a lentivirus shControl

The L4/L5 dorsal root ganglia in the ipsilateral group are those ganglia ipsilateral to the surgery in the spare nerve injury group

Sprague-Dawley;Dorsal root ganglia;17 days;Spare nerve injury;Young Ipsilateral

L4/L5 dorsal root ganglia from young rats (10 days old) 7 days after SNI surgery

Technical replicate #1 of ATF2 wildtype. These mice are mixed background of FVB and C57bl6 and the age when they got the papillomas was about 9 months.

Technical replicate #2 of ATF2 wildtype. These mice are mixed background of FVB and C57bl6 and the age when they got the papillomas was about 9 months.

One of three samples from the same patient, different visits.

Celecoxib (Sigma) was dissolved in DMSO and 10mM stock was prepared. AGS cells were treated with 20μM celecoxib in separate wells and incubated for 24 hours.

AGS cells purchased from NCCS Pune were grown in DMEM/F12 media supplemented with 10% FBS, 2mM Glutamine, 100U/ml penicillin, 100μg/ml streptomycin antibiotics and incubated in 5% CO2 incubator at 37⁰C. At 90% confluency, cells were trypsinized, counted and 3x10⁵ cells were seeded in 6 well plates and further incubated for 48 hours

The raw data was normalized in Affymetrix Expression Console (v.1.1), using RMA algorithm

After 24 hours incubation, cells were rinsed once with 1X PBS. For each well, 1ml of Trizol (Invitrogen)was added for the extraction of total RNA as per manufacturer's instructions. RNA integrity was evaluated using MultiNA nucleic acid analyzer then control and celecoxib treated samples were pooled.

Following fragmentation, single stranded DNA obtained from 10 mg of cRNA were hybridized for 16 hr at 45°C inAffymetrix “HuGene-1_0-st” (Human Gene 1.0 ST ) array GeneChip with Hybridization Oven 640. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

Biotin labelled fragmented single stranded DNA was prepared from 250 ng of total RNA. The steps were followed as per the instructions in the user manuals of Ambion® WT Expression Kit, GeneChip® WT Terminal Labeling and Hybridization kit (Affymetrix).

AGS;stomach;human gastric carcinoma cells;20μM celecoxib for 24hrs

Data was processed/normalized by MAS 5.0 using Affymetrix Expression Console version 1.1.

Primary culture of type II cells collected from SPC KO lung adult;adult;type II lung epithelial;Surfactant Proteiin C KO;129S6/SvEvTac

Primary culture of typeII cells collected from SPC KO lung adult;adult;type II lung epithelial;Surfactant Proteiin C KO;129S6/SvEvTac

ACRL_SN__Treated_B

RNA was isolated from unstimulated HMEC (passage 3) cultured for 5 h.

Normoxic untreated control for evaluation of hypoxic response in hepatocytes

Normoxic adeno treated control for evaluation of hypoxic response in hepatocytes

48 hours after plating, cells were treated with ER ligands using 1 nM final concentration vehicle (ethanol) or E2 in the presence of vehicle (ethanol) or 27HC (1uM).  After 24 hours treatment, cells were washed once in PBS prior to lysis.

MCF7 cells were plated in 6 well culture dishes at a density of 4x105 cells per well.

Raw data was background corrected with RMA, Log2 transformed, and summarized by median polish using the Affy package (v.1.36.1) in Bioconductor (v.2.15.2).
Log2 RMA, quantile normalization, summary by median polish, adjusted for batch effects.

RNA isolation (BioRad, Aurum total RNA mini kit) was performed per kit manufacturer’s instructions.

MCF-7;human breast adenocarcinoma cells;1 nM final conc. E2 + 1 uM 27-Hydroxycholesterol (27HC) for 24hr;3

normal;IA, IB, II, IIIA, IIIB, or IV=IA;45;female, male:male;early gastric cancer or advanced gastric cancer=early gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

normal;IA, IB, II, IIIA, IIIB, or IV=IA;58;female, male:female;early gastric cancer or advanced gastric cancer=early gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

normal;IA, IB, II, IIIA, IIIB, or IV=IA;64;female, male:male;early gastric cancer or advanced gastric cancer=early gastric cancer;moderately differentiated or poorly differentiated=moderately differentiated;intestinal type, diffuse type, mixed type, or not determined=intestinal type

normal;IA, IB, II, IIIA, IIIB, or IV=IA;56;female, male:male;early gastric cancer or advanced gastric cancer=early gastric cancer;moderately differentiated or poorly differentiated=moderately differentiated;intestinal type, diffuse type, mixed type, or not determined=intestinal type

normal;IA, IB, II, IIIA, IIIB, or IV=IB;39;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=moderately differentiated;intestinal type, diffuse type, mixed type, or not determined=intestinal type

normal;IA, IB, II, IIIA, IIIB, or IV=IA;41;female, male:female;early gastric cancer or advanced gastric cancer=early gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

normal;IA, IB, II, IIIA, IIIB, or IV=IA;55;female, male:male;early gastric cancer or advanced gastric cancer=early gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

normal;IA, IB, II, IIIA, IIIB, or IV=IA;68;female, male:male;early gastric cancer or advanced gastric cancer=early gastric cancer;moderately differentiated or poorly differentiated=moderately differentiated;intestinal type, diffuse type, mixed type, or not determined=intestinal type

normal;IA, IB, II, IIIA, IIIB, or IV=IB;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=moderately differentiated;intestinal type, diffuse type, mixed type, or not determined=intestinal type

Total RNA was obtained using the RNeasy kit (Quiagen) according to the manufacturer’s instructions.

transfection of esiRNA with Lipofectamine 2000 (Invitrogen)
RNA isolation 24 h after transfection

Data analysed with PARTEK Genomic Suite software with standard parameters

E14.5;male;dorsal telencephalon;histone methyltransferase ESET KO;C57BL\6

bone marrow;CD34+ hematopoietic stem cells (HSC);myelodysplastic syndromes (MDS);refractory anemia with excess blasts 2 (RAEB2);trisomy8

bone marrow;CD34+ hematopoietic stem cells (HSC);myelodysplastic syndromes (MDS);refractory anemia with ringed sideroblasts (RARS);trisomy8

Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

Heart dissected from E12.5 fetus with a null mutation for the Sp3 transcription factor.

Total RNA isolated from single hearts stored at -80 degrees Celsius, according to standard Affymetrix protocol (GeneChip® Expression Analysis Technical Manual)

After hybridization, signal intensities were calculated using the Affymetrix GeneChip® software MAS 5.0

Total RNA was extracted from frozen individual cerebellum
and treated with DNase using RNeasy Midi kit (Qiagen).
The quality of each RNA sample was then checked using
the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.,

Biotinylated cRNA were hybridized to Affymetrix Murine Genome U74A version 2 microarrays (Affymetrix, Inc., Santa Clara, CA, USA) on the Curie Institute Affymetrix microarray platform (Paris, France), according to the Affymetrix procedures. Each pool was hybridized in duplicate on independent U74Av2 microarrays.

An aliquot 20µg of total RNA from each pool was
converted to cDNA and then to biotinylated cRNA according to the Affymetrix procedures.

Pool of total RNA from 3 euploid cerebella at P0 postnatal stage
Keywords = Down syndrome
Keywords = Chromosome 21
Keywords = Transcriptome
Keywords = Brain
Keywords = Cerebellum
Keywords = Development

Clinical information: Sample.ID=763;Tumor.type=D;Size=1.8;Grade=2;Nodes=0/14;ER=Pos;PR=Pos;HER2=ND;Age=63;DFS=118;Status=non-recur

Clinical information: Sample.ID=772;Tumor.type=D;Size=2.5;Grade=2;Nodes=0/18;ER=Pos;PR=Pos;HER2=Neg;Age=68;DFS=69;Status=recur

Clinical information: Sample.ID=655;Tumor.type=D;Size=2;Grade=3;Nodes=ND;ER=Pos;PR=Pos;HER2=ND;Age=73;DFS=143;Status=non-recur

Clinical information: Sample.ID=662;Tumor.type=D;Size=1;Grade=3;Nodes=6/11;ER=Pos;PR=Pos;HER2=Neg;Age=79;DFS=27;Status=recur

Clinical information: Sample.ID=687;Tumor.type=D;Size=3.5;Grade=3;Nodes=3/16;ER=Pos;PR=Pos;HER2=Neg;Age=73;DFS=142;Status=non-recur

Clinical information: Sample.ID=749;Tumor.type=D;Size=1.8;Grade=2;Nodes=2/9;ER=Pos;PR=Neg;HER2=Neg;Age=61;DFS=137;Status=non-recur

Pool of total RNA from 2 euploid cerebella at P30 postnatal stage

Fbn1C1039G mutant;intact TGF-β signaling;ascending aorta;6 weeks

female;juvenile, 8 weeks (P58);Sv129 / C57BL/6N mixed background;Cldn16 +/-;renal tissue

FBN+/+.TGFBRIIko_5
Gene expression data from Tgfbr3 knockout mice

Fbn1 wild-type;conditional disruption of Tgfbr2;ascending aorta;6 weeks

No additional treatments were applied to the cultured cell lines

Primary cultures of LFs were isolated from the distal parenchyma of patients from unaffected donor controls (lung cancer patients) and patients with IPF as previously described [Hogaboam CM, Carpenter KJ, Evanoff H, Kunkel SL (2005), Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. All fibroblast cell lines were completely de-identified from the patients they were grown from prior to characterization in this study.  The IPF lung tissue was obtained and the diagnosis of Usual Interstitial Pneumonia (UIP) / IPF achieved as previously outlined [Pechkovsky DV, Prele CM, Wong J, Hogaboam CM, McAnulty RJ, et al. (2012)]. Normal human lung tissue was obtained from macroscopically tumor-free lung resections of patients with lung cancer.  The human lung tissue collection was approved by the ethics committees of all institutions involved. In this study we characterized fibroblasts cell lines originated from 14 donors across 3 phenotypes: non-IPF control (n = 4), stable IPF (n = 6), and rapidly progressing IPF (n = 4) subjects. Cells from these lines were plated and passaged (up to the 11th passage).

Array washing, staining and scanning was performed according to standard Affymetrix protocols .

Probe level data was curated by first mapping individual probe sequences to their most current genome sequences. Probes which were non-uniquely mapped to specific genes or contained outdated mappings were discarded, and the remaining probes were summarized into probesets and normalized using Robust Multi-array Average (RMA). Probes expressed at low levels across all samples were subsequently discarded.

Total RNA was isolated and homogenized in QIAzol reagent. Purified RNA was then amplified and labeled using NuGen Ovation kits

Purified total RNA was amplified and labeled using NuGen Ovation kits (NuGEN Technologies, Inc., San Carlos, CA) and RNA from samples was hybridized to Affymetrix HG-U133 plus 2.0 arrays.

Agilent TIFF High File = US22502532_251486820842_S01_H.tif
Agilent TIFF Low File = US22502532_251486820842_S01_L.tif

C57BL/6;wild type;male;5 Month old;Liver;35% Fat Diet (High Fat Diet; HFD)

Cells were transiently transfected with either a BCL6-specific or a non-target control siRNA

Data was normalized and probe-sets summarized with the MAS5 algorithm implemented in the R-system affy package and the variance was stabilized by performing a log-base2 transformation.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip H-GU-133 Plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Affymetrix, Santa Clara, CA).

Gene expression data from Pfeiffer DLBCL cell line 48h after transfection with BCL6 targeting siRNA oligos

Gene expression data from Pfeiffer DLBCL cell line 48h after transfection with NT-control siRNA oligos

Gene expression data from OCI-Ly7 DLBCL cell line 48h after transfection with BCL6 targeting siRNA oligos

Gene expression data from OCI-Ly7 DLBCL cell line 48h after transfection with NT-control siRNA oligos

Early passage cells at confluence were treated with interleukin-1-beta (10 ng/ml) for 1 or 8 h, whereas control cells were treated with serum-free medium only.

Primary cultures of human amnion mesenchymal cells were prepared from amnion membranes obtained prior to labor at term.  Cells were cultured in DMEM (25 mM glucose) supplemented with 10% fetal bovine serum, 2mM L-glutamine, 1mM sodium pyruvate, 50 ug/ml of gentamicin sulfate, and 0.5 mg/ml of amphotericin B at 37C in a 5% CO2 atmosphere.

The data were analyzed with R statistics package version 2.7.1 using robust multichip average (RMA) as normalization method.

Total RNA from control and experimental groups were extracted using Trizol reagent and the RNeasy Mini Kit (Qiagen) as according to the manufacturer's instructions.

Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Human Genome U133A 2.0 Arrays (Platform GPL571). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (GeneChip Expression Analysis Technical Manual, 2004, Affymetrix).

Gene expression data from amnion mesenchymal cells with no treatment
AMC_veh-1

amnion mesenchymal cells, 1h interleukin-1-beta, biological rep1

Gene expression data from amnion mesenchymal cells treated with interleukin-1-beta for 1h
AMC_1h-1

amnion mesenchymal cells, 1h interleukin-1-beta, biological rep2

AMC_1h-2

AMC_veh-2

AMC_veh-3

amnion mesenchymal cells, 1h interleukin-1-beta, biological rep3

AMC_1h-3

amnion mesenchymal cells, 8h interleukin-1-beta, biological rep1

Gene expression data from amnion mesenchymal cells treated with interleukin-1-beta for 8h
AMC_8h-1

5445316044_F
normal;induced pluripotent stem cell;CRL-1502 C29;rep3

5445316044_E
normal;induced pluripotent stem cell;CRL-1502 C29;rep2

5445316044_D
normal;induced pluripotent stem cell;CRL-1502 C29;rep1

5445316044_C
normal;induced pluripotent stem cell;CRL-2429 C16;rep3

5445316044_B
normal;induced pluripotent stem cell;CRL-2429 C16;rep2

5445316044_A
normal;induced pluripotent stem cell;CRL-2429 C16;rep1

Day: 3; Drug: Methamphetamine; Phase: Drug treatment; Replicate: 3

Day: 1; Drug: Methamphetamine; Phase: Drug treatment; Replicate: 2

RMA signal intensities obtained using BRB-arraytool software which calculates the RMA-values with the affy package from Bioconductor.

KU-812 leukemia cells were incubated with 10 µM STI571 (Imatinib) for 16 hours.
For more information about the cell line, please check: www.dsmz.de
Q249_A_HG_U133_Plus_2_01_1__UU812_STI_.CEL

JURL-MK1 leukemia cells were cultured in absence of STI571 (Imatinib).
Q250_A_HG_U133_Plus_2_01_1__3WL_.CEL

JURL-MK1 leukemia cells were incubated with 10 µM STI571 (Imatinib) for 16 hours.
Q251_A_HG_U133_Plus_2_01_1__3WL_STI_.CEL

LNCaP cells were infected with ELK1 shRNA lentivirus or non-target control lentivirus, and  grown in hormone-free media to deplete androgen. 96h after infection the cells were cells were grown for 48 h with either vehicle or R1881 (1nM) and harvested to obtain total RNA.

Cells were routinely cultured at 37°C and in 5% CO2 in RPMI 1640 medium supplemented with FBS (10%), penicillin (100units/mL), streptomycin (100 mg/mL), L-glutamine (2mM), and sodium pyruvate (1mM). For hormone depletion, cells were grown in phenol-red free RPMI-1640 with 10% charcoal stripped FBS, penicillin (100 units/ml)/streptomycin (100 µg/ml)/L-glutamine (2mM) mix for 48 h before the experiments.,

Gene expression data from LNCaP cells treated with vehicle and ELK1 shRNA

Gene expression data from LNCaP cells treated with R1881 and control shRNA

Gene expression data from LNCaP cells treated with vehicle and control shRNA

Gene expression data from LNCaP cells treated withR1881 and ELK1 shRNA

244;Seratide Bricanyl BFZ;1/29/55;M;CAUCASIAN;1/1/03;6/16/03;FALSE;FALSE;FALSE;NO;FALSE;FALSE;3/29/05;1;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;BOTH;BOTH;BOTH;3/29/05;BOTH;BOTH;BOTH;BOTH;BOTH;6/1/05;DISEASE IN REMISSION;ex;1/1/94;15-24;Asthma Hypertension;UC;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

244;Seratide Bricanyl BFZ;1/29/55;M;CAUCASIAN;1/1/03;6/16/03;FALSE;FALSE;FALSE;NO;FALSE;FALSE;3/29/05;1;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;BOTH;BOTH;BOTH;3/29/05;BOTH;BOTH;BOTH;BOTH;BOTH;6/1/05;DISEASE IN REMISSION;ex;1/1/94;15-24;Asthma Hypertension;UC;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

242;Salazopyrin Folic acid;10/18/39;F;CAUCASIAN;1/1/75;1/1/75;FALSE;FALSE;FALSE;NO;FALSE;FALSE;3/22/05;2;0;0;0;0;0;0;0;TRUE;0;BOTH;BOTH;unknown;unknown;unknown;3/22/05;BOTH;BOTH;unknown;unknown;unknown;7/7/05;DISEASE IN REMISSION;ex;1/1/95;0-4;None;UC;8-9-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

242;Salazopyrin Folic acid;10/18/39;F;CAUCASIAN;1/1/75;1/1/75;FALSE;FALSE;FALSE;NO;FALSE;FALSE;3/22/05;2;0;0;0;0;0;0;0;TRUE;0;BOTH;BOTH;unknown;unknown;unknown;3/22/05;BOTH;BOTH;unknown;unknown;unknown;7/7/05;DISEASE IN REMISSION;ex;1/1/95;0-4;None;UC;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

253;Asacol 800mg BD;3/14/58;M;CAUCASIAN;8/24/97;9/4/97;FALSE;FALSE;FALSE;unknown;FALSE;FALSE;5/24/05;1;0;0;0;0;0;0;0;TRUE;0;12;12;12;12;12;11;11;11;12;BOTH;BOTH;BOTH;BOTH;BOTH;5/24/05;BOTH;BOTH;BOTH;BOTH;BOTH;8/3/05;FAILURE OF THERAPY;never;unknown;None;UC;11-15-01;ascending colon;Inflamed;total RNA from 10 human cell lines

250;Asacol 2.4g/d;1/27/58;M;ASIAN;1/1/94;5/30/94;FALSE;FALSE;FALSE;NO;FALSE;FALSE;4/29/05;3;0;0;0;0;0;0;0;FALSE;0;11;11;11;11;11;11;11;11;11;BOTH;BOTH;BOTH;unknown;unknown;4/29/05;BOTH;BOTH;BOTH;BOTH;BOTH;5/30/05;DISEASE IN REMISSION;ex;1/1/95;5-14;None;UC;11-15-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

250;Asacol 2.4g/d;1/27/58;M;ASIAN;1/1/94;5/30/94;FALSE;FALSE;FALSE;NO;FALSE;FALSE;4/29/05;3;0;0;0;0;0;0;0;FALSE;0;11;11;11;11;11;11;11;11;11;BOTH;BOTH;BOTH;unknown;unknown;4/29/05;BOTH;BOTH;BOTH;BOTH;BOTH;5/30/05;DISEASE IN REMISSION;ex;1/1/95;5-14;None;UC;11-15-01;descending colon;Inflamed;total RNA from 10 human cell lines

244;Seratide Bricanyl BFZ;1/29/55;M;CAUCASIAN;1/1/03;6/16/03;FALSE;FALSE;FALSE;NO;FALSE;FALSE;3/29/05;1;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;BOTH;BOTH;BOTH;3/29/05;BOTH;BOTH;BOTH;BOTH;BOTH;6/1/05;DISEASE IN REMISSION;ex;1/1/94;15-24;Asthma Hypertension;UC;8-9-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

253;Asacol 800mg BD;3/14/58;M;CAUCASIAN;8/24/97;9/4/97;FALSE;FALSE;FALSE;unknown;FALSE;FALSE;5/24/05;1;0;0;0;0;0;0;0;TRUE;0;12;12;12;12;12;11;11;11;12;BOTH;BOTH;BOTH;BOTH;BOTH;5/24/05;BOTH;BOTH;BOTH;BOTH;BOTH;8/3/05;FAILURE OF THERAPY;never;unknown;None;UC;11-15-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

253;Asacol 800mg BD;3/14/58;M;CAUCASIAN;8/24/97;9/4/97;FALSE;FALSE;FALSE;unknown;FALSE;FALSE;5/24/05;1;0;0;0;0;0;0;0;TRUE;0;12;12;12;12;12;11;11;11;12;BOTH;BOTH;BOTH;BOTH;BOTH;5/24/05;BOTH;BOTH;BOTH;BOTH;BOTH;8/3/05;FAILURE OF THERAPY;never;unknown;None;UC;11-15-01;descending colon;Inflamed;total RNA from 10 human cell lines

peripheral blood;sickle-cell patient;PAXgene Globin reduced;Globin-depleted RNA

Cells were grown in DMEM/F12 media supplemented with 1% non-essential aminoacids, 15% fetal bovine serum and 1% penicilin/streptomicin

The data were analyzed with GenomeStudio using Illumina default analysis settings. No normalization and background correction are performed first, then quantile normalization and background correction are done.

Following fragmentation, cRNA were hybridized for Illumina GX human HT12 Array. Slides were washed and stained in the Illumina instrument.

Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.

Gene expression data from motor neurons of the sacral rat spinal cord 60 days post sham operation

100-200 motor neurons, sacral spinal cord, 60 days post sham opration

500ng of total RNA was amplified by using MessageAmpTM-Biotin Enhanced Kit from Ambion

Targeted deletion of skNAC in mice rsulted in embryonic lethality with cardiac defects by E12.5.  In order to investigate the molecular mechanism of the cardiac defect, we compared gene expression profiles of the knockout heart and wild type heart.

proband i, past exhaustive exercise, white blood cells, male, healthy, no medicamentation

proband k, past moderate exercise, white blood cells, male, healthy, no medicamentation

proband a, past moderate exercise, white blood cells, male, healthy, no medicamentation

proband a, past exhaustive exercise, white blood cells, male, healthy, no medicamentation

proband i, before moderate exercise, white blood cells, male, healthy, no medicamentation

proband i, before exhaustive exercise, white blood cells, male, healthy, no medicamentation

proband k, before exhaustive exercise, white blood cells, male, healthy, no medicamentation

proband i, past moderate exercise, white blood cells, male, healthy, no medicamentation

proband k, before moderate exercise, white blood cells, male, healthy, no medicamentation

proband k, past exhaustive exercise, white blood cells, male, healthy, no medicamentation

JLI_73

JLI_72

JLI_71

JLI_69

JLI_68

JLI_67

JLI_66

JLI_65

White and grey matter in the distribution of the middle cerebral artery after one hour of ischemia followed by treatment (IV) with the catalytic antioxidant AEOL 10150 and then 6 hours of reperfusion; mRNA from a single brain #16.

COLO829 melanoma cell line;MITF knockdown;BRAF inhibitor PLX4032 (Vemurafenib)

BxPC3 cells were transfected with either control vector or vector expressing shJMJD3.

Cells were grown in RPMI with 10% fetal bovine serum, and maintained at 37C in 5% CO2 in a humidified environment.

The hybridized array slides were scanned on an Agilent Microarray Scanner. Scanned images were quantified using Agilent Feature Extraction software (ver. 10.5.1.1).

Microarray signal and background information were retrieved using Agilent Feature Extraction software (ver. 10.5.1.1). Extracted intensities were background-corrected and normalized by the quantile normalization method using statistical software R (http://www.R-project.org) and the Bioconductor package “Agi4x44PreProcess” (Pedro Lopez-Romero) (http://www.bioconductor.org/packages/2.3/bioc/html/Agi4x44PreProcess.html). Probes were filtered based on the Quality Flags provided by Agilent FE using the function "filter.probes" in the "Agi4x44PreProcess" package. Replicated probes were summarized using the function "summarize.probe".

Total RNA was extracted from cells with the RNeasy mini kit (Qiagen) following the manufacturer’s instructions, and was quantified by Nanodrop.

Labeled cRNA was incubated with Blocking agent and Fragmentation buffer (Agilent Gene Expression Hybridization Kit) for 30min at 60°C. GE Hybridization Buffer HI-RPM was then added to the mixture. Samples were applied to microarrays using hybridization chambers and hybridized at 65°C for 16h. After hybridization, slides were washed sequentially with Agilent Gene Expression Wash Buffer.

Cyanine-3 (Cy3) labeled cRNA was prepared from 500ng RNA using the Quick Amp Labeling Kit (One colour, Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).

Gene expression after transfection of vector expressing shJMJD3 in BxPC3 cells.

human pancreatic cancer cell line BxPC3 transfected with vector expressing shJMJD3

Gene expression after transfection of control vector in BxPC3 cells.

human pancreatic cancer cell line BxPC3 transfected with control vector

14 days hindlimb suspended

PBMCs enriched for CD8+ cells from normal control subject K (KCD8)

Gene expression data from PBMC of normal control subject K enriched for CD8+ T cells

Expression Console (Affymetrix)
affymetrix-algorithm-name = rma-gene-default.

C57BL/6x129Sv;female;hCAR transgenic in mCAR knockout background;TCPOBOP; 1,4-bis[2-(3, 5-dichloropyridyloxy)]benzene

C57BL/6x129Sv;female;mCAR knockout;TCPOBOP; 1,4-bis[2-(3, 5-dichloropyridyloxy)]benzene

iPSC derived from healthy control fibroblast WT1, biological rep2

iPSC derived from healthy control fibroblast WT1, biological rep3

iPSC derived from healthy control fibroblast WT2, biological rep4

iPSC derived from healthy control fibroblast WT2, biological rep5

iPSC derived from healthy control fibroblast WT1, biological rep1

iPSC derived from healthy control fibroblast WT2, biological rep6

iPSC derived from healthy control fibroblast WT2, biological rep7

Embryoid bodies were dissociated to single cells by a 1 hour incubation with 0.2% Collagenase B containing 20% serum followed by a 2 minute incubation with trypsin (0.05% trypsin-EDTA) at 37ºC. After enzymatic treatment, 1 ml serum was added and the embryoid bodies were disaggregated to single cells by multiple passages through a 20-gauge needle. Cells were stained with anti-human CD41 and CD235, and flow cytometrically sorted for the double positive population to extract RNA.

For hematopoietic differentiation, embryoid bodies were generated by culturing small aggregates of feeder-depleted iPSCs in 6 well low-cluster plates in StemPro-34 (Invitrogen) media supplemented with glutamine, ascorbic acid, transferrin, monothioglycerol, and with the following cytokines: bone morphogenic protein 4 (BMP4) 25 ng/ml and vascular endothelial growth factor (VEGF) 50 ng/ml on days 0-2; BMP4 25 ng/ml, VEGF 50 ng/ml, stem cell factor (SCF) 50 ng/ml, thrombopoietin (TPO) 50 ng/ml, Flt3 ligand (FLT3) 50 ng/ml, and fibroblast growth factor (bFGF) 20 ng/ml on days 2-4; VEGF 50 ng/ml, SCF 50 ng/ml, TPO 50 ng/ml, FLT3 50 ng/ml, and bFGF 20 ng/ml on days 4-8.

The raw intensity values from CEL files were processed using RMA method implemented by the Bioconductor R oligo package. RMA processing resulted in 33,297 probesets, that were then mapped to 19,392 RefSeq genes. In cases where several probesets mapped to one RefSeq gene the expression values were averaged to obtain one value per gene.

Total RNA was extracted with the Qiagen miRneasy kit per manufacturer's instructions.

cRNA was hybridized according to the Affymetrix GeneChip Technical Manual.

Biotinylated cRNA was prepared according to manufacturer instructions for the NuGEN WT-Ovation Pico RNA kt .

CD43+/41+/235+ progenitors generated from euploid iPSC line, biological rep1

CD43+/41+/235+ progenitors generated from euploid iPSC line, biological rep2

CD43+/41+/235+ progenitors generated from euploid iPSC line, biological rep3

CD43+/41+/235+ progenitors generated from T21 iPSC line, biological rep1

CD43+/41+/235+ progenitors generated from T21 iPSC line, biological rep2

CD43+/41+/235+ progenitors generated from T21 iPSC line, biological rep4

Male;75;9h;6.3;schizophrenic;superior temporal cortex (Brodmann Area 22, BA22)

The human studies have been approved by the Institutional Review Board (IRB) of the State University of New York at Buffalo and Women and Children’s Hospital of Buffalo. Liver biopsies were obtained, with prior informed consent, from parents of patients suspected of having NASH as part of regular medical care. Patients from 7 to 18 years of age signed an assent to the research. Diagnosis of NASH was based on hepatic fat infiltration, inflammation and fibrosis as revealed by liver biopsy. Only children and adolescents were included in this study to ensure that our patients were not sustained alcohol users. All NASH patients included in this study exhibited significant insulin resistance (IR). IR was calculated based on the “homeostasis model assessment (HOMA)” method.

The human studies have been approved by the Institutional Review Board (IRB) of the State University of New York at Buffalo and Women and Children’s Hospital of Buffalo.  Liver biopsies were obtained, with prior informed consent, from parents of patients suspected of having NASH as part of regular medical care.  Patients from 7 to 18 years of age signed an assent to the research.  Diagnosis of NASH was based on hepatic fat infiltration, inflammation and fibrosis as revealed by liver biopsy.  Only children and adolescents were included in this study to ensure that our patients were not sustained alcohol users.  All NASH patients included in this study exhibited significant insulin resistance (IR).  IR was calculated based on the “homeostasis model assessment (HOMA)” method

These samples were derived from liver grafts of normal subjects with normal body mass index.  The ages of these normal controls were matched with our NASH patients.  No liver diseases were diagnosed with these normal controls.  Although the biochemistry data provided by Admet were limited, the healthy status of these livers was ascertained by the lower transcription levels of marker genes for inflammation and fibrosis.

Peripheral blood mononuclear cells;healthy control;GTE6;97min;White;Female

Peripheral blood mononuclear cells;healthy control;GTE6;145min;White;Female

Peripheral blood mononuclear cells;healthy control;GTE6;140min;White;Male

Peripheral blood mononuclear cells;healthy control;GTE6;100min;White;Male

Peripheral blood mononuclear cells;healthy control;LT6;90min;White;Female

Peripheral blood mononuclear cells;healthy control;GTE6;140min;White;Female

Peripheral blood mononuclear cells;healthy control;GTE6;100min;White;Female

Peripheral blood mononuclear cells;healthy control;GTE6;130min;White;Male

Rats were given water (vehicle, n = 4) or 1 mL of D-penicillamine dissolved in tap water in a single dose of 150 mg/kg by oral gavage (n = 8).  Animals were sacrificed 6 hours after initial dosing.

Male Brown Norway (BN) rats weighing 150-170 g were purchased from Charles River (Montreal, QC). All animals were housed in plastic cages (two/cage) with wooden chips as bedding in a 12:12 h light:dark cycle at 22 °C. Rats were given access to standard rat chow (Agribrands, Purina Canada, Strathroy, ON) and ad libitum access to tap water for 1 week (acclimatization period) before starting experiments.

Total RNA was isolated from frozen liver tissues of individual rats using Qiagen RNeasy mini kits as described by the manufacturer. RNA concentrations and purity were determined spectrophotometrically. RNA quality was further assessed by capillary electrophoresis using the Agilent Bioanalyzer. We used 10 micrograms of total RNA from each individual animal for microarray analysis.

Rattus norvegicus;Brown Norway;150-170 grams;liver;male;6 hours;D-penicillamine 150 mg/kg by oral gavage

Rats were given water (vehicle, n = 4) or 1 mL of D-penicillamine
dissolved in tap water in a single dose of 150 mg/kg by oral
gavage (n = 8).  Animals were sacrificed 6 hours after initial dosing.

Male Brown Norway (BN) rats weighing 150-
170 g were purchased from Charles River (Montreal, QC). All
animals were housed in plastic cages (two/cage) with wooden
chips as bedding in a 12:12 h light:dark cycle at 22 °C. Rats
were given access to standard rat chow (Agribrands, Purina
Canada, Strathroy, ON) and ad libitum access to tap water for
1 week (acclimatization period) before starting experiments.

Total RNA was isolated from frozen liver
tissues of individual rats using Qiagen RNeasy mini kits as
described by the manufacturer. RNA concentrations and purity
were determined spectrophotometrically. RNA quality was
further assessed by capillary electrophoresis using the Agilent
Bioanalyzer. We used 10 micrograms of total RNA from each individual
animal for microarray analysis.

Expression profiles generated from the white portion of the gastrocnemicus muscle from wild type littermates to AMPK gamma3 knock-out mice

C57BL/6;wild type;F7;male;white portion of the gastrocnemius muscle;fasted

Differentiation of hES cells line SA01 towards MPC-like cells;Mesenchymal stem cells phenotype

Mesodermal Precursor Cells derived from hES cells line SA01, biological replicate 2

Mesodermal Precursor Cells derived from hES cells line SA01, biological replicate 1

Gene expression data from brain of Npc1+/- mouse1 of age 81 days

microarray analysis of gene expression after transverse aortic constriction in mice - 48 hours TAC group No.5

microarray analysis of gene expression after transverse aortic constriction in mice - 48 hours TAC group No.2

microarray analysis of gene expression after transverse aortic constriction in mice - 48 hours sham group No.4

microarray analysis of gene expression after transverse aortic constriction in mice - 48 hours sham group No.3

Gene expression data from SW480 cells treated with MEK inhibitor for 4h

Gene expression data from SW480 cells treated with TNKS inhibitor for 4h

gemcitabine resistant Calu3 were treated over 10 consecutive 10-day treatment cycles with 50 nM gemcitabine for the first 3 days of the cycle followed by 7 days of vehicle

gemcitabine resistant Calu3 cells, treated for 10 cycles of 10 days each with gemcitabine (still gemcitabine resistant)

gemcitabine resistant Calu3 were treated over 10 consecutive 10-day treatment cycles with continuous exposure to 1 micromolar bexarotene

gemcitabine resistant Calu3 cells, resensitized to gemcitabine after treatment for 10 cycles of 10 days each with bexarotene

Ulcerative Colitis (59 year old caucasian female, SAK_1286565132)

Subject Age : 59

Ulcerative Colitis (27 year old caucasian female, SAK_1286587485)

Ulcerative Colitis (33 year old hispanic female, SAK_1285179246)

Subject Race : HISPANIC

Ulcerative Colitis (62 year old caucasian female, SAK_1305735600)

Ulcerative Colitis (40 year old caucasian female, SAK_1285156893)

Control hippocampus 1

Ulcerative Colitis (57 year old caucasian female, SAK_1286542779)

Subject Age : 57

cells were grown in macrophage-SFM medium (Gibco) containing 10% FCS and 30% L-929R-cell-conditioned medium at 37°C in a humidified CO2 (5%) incubator

bone marrow macrophages from 1 female and 2 male wild type Balb/c mice

tumor tissue from cancer patients;p53 mutant;Microsatellite Stable Stage III Colorectal adenocarcinoma

lung tissue;CD-1_Nrf2 -/-;13 weeks + 2 month;2R4F whole mainstream smoke 750 µg/ml, treatment over 2 month, 3x1h exposure per day

lung tissue;CD-1;13 weeks + 5 month;fresh air, treatment over 5 month, 4x1h exposure per day

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Estradiol + medroxyprogesterone acetate treated. Patient 4.

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Estradiol treated. Patient 13.

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Estradiol treated. Patient 8.

C57BL/6GT(ROSA)26tm9(creEsr1)Arte (TamoxCre) and PDK1fl/fl C57BL/6GT(ROSA)26tm9(creEsr1)Arte (PDK1fl/fl TamoxCre) T-cells were activated for 48h and then cultured for 5days, supplimented with 0.6μM 4OHT for the last 72h of culture.
Alternatively T-cells from C57/B6 mice were were activated for 48h and then cultured for 5days with half the cells from each biological replicated being treated with 1μM AktI-1/2 for the last 48h of culture.

CTL were generated by activating Splenic T-cells for 48h in RPMI 1640/10% heat-inactivated fetal calf serum (FCS) penicillin/streptomycin (Gibco), 50μM β-mercaptoethanol (β-ME) (Sigma)  with 0.5μg/ml CD3 antibody (2C11) in the presence of 20ng/ml IL2.
Cells were then washed free of activating agent and thereafter maintained in 20ng/ml IL2 at a density of approximately 0.3×106/ml at 37°C

GeneChip Scanner 3000 7G with AutoLoader was used to scan the arrays.

Affymetrix GeneChip Command Console (AGCC) 1.1 was used to control GeneChip Fluidics Stations and Scanner and in summarizing probe cell intensity data (.CEL file generation).
After hybridization quality was checked with AGCC and Expression Console TM 1.1.
Data was normalized using the Affymetrix Expression Console v1.1 (Affymetrix) implementation of the robust multichip averaging algorithm using default analysis settings and quantile normalisation.

RNA was extracted from cells with the RNeasy RNA purification minikit (Qiagen) according to the manufactures protocol.

Each sample was hybridized to GeneChip®Mouse Genome 430 2.0 Array at +45°C overnight (16 h) according to GeneChip® Expression Analysis Technical Manual (With Specific Protocols for Using the GeneChip® Hybridization, Wash and Stain Kit)
GeneChip Fluidics Station 450 was used to wash and stain the arrays.

Biotinylated cRNA were prepared from 2μg RNA according to the standard One-cycle target labelling protocol from GeneChip Expression Analysis Technical Manual (with specific protocols for using the GeneChip hybridization, Wash and Stain Kit)

Gene expression data from wild-type CTL from mouse 1 treated with AktI
2_153IL2Akti

C57BL/6;cytotoxic T-lymphocytes (CTL);wild type;Akt inhibitor AktI-1/2

Gene expression data from wild-type CTL from mouse 3 treated with AktI
6_157IL2Akti

Gene expression at 6h after treatment with IFNg in WT mouse neurons

Gene expression at 24h after treatment with IFNg in WT mouse neurons

Gene chips were scanned using the Affymetrix gene chip scanner 3000 7G

Data were analyzed using the Affymetrix Expression Console (algorithm-name = rma-gene-default) and then furhter analyzed using Microsoft Excel

Total RNA was isolated from mouse livers with TRIZOL (Invitrogen, Carlsbad CA) extraction, followed by purification with RNeasy Mini Column (QIAGEN, Valencia CA).

Each sample was then hybridized to an Affymetrix Mouse Gene 1.0 ST array by standard procedures.

Total RNA from 3 8-week old male and 3 female JAK2L and littermate control livers was prepared as above. RNA was analyzed using the Agilent 2100 BioAnalyzer. All samples were prepared using Affymetrix WT cDNA Synthesis and Amplification Kits for cDNA.synthesis, cRNA amplification and conversion to sense strand DNA products according to manufacturer's instructions. Samples were then fragmented and end labeled using Affymetrix WT Target Labeling and Control Reagents Kits according to manufacturer's instructions.

mixed (C57Bl/6:129Sv) background;female;Liver;131;JAK2 KO;8 weeks

mixed (C57Bl/6:129Sv) background;female;Liver;141;JAK2 KO;8 weeks

Cells expressing IkBa dominant negative cultured in presence of dox, TNF stimulation for 3h

Cells expressing IkBa dominant negative cultured in presence of dox, TNF stimulation for 1h

Cells expressing IkBa dominant negative cultured in absence of dox, TNF stimulation for 0h

sample of normal skin (no_19):
Keywords = Non-melanoma skin cancer
Keywords = cDNA-microarray
Keywords = expression profiling
Keywords = expressed sequence tag (EST)

sample of normal skin (no_18):

Cells expressing IkBa dominant negative cultured in presence of dox, TNF stimulation for 0h

Cells expressing IkBa dominant negative cultured in absence of dox, TNF stimulation for 6h

sample of actinic keratoses (ak_12):

sample of actinic keratoses (ak_09+15):

sample of normal skin (no_17):

sample of normal skin (no_02+05+08):

sample of actinic keratoses (ak_04):

sample of actinic keratoses (ak_03):

Carcinogenesis is a multi-step process indicated by several genes up- or down-regulated during tumor progression. The type and number of genes involved in non-melanoma skin cancer (NMSC) are still unclear. This study examined and identified different expressed genes in NMSC. Fifteen snap-frozen biopsies of five immunosuppressed organ-transplanted recipients each normal skin, actinic keratosis (AK) and invasive squamous cell carcinoma (SCC) were analysed. Total RNA was extracted reverse transcribed and biotin-labeled cRNA was used for hybridization with Affymetrix HG-U133A gene expression cDNA-microarrays containing 22,283 known genes. Confocal scanner evaluated the signals twice and data analysis was performed by predicition analysis of microarrays (PAM) using nearest shrunken centroids with the threshold 3.5 to identify genes best characterizing normal skin and skin cancer. ANOVA analysis was performed as a second independent method to identify differentially expressed genes (p<0.05, and p<0.15). Quantitative verification of 13 up- or down-regulated genes was performed by real-time RT-PCR and genes were confirmed by sequencing. Broad coherent patterns in normal skin vs. AK and SCC were observed for 118 genes. Some of the genes (e.g. annexin, lamin, and metalloproteinases) up-regulated in carcinomas in our study have previously reported as over-expressed in NMSC. In total 42 genes were up-regulated and 76 genes were down-regulated in non-melanoma skin cancer. The majority of genes identified have not been previously reported different expressed during non-melanoma skin carcinogenesis.

In situ IP was performed in A2BAR-/- mice and matched littermate controls. IP consisted of 4 cycles of 5 min myocardial ischemia and 5 min reperfusion followed by 2 h of reperfusion. The area at risk was excised and shock frozen in liquid nitrogen. Controls were sham operated.

male wildtype BL6/C57 mice were ordered from Jackson Laboratories. A2BAR deficient mice (BL6/C57 background) were bred in house. 12 week old male were used for the study.

After hybridization and staining, the arrays were scanned using a GCS3000 with the latest 7G upgrade

heart tissue treated with 4 cycles of 5 min ischemia/5 min reperfusion followed by 2 h of reperfusion

Control and Rif1 virus or siRNA were applied and selected for further culture and analysis.

ES cells were cultured on feeder plates following standard ES cell culture protocol.

Analyzed by MAS 5.0 using Affymetrix default settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Hierarchical clustering was performed using cluster software (version 3) and by applied mean centering and normalization of genes and arrays before average linkage clustering. Significantly different genes were identified using a 1-class unpaired significance analysis of microarrays (SAM) and fold change.

Rif1 shRNA;Stable F1 Rif1 knockdown ES cells at passage 16;C57BL/6xC3H

control shRNA;Stable F1 Rif1 knockdown ES cells at passage 16;C57BL/6xC3H

Untreated 1 hour control sample.
Treatment, type=time_course, measurement=1.0 h

The untreated control sample for SH-SY5Y treated with 1mM nicotine for 24 hour.

Total RNA extracted from SH-SY5Y treated with 1mM nicotine for 1 hour.

After cleanup (Qiagen, Hilden, Germany), the biotin-labeled cRNA was fragmented by alkaline treatment (40 mmol/L Trisacetate (pH 8.2), 100 mmol//L potassium acetate, and 50 mmol//L magnesium acetate) at 94°C for 35 minutes. 15 µg of each cRNA sample was hybridized for 16 hours at 45°C to an Affymetrix Human Genome U133 Plus 2.0 GeneChip Array. Chips were washed and stained with streptavidin-phycoerythrin using a fluidics station according to protocols recommended by Affymetrix.

C57BL/6N;Sta1 Wildtype (wt);Bone marrow derived macrophages (BMMs);6h IFNg

Cells were transduced two consecutive days with  MSCV-based retroviruses and sorted on GFP 48 hours later.

Fetal liver cells were removed, subjected to red cell lysis, and grown for 48h in RPMI 20% FBS, 1% L-Glutamine supplemented with 10 ng/mL interleukin-6, 100 ng/mL SCF, 6 ng/mL IL3, 50 ng/mL FLT3 ligand and 10 ng/mL TPO

Raw probe intensities were background-corrected, quantile-normalized, and summarized using the R function rma.

1_DMSO-1_(Mouse430_2)

4_DMSO-4_(Mouse430_2)

3_DMSO-3_(Mouse430_2)

Endocrine independent cell line pII was established by transfection of MCF7 with ER directed shRNA plasmid. Another transfected cell line designated E2 was established that had retained sensitivity to estrogen and tamoxifen (presumably as a result of failure to produce siRNA) was used as an additional control.

MCF7 derived from the ATCC (American Type Culture Collection, (VA, USA) were maintained at 37˚C in a humidified atmosphere of 5% CO2 in DMEM supplemented with 10% foetal bovine serum (FBS), 600 μg/ml L-glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin and 6 ml/500 ml 100 x non-essential amino acids (Invitrogen, CA, USA).

The data were analyzed with Partek Genomics Suite V 6.5 for RMA background correction, quantile normalisation with GC content adjustment

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human U133 Plus 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Gene expression data from MCF7 breast cancer cell line with silenced Estrogen receptor

Gene expression data from MCF7 breast cancer cell line expressing Estrogen receptor

mIMCD3 cells were treated for 1 hour with vehicle (control) or aldosterone. Total RNA was isolated and used as template to generate the eventual cRNA target. The experiment was repeated a total of three times. Six cRNA samples, three control and three treated, were generated and used in a total of six hybridizations. This data set represents the control sample for replication 1.

mIMCD3 cells were treated for 1 hour with vehicle (control) or aldosterone. Total RNA was isolated and used as template to generate the eventual cRNA target. The experiment was repeated a total of three times. Six cRNA samples, three control and three treated, were generated and used in a total of six hybridizations. This data set represents the aldosterone-treated sample for replication 1.

mIMCD3 cells were treated for 1 hour with vehicle (control) or aldosterone. Total RNA was isolated and used as template to generate the eventual cRNA target. The experiment was repeated a total of three times. Six cRNA samples, three control and three treated, were generated and used in a total of six hybridizations. This data set represents the control sample for replication 2.

mIMCD3 cells were treated for 1 hour with vehicle (control) or aldosterone. Total RNA was isolated and used as template to generate the eventual cRNA target. The experiment was repeated a total of three times. Six cRNA samples, three control and three treated, were generated and used in a total of six hybridizations. This data set represents the aldosterone-treated sample for replication 2.

mIMCD3 cells were treated for 1 hour with vehicle (control) or aldosterone. Total RNA was isolated and used as template to generate the eventual cRNA target. The experiment was repeated a total of three times. Six cRNA samples, three control and three treated, were generated and used in a total of six hybridizations. This data set represents the control sample for replication 3.

OVA-induced asthma model:OVA challenged and agonist of PGE receptor EP3 subtype treated  #2

OVA-induced asthma model:OVA challenged and agonist of PGE receptor EP3 subtype treated  #3

WI-38 cells, at 24 h after exposure to 0.5 uM BPDE, biological rep2

WI-38 cells, at 24 h after exposure to 0.5 uM BPDE, biological rep1

retina
Treatment, type=pharmacogenomic_treatment, description=Retinas were dissected from control and transgenic animals. The transgenic animals expressed myocilin in their aqueous humor. A part of the aqueous humor also is present in the back of the eye. High levels of myocilin would be present around the retina.

retina--technical replicate for Control 1

128;Pentaza;3/19/81;M;JEWISH;FALSE;FALSE;FALSE;FALSE;FALSE;4/1/05;IBS Type symptoms;0;TRUE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;terminal ileum;Uninflamed;total RNA from 10 human cell lines

128;Pentaza;3/19/81;M;JEWISH;FALSE;FALSE;FALSE;FALSE;FALSE;4/1/05;IBS Type symptoms;0;TRUE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

122;Venlafaxine;7/10/61;M;JEWISH;FALSE;FALSE;FALSE;FALSE;FALSE;2/10/05;FH Colon Ca;0;TRUE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

124;OCP;6/25/77;F;JEWISH;FALSE;FALSE;FALSE;FALSE;FALSE;3/1/05;IBS Type symptoms;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

124;OCP;6/25/77;F;JEWISH;FALSE;FALSE;FALSE;FALSE;FALSE;3/1/05;IBS Type symptoms;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

124;OCP;6/25/77;F;JEWISH;FALSE;FALSE;FALSE;FALSE;FALSE;3/1/05;IBS Type symptoms;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

125;OCP;3/17/78;F;JEWISH;FALSE;FALSE;FALSE;FALSE;FALSE;3/1/05;Diarrhoea predominant IBS;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;terminal ileum;Uninflamed;total RNA from 10 human cell lines

125;OCP;3/17/78;F;JEWISH;FALSE;FALSE;FALSE;FALSE;FALSE;3/1/05;Diarrhoea predominant IBS;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

126;None;4/4/87;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;3/1/05;FH of Crohn's disease, Symtom free at procedure;0;TRUE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

127;Prednisolone 10mg Heparin Questran Gabapentin FA;9/9/36;M;JEWISH;FALSE;FALSE;FALSE;FALSE;FALSE;3/29/05;Pseudomembranous Colitis;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

Gata4Loxp/-VillinCre adult male jejunum (6-8wk). Gata4 conditional knockout (mutant) sample.

Female (age range 33-49), skin biopsy from upper nates taken 7 hours after nickel exposure

RNA was isolated after the third passage of cells.

normal esophageal tissue of surgically resected human esophagus;fibroblast

fibroblast cultured from esophageal squamous cell carcinoma tissue_HECaF_2111

surgically resected esophageal squamous cell carcinoma tissue;fibroblast

fibroblast cultured from esophageal squamous cell carcinoma tissue

Dmbo mice were backcrossed with C57BL/6JWT to remove the Rd1 mutation. Wild-type and dumbo mice were maintained in a 12-hours light/12-hours dark cycle with free access to food and water. Animals were killed at P15 by cervical dislocation.

The arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix) and raw data were extracted from the scanned images and analyzed with the Affymetrix Power Tools software package.

Normalized expression signals were calculated from Affymetrix CEL files using RMA normalization method.

Retinas were isolated under a microscope to remove extra retinal tissue and snap-frozen at -80°C. Total RNA was individually isolated from each whole retina and purified using the RNeasy minikit as described by the manufacturer. RNA quantities were assessed by NanoDrop®ND-1000 spectrophotometer

Affymetrix Mouse Gene 1.0 ST arrays were hybridized according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007).

For each sample, 100ng of total RNA were amplified using the WT sense strand Target Labelling kit (Affimetryx). The resulting sense cDNA was fragmented by UDG and APE 1 and biotin-labelled with TdT using the GeneChip® WT Terminal labelling kit (Affymetrix).

Sample name: WT_HFD_6

C57BL/6;WT;male;cerebellum;1 year;high-fat diet consisting of AIN-93G with 60% of calories from fat (HFD; carbohydrate:protein:fat ratio of 16:23:61) ad libitum for 8 months

Sample name: WT_HFD_5

Sample name: WT_CR_4

C57BL/6;WT;male;cerebellum;1 year;40% caloric restriction of SD diet for 8 months

Sample name: WT_CR_3

Sample name: CSB_SD_6

Sample name: CSB_SD_5

Sample name: WT_HFD_4

Sample name: WT_HFD_3

Sample name: WT_CR_6

Sample name: WT_CR_5

Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure.

Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip  3’ IVT Express Kit manual (Rev. 6)

1x10^6 cells were subcutaneously injected into five-week-old female nude mice with a BALB/c genetic background. When the tumor size reached at least 5 mm in diameter, mice were euthanized and tumor tissue was collected.

Gene-level expression signals were obtained by processing of raw data with the RMA procedure using GeneSpring GX (Agilent Technologies).

RNA extraction from tumor xenografts were performed by using the RNeasy kit and Tissue Lyser (Qiagen) according to the manufacturer’s protocol.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA.

HL-60 cell line infected with GSK3B Construct 2 shRNA, biological rep1
Sample name: HL60_GSK3B_2-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A04_596674.CEL

HL-60 cell line infected with GSK3B Construct 1 shRNA, biological rep2
Sample name: HL60_GSK3B_1-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A08_596694.CEL

Rat Retinal Müller cells from healthy rats.  Müller cells were isolated from the pooled retinas of 12 rats.

Rat Retinal Müller cells from diabetic rats (diabetes duration 6 months).  Diabetes was induced by streptozotozine.  Diabetic rats were treated with small doses of insulin to prevent catabolism.  Müller cells were isolated from the pooled retinas of 12 rats.

48B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

47B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

46B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; not assessable

45B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

49B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

pre-iPSC- siRNA to Ehmt1, Ehmt2 and Setdb1- biological replicate1

RE1_H20_1950_U133Plus2.0.CEL

RE1_H5_1332_U133Plus2.0.CEL

RE1_H2_1279_U133Plus2.0.CEL

RE1_H10_1594_U133Plus2.0.CEL

RE1_H9_1575_U133Plus2.0.CEL

RE1_H11_1610_U133Plus2.0.CEL

MO-WT U1
Gene expression data from PBS-injected NT mice brain at 5 d.p.i.

C57BL/6;non-transgenic;brain (right cerebral hemisphere);7 days;PBS control;5

RE1_H6_1346_U133Plus2.0.CEL

MO-Tg U4

male;60 years;upper arm;9.9x7x7;dedifferentiated liposarcoma;medium;G2;local recurrence;yes;no

male;74 years;thigh;16.5x9x7;dedifferentiated liposarcoma;medium;G2;primary tumor;no;no

male;37 years;thigh;7x14x9;myxoid/roundcell liposarcoma;medium;G2;primary tumor;no;yes

female;70 years;thorax;1.9x1.3x1;pleomorphic liposarcoma;medium;G2;residual tumor;no;no

wt_off_15_11

Clinical information: Sample.ID=140;Tumor.type=L;Size=>2.0;Grade=2;Nodes=18/28;ER=Pos;PR=Pos;HER2=Neg;Age=63;DFS=43;Status=recur

Clinical information: Sample.ID=180;Tumor.type=D;Size=1.6;Grade=2;Nodes=2/19;ER=Pos;PR=Pos;HER2=Neg ;Age=69;DFS=169;Status=non-recur

Clinical information: Sample.ID=59;Tumor.type=L;Size=3;Grade=2;Nodes=33/38;ER=Pos;PR=Pos;HER2=ID (+2);Age=70;DFS=21;Status=recur

Clinical information: Sample.ID=68;Tumor.type=D;Size=3;Grade=2;Nodes=0/17;ER=Pos;PR=Pos;HER2=Neg;Age=53;DFS=38;Status=recur

A549 cells were transfected  one day after plating using 50 nM siRNAs (Ambion non-targeting siRNA (AM4637); FAM60A siRNA (s33909)) and Dharmafect 1 transfection reagent.

7.5x10^4 A549 cells were plated in each well of a 6-well plate.  Cells were plated in F-12K media (Cellgro) with 10% FBS in triplicate.

GeneChips were scanned using the GeneChip Scanner 3000 and processed with AGCC v3.0 software.

Array intensities were processed using the RMA algorithm in R/bioconductor.

Cells were lysed in Trizol (Invitrogen) three days after transfection, RNA was extracted and then processed through an RNeasy column (QIAGEN) using the RNA clean-up protocol.

Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA was prepared according to the Ambion Biotin Enhanced MessageAmp II aRNA amplification kit (according to manual rev. C rev 5/16/2008) from 1 ug total RNA.

Gene expression from A549 cells after transfection with SDS3 targeting siRNA, replicate 1

Gene expression from A549 cells after transfection with non-targeting siRNA, replicate 3

Gene expression from A549 cells after transfection with non-targeting siRNA, replicate 2

Gene expression from A549 cells after transfection with non-targeting siRNA, replicate 1

Gene expression from A549 cells after transfection with SDS3 targeting siRNA, replicate 3

Gene expression from A549 cells after transfection with SDS3 targeting siRNA, replicate 2

total RNA from biosource CC#42a

total RNA from biosource CC#18

total RNA from biosource CC#31

total RNA from biosource CC#36

total RNA from biosource CC#1

total RNA from biosource CC#17

total RNA from biosource CC#5

PBMC isolated by Ficoll gradient centrifugation from JSpA patient
Keywords = Juvenile spondyloarthropathy (JSpA), peripheral blood mononuclear cells (PBMC)

Microarray experiments were performed using whole-mouse-genome oligoarrays (Mouse430a, Affymetrix). Array data were analyzed using MAYDAY (Version 2.10). Array data were subjected to robust multi-array average (RMA) normalization. Normalized data were used for calculating fold changes of up- and down-regulated genes using Student's T-test. Data underwent z-score transformation for display.

HIV seropositive, CD4 cells increase over time, sampled at time point2

Uterus isolated from wild-type ovariectomized mice treated with vehicle for 40h.

Uterus isolated from wild-type ovariectomized mice treated with progesterone for 40h.

Uterus isolated from PRKO ovariectomized mice treated with vehicle for 40h.

Uterus isolated from PRKO ovariectomized mice treated with progesterone for 40h.

lung, upper lobe;explant;advanced idiopathic pulmonary fibrosis (IPF);female;67

lung, lower lobe;surgical biopsy;early idiopathic pulmonary fibrosis (IPF);male;68

lung, lower lobe;explant;advanced idiopathic pulmonary fibrosis (IPF);female;67

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D14;P1

blast count: 37

blast count: 65

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D21;13

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D72 (30 days post-EBRT);13

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D1;P1

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D1;5

male;non-metastatic prostate cancer;peripheral blood;white blood cells;baseline;5

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D72 (30 days post-EBRT);4

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D42;4

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D21;4

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D14;4

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D7;4

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D1;4

shRNA sequences present in pENTR plasmid vector transfected by electroporation (0.35 kV, with 550 _F capacitance). RNA harvested 48 hours after electroportation.

Cell line, grown invitro; Tissue derivation: Adenoid cystic carinoma of the parotid gland

Air
1
1

Air
1
1

Air
1
0.5

liver cells from wildtype 8wk male mouse 8 challenged with vehicle (saline)_8

liver cells from wildtype 8wk male mouse 8 challenged with vehicle (saline)_9

liver cells from wildtype 8wk male mouse 8 challenged with acetaminophen (APAP)_13

liver cells from wildtype 8wk male mouse 8 challenged with acetaminophen (APAP)_14

liver cells from wildtype 8wk male mouse 8 challenged with vehicle (saline)_10

liver cells from wildtype 8wk male mouse 8 challenged with acetaminophen (APAP)_12

liver cells from txnrd1 liver-null 8wk male mouse 8 challenged with vehicle (saline)_4

liver cells from txnrd1 liver-null 8wk male mouse 8 challenged with vehicle (saline)_5

15(+) 12d (II)
Gene expression data from clone#15 (12 days after tamoxifen treatment: Rybp-KO)

15(-) 12d (II)

15(+) 4d (II)
Gene expression data from clone#15 (4 days after tamoxifen treatment: Rybp-KO)

15(-) 4d (II)

10(+) 12d (II)
Gene expression data from clone#10 (12 days after tamoxifen treatment: Rybp-KO)

10(-) 12d (II)
Gene expression data from clone#10 (without tamoxifen treatment; Wild-type control)

C57Bl/6;AIRE ko;Cells cultured 96h with allogenic APC and anti CD3 antibody

Gene expression data from cells treated with TGF-alpha for 48 hours

normal breast cell line with stably transfected full-length chimeric human HER2 receptor with FKBP and HA tags;MCF10A;TGF-alpha

Gene expression data from cells treated with AP1510 for 48 hours

normal breast cell line with stably transfected full-length chimeric human HER2 receptor with FKBP and HA tags;MCF10A;AP1510

normal breast cell line with stably transfected full-length chimeric human HER2 receptor with FKBP and HA tags;MCF10A;Untreated

Total RNA from testis of Ku86(-/-);G3-Terc(-/-) mice; experiment 2

Total RNA from testis of Ku86(-/-);Terc(+/+) mice; experiment 1

Total RNA from testis of Ku86(-/-);G3-Terc(-/-) mice; experiment 1

We transfect siRNA using Lipofectamine 2000 (invitrogen) according to its manual and siRNA final concentration in the medium was 20nM. After culturing for 48hr, transfection medium was changed to fresh antibiotic containing medium. Then the cells were incubated for additional 12hr

HeLa S3 cells were seeded on 6-well plate at 4 x 104 cells per well in 2ml antibiotic free DMEM medium before 24hr transfection.

The data were analyzed with RMA using GeneSpring software. Base line was created as median of all sample.

Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;Control;6h;1;4421339030

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;HA1077;2h;1;4421339030

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;Control;12h;1;4421339030

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;HA1077;6h;1;4421339030

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;Control;24h;1;4421339030

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;HA1077;12h;1;4421339030

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;Control;2h;1;4421339032

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;HA1077;24h;1;4421339030

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;Control;6h;2;4421339032

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;HA1077;2h;1;4421339032

BALB-c mice were given intratracheal bleomycin (1.5U per kg) or saline control.  Lungs were harvested and frozen at 24h.
Lot batch =

BALB-c mice were given intratracheal bleomycin (1.5U per kg).  Lungs were harvested and frozen at 72h.
Lot batch =

BALB-c mice were given intratracheal saline.  Lungs were harvested and frozen at 14d.
Lot batch =

BALB-c mice were given intratracheal bleomycin (1.5U per kg).  Lungs were frozen at 24hr 72hr 10d 14d
Lot batch =

LaserPower: 2.54;; 1.34
Temperature: 34.13

LaserPower: 2.49;; 1.34
Temperature: 33.84

LaserPower: 2.5;; 1.33
Temperature: 34.93

LaserPower: 2.54;; 1.58
Temperature: 32.62

LaserPower: 2.56;; 1.3
Temperature: 31.37

C57BL-6J were given intratracheal bleomycin (1.5U per kg).  Lungs were harvested and frozen at 14d.
Lot batch =

Gene expression data from MCF7 (BUS stock) exposed to 100 pM 17beta-estradiol for 48 hours.

Gene expression data under ER stress from lymphoblastoid cells of twin 1756:1 treated with DMSO.

lymphoblastoid cell line;1756;GM14581;Twin number 1;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1756:1 treated with 500nM thapsigargin.

lymphoblastoid cell line;1756;GM14581;Twin number 1;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1752:2 treated with DMSO.

lymphoblastoid cell line;1752;GM14569;Twin number 2;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1752:2 treated with 500nM thapsigargin.

lymphoblastoid cell line;1752;GM14569;Twin number 2;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1752:1 treated with DMSO.

lymphoblastoid cell line;1752;GM14568;Twin number 1;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1752:1 treated with 500nM thapsigargin.

lymphoblastoid cell line;1752;GM14568;Twin number 1;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1740:2 treated with DMSO.

lymphoblastoid cell line;1740;GM14521;Twin number 2;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1740:2 treated with 500nM thapsigargin.

lymphoblastoid cell line;1740;GM14521;Twin number 2;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1740:1 treated with DMSO.

lymphoblastoid cell line;1740;GM14520;Twin number 1;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1740:1 treated with 500nM thapsigargin.

lymphoblastoid cell line;1740;GM14520;Twin number 1;thapsigargin;500nM;4 hours

Cells were transfected with the control vector or Gli3T expressing vector using Lipofectamine 2000 reagent.

Statistical analyses were performed using R, a system for statistical computation and graphics (Ihaka and Gentleman 1996; http://www.r-project.org). The RMA method in the oligo package from Bioconductor was used in R to summarize probe level data and to normalize the dataset to remove across array variation (Irizarry et al. 2003a,b;Bolstad et al., 2003). Log transformed data were used in subsequent analysis and plotting. To determine differentially expressed genes between control and knockdown, moderated T Statistics in limma (Smyth2004) was used. To adjust for multiple comparisons, p-values were adjusted using B-H method (Benjamini & Hochberg 1995) and genes with adjusted p-value <0.05 and absolute fold change >1.5 were considered potential targets for further investigation ['differentially_expressed.txt' on Series record].

RNA was isolated from FACS sorted cells using Qiagen RNAeasy kit according to manufacturer protocol

Samples were hybridized using Affymetrix hybridization kit materials. Cocktails were heated  at 99° for 5 minutes, then 45° for 5 minutes, and centrifuge at max speed for 1 minute. 200μl of hyb solution transfered to each array. Hybridize 16 hours at 45° at 60rpm. Fluidics washing is FS450

Short hairpin RNA targeting human TRAF6 was expressed in pLKO.1-puro lentiviral expression vector, and provided by the Lenti-shRNA library core CCHMC. The clones for TRAF6 is TRCN0000007348. Puromycin resistance gene was replaced by green fluorescent protein (GFP). The vector targeting scramble sequences was used as control. All the plasmids were packaged into pseudo lentivirus for transient and stable knockdown. Lentiviruses were pseudotyped with VSV-G, produced by 293-FT cells, and concentrated through ultracentrifugation at 20,000rpm for 2 hours at 4°C. Cells at 1×10^5/mL were transduced with lentivirus at an multiplicity of infection (MOI) of 0.5~1 and in the presence of 8μg/mL of polybrene (No. TR-1003-G; Millipore). At 2.5 days post-transduction, GFP positive cells were purified via fluorescence-activated cell sorting (FACS).

TF-1 cells were cultured in RPMI1640 supplemented with 10% fetal bovine serum, 100U/mL Penicillin and 100ug/mL Streptomycin, and 10ng/mL hIL-3.

Genechips were scanned using the Affymetrix GeneChip Scanner 3000 7G, and data were collected with Genechip Operating Software (Affymetrix).

Use RMA to normalize all arrays (samples) for a project. Average means of replicate samples. Create interpretations to compare different groups. Filter raw data to remove entities (genes) not being expressed. Perform fold change analysis, create list of genes with a  FC  1.5 or higher. Then use a statistical test, T Test unpaired with a p-value cutoff of 0.05 and multiple testing correction using Benjamini-Hochberg.
probe group file: HuGene-1_0-st-v1.pgf
meta-probeset file: HuGene-1_0-st-v1.csv

Total RNA was extracted and purified with Quick-RNA MiniPrep Kit from Zymo Research (Cat#R1054) according to the manufacturer's instructions.

Hybridizations were with the standard Probe Array Cartidge (GeneChip Human Gene 1.0 ST Array; Affymetrix). Create a hybridization cocktail for a single probe array that contains 2.5 µg of fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20× Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 10% DMSO, and 1× Hybridization Buffer.  Heat hybridization cocktail to 99°C for 2 minutes, to 45°C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 90 µL of 1× Hybridization Buffer. Incubate at 45°C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1× Hybridization Buffer and fill probe array with 90 µL of the hybridization cocktail. Incubate at 45°C for 18 hrs in the Hybridization Oven rotating at 60 rpm.

A total of 1-20ng of total RNA was reversed transcribed and labeled with the Ovation Pico WTA System (Nugen), the WT-Ovation Exon Module v1.0 (NuGEN), and the Encore Biotin Module (NuGEN).

RNA extracted from cultured lymphoblastic cell line of FCHL patient

brain (frontal cortex);schizophrenia;32 yr;white;295.9;29 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);schizophrenia;24 yr;white;295.9;20 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);schizophrenia;39 yr;white;295.3;17 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);schizophrenia;43 yr;white;295.9;18 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);schizophrenia;33 yr;white;295.9;19 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);schizophrenia;47 yr;white;295.9;20 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);schizophrenia;35 yr;white;295.3;14 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);schizophrenia;53 yr;white;295.9;23 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);schizophrenia;36 yr;white;295.9;33 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

BALB/c;4T1.2;pMSCV retroviral expression vector system the base vector (BV);base vector (BV);Mammary Tumour

Rb-/- prostate epithelial cell line maintained in RPMI-1640 medium supplemented with 5% fetal bovine serum

Male;54;12h;6.6;control;superior temporal cortex (Brodmann Area 22, BA22)

Male;91;13h;6.3;control;superior temporal cortex (Brodmann Area 22, BA22)

Female;87;14.5h;6.5;control;superior temporal cortex (Brodmann Area 22, BA22)

Female;90;12.5h;5.7;control;superior temporal cortex (Brodmann Area 22, BA22)

Female;94;9.5h;6.3;control;superior temporal cortex (Brodmann Area 22, BA22)

differentiated U937 cells, ROS exposed, 1uM curcumin treated, 4h

GeneChips were scanned using the GeneChip Scanner 3000 7G System.

The data were analyzed with GeneChip Operating Software Ver. 1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

MCF10A cells were infected with retrovirus constructs (vector or YAP) and puromycin was used to select for transduced cells. Cells were split and grown to ~60-75%% confluency at which point they were harvested for RNA.

vLow_24h_1

vLow_8h_4

Ishikawa;39-year-old parous Japanese female diagnosed with endometrial adenocarcinoma stage 2.;bisphenol A;1 pM;8 hours

vHigh_48h_3

Ishikawa;39-year-old parous Japanese female diagnosed with endometrial adenocarcinoma stage 2.;bisphenol A;1 uM;48 hours

vHigh_48h_2

vHigh_48h_1

vHigh_24h_4

Ishikawa;39-year-old parous Japanese female diagnosed with endometrial adenocarcinoma stage 2.;bisphenol A;1 uM;24 hours

vLow_8h_3

vLow_8h_2

vLow_8h_1

vHigh_48h_4

Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16662.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16834.gif

mixed reference (MR = CRG + FR);ARD842, CAIS, proliferating cells, 24h 1000nM DHT

Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15743.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15581.gif

mixed reference;nGSF56, 14 days DMEM F12 12.9% D/S FCS + 6 x ETOH

Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15719.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17291.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15582.gif

mixed reference;nGSF56, 14 days DMEM F12 12.9% D/S  FCS + 6 x 100nM DHT

Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16724.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17292.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17277.gif

K562 cells (CML cell line) treated with IC50 concentration of AMN107 (Nilotinib) (0.05 µM) for 24 hours

109;None;10/10/57;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;12/2/04;FH of Colon Cancer;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

107;None;07/28/1060;M;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;11/25/04;FH Colon Cancer;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

111;Paracetamol;9/5/82;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;12/3/04;FH of CD, Path Increased lymphiod in TI Bx.;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

110;None;3/13/54;M;JEWISH;FALSE;FALSE;FALSE;FALSE;FALSE;12/2/04;Diarrhoea;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

103;None;6/30/65;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;11/9/04;Diarrhoea, now settled, Mum has UC;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

117;Loperamide;3/31/67;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;12/21/04;IBS type symptoms;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

105;None;7/29/84;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;11/15/04;IBS type symptoms;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

104;None;1/2/72;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;11/15/04;IBS type symptoms;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

114;None;6/27/36;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;12/14/04;Altered bowel habit, Alcohol excess;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

112;None;7/5/81;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;12/7/04;Altered bowel habit;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

Sample_ID:t06 // Patient:J-111 // Histology:Intestinal // Metastasis:+ // p53_mut:++ // E-cadherin_mut:+ // beta-Catenin_mut:++

Affymetrix GCOS 1.4 software (Affymetrix); Probability scores and fold changes were calculated using the Rosetta Resolver software (Rosetta Biosoftware, Seattle, WA).

Biotinylation; IVT Labeling Kit (Affymetrix Inc., Santa Clara, CA)

In 6-well plates, cells were pre-incubated with 10 µM ubiquinol (Q10H2), or the respective vehicle controls (KANEKA Corporation, Japan). After 24 hours, cell culture medium was removed and fresh lipopolysaccharide (LPS, E. coli, O55:B5, Sigma Aldrich, Taufkirchen, Germany) containing medium (1 µg/ ml) was added for 4 hours, except in the negative control wells (-LPS).

myeloid monocytic cells;24h Q10H2 preincubation, 4h LPS stimulation

STAT1-deficient naïve T cells stimulated for 3 hours with medium alone 2

Gene expression data from STAT1KO naïve CD4+ T cells stimulated for 3 hours with medium alone

CD4+ T;C57BL/6J;C57BL6-STAT1<tm1Dlv> (STAT1KO);stimulated for 3 hours with medium alone

STAT1-deficient naïve T cells stimulated for 3 hours with medium alone 3

Gene expression data from wild type naïve CD4+ T cells stimulated for 3 hours with IL-27

CD4+ T;C57BL/6J;wild type;stimulated for 3 hours with IL-27 (20 ng/ml)

STAT1-deficient naïve T cells stimulated for 3 hours with medium alone 1

Gene expression data from wild type naïve CD4+ T cells stimulated for 3 hours with IL-6

CD4+ T;C57BL/6J;wild type;stimulated for 3 hours with IL-6 (20 ng/ml)

STAT1-deficient naïve T cells stimulated for 3 hours with IL-6 1

Gene expression data from STAT1KO naïve CD4+ T cells stimulated for 3 hours with IL-6

CD4+ T;C57BL/6J;C57BL6-STAT1<tm1Dlv> (STAT1KO);stimulated for 3 hours with IL-6 (20 ng/ml)

STAT1-deficient naïve T cells stimulated for 3 hours with IL-6 2

U2OS;osteosarcoma cells;nonspecific siRNA (SiNS);dexamethasone (Dex) for 24h

Rat230_2;15;ul;1.626;0.845;1.91;1:5;8.4;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;75;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.843;0.95;1.9;1:5;8.3;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;52;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;2.242;1.132;1.95;1:5;7.8;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;50;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;2.692;1.387;1.91;1:5;8.2;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;49;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 5, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 0, Units of Dose or Concentration: ppm

nasal epithelium, formaldehyde inhalation exposure, air control, 6 hours per day, 5 days per week, 5 day time point

Rat230_2;15;ul;1.549;0.803;1.9;1:5;7.9;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;63;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.542;0.787;1.93;1:5;7.7;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;62;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.894;0.979;1.9;1:5;7.8;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;61;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.163;0.612;1.87;1:5;7.8;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;60;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

in vivo Treatment: Formaldehyde, Vehicle for Chemical: Water, Amount of Vehicle: 40, Route of Exposure: Instillation (nasal), Units of Amount of Vehicle: ul per nostril, Dose or Concentration: 0, Units of Dose or Concentration: mM

nasal epithelium, formaldehyde instilation exposure, vehicle control, single exposure, 6 h time point

Rat230_2;15;ul;3.701;1.82;1:5;8.3;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;354;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;3.678;1.857;1.95;1:5;7.5;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;352;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

The transgenic Crx-Nr2e3-Nrl-ko-Gfp samples were compared to Nrl-ko-Gfp
at 4weeks. The Nrl-ko-Gfp data has already been submitted to GEO with series entry GSE4051

C57BL/6;mouse bone marrow;wild type;1x10^6 cells in a 12-well plate co-cultured overnight with 1x10^6 E0771 tumor cells in an sterile insert

A673 treated with DMSO vehicle control for 5 days, biological rep5

Gene expression data from A673 cell line that has been treated with DMSO vehicle control for 5 days.

A673 cell line that has been treated with DMSO vehicle control for 5 days.

A673 treated with DMSO vehicle control for 5 days, biological rep4

A673 treated with cytarabine (ARA-C) for 24 hours with concentration of 0.17 uM (EC50), biological rep1

Gene expression data from A673 cell line that has been treated with cytarabine (ARA-C) for 24 hours with concentration of 0.17 uM (EC50).

A673 cell line that has been treated with cytarabine (ARA-C) for 24 hours with concentration of 0.17 uM (EC50).

A673 treated with DMSO vehicle control for 5 days, biological rep6

A673 treated with DMSO vehicle control for 5 days, biological rep1

A673 treated with DMSO vehicle control for 3 days, biological rep6

A673 treated with DMSO vehicle control for 5 days, biological rep3

A673 treated with DMSO vehicle control for 5 days, biological rep2

A673 treated with cytarabine (ARA-C) for 24 hours with concentration of 0.17 uM (EC50), biological rep3

A673 treated with cytarabine (ARA-C) for 24 hours with concentration of 0.17 uM (EC50), biological rep2

SMhu004

SMhu006

SMhu001

SMhu002b

SMhu003

SMhu001b

SMhu002

Gene expression data from small intestine treated with irinotecan

Gene expression data from large intestine not treated with irinotecan

LT-HSCs were FACS-sorted from three Lrf knockout (Zbtb7a Flox/Flox Mx1-Cre+) and two control (Zbtb7a Flox/+ Mx1-Cre+) mice, nine days after the first pIpC injection. pIpC (250μg) was injected twice to induce Cre recombinase.

Affymetrix GeneChip images were scanned using a high-resolution GeneChip Scanner 3000 (Hewlett-Packard).

The raw data is normalized by Robust Multi-array Average (RMA) using Affymetrix Expression Console.

RNA samples were prepared using the Absolutely RNA Microprep Kit (Stratagene).

Affymetrix GeneChip Mouse Genome 430 v2.0 arrays (Affymetrix, Santa Clara, CA) were hybridized with fragmented cRNA targets (20 μg) and washed and stained with streptavidin-PE.

Biotinylated cRNA was generated using two rounds of in vitro transcription by T7 RNA polymerase.

B657_MG430 2-(5_2950FF)
Gene expression data from FACS-sorted LT-HSCs (LSK IL7Ra-Flt3-CD150+CD48-).

C57BL/6;Zbtb7a Flox/Flox Mx1-Cre+ (LRF homozygous knockout);4 weeks;FACS-sorted LT-HSCs (LSK IL7Ra-Flt3-CD150+CD48-);9 days after 1st pIpC injection

B656_MG430 2-(4_2846FF)

B655_MG430 2-(2_2849F+)

C57BL/6;Zbtb7a Flox/+ Mx1-Cre+ (LRF heterozygous);4 weeks;FACS-sorted LT-HSCs (LSK IL7Ra-Flt3-CD150+CD48-);9 days after 1st pIpC injection

mouse NSCs were nucleofected either with miR-128 mimic or miR-Control

mouse NSCs were grown as neurospheres and in proliferation conditions.

Image analysis was performed using the standard Affymetrix protocols (GeneChip® Expression Wash, Stain and Scan User Manual (P/N 702731)). Scanning was performed using the GeneChip® Scanner 3000 and Affymetrix® GeneChip® Command Console® (AGCC).

The raw CEL files were imported into R using the 'affy' package. Arrays were processed using RMA background correction, quantile normalization, and median polish summarization using only the perfect match (PM) probes.

GeneChip® Hybridization, Wash and Stain Kit  was used to prepare samples for hybridization to the Gene 1.0 ST Array. More information about this protocol can be found on the Affymetrix website.

One μg of total RNA was labeled following the GeneChip® Whole Transcript (WT) Sence Target Labeling Protocol (P/N 701880)

B654_MG430 2-(1_2823F+)

B658_MG430 2-(6_2851+2821FF)

The left hippocampus was dissected out of a male, 12 month-old mouse overexpressing amyloid precursor protein with the Swedish mutation (Tg2576; APPSw).  Total RNA was extracted and the data were analyzed with MAS 5.0 and scaled to 2500.

The left hippocampus was dissected out of a male, 12 month-old nontransgenic control mouse (C57B6/SJL).  Total RNA was extracted and the data were analyzed with MAS 5.0 and scaled to 2500.

For stimulation, B cells (0.4 x 106) were cultured in 24-well plates and stimulated with LPS (20 µg/ml; Sigma) and mouse recombinant IL-4 (10 ng/ml; Pharmingen) for 2 days.

B cells from spleen were isolated by negative selection using CD43 microbeads (MACS; Milteny). The purity of the different subpopulations was above 98% as assayed by flow cytometry.B cells were grown in RPMI with Glutamax containing 10% FCS (Invitrogene), nonessential amino acids (0.1 mM), sodium pyruvate (1 mM), penicillin (100 U/ml)/streptomycin (100 µg/ml) and 50 µM b-mercaptoethanol and were maintained at 37 ºC in an atmosphere at 5% CO2.

GeneChip intensities were background-corrected, normalized and sumarized by RMA method, using the “Affy” package from Bioconductor.

RNA was prepared using TRIzol (Invitrogen) and the RNeasy Mini Kit (Qiagen). RNA was quantified and the RNA quality was assessed with a 2100 Bioanalyzer from Agilent Technologies

Following fragmentation, 10 µg of biotinylated cRNA were hybridized to Affymetrix chips (GeneChip Mouse Genome 430 2.0 Array). Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino)ethanesulfonic acid, 1 M Na+, and 20mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05 µg/ml. Hybridization was performed for 16 h at 45ºC . Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix).

Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 4 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

Wild Type;stimulated with LPS and mouse recombinant IL-4 (day 2);B cells

Study of rat femur fracture healing in old rats (52 weeks old at fracture) at 6 weeks after fracture.  RNA from 2 rats was pooled for each array.  Sample is middle third of femur with external callus, cortical bone and marrow elements.

Skin removed from back region of embryonic day 16.5 mouse, Tcfap2c mutation

Female;6 months;additional patient information found in Series supplementary file

Female;8 months;additional patient information found in Series supplementary file

Male;18 months;additional patient information found in Series supplementary file

3239_H1299_1uM-Dac_2.CHP
H1299 1D
3239_H1299_1uM-Dac_2.CEL

Treated with vehicle for 24 hrs
Treatment on a different day than original treatments-associated with high dose quinolones

This vehicle is associated with GSM231517 and GSM231518.

This vehicle is associated with GSM231528 and GSM231529

Brg1_cKO1;mixed background (Gebuhr TC, Kovalev GI, Bultman S, Godfrey V, Su L, Magnuson T. The role of Brg1, a catalytic subunit of mammalian chromatin-remodeling complexes, in T cell development. J Exp Med. 2003 Dec 15;198(12):1937-49.);P1

Female SJL/J mice were purchased from Charles River Laboratories (Sulzfeld, Germany) at age 4-6 weeks and kept in a pathogen free environment. The microarray experiments were performed in mice 32 - 34 weeks of age. The SJL/J mouse strain has been derived from non-inbred Swiss Websterstock by brother-sister mating for 30 generations (Murphy, ED. Proc Am Assoc Cancer Res 4:46, 1963) and is a naturally occurring model for autosomal recessive muscular dystrophy (Bittner, RE et al. Nature Genet 23, 141-142, 1999). The SJL/J mice develop a spontaneously occurring myopathy resulting in muscle weakness (Weller, AH et al. Muscle Nerve 20, 72-82, 1997). This is due to a 171-bp deletion in the dysferlin gene of SJL mice resulting in an in-frame deletion and removal of 57amino acids (Bittner, RE et al. Nature Genet 23, 141-142, 1999). RNA was extracted from the left ventricle of heart of 5 SJL/J mice using TRIzol reagent (Invitrogen, Life Technologies, Carlsbad, USA). Total RNA was purified following the TRIzol standard protocol. Total RNA was treated by deoxyribonuclease I (Invitrogen) and purified using the RNeasy Mini Kit (Qiagen GmbH, Hilden, Germany) according to the manufacture's protocol. RNA integrity was checked by denaturating agarose gel electrophoresis, and only RNA with absorbance ratios 260 nm/280 nm between 1.9 and 2.1 was used. 8 µg RNA were transcribed in double-stranded cDNA by cDNA Synthesis System (Roche Diagnostics GmbH, Mannheim, Germany). cRNA was produced by MEGAscript TM High Yield Transcription Kit (Ambion, Austin, USA) and labelled with biotin-11-CTP and biotin-16-UTP nucleotides (Perkin Elmer Life Sciences, Boston, USA). 5 left ventricle biological replicates were analyzed using standard Affymetrix procedures.
Keywords = Mus musculus,  SJL/J, cardiac muscle, left ventricle, effect of deleted gene dysferlin

Keywords = Mus musculus,  SJL/J,  cardiac muscle, left ventricle, effect of deleted gene dysferlin

Female C57BL/6 mice were purchased from Charles River Laboratories (Sulzfeld, Germany) at age 4-6 weeks and kept in a pathogen free environment. The microarray experiments were performed in mice 32 - 34 weeks of age. RNA was extracted from the left ventricle of heart of 5 C57BL/6 mice using TRIzol reagent (Invitrogen, Life Technologies, Carlsbad, USA). Total RNA was purified following the TRIzol standard protocol. Total RNA was treated by deoxyribonuclease I (Invitrogen) and purified using the RNeasy Mini Kit (Qiagen GmbH, Hilden, Germany) according to the manufacture's protocol. RNA integrity was checked by denaturating agarose gel electrophoresis, and only RNA with absorbance ratios 260 nm/280 nm between 1.9 and 2.1 was used. 8 µg RNA were transcribed in double-stranded cDNA by cDNA Synthesis System (Roche Diagnostics GmbH, Mannheim, Germany). cRNA was produced by MEGAscript TM High Yield Transcription Kit (Ambion, Austin, USA) and labelled with biotin-11-CTP and biotin-16-UTP nucleotides (Perkin Elmer Life Sciences, Boston, USA). 5 left ventricle biological replicates were analyzed using standard Affymetrix procedures.
Keywords = Mus musculus,  C57BL/6, cardiac muscle, left ventricle, effect of deleted gene dysferlin

This is wt-Gfp 4 weeks replicate 2.

Keywords = Mus musculus,  C57BL/6,  cardiac muscle, left ventricle, effect of deleted gene dysferlin

Keywords = C57BL/6
Keywords = cardiac muscle
Keywords = left ventricle
Keywords = effect of deleted gene dysferlin

Animals were exposed to air or ozone, for 6, 24, 48 or 72 hours.

GeneChips were scanned in an Affymetrix GCS3000 scanner with autoloader.

The data were analyzed with GCOS 1.4 software. All probe sets scaling was performed with a target signal value of 500. No normalization was performed.

Total RNA was extracted from individual lungs homogenized in TRIZOL. RNA was column-purified using the Qiagen RNeasy Mini Kit.

10ug fragmented, biotinylated cRNA was hybridized to MOE430A GeneChips for 16hours at 45oC and 60rpm. The signal amplification protocol for washing/staining was performed in a FS450 automated fluidics station according to Affymetrix protocol.

7.5 ug total RNA was processed according to the Affymetrix Technical manual Rev3 protocol. Biotinylated cRNA was prepared using the ENZO BioArray High Yield RNA Transcript Labeling Kit.

Gene expression data from HSF1+/+ T cells activated at 40oC for 5h with plate bound anti-CD3.

breast cancer derived cell line treated with 20 uM of etoposide for 12 hours

breast cancer derived cell line treated with 30 uM of etoposide for 36 hours

breast cancer derived cell line treated with 40 uM of etoposide for 12 hours

breast cancer derived cell line treated with 10 uM of etoposide for 36 hours

breast cancer derived cell line treated with 20 uM of etoposide for 36 hours

Cyclophosphamide-treated peripheral blood leukocytes 1 day - Biological Replicate 1 - Technical Replicate 2

Biological replicate 1 of 4. Technical Replicate 2 of 2. Peripheral blood leukocytes,  CTX-treated day 1

Cyclophosphamide-treated peripheral blood leukocytes 1 day - Biological Replicate 1 - Technical Replicate 1

Biological replicate 1 of 4. Technical Replicate 1 of 2. Peripheral blood leukocytes, CTX-treated day 1

Control peripheral blood leukocytes - Biological Replicate 2 - Technical Replicate 2

Biological replicate 2 of 4. Technical Replicate 2 of 2. Control Peripheral blood leukocytes, untreated

Control peripheral blood leukocytes - Biological Replicate 2 - Technical Replicate 1

Biological replicate 2 of 4. Technical Replicate 1 of 2. Control Peripheral blood leukocytes, untreated

Control peripheral blood leukocytes - Biological Replicate 1 - Technical Replicate 2

Biological replicate 1 of 4. Technical Replicate 2 of 2. Control Peripheral blood leukocytes, untreated

Control peripheral blood leukocytes - Biological Replicate 1 - Technical Replicate 1

Biological replicate 1 of 4. Technical Replicate 1 of 2. Control Peripheral blood leukocytes, untreated

Control peripheral blood leukocytes - Biological Replicate 4 - Technical Replicate 2

Biological replicate 4 of 4. Technical Replicate 2 of 2. Control Peripheral blood leukocytes, untreated

Control peripheral blood leukocytes - Biological Replicate 4 - Technical Replicate 1

Biological replicate 4 of 4. Technical Replicate 1 of 2. Control Peripheral blood leukocytes, untreated

Control peripheral blood leukocytes - Biological Replicate 3 - Technical Replicate 2

Biological replicate 3 of 4. Technical Replicate 2 of 2. Control Peripheral blood leukocytes, untreated

Control peripheral blood leukocytes - Biological Replicate 3 - Technical Replicate 1

Biological replicate 3 of 4. Technical Replicate 1 of 2. Control Peripheral blood leukocytes, untreated

LOX-1:113503;GFP_Untreated_24hr:113503;Classification:Good;Gradient Severity:0.04;Distortion Severity:0.04;Defective Area (%):0.01;Outlier Area (%):0.04;3'/5' Mean:1.66;Background Mean Dev.:0.36;Absent (%):58.28;Absent (%) Dev.:0.02;Scaling Factor:0.65;Scaling Factor Dev.:0.34;GFP;24 hours;(Not applicable);113503;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;GFP_Untreated_24hr;282295853

LOX-1:113202;GFP_Untreated_2hr:113202;Classification:Medium;Gradient Severity:0.06;Distortion Severity:0.07;Defective Area (%):0.01;Outlier Area (%):0;3'/5' Mean:1.75;Background Mean Dev.:2.27;Absent (%):59.11;Absent (%) Dev.:0.67;Scaling Factor:0.55;Scaling Factor Dev.:0.5;GFP;2 hours;(Not applicable);113202;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;GFP_Untreated_2hr;282295483

LOX-1:113301;GFP_Untreated_6hr:113301;Classification:Medium;Gradient Severity:0.04;Distortion Severity:0.09;Defective Area (%):0.01;Outlier Area (%):0;3'/5' Mean:1.52;Background Mean Dev.:1.13;Absent (%):61.55;Absent (%) Dev.:2.56;Scaling Factor:0.77;Scaling Factor Dev.:1.36;GFP;6 hours;(Not applicable);113301;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;GFP_Untreated_6hr;282295593

LOX-1:113501;GFP_Untreated_24hr:113501;Classification:Good;Gradient Severity:0.04;Distortion Severity:0.09;Defective Area (%):0;Outlier Area (%):0.01;3'/5' Mean:1.66;Background Mean Dev.:0.38;Absent (%):56.87;Absent (%) Dev.:1.07;Scaling Factor:0.52;Scaling Factor Dev.:0.75;GFP;24 hours;(Not applicable);113501;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;GFP_Untreated_24hr;282295833

LOX-1:213403;LOX1_Untreated_12hr:213403;Classification:Good;Gradient Severity:0.1;Distortion Severity:0.04;Defective Area (%):0.08;Outlier Area (%):0;3'/5' Mean:1.79;Background Mean Dev.:0.74;Absent (%):59.36;Absent (%) Dev.:0.86;Scaling Factor:0.66;Scaling Factor Dev.:0.42;LOX1;12 hours;(Not applicable);213403;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;LOX1_Untreated_12hr;282295793

LOX-1:213302;LOX1_Untreated_6hr:213302;Classification:Bad;Gradient Severity:0.08;Distortion Severity:0.08;Defective Area (%):0;Outlier Area (%):0.01;3'/5' Mean:1.67;Background Mean Dev.:0.99;Absent (%):60.73;Absent (%) Dev.:1.92;Scaling Factor:1.1;Scaling Factor Dev.:4.2;LOX1;6 hours;(Not applicable);213302;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;LOX1_Untreated_6hr;282295663

LOX-1:113403;GFP_Untreated_12hr:113403;Classification:Good;Gradient Severity:0.05;Distortion Severity:0.04;Defective Area (%):0.04;Outlier Area (%):0;3'/5' Mean:1.7;Background Mean Dev.:1.04;Absent (%):57.99;Absent (%) Dev.:0.2;Scaling Factor:0.48;Scaling Factor Dev.:1.14;GFP;12 hours;(Not applicable);113403;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;GFP_Untreated_12hr;282295733

LOX-1:113502;GFP_Untreated_24hr:113502;Classification:Medium;Gradient Severity:0.12;Distortion Severity:0.08;Defective Area (%):0.01;Outlier Area (%):0.01;3'/5' Mean:1.46;Background Mean Dev.:0.06;Absent (%):60.04;Absent (%) Dev.:1.38;Scaling Factor:0.87;Scaling Factor Dev.:2.22;GFP;24 hours;(Not applicable);113502;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;GFP_Untreated_24hr;282295843

LOX-1:221402;LOX1_oxLDL_12hr:221402;Classification:Good;Gradient Severity:0.04;Distortion Severity:0.02;Defective Area (%):0;Outlier Area (%):0.01;3'/5' Mean:1.56;Background Mean Dev.:0.89;Absent (%):56.53;Absent (%) Dev.:1.34;Scaling Factor:0.54;Scaling Factor Dev.:0.58;LOX1;12 hours;Oxidized LDL;221402;HAECT;50 ug/ml;Endothelial;Human:Homo sapiens;LOX1_oxLDL_12hr;282295813

WI-38 cells, at 24 h after exposure to DMSO vehicle control, biological rep4

C57BL/6;male;embryonic day E15.5;Gadd45a-/- Ing1-/-;mouse embryonic fibroblasts (MEF cells)

C57BL/6;male;embryonic day E15.5;Gadd45a-/-;mouse embryonic fibroblasts (MEF cells)

NB194

aortic biopsy stiff

aortic biopsy medium

Affymetrix GeneChip experiment performed on mRNA from adrenal glands of the hypotensive mouse strain, BPL ("Blood Pressure Low"). Replicate 1 of 3.

Affymetrix GeneChip experiment performed on mRNA from adrenal glands of the hypotensive mouse strain, BPL ("Blood Pressure Low"). Replicate 2 of 3.

Affymetrix GeneChip experiment performed on mRNA from adrenal glands of the hypertensive mouse strain, BPH ("Blood Pressure High"). Replicate 1 of 3.

Affymetrix GeneChip experiment performed on mRNA from adrenal glands of the hypertensive mouse strain, BPH ("Blood Pressure High"). Replicate 2 of 3.

Affymetrix GeneChip experiment performed on mRNA from adrenal glands of the hypertensive mouse strain, BPH ("Blood Pressure High"). Replicate 3 of 3.

Balb/C;female;pancreas;30 days old;Isocaloric low protein diet;streptozotocin

Mice were euthanized and spleen tissue was collected and stored in RNAlater for microarray analysis

Microarrays were scanned using a Beadstation 500 at Green factor level 2

Data was analysed using BeadStudio and Genespring GX; Values reported were derived using Illumina BeadStudio v3 and represent relative signal intensity normalized to background, Genespring GX was used to normalise each chip to the 50th percentile and each gene to the median and uninfected controls, measurements less than 0.01 were set to 0.01

Total RNA was extracted from spleen tissue by phase separation with Trizol (Invitrogen, USA) and column chromatography using an Rneasy Mini kit (Qiagen Inc, USA), RNA quantity was measured using a Nanodrop (Nanodrop Technologies, USA) and quality was assessed using an Agilent Bioanalyzer Nanochip (Agilent Technologies, USA)

cRNA was hybridised to Illumina mouse-6 v1.1 expression beadchips according to the manufacturers instructions

cRNA was synthesised from 250ng of pooled total RNA with an Illumina Total Prep RNA Amplification Kit (Ambion Inc., USA) according to the manufacturers instructions

Gene expression in the spleen of C57BL/6 mice 4 weeks post infection with Schistosoma japonicum

C57BL/6;Female;6 weeks;Spleen;Schistosoma japonicum;4 weeks post infection 20 cercariae

Gene expression in the spleen of C57BL/6 mice 6 weeks post infection with Schistosoma japonicum

C57BL/6;Female;6 weeks;Spleen;Schistosoma japonicum;6 weeks post infection 20 cercariae

Gene expression in the spleen of C57BL/6 mice 7 weeks post infection with Schistosoma japonicum

C57BL/6;Female;6 weeks;Spleen;Schistosoma japonicum;7 weeks post infection 20 cercariae

Around 1x10^5 ES cells/well in 24-well plates are infected with lentiviral vectors at 10 MOI. 48 hours after transduction, puromycin (2ug/ml) is added to the medium for selecting transduced cells.

E14 mESCs are cultured on the 0.1% gelatin coated plates in the DMEM medium (Sigma) supplemented with 100U/ml penicillin/streptomycin, 15% fetal bovine serum (Sigma), 1x nonessential amino acid, 1x sodium pyruvate, 1x GlutaMax, 1x beta-mercaptoethanol (Invitrogen) and 1000 units/ml leukemia inhibitory factor (ESGRO, EMD Millipore).

GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G by Functional Genomics Core Facility in UNC-CH using standard protocol.

Primary analysis was carried out by Functional Genomics Core Facility in UNC-CH using Affymetrix Expression Console software.

Total RNA was extracted from the control and Kdm2b knockdown mESCs using RNeasy mini kit (QIAGEN) following manufacture's instructions.

Hybridization to Affymetrix MoGene-1_0-st-v1 array was carried out by Functional Genomics Core Facility in UNC-CH using standard protocol.

Biotin labeling was carried out by Functional Genomics Core Facility in UNC-CH using GeneChip WT Sense Target Labeling and Control Reagents and standard protocol.

C57/B6 subjected to cecal ligation and puncture (CLP) and samples taken 24hr after surgery.

C57/B6 mouse was subjected to sham laparotomy and sample taken 24hr after surgery.

Gene expression data from Rptr KO, YFP+ muscle stem cells isolated from a noninjured animal

mixed C57BL6;Rptrflox/flox;Pax7CreER/+;Rosa26REYFP/+;3-5 months old;noninjured;hindlimb muscle;QSC;control

Whole embryonic kidneys were isolated from E12.5 pregant female wild-type and knockout mice.

RNA was extracted with the Qiagen RNEasy Micro kit according to the manufacturer's instructions.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hrs at 45C on GeneChip Mouse Genome Array (430 2.0).  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2-5 ug total RNA (Expression Analysis Technical Manual, 2011, Affymetrix)

C57BL/6;Ret Deficient;whole embryonic kidney;gestational day 12.5 (E12.5)

mouse E12.5 embryonic kidney isolated from Ret-knockout pregnant female

C57BL/6;Wildtype;whole embryonic kidney;gestational day 12.5 (E12.5)

mouse E12.5 embryonic kidney isolated from wild-type pregnant female

Gene expression data from cMet KO, YFP+ muscle stem cells isolated from a noninjured animal

C57BL6 mixed FVB;cMetflox/flox;Pax7CreER/+;Rosa26REYFP/+;3-5 months old;noninjured;hindlimb muscle;QSC;control

Gene expression data from Rptr KO, YFP+ muscle stem cells, isolated from hindlimb that was contralateral to an hindlimb were we induced a muscle injury, 2.5 days post injury

mixed C57BL6;Rptrflox/flox;Pax7CreER/+;Rosa26REYFP/+;3-5 months old;BaCl2 muscle injury;hindlimb muscle contralateral to BaCl2 muscle injury;CSC;2.5 days post injury

whole blood;Unaffected control;Male;3;n/a;n/a;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Unaffected control;Female;1;n/a;n/a;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Unaffected control;Male;4;n/a;n/a;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Unaffected control;Female;4;n/a;n/a;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Cutaneous psoriasis without arthritis;Female;4;4;24;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Cutaneous psoriasis without arthritis;Female;3;13;25;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Unaffected control;Female;3;n/a;n/a;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

Empty vector-non silencing-pGIPZ, OpenBiosystems (EV), human osteoblast cell line (hOB)

SAM630144;C57BL/6;spr881;IL17RC Knock out;pooled mouse reference RNA

SAM630146;C57BL/6;spr881;IL17RC Knock out;pooled mouse reference RNA

brain (frontal cortex);schizophrenia;42 yr;white;295.3;18 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);schizophrenia;53 yr;white;295.9;29 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);schizophrenia;52 yr;white;295.1;28 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

Synovial biopsies (n = 4 to 6), obtained by needle arthroscopy from the swollen knee of a patient with seronegative arthritis

Bipolar disorder;56;Female;14;42;6.58;26;Left;25000;No;Yes;No;No;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): 5

Bipolar disorder;35;Female;21;14;6.10;17;Right;3000;No;No;No;Yes;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): 1

Bipolar disorder;44;Male;33;11;6.74;19;Right;0;No;Yes;No;Yes;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): 2

Bipolar disorder;48;Male;31;17;6.90;23;Left;0;Yes;No;No;Yes;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): 5

Bipolar disorder;48;Female;33;15;6.50;18;Left;0;No;No;No;No;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): 1

Bipolar disorder;42;Male;18;24;6.65;32;Right;0;No;No;No;No;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): 5

Bipolar disorder;54;Male;45;9;6.50;44;Left;0;No;Yes;No;Yes;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): 2

Bipolar disorder;43;Female;25;18;6.74;39;Left;4500;No;No;No;Yes;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): 2

Bipolar disorder;41;Male;22;19;6.71;70;Left;0;Yes;Yes;No;Yes;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): 5

Bipolar disorder;35;Male;19;16;6.30;35;Right;30000;Yes;No;No;No;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): 1

Human melanoma cell line;M238;V600E BRAF mutant;1 uM PLX4032 for 6h

Human melanoma cell line;M238_R1;V600E BRAF mutant;1 uM PLX4032 for 6h

Human melanoma cell line;M249;V600E BRAF mutant;1 uM PLX4032 for 6h

Lot batch = 5270

Lot batch = 5253

At day 14-16, T cell clones were left one day without IL2.  Cells were then left unstimulated (t0) or stimulated for 72hrs (72h) with anti-CD3 immoblized (10 mg/ml) in Tris-HCL 0.1M and soluble anti-CD28 mAB (1 mg/ml)

CD4+ T cell clones were stimulated by a feeder cell mixture containing 10^6 PBMCs from 3 different healthy donors/ml (irradiated with 6000 rads), 10^5 JY(Epstein Bar virus immortalized B cell limphoblastoid cell line)/ml (irradiated 10000 rads) and PHA (Roche Diagnostics 0.1 mg/ml). T cell clones were stimulated every 21 days with the same feeder mixture.

Hybridized arrays were washed and stained on a gene Chip Fluidics Station 450 and finally scanned on a Gene Chip Scanner 3000 7G (Affymetrix), generating an intensity file (*.CEL) for each array

Data preprocessing was done using RMA quantile normalization by the <oligo> R package and differential gene expression was assesd by <limma> R package.

Total RNA was extracted with Rnaesy Plus MINI Kit (Quiagen, Hilden, Germany) according to manufacture's instructions.

About 5.5 μg of fragmented and labeled DNA target was hybridized to the Affymetrix GeneChip Human Gene 1.0 ST Array at 45°C for 17 h on a GeneChip Hybridization Oven 640 (Affymetrix).

DNA was fragmented and end-labeled using the GeneChip WT Terminal Labeling Kit (Affymetrix)

Gene expression data from T effector cells with or without FOXP3 expression

NO;CD4+/CD25- T effector cell;IPEX disease carrier;FOXP3 2T>C(mut);female;none

YES;CD4+/CD25- T effector cell;IPEX disease carrier;FOXP3 wild type;female;none

Lot batch = 5197

Lot batch = 5213

Lot batch = 5227

NO;CD4+/CD25- T effector cell;IPEX disease carrier;FOXP3 2T>C(mut);female;anti-CD3, anti-CD28 for 72 h

TNFa-OMe-P siRNA-C;09/06/16;09/06/29;6.4;162;2.53;0.815;colon;5% DSS

A total of 5 x 105 MEFs were plated on multiple 100-mm dishes for each line in 10% fetal calf serum and Dulbecco's Modified Eagle's Medium (DMEM).

Three pairs of wild-type and Zmpste24-/- MEFs were generated from E13.5 embryos at passage 0, subcultured into passage 3 and collected for total RNA extraction.

According to The GeneChip® Mouse Genome 430 2.0 protocol.  Array

RNA was isolated by TRIzol (Invitrogen) following the manufacturer protocol.

gene expression data from early passage mouse embryonice fibroblsts

expression profile pre-treatment a 65 year-old patient with clinical dermatomyositis

MxCre Notch1 lox/lox mice or Notch 1 lox/lox wildtype (WT) mice on a C57Bl/6 background were injected with 300ug of polyiosinic-polycytidylic acid at the age of 4 weeks at day 0, 3, and 6 to induce Cre expression for deletion of the loxP-flanked exon encoding the signal peptide of Notch 1 as previously described. Mice were euthanised by CO2 inhalation and liver samples were collected and snap-frozen for RNA extraction. For the establishment of angiosarcoma (AS) cell lines, hepatic endothelial cells were isolated from Notch1 knockout (KO) mice harbouring a visible AS. Longterm culturing of the primary cells selected malignant AS cells based on their atypical growth capacity and eventually lead to a uniform cell population.

Affymetrix GeneChip Scanner 3000 7G was used to scan the arrays.

Microarray data were preprocessed using standard RMA algorithm as implemented in the OLIGO package of Bioconductor libraries of R statistical environment.

Total RNA was extracted from the PHH using Qiazol reagent and miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction

The Hybridization, Wash and Stain Kit (Affymetrix) was used to hybridize all samples for 17 hours at 45°C in Affymetrix hybridization oven 645. The arrays were washed and stained on Fluidics station 450 using wash protocol FS450_0007 (Affymetrix).

250 ng of total RNA was reverse transcribed and biotinylated with the whole-transcript Expression Kit (Ambion) and whole-transcript Terminal Labeling Kit (Affymetrix) according to the manufacturer’s instructions.

RNA oligos for interference (RNAi) were purchased from Dharmacon.

Human glioblastoma cell line U87MG were grown in DMEM supplemented with 10% FBS, penicillin (100 U/mL), glutamine (2 mmol/L), and streptomycin (100 μg/mL) at 37°C in 5% CO2 atmosphere.

Data processing was performed with BioConductor packages (http://www.bioconductor.org/). Robust Multi-Array Average (RMA) normalization was applied. Normalized intensity values for all probes on the Affymetrix chip are presented in the Matrix table. Data analysis was performed using the t-test as implemented in the R statistical package. A minimum standard deviation was assumed corresponding to the median percentile of all standard deviations in order to avoid fortuitously large t statistics. Differentially expressed genes were selected based on >1.5 fold change and P<0.05.

Labeled cRNA was hybridized on Affymetrix GeneChip Human Gene 1.0 ST Array.

RNA sample was labeled according to the standard one cycle amplification and labeling protocol (Affymetrix).

Human glioblastoma cell line U87MG treated with a siRNA against CASP2

isolated from spleen;memory CD8 T cells;C57/BL6;TCF-1-deficient;over 80 days after infection

in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 5, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 0.7, Units of Dose or Concentration: ppm

nasal epithelium, formaldehyde inhalation exposure, 0.7 ppm, 6 hours per day, 5 days per week, 5 day time point

Rat230_2;15;ul;2.434;1.353;1.88;1:5;7.6;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;140;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.588;0.789;1.99;1:5;8.5;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;127;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Low_24h_1

Station	1
Module	4
[Scanner]
Filter	570
Scan Date	Sep 07 2006 01:43PM

Low_24h_3

Station	1
Module	2
[Scanner]
Filter	570
Scan Date	Sep 07 2006 01:18PM

Low_8h_1

High_48h_4

Ishikawa;39-year-old parous Japanese female diagnosed with endometrial adenocarcinoma stage 2.;bisphenol A;10 nM;48 hours

flow-cytometry: B220+, CD5–, CD19+, CD25+, CD69+, B7-1+, B7-2+, IgDlo, sIgMlo; clinical-signs: none

65N

90N

97N

This is the homozygous sample number three of three.
Experiment compares 129 Wt mouse pineal gland gene expression at P0 versus P0 pineal gland gene expression in NeuroD1 knockout mice.

The mRNA was extracted from rat livers collected 1 hour after inflicting with a burn injury

The mRNA was extracted from rat livers collected 4 hour after inflicting with a burn injury

Crohn's Disease subject (21 year old caucasian female, SAK_1261327175)

Crohn's Disease subject (34 year old caucasian female, SAK_1288197141)

in vivo Treatment: MEHP, Treatment Duration: 12, Units of Duration: hours, Treatment Time: 6:20, Units of Treatment Time: am, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.24, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

KJ_1_12_59_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

in vivo Treatment: MEHP, Treatment Duration: 1, Units of Duration: hour, Treatment Time: 1:00, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.23, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg oodyweight

KJ_1_1_37_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

in vivo Treatment: Corn Oil, Treatment Duration: 3, Units of Duration:  hour, Treatment Time: 1:34, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.22, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

KJ_0_3_54_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

in vivo Treatment: corn oil, Treatment Duration: 6, Units of Duration: hours, Treatment Time: 10:15, Units of Treatment Time: am, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.28, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

KJ_0_6_34_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

in vivo Treatment: Corn Oil, Treatment Duration: 3, Units of Duration: hours, Treatment Time: 1:22, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.24, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

KJ_0_3_52_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

in vivo Treatment: Corn Oil, Treatment Duration: 3, Units of Duration: hours, Treatment Time: 1:28, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.24, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

KJ_0_3_53_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

in vivo Treatment: MEHP, Treatment Duration: 12, Units of Duration: hours, Treatment Time: 6:10, Units of Treatment Time: am, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.21, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

KJ_1_12_57_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

in vivo Treatment: MEHP, Treatment Duration: 12, Units of Duration: hours, Treatment Time: 6:15, Units of Treatment Time: am, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.265, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

KJ_1_12_58_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

in vivo Treatment: corn oil, Treatment Duration: 6, Units of Duration: hours, Treatment Time: 10:20, Units of Treatment Time: am, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.285, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

KJ_0_6_35_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

in vivo Treatment: Corn oil, Treatment Duration: 6, Units of Duration: hours, Treatment Time: 10:25, Units of Treatment Time: am, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.305, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

KJ_0_6_36_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

long access to cocaine, lateral hypothalamus, 6 hrs/day access to cocaine

short access to cocaine, lateral hypothalamus, 1 hr/day access to cocaine

Calu-3 human lung epithelial cells were seeded onto 6-well plates and grown to about 80% confluency. Epithelial monolayers were infected with 10**8 CFUs per ml of one of the bacterial strains (FRD1, FRD440, FRD875, or FRD1234) for 60 min and then washed extensively with phosphate-buffered saline. The cultures were subsequently incubated in fresh RPMI 1640 medium supplemented with 10% fetal bovine serum and 100 µg/ml gentamicin. After 6 h, total RNA from the cells was prepared with RNAzol and further purified with RNEasy (Qiagen) for microarray hybridization. Control samples of Calu-3 cells were treated similarly, but not infected with bacteria. Single array image analysis was performed using MAS 5 (Affymetrix) to derive probeset intensities and detection p-values. All arrays were globally scaled to 500.
Keywords = CF, Cystic Fibrosis, Pseudomonas, Alginate, Flagellin

Female;36;PBMC;Patient 116;REBIF;3 month of REBIF;multiple sclerosis;NAB-

Female;36;PBMC;Patient 116;baseline;baseline;multiple sclerosis;NAB-

Female;36;PBMC;Patient 116;REBIF;24 month of REBIF;multiple sclerosis;NAB-

Female;36;PBMC;Patient 116;REBIF;12 month of REBIF;multiple sclerosis;NAB-

Day: 3; Drug: Methamphetamine; Phase: Drug treatment; Replicate: 1

Cells transfected with sirtuin 6 and stimulated with TNFa, biological rep1

Gene expression data from HEK293 cells transfected with SIRT6 construct  and stimulated with TNFa

HEK293 cells transfected with SIRT6 construct  and stimulated with TNFa

Gene expression data from HEK293 cells transfected with SIRT6 construct  and unstimulated

Cells transfected with sirtuin 6 and stimulated with TNFa, biological rep3

Cells transfected with sirtuin 6 and stimulated with TNFa, biological rep2

Gene expression data from purified clock positive bulge stem cells

Dorsal skin bulge epidermal stem cells;Venus GFP positive Bulge cells (alpha6bright/CD34+/Venushigh population)

Venus GFP positive Bulge cells (alpha6bright/CD34+/Venushigh population) isolated from the dorsal skin of P18-19 mice

Only sedentary male subjects were recruited. Patients with type 2 diabetes were either treated by diet alone or in combination with sulphonylurea or metformin, which were withdrawn one week prior to the study. The patients were all GAD65 antibody negative and without signs of diabetic retinopathy, nephropathy, neuropathy or macrovascular complications.

08-34_ACCX1
Gene expression data from human adenoid cystic carcinoma xenograft

adenoid cystic carcinoma grown as xenograft tumor;primary;nasal cavity;male

08-34_ACCX11
Gene expression data from human adenoid cystic carcinoma xenograft.

adenoid cystic carcinoma grown as xenograft tumor;primary;maxilla;female

female;1;42;Severe_8;33;94;Prednisolone 5mg od, Aminophylline 225mg bd,Seretide 500 2pbd,doxycycline, Tiotropium;CD8+ T-cells

epithelial cells (keratinocytes);hTERT-immortalized, non-transformed;STR-pGIPZ shNotch3;Ca 0.6mM, 72 h

A549 human lung cancer cells (1X10^5 per T-25 flask in 7 mL complete RPMI 1640 medium) were seeded eights days prior to treatment of non-cycling plateau phase cultures with drug.  At four hours prior to RNA isolation, actinomycin D (5 ug/mL final concentration) was added to the culture.  After incubation for four hours, the culture was washed twice with HBSS supplemented with 0.5% BSA and total RNA was isolated.

Actinomycin D treated A549 human lung cancer cell cultures replicate A

We used the Affymetrix GeneChip® Scanner 3000 according to the manufacturer's recomended protocols.

We used the RNA Stat-60 reagent (Tel-Test, Inc.) according to the manufacturer's recomended protocols.

We used the Affymetrix Hybridization Oven 640 and GeneChip® Fluidics Station 450 according to the manufacturer's recomended protocols.

We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recomended protocols.

epithelial cells (keratinocytes);hTERT-immortalized, non-transformed;STR-pGIPZ shNotch3;Ca 0.09mM, 72 h

epithelial cells (keratinocytes);hTERT-immortalized, non-transformed;STR-pGIPZ scramble;Ca 0.6mM, 72 h

Total RNA was extracted from lymphoblastoid cells of AU039305 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;AU039305 is a male with autism and full mutation of FMR1.

Total RNA was extracted from lymphoblastoid cells of AU039304 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;AU039304 is a male with autism and full mutation of FMR1.

Total RNA was extracted from lymphoblastoid cells of AU046703 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;AU046703 is a male with autism and full mutation of FMR1.

control;2;28;Human liver slices (diameter 4 mm, thickness 250 µm)

diclofenac;2;28;Human liver slices (diameter 4 mm, thickness 250 µm)

control;3;29;Human liver slices (diameter 4 mm, thickness 250 µm)

diclofenac;3;29;Human liver slices (diameter 4 mm, thickness 250 µm)

Minimum Essential Medium containing glutamine (MEM-GlutaMAXTM-I) (Gibco, Darmstadt, Germany) supplemented with 10% tetracycline-negative fetal bovine serum (PAA, Pasching, Austria) and 1% penicillin/streptomycin (Invitrogen, Darmstadt, Germany). All cells were maintained at 37 °C and 5% CO2 in a 95% air-humidified incubator.

RMA normalization by apt-probeset-summarize.exe from Affymetrix.

Affymetrix WT cDNA Synthesis and Amplification and Terminal labeling kits.

MEFs were isolated from E13.5 embryos and passaged 3 times prior to experiment plating and collection.

MEFs cells were passaged in DMEM supplemented with 10% FBS and pen/strep.

Following QC checks, microarray probe level data were normalized, background adjusted, and summarized with the RMA algorithm (Robust Multichip Analysis)

Total RNA was extracted from MEFs using RNeasy Kits (Qiagen) according to manufacturer's instructions.

Four replicates of each group were prepared, labeled, and hybridized to Affymetrix mouse 430 2.0 GeneChip

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA.  RNA was reverse transcribed with T7-oligo(dT) primer and biotin-labeled

Gene expression data fromBmpr1a-/- cells in N2B27
Bmpr1a-/- ESCs

left ventricle after 7 weeks of treadmill running
Keywords = heart, left ventricle, hypertrophy

Sample name: TM-98-10R

Sample name: TM-131-10R

Sample name: TM-1039-11R
Gene expression data from PTC without a BRAF mutation

Sample name: TM-1098-11R

Sample name: TM-197-12R

Sample name: TM-155-12R

Sample name: TM-187-11R

Sample name: TM-602-11R

Sample name: TM-681-11R

lung tissue;CD-1_Nrf2 -/-;13 weeks + 5 month + 1 day;fresh air, treatment over 5 month + 1 day recovery, 4x1h exposure per day

SUDHL-1 Cells derived from the a patient with Anaplastic Large Cell Lymphoma;ALK inhibitor CEP-14083

T09
JLP_T09_U133_2.CEL

T08
JLP_T08_U133_2.CEL

T10
JLP_T10_U133_2.CEL

Three control mice and three mutant mice were treated with tamoxifen (two consecutive intraperitoneal injections, 0.1 mg/g of body weight) to activate CreER recombinase.

Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions.

The quality of hybridization and overall chip performance were monitored by visual inspection of both internal quality control checks and the raw scanned data. Raw data were extracted using the software provided by the manufacturer(Illumina GenomeStudio v2009.2 (Gene Expression Module v1.5.4)).   Array data were filtered by detection p-value < 0.05 (similar to signal to noise) in at least 50% samples (we applied a filtering criterion for data analysis; higher signal value was required to obtain a detection p-value < 0.05).    Selected gene signal value was transformed by logarithm and normalized by quantile method. The comparative analysis between test sample and control sample was carried out using fold-change.   Go-ontology analysis for significant probe list was performed using PANTHER (http://www.pantherdb.org/panther/ontologies.jsp), using text files containing Gene ID list and accession number of illumina probe ID.   All data analysis and visualization of differentially expressed genes was conducted using R 2.4.1(www.r-project.org).

Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol. After processing with DNase digestion, clean-up procedures, RNA samples were quantified, aliquot and stored at -80°C until use. For quality control, RNA purity and integrity were evaluated by denaturing gel electrophoresis, OD 260/280 ratio, and analyzed on Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

750 ng of labeled cRNA samples were hybridized to each mouse-8 expression bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA). Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual.

Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions. Briefly, 550 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed, and labeled with biotin-NTP. After purification, the cRNA was quantified using the ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA).

Btk KO/CBA were created by back-crossing Btk KO/SW129 mice on CBA background strain for 9 generations

2.5 x 105/well KB cells in 6 well-plates were transfected with 60 pmol p53R2 siRNA or scramble siRNA by Lipofectamine RNAiMAX (Invitrogen) according to the manufacturer's instructions.

Arrays were scanned at 5um resolution with Affymetrix scanner 3000 7G.

All data processing was done using Bioconductor or APT tools; GCBG using background probes; Sketch Quantile to standardize arrays. Transformation: Log2 with offset of 1 to prevent negative numbers.

RNA-Easy kit (Qiagen) of total RNA was performed according to the manufacturer's instructions.

Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

Gene expression data from KB cancer cells transfected with p53R2 specific siRNA to knockdown its expression

Gene expression data from KB cancer cells transfected with p53R3 specific siRNA to knockdown its expression

Gene expression data from KB cancer cells transfected with control siRNA

Panc-1 human pancreatic carcinoma cell line, grown in mice;GSK3B shRNA

Gene expression data from skeletal muscle of two-month-old mouse deficient in dystrophin.
82mdx Skeletal Muscle

Gene expression data from skeletal muscle of two-month-old mouse deficient in Neu5Gc sialic acid.
10 Cmah KO Skeletal Muscle

340mdx Skeletal Muscle

336mdx Skeletal Muscle

61WT Skeletal Muscle

65WT Skeletal Muscle

7Cmah KO Skeletal Muscle

5Cmah KO Skeletal Muscle

7Cmah KO mdx Skeletal Muscle

6Cmah KO mdx Skeletal Muscle

ID = N5
Total RNA

ID = N17
Total RNA

ID = N8
Total RNA

ID = N6
Total RNA

ID = N10
Total RNA

ID = C540
Stage 1B
Total RNA

ID = N14
Total RNA

ID = N13
Total RNA

ID = N9
Total RNA

SKI-DLCL cells were treated with AraC alone at concentration 20nM for 24h. Total RNA was isolated.

SKI-DLCL cells were treated with Aplidin 1.5nM and AraC 5.0 nM combination for 24h. Total RNA will be extracted.

SKI-DLCL cells were treated with Aplidin 1.5nM and AraC 5 nM combination for 24h. Total RNA was isolated.

External controls (spikes): A 15 ul aliquot of a 20X mixture of in-vitro transcripts of bacterial genes BioB BioC BioD and cre  were added to the cocktail to give final concentrations of 1.5, 5, 25 and 100pM respectively. Control oligonucleotide (5 ul) was added to a final concentration of 50pM.

Hybridization: Sample Hyridization cocktails (300 ul) were removed from storage at �20C and thawed in a 45C temperature block. The samples were incubated at 45C for 5 min, incubated at 45C for 5 min and then centrifuged at 15,000g for 5 min.

Meanwhile,  the Affymetrix chip arrays were taken from their storage at 4C and allowed to come to room temperature. The chamber was filled with 1X hybridization buffer (final concentrations : 100mM MES, 1M [Na+], 20mM EDTA, 0.01% Tween 20). The chip was then preconditioned by incubation in the hybridization oven at 45C for 10 min. The chip was removed and the chamber drained.  Sample cocktails (200 ul) were then introduced into the chamber of the chips. The ports were sealed with tough-spots stickers and placed in the hybridization oven and incubated at 45C with rotation overnight.

Next day (16hr later), the incubation was terminated and the chips removed from the oven.  Samples were retrieved from the chips and stored again in a freezer at -20C. The chips were filled with buffer A and placed in a module of Fluidics 400 wash station.

The chips were subjected to the Affymetrix  �EuKws4 ver 2� programmed series of stringent post hybridization washes, staining and post-staining washes in accordance with Affy protocols.

Upon completion of the wash series (approximately 2 hrs), the chips were removed from the Fluidics station. The chips were inspected

Gene expression data under ER stress from lymphoblastoid cells of twin 1733:2 treated with DMSO.

lymphoblastoid cell line;1733;GM14502;Twin number 2;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1733:2 treated with 500nM thapsigargin.

lymphoblastoid cell line;1733;GM14502;Twin number 2;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1727:1 treated with DMSO.

lymphoblastoid cell line;1727;GM14480;Twin number 1;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1727:1 treated with 500nM thapsigargin.

lymphoblastoid cell line;1727;GM14480;Twin number 1;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1725:2 treated with DMSO.

lymphoblastoid cell line;1725;GM14477;Twin number 2;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1725:2 treated with 500nM thapsigargin.

lymphoblastoid cell line;1725;GM14477;Twin number 2;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1733:1 treated with DMSO.

lymphoblastoid cell line;1733;GM14501;Twin number 1;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1733:1 treated with 500nM thapsigargin.

lymphoblastoid cell line;1733;GM14501;Twin number 1;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1727:2 treated with DMSO.

lymphoblastoid cell line;1727;GM14481;Twin number 2;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1727:2 treated with 500nM thapsigargin.

lymphoblastoid cell line;1727;GM14481;Twin number 2;thapsigargin;500nM;4 hours

Lot batch = 0174-5k

Lot batch = 0175-5k

Lot batch = 0166-5k

Lot batch = 0167-5k

Lot batch = 0132-5k

Lot batch = 0165-5k

Lot batch = 0129-5k

Lot batch = 0130-5k

Lot batch = 0095-5k

Lot batch = 0096-5k

Notch3 knockout mouse cerebellar microvascular fragments, biological rep3

Gene expression data from mouse Notch3 knockout cerebellar microvascular fragments

C57BL/6;cerebellar microvascular fragments;Notch3 knockout;2 months

LSK and CMP cells were sorted from Tet2+/+ Mx+, Tet-/-Mx+ littermate mice 4 weeks post deletion via pIC injection. Additionally cells were obtained from serial replating of CD150+ sorted Tet2 deficient cells.

Qiagen RNEasy Plus Kit  was used to extract total cellular RNA according to the manufacturer's protocol, and the RNA was amplified and converted into cDNA using the Ovation Amplification v2 and Biotin cDNA Biotin systems

Tet2 deficient Lineage negative, c-Kit positive and Sca1 (LSK) negative FCgammaReceptor Low CD34 positive expressing bone marrow progenitors-repeat1
Gene expression data from Tet2 deficient Lineage negative, c-Kit positive and Sca1 (LSK)negative FCgammaReceptor Low CD34 positive expressing bone marrow progenitors-repeat1

B6/129;Tet2 KO;Lineage negative, c-Kit positive and Sca1 (LSK) negative FCgammaReceptor Low CD34 positive expressing bone marrow progenitors CMP

Tet2 deficient Lineage negative, c-Kit positive and Sca1 (LSK) negative FCgammaReceptor Low CD34 positive expressing bone marrow progenitors-repeat2
Gene expression data from Tet2 deficient Lineage negative, c-Kit positive and Sca1 (LSK)negative FCgammaReceptor Low CD34 positive expressing bone marrow progenitors-repeat2

WT Lineage negative, c-Kit positive and Sca1 (LSK) negative FCgammaReceptor High CD34 positive expressing bone marrow progenitors-repeat1
Gene expression data from WT Lineage negative, c-Kit positive and Sca1 (LSK)negative FCgammaReceptor High CD34 positive expressing bone marrow progenitors-repeat1

B6/129;WT;Lineage negative, c-Kit positive and Sca1 (LSK) negative FCgammaReceptor High CD34 positive expressing bone marrow progenitors GMP

WT Lineage negative, c-Kit positive and Sca1 (LSK) negative FCgammaReceptor High CD34 positive expressing bone marrow progenitors-repeat2
Gene expression data from WT Lineage negative, c-Kit positive and Sca1 (LSK)negative FCgammaReceptor High CD34 positive expressing bone marrow progenitors-repeat2

Tet2 deficient Lineage negative, c-Kit and Sca1 (LSK) positive expressing bone marrow progenitors-repeat1
Gene expression data from Tet2 deficient Lineage negative, c-Kit and Sca1 (LSK) positive expressing bone marrow progenitors-repeat1

B6/129;Tet2 KO;Lineage negative, c-Kit and Sca1 (LSK) positive expressing bone marrow progenitors

Tet2 deficient Lineage negative, c-Kit and Sca1 (LSK) positive expressing bone marrow progenitors-repeat2
Gene expression data from Tet2 deficient Lineage negative, c-Kit and Sca1 (LSK) positive expressing bone marrow progenitors-repeat2

WT Lineage negative, c-Kit positive and Sca1 (LSK) negative FCgammaReceptor Low CD34 positive expressing bone marrow progenitors-repeat1
Gene expression data from WT Lineage negative, c-Kit positive and Sca1 (LSK)negative FCgammaReceptor Low CD34 positive expressing bone marrow progenitors-repeat1

B6/129;WT;Lineage negative, c-Kit positive and Sca1 (LSK) negative FCgammaReceptor Low CD34 positive expressing bone marrow progenitors CMP

WT Lineage negative, c-Kit positive and Sca1 (LSK) negative FCgammaReceptor Low CD34 positive expressing bone marrow progenitors-repeat2
Gene expression data from WT Lineage negative, c-Kit positive and Sca1 (LSK)negative FCgammaReceptor Low CD34 positive expressing bone marrow progenitors-repeat2

Tet2 deficient  Lineage negative, c-Kit positive and Sca1 (LSK) negative FCgammaReceptor High CD34 positive expressing bone marrow progenitors-repeat1
Gene expression data from Tet2 deficient Lineage negative, c-Kit positive and Sca1 (LSK)negative FCgammaReceptor High CD34 positive expressing bone marrow progenitors-repeat1

B6/129;Tet2 KO;Lineage negative, c-Kit positive and Sca1 (LSK) negative FCgammaReceptor High CD34 positive expressing bone marrow progenitors GMP

Tet2 deficient  Lineage negative, c-Kit positive and Sca1 (LSK) negative FCgammaReceptor High CD34 positive expressing bone marrow progenitors-repeat2
Gene expression data from Tet2 deficient Lineage negative, c-Kit positive and Sca1 (LSK)negative FCgammaReceptor High CD34 positive expressing bone marrow progenitors-repeat2

Breast adenocarcinoma;MCF-7;trans-hydroxy-tamoxifen TOT;FOXM siRNA

wild-type littermate of B6.BKS Ighmbp2nmd-2J mice;6 weeks of age;male

Peripheral blood mononuclear cells;oligoarticular JIA;GTE6;180min;White;Female

Peripheral blood mononuclear cells;oligoarticular JIA;LT6;70min;White;Female

Peripheral blood mononuclear cells;oligoarticular JIA;GTE6;97min;White;Female

Peripheral blood mononuclear cells;oligoarticular JIA;LT6;165min;White;Female

The array images were analyzed with Microarray Suite 5.0 (Affymetrix) software. All chips were scaled (global scaling) to target intensity of 50 to minimize differences between chips caused by physical differences in chips, hybridization efficiencies and manual laboratory work. The data was subjected to robust normalization that reduces the errors, which are caused by binding capacity and linearity differences between probe sets.

Total RNA was extracted from the cardiac muscle with Trizol Reagent (Invitrogen, Carlsbad, CA) and further purified with RNeasy columns (Qiagen, Valencia, CA) according to the manufacturers' protocols. Concentration and purity of RNA was determined by measuring absorbances at wavelengths 260 and 280 nm. Integrity of the RNA was checked with agarose gel electrophoresis. RNA samples were pooled within each group for microarray analyses. Concentration, purity and integrity of pooled RNA samples were checked as described above.

Effects of diabetes, physical training, and their combination on the gene expression of cardiac muscle

Gene expression data from mouse CD3+ Wt T-cells with anti-CD3 and anti-CD28 stimulation

Replicate 2 after stimulation for 100 minutes with 10 ng/ml IL-6.

Replicate 2 unstimulated.

Human lung adenocarcinoma cell lines of CL1-0 JAG1-transfected and CL1-0 vector control were grown in DMEM with 10% fetal bovine serum at 37¢XC, 20% O2, 5% CO2 and 1000 £gg/ml G418.

The mRNA profiles from vector control transfectants and JAG1 overexpressed transfectants were analyzed using Affymetrix Human Genome U133 plus 2.0 GeneChip according to the Manufacturer¡¦s protocols (Santa Clara, CA, USA, http://www.affymetrix.com).

Affymetrix Human Genome U133A 2.0 array was scanned on Affymetrix’s GeneChip Scanner 3000 7G and reviewed for quality control.

HG-U133A 2.0 microarray was analyzed with Affymetrix Microarray Suite v5.0 and GeneSpring v5.0.3 (Silicon Genetics) software.

Total RNA was extracted using Invitrogen's TRIzol reagent and purified with RNeasy mini columns (Qiagen), following the manufactures protocols.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133A 2.0 expression array.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (GeneChip Expression Analysis Technical Manual, Affymetrix).

Gene expression data from the inferior olivary nucleus in a control subject.

Gene expression data from the Inferior olivary nucleus in a Parkinson's disease subject.

Gene expression data from the dorsal motor nucleus of the vagus in a control subject.

#15;Control case #5;T-2017;74;Male;Dorsal motor nucleus of the vagus

neuro 2A (N2A);neuroblastoma cell line;transiently transfected with non-targeting vector

Clinical information: Sample.ID=1389;Tumor.type=D;Size=1.7;Grade=2;Nodes=0/1;ER=Pos;PR=Pos;HER2=Neg;Age=80;DFS=94;Status=non-recur

Clinical information: Sample.ID=1405;Tumor.type=D;Size=1;Grade=3;Nodes=ND;ER=Pos (<10%);PR=Pos;HER2=Neg;Age=81;DFS=95;Status=non-recur

Clinical information: Sample.ID=1419;Tumor.type=D;Size=2.5;Grade=2;Nodes=1/8;ER=Pos;PR=Pos;HER2=Neg;Age=59;DFS=86;Status=non-recur

Clinical information: Sample.ID=1437;Tumor.type=D;Size=1.7;Grade=2;Nodes=2/22;ER=Pos;PR=Pos;HER2=Neg;Age=67;DFS=89;Status=non-recur

Clinical information: Sample.ID=1507;Tumor.type=D;Size=3.7;Grade=3;Nodes=0/40;ER=Pos;PR=Pos;HER2=Neg ;Age=70;DFS=70;Status=non-recur

Animals received humane care according to the criteria outlined in the “Guide for the Care and Use of Laboratory Animals” of the National Academy of Sciences. All animals were maintained in accordance with the institutional guidelines of the Massachusetts General Hospital Subcommittee on Research Animal Care. Strain A/J male mice (Jackson Laboratory, Bar Harbor, ME) were treated three times a week for 18 weeks with either 0.1cc of a 40 percent solution of CCl4 (Sigma) in olive oil or with vehicle control by oral gavage.  Mice were sacrificed at 19 weeks after a one-week washout to eliminate acute effects of CCl4.  The liver was sectioned and fixed in phosphate-buffered 10% formaldehyde for histological analysis.  The remaining portions of the liver were collected in RNase-free tubes and snap-frozen in liquid nitrogen.  Frozen tissues were stored at -80°C until use.

U-33 cells stably transfected with an empty vector control (U-33/c cells);2 hrs;Rosiglitazone present

U-33 cells stably transfected with an empty vector control (U-33/c cells);2 hrs;No Rosiglitazone present

U-33 cells stably transfected with a PPARg2 expression construct (U-33/g2 cells);2 hrs;Rosiglitazone present

U-33 cells stably transfected with a PPARg2 expression construct (U-33/g2 cells);2 hrs;No Rosiglitazone present

Approximately10-14 wild-type mice were dissected and the fundus was used to isolate parietal cells and purified by flow cytometry. Total RNA was extracted from the purified parietal cells by Trizol followed by an RNeasy kit (Qiagen).

HEK293 cells were transfected with pcDNAI/Neo (Invitrogen) plasmid containing HCaRG. Stable transfectants, overexpressing HCaRG, were synchronized and grown in the presence of 10% FBS for 48 h. Total RNAs were purified with the mini RNeasy kit (Qiagen).

C57BL/6N;Sta1 Wildtype (wt);Bone marrow derived macrophages (BMMs);24 h IFGg

C57BL/6N;Stat1 KO (ko);Bone marrow derived macrophages (BMMs);24 h IFGg

C57BL/6N;Stat1 delta beta (db);Bone marrow derived macrophages (BMMs);24 h IFGg

C57BL/6N;Stat1 delta alpha (da);Bone marrow derived macrophages (BMMs);24 h IFGg

C57BL/6N;Stat1 delta beta (db);Bone marrow derived macrophages (BMMs);6h IFNg

C57BL/6N;Stat1 delta alpha (da);Bone marrow derived macrophages (BMMs);6h IFNg

Gene expression data from MCF-7cells treated with vehicle and ER siRNA
MD38

MD37

Gene expression data from MCF-7cells treated with 500 nM 4-hydroxytamoxifen and scrambled siRNA
MD36

MCF-7 breast cancer cell line;control (scrambled siRNA);4-hydroxytamoxifen;500 nM

MCF-7cells treated with 500 nM 4-hydroxytamoxifen and scrambled siRNA

MD35

Gene expression data from MCF-7cells treated with 100 nM 4-hydroxytamoxifen and scrambled siRNA
MD34

MCF-7 breast cancer cell line;control (scrambled siRNA);4-hydroxytamoxifen;100 nM

MCF-7cells treated with 100 nM 4-hydroxytamoxifen and scrambled siRNA

MD33

MD32

MD31

MD39

Gene expression data from spleen of Npc1+/- mouse1 of age 25 days

Gene expression data from spleen of Npc1-/- mouse1 of age 20 days

251486838940_1_3

Gene expression after 6 h in phenobarbital-treated WT mouse liver
251486838932_1_4

251486838941_1_2

251486838940_1_2

251486838932_1_3

251486838941_1_1

Gene expression data from liver of Npc1+/- mouse1 of age 55 days

Gene expression data from liver of Npc1-/- mouse1 of age 54 days

Gene expression data from liver of Npc1-/- mouse1 of age 55 days

Gene expression data from liver of Npc1+/- mouse1 of age 67 days

Gene expression data from liver of Npc1-/- mouse1 of age 67 days

Gene expression data from liver of Npc1-/- mouse1 of age 71 days

Gene expression data from spleen of Npc1+/- mouse1 of age 20 days

Dox_Veh_1

Veh_PMA_1

Dox_PMA_1

Veh_Veh_2

Dox_Veh_2

Veh_PMA_2

Gene expression data from CUTLL1 cells treated with compound E for 3days and mockwash with medium containing compound E and cycloheximide for 4 hours

gene expression data from wildtype mouse liver

Gene expression data from CUTLL1 cells treated with compound E for 3days and mockwash with medium containing compound E and cycloheximide for 2hours

Lot batch = Joslin core 649

Macrophages were prepared from bone marrow by growth for 6 days in the presence of recombinant human M-CSF

GeneChips were scanned using the Affymetrix GeneChip Scanner 3000G.

Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

MyD88 deficient bone marrow-derived macrophages with and without Zymosan stimulation

Bone marrow-derived macrophages from mice deficient in signaling adaptor molecule MyD88

Bone marrow-derived macrophages, MyD88 -/-, Zymosan stimulated, 120 minutes

Cells were transduced with lentiviral supernatant containing pLL p63shRNA or empty vector (control), and harvested ~65 hours later.

Cells were grown in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% Fetal Bovine Serum.

Data were processed by Affymetrix GeneChip Operating Software (GCOS), followed by global median normalization.

Biotinylated cRNA was hybridized to the Affymetrix HG-U133 plus 2.0 GeneChip, washed, and stained according to manufacturer’s instructions.

Total RNA was converted to cDNA using T7-oligo(dT) and in vitro transcribed to obtain biotin-labeled cRNA for hybridization.

(CML) chronic myeloid leukaemia / CD34+ stem cells before Glivec therapy

Rats were sacrificed six hours after the injection with methylprednisolone

Rats were sacrificed five hours after the injection with methylprednisolone

Rats were sacrificed four hours after the injection with methylprednisolone

12 hour control, replicate 3

12 hour control, replicate 2

L428-PAX5;Mifepristone + 5-aza-2′-deoxycytidine + Trichostatin A (MAT);5 days

6 hour control, replicate 3

6 hour control, replicate 2

12 hour control, replicate 1

6 hour RA treated, replicate 3

6 hour RA treated, replicate 2

6 hour RA treated, replicate 1

lymphoblastoid cell line from F6.01, one out of seven of sensitive group, 50*10e6 cells;Pooled RNA from a number of lymphoblastoid cell lines (with and without bleo treatment) and head and neck cancer cell lines.

lymphoblastoid cell line from F6.04, one out of seven of sensitive group, 50*10e6 cells;Pooled RNA from a number of lymphoblastoid cell lines (with and without bleo treatment) and head and neck cancer cell lines.

lymphoblastoid cell line from T4.02, one out of seven of insensitive group, 50*10e6 cells;Pooled RNA from a number of lymphoblastoid cell lines (with and without bleo treatment) and head and neck cancer cell lines.

lymphoblastoid cell line from F1.02, one out of seven of sensitive group, 50*10e6 cells;Pooled RNA from a number of lymphoblastoid cell lines (with and without bleo treatment) and head and neck cancer cell lines.

lymphoblastoid cell line from F6.06, one out of seven of sensitive group, 50*10e6 cells;Pooled RNA from a number of lymphoblastoid cell lines (with and without bleo treatment) and head and neck cancer cell lines.

gastrointestinal stromal tumor;Female;MEDIUM;PDGFRA mutation detected

15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2).  Pyramidal neurons were selected based on staining and morphology.

The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software

Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.

Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions

Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..

RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).

endothelial, age:42, gender:male, diagnostic group: schizophrenia, PMI:19h

human endothelial cells isolated from postmortem dorsolateral prefrontal cortex

endothelial, age:47, gender:male, diagnostic group: control, PMI:11h

endothelial, age:55, gender:male, diagnostic group: control, PMI:31h

endothelial, age:34, gender:male, diagnostic group: control, PMI:22h

endothelial, age:19, gender:male, diagnostic group: schizophrenia, PMI:28h

endothelial, age:47, gender:female, diagnostic group: schizophrenia, PMI:35h

endothelial, age:54, gender:female, diagnostic group: schizophrenia, PMI:42h

endothelial, age:47, gender:female, diagnostic group: schizophrenia, PMI:30h

neuronal, age:47, gender:male, diagnostic group: control, PMI:11h

human neurons isolated from postmortem dorsolateral prefrontal cortex

neuronal, age:39, gender:female, diagnostic group: control, PMI:58h

A pool of two pure subsets of peripheral blood CD8+ T cells (CD19- CD3+ CD4- CD8+ CD16- CD56-), stringently sorted by flow cytometry, from two age and gender matched stage IV (American Joint Committee on Cancer) melanoma patients.;Pooled RNA from the total peripheral lymphocyte fraction from 20 healthy donors, used as a common reference.

5x105 Huh7 cells were seeded in 25cm2 culture flasks and infected in triplicate either with the genotype 2a HCV clone, JFH-1 at a multiplicity of infection (MOI) of 3 or mock infected with an equal volume of concentrated conditioned growth medium

Huh7 cells: Huh7 cells were grown in Dulbecco’s modified Eagles Medium (DMEM) supplemented with 10% foetal calf serum, 100U/ml penicillin and 100µg/ml streptomycin (Invitrogen) at 37°C, 5% CO2. HCV JFH-1 production: Full-length JFH-1 virus was produced using Huh7.5 cells transfected with RNA transcribed from the pJFH-1 plasmid.  Transfected cells were maintained for 21 days and growth medium containing infectious JFH-1 was serially passaged onto naive Huh7.5 cells every four days. Culture medium containing virus was harvested at each passage, clarified by centrifugation and 0.45µm filtration, and concentrated using Amicon Ultra-15 centrifugal filter units (Millipore).

The stained array chips were scanned using the Affymetrix genechip scanner 3000 which was operated using the Affymetrix GeneChip Operating System (GCOS).

Raw microarray expression data was analyzed with Array Studio software (Omicsoft, USA) using MicroArray data default settings and RMA signal extraction method.  Two samples (Mock_6hrs_1 and JFH-1_6hrs_1) did not pass our data quality control measures and were excluded from the analysis.  Data was analyzed on the log2 scale, using analysis of variance (ANOVA), followed by pre-specified contrast statements.  Fold changes were obtained from the estimated least squares mean differences.  Host genes demonstrating at least a 2 fold change in expression, a significant differential expression at a raw p-value level of 0.05, and an intensity level above 32 (5 on the log2 scale) for at least one of the treatment means were selected for further investigation.

3ml of TRIzol reagent (Invitrogen) was added to the cells in each T25 flask. RNA was extracted according to the manufacturer’s protocol.

Hybridisation of cRNA was performed using a hybridisation cocktail of 15ug cRNA, 50pM control oligonucleotide B2, Eukaryotic hybridisation controls (1.5pM bioB, 5pM bioC, 25pM bioD and 100pM cre), 0.1mg/ml Herring sperm DNA, 0.5mg/ml BSA, 1x hybridisation buffer and 10% DMSO. The hybridisation cocktail was heated to 99°C for 5 minutes followed by 45°C for 5 minutes. The array was filled with 1x hybridisation buffer and heated to 45°C for 10 minutes. Hybridisation buffer was removed from the array and the hybridisation cocktail was added and incubated for 16 hours at 45°C. Following hybridisation, arrays were washed using both non-stringent and stringent wash buffers. The array was then stained using 10ug/ml streptavidin phycoerythrin diluted in stain buffer with 2mg/ml BSA for 10 minutes, followed by incubation with goat anti-streptavidin biotinylated antibody diluted in stain buffer containing 2mg/ml BSA and 0.1mg/ml goat IgG stock for 10 minutes and a second round of staining with 10ug/ml streptavidin phycoerythrin diluted in stain buffer with 2mg/ml BSA for 10 minutes.The array was washed again with non-stringent wash buffer and was placed onto the scanner.

Total RNA was first reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip expression arrays. Quality of labeled RNA was assessed using the Agilent Bioanalyser.

Gene expression data from Huh7 cells Infected with JFH-1 for 24 hours

Gene expression data from Huh7 cells Infected with JFH-1 for 18 hours

Gene expression data from Huh7 cells Infected with JFH-1 for 12 hours

Gene expression data from Huh7 cells Infected with JFH-1 for 6 hours

Human male subjects with familial combined hyperlipidemia (FCH), peripheral blood monocytes

10-week old male C57BL6 mice were fasted for 16 h overnight and then given either saline or IL-6 (100 ng/mouse) injections intraperitoneally for 1 h. Mice were euthanized using CO2, and the livers were collected and snap-frozen in liquid nitrogen and stored at -80 C until further use.

Tissues were homogenized in STAT60 reagent (TelTest Inc) using a Tissue Lyser (Qiagen) at 30 Hz for 2 min. RNA was extracted according to the manufacturer’s protocol.

Well-differentiated human lung epithelial cells, infected with KY/136 (pdmH1N1) for 36h

seasaonal H1N1 Influenza virus;cultured primary human lung epithelial cells

Well-differentiated human lung epithelial cells, infected with BN/59 (seasonal H1N1) for 36h

total RNA extracted from cells obtained using biopsy of the colon in a healthy control

TTF=135min;Race=Black or African American;Sex=Female;Group=B;Prototype_N

TTF=122min;Race=Black or African American;Sex=Female;Group=A;Prototype_N

Peripheral blood mononuclear cells;RF- polyarticular JIA;GTE6;165min;Caucasian/White;Female;A;Y

C57BL/6J female number 1, DNFB-treated allergic ear (#4_Wt-Tr-3)

C57BL/6J female number 1, 2 months old, whole ear tissue, DNFB-treated allergic ear

Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 96 hours, replica 2

Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 72 hours, replica 2

spinal cord, ventral spinal cord: EP144/L - G93R(Roth)/e14-mutant hSOD1_le2

AZ521;inducible dnSox2;gastric cancer cell line;doxycycline induced;24h

Typically Developing Control, Semitendinosus, Patient Replicate 5

Typically Developing Control, Semitendinosus, Patient Replicate 3

Typically Developing Control, Semitendinosus, Patient Replicate 4

Typically Developing Control, Semitendinosus, Patient Replicate 1

Typically Developing Control, Semitendinosus, Patient Replicate 2

RNA was isolated using Trizol 7 days after infection.  RNA was further prepared by passage over an RNeasy column.  cDNA synthesis, biotinylation of cRNA and hybridization to mouse Genechip 430A v2 containing 39,000 probes was performed according to the manufacturer’s instructions (Affymetrix, Santa Clara).

Total RNA pooled from 4 mice: BTBR-ob/ob 215, BTBR-ob/ob 301, BTBR-ob/ob 347, BTBR-ob/ob 348

Five days after initial plating, cultures were inoculated with SeV (Sendai virus, MOI 20) for 4 d.

Cells were grown in 8-well Labtek chambers (2 x 105 cells per well) in RPMI medium with 10% FBS, 2 mM L-glutamine, and 1 mM non-essential amino acids. This method provided cultures in which 98.9 ± 0.7% of cells were CD68-positive and 100% of adherent cells were viable.

Macrophage RNA was isolated using RNAqueous (Ambion, Austin, TX) and converted to Poly(A)+ RNA. RNA was assessed by formaldehyde agarose gel electrophoresis. Poly(A)+ RNA was amplified using RiboAmp (Arcturus, Mountain View, CA).

RNA was labelled with biotin by using the BioArray High Yield RNA Transcript Labeling Kit (Enzo, Farmindale, NY).

Microarray normalization and statistical analysis were carried out using packages from the Bioconductor project (Gentleman RC et al, 2004), executed in the R programming environment. Data was normalized using the empirical Bayes version of the GCRMA algorithm as implemented in the GCRMA package (Wu Z et al, 2004). Differential expression was assessed by using linear models and empirical Bayes moderated F statistics as implemented in the LIMMA package (Smyth GK, 2004). Differences in gene expression were considered significant if the P values were <0.05 after adjustment for multiple testing (Benjamini & Hochberg, 1995), and thus, false discovery rate was controlled to be <5%. Visualization and plotting were performed using Spotfire DecisionSite for Functional Genomics (Spotfire, Somerville, MA).

Macrophage cultures were prepared from C57BL/6J, male, mouse peripheral blood by Optiprep (Accurate Chemical and Scientific, Westbury, NY) gradient centrifugation.

Total RNA pooled from 4 mice: BTBR-ob/ob 229, BTBR-ob/ob 309, BTBR-ob/ob 318, BTBR-ob/ob 346

bone marrow;CD34+ hematopoietic stem cells (HSC);myelodysplastic syndromes (MDS);refractory anemia with excess blasts 2 (RAEB2);del5q plus monosomy7/del7q plus other

Gene expression data of gastrocnemius muscle mRNA from young (10 week old) knock-out mice

Gastrocnemius muscle mRNA from young (10 week old) knock-out mice

Gene expression data of gastrocnemius muscle mRNA from old (24 month old) wild-type mice

Gastrocnemius muscle mRNA from old (24 month old) wild-type mice

Gene expression data of gastrocnemius muscle mRNA from old (24 month old) knock-out mice

Gastrocnemius muscle mRNA from old (24 month old) knock-out mice

Bipolar disorder;64;Male;19;45;6.10;16;Right;130000;No;Yes;No;No;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): 0

Bipolar disorder;58;Female;27;31;6.50;35;Left;12000;Yes;No;No;Yes;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): 1

Bipolar disorder;42;Female;20;22;6.65;49;Left;15000;No;No;No;No;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): 4

Bipolar disorder;63;Female;43;20;6.97;32;Left;0;No;No;No;No;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): 0

Bipolar disorder;44;Female;26;18;6.37;37;Right;30000;No;Yes;No;No;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): 0

Bipolar disorder;43;Female;29;14;5.92;57;Left;10000;No;No;No;No;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): 4

Bipolar disorder;19;Male;17;2;5.97;12;Right;2000;No;No;No;No;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): 2

Bipolar disorder;59;Male;25;34;6.65;84;Right;500;No;Yes;Yes;No;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): 1

Bipolar disorder;41;Female;14;27;6.44;28;Left;3000;No;Yes;No;No;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): 4

Bipolar disorder;49;Female;20;29;6.39;38;Right;0;No;No;No;No;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): 5

Gene expression data from Deltoid, control, cohort 22, subject 22U

skeletal muscle;insulin sensitive;untreated;128;117;1790;78.3;20;60.4;1566

skeletal muscle;insulin sensitive;untreated;69.9;10.4;61.2;726.96

Cells immortalized through SV40 driven largeT antigen expression

immortalized cells derived from brown fat tissue of mouse of mixed background.;4

Expression comparison of primary normal human mammary epithelial cells between 50 years old and 41 years old donors

Expression comparison between primary normal human mammary epithelial cell from 50 years old donor and  human breast cancer cell line T47D

Expression comparison of primary normal human mammary epithelial cells between 50 years old and 21 years old donors

Expression comparison between primary normal human mammary epithelial cell from 50 years old donor and  human breast cancer cell line ZR-75-1

Expression comparison between primary normal human mammary epithelial cell from 50 years old donor and  human breast cancer cell line MCF7

Quadriceps muscle;P.q.1;Pompe;rhGAA;00 Weeks;M;5m;No gains;Increased;Poor Clinical Outcome

skeletal muscle;insulin sensitive;untreated;0.93;330;22;1930;84.5;35.2;54;2974.4

Mc3T3-E1_T0-3
MOE4302_042809H_RH5_Ctl3

For the initial normalization and analysis steps, data were retrieved on Affymetrix GCOS software. The frequency of positive genes (genes with a flag present) was between 40 and 50% on each slide. After scaling of all probe sets to a value of 100, the range of the reported amplification scales was between 0,8 and 6,7. The signals yielded by the poly-A RNA, hybridization and housekeeping controls (GADPDH 3’/5’ ratio < 2.3 in all the slides) were indicated of the good quality of the amplification and hybridization procedures.

baseline;F;68;synovial knee biopsy;rheumatoid arthritis;EULAR Good-responder;synovium

Human synovial biopsies from the knee of a patients with RA prior to (T0) or after (T12) RTX therapy (EULAR Good-responder).

CD133+ and CD133- glioma cells were separated from tumor xenografts (4105 and 4302), cultured in serum-free media for 48 hours in the presence of absence of laminin, which led to adherent growth of glioma stem cells while preserving stemness.

The data were analyzed with RMA (Robust Multichip Average) using Bioconductor

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133A plus 2.0 arrays. Affymetrix GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared using Ambion MessageAmp Premier labeling kit.

Mc3T3-E1_T1-1
MOE4302_042809H_RH2_AA1
Gene expression data from Mc3T3-E1 cells stimulated with AA for 5 days

Mc3T3-E1;osteoblastic cells;50µg of Ascorbic Acid (AA) for 5 days

baseline;F;33;synovial knee biopsy;rheumatoid arthritis;EULAR Moderate-responder;synovium

Human synovial biopsies from the knee of a patient with severe rheumatoid arthritis

RE1_H14_1659_U133Plus2.0.CEL

2B1 Otic vesicle cell line transiently transfected with Dlx5 and GFP expression vector and differentiated for 4 days at 37oC without gamma-interferon, replicate2

2B1 Otic vesicle cell line transiently transfected with Dlx5 and GFP expression vector and differentiated for 4 days at 37oC without gamma-interferon, replicate1

2B1 Otic vesicle cell line transiently transfected with an empty vector only containing GFP and differentiated for 4 days at 37oC without gamma-interferon, replicate2

RE1_H4_1328_U133Plus2.0.CEL

MS-3

RE1_H16_1717_U133Plus2.0.CEL

Gene expression data from PPTA knockout mice 8 h after cecal ligation and puncture surgery.
M-2

lung;PPTA knockout;cecal ligation and puncture surgery;8-10 weeks

mouse PPTA knockout lung 8 h after cecal ligation and puncture surgery

M-1

M-3

Day: 6; Drug: Methamphetamine; Phase: Drug treatment; Replicate: 1

Station	1
Module	4
Hybridize Date	Dec 22 2005 11:27AM

Station	1
Module	2

Station	1
Module	4
Hybridize Date	Dec 14 2005 11:09AM

Station	1
Module	1
Hybridize Date	Dec 14 2005 11:08AM

Station	1
Module	2

Cells were transduced with lentivirus containing either a shRNA-cassette targeting human YAP or the empty pLKO.1 backbone. Cells stably expressing the constructs were selected using puromycin selection (3,0 µg/ml) and were constantly grown in the presence of selection antibiotic.

The human ccRCC cell line MZ1774 was grown in RPMI 1640 medium supplemented with 10% FCS, 100 I.U./ml penicillin, 100 µg/ml streptomycin as well as 5 µg/ml plasmocin (InvivoGen).

Total RNA was extracted from MZ1774 cells using the RNAeasy Mini Kit (Qiagen) with on column Dnase digest.

24 hrs tetracycline (1000 ng/ml) to induce expression of the transcription factors.

HEK293 cell line carrying the tetracycline inducible transgenes were generated and grown essentially as described in the Flp-In T-REx Core Kit Manual from Invitrogen.

Arrays were scanned with an Affymetrix GeneArray 2500 scanner after the second staining step. GeneChip CEL files are deposited in the GEO raw data depository.

Data extraction and normalization: Signals and detection calls were determined by single array analysis using the statistical algorithm implemented in the Affymetrix Microarray Suite 5.0 software. Global scaling to a target intensity of 1000 units was chosen as a normalization procedure.

Total RNA was extracted using  TRIzol (Invitrogen). RNA quality was checked by agarose gel electrophoresis and found to show no signs of degradation. All cRNAs hybridized displayed 3’/5’-ratos for beta Actin below 2.0.

Hybridization, washing and staining of HG-U133A arrays (EukGE-WS2v4 protocol) was performed exactly as described in the Affymetrix Expression Technical Manual (rev. 3). Biotinylated hybridization controls (BioB, BioC, BioDN, CreX) from Affymetrix were included in the hybridization cocktail as recommended by Affymetrix.

Biotinylated cRNA targets were prepared starting with 13.5 microgram of total RNA exactly as described in the Affymetrix Expression Technical Manual (rev. 3). Polyadenylated B. subtilis DapX, LysX, PheX, ThrX, and TrpnX transcripts were added in staggered concentrations as polyA+ spike-in controls prior to cDNA synthesis.

Hepatocyte nuclear factor 1beta (HNF1beta, TCF2) is a tissue-specific transcription factor whose mutation in humans leads to renal cysts, genital malformations, pancreas atrophy and maturity onset diabetes of the young (MODY5). Furthermore, HNF1beta overexpression has been observed in clear cell cancer of the ovary. To identify potential HNF1beta target genes whose activity may be deregulated in human patients we established a human embryonic kidney cell line (HEK293) expressing HNF1beta conditionally. Using Flp recombinase we introduced wildtype or mutated HNF1beta at a defined chromosomal position allowing a most reproducible induction of the HNF1beta derivatives upon tetracycline addition. By oligonucleotide microarrays we identified 25 HNF1beta regulated genes. By an identical approach we identified that the closely related transcription factor HNF1alpha (TCF1) affects only nine genes in HEK293 cells and thus is a less efficient factor in these kidney cells. The HNF1beta target genes dipeptidyl peptidase 4 (DPP4), angiotensin converting enzyme 2 (ACE2) and osteopontin (SPP1) are most likely direct target genes, as they contain functional HNF1 binding sites in their promoter region. Since nine of the potential HNF1beta target genes are deregulated in clear cell carcinoma of the ovary, we propose that HNF1beta overexpression in the ovarian cancer participates in the altered expression pattern.

Flp-InTMT-RExTM-293 (Invitrogen) cell line derived from the human embryonic kidney cell line HEK293 carrying tetracycline inducible transgene

stably expressing shRNA directed against YAP;human ccRCC cell line

Renal failure. Othe ocular diseases: cataracts. IOP: 17-28. Drug therapy: Xalatan

renal failure. Other ocular diseases: cataracts. IOP: 15-25. Drug therapy: Xalatan, cosopt.

total RNA of human coronary artery smooth muscle (hcaSMC) cultivated in SMGM-2-MV bulletkit medium were isolated after incubation with control medium for 72 hours using Trizol and purified with RNeasy spin columns.

human coronary artery smooth muscle Cells, untreated control, replicate 3

coronary smooth muscle cells (hcaSMC), treated with control medium for 72 hours

total RNA of human coronary artery smooth muscle (hcaSMC) cultivated in SMGM-2-MV bulletkit medium were isolated after incubation with metoprolol for 72 hours using Trizol and purified with RNeasy spin columns.

human coronary artery smooth muscle Cells, treated with metoprolol, replicate 1

coronary smooth muscle cells (hcaSMC), treated with metoprolol for 72 hours

human coronary artery smooth muscle Cells, untreated control, replicate 1

human coronary artery smooth muscle Cells, untreated control, replicate 2

plaque type psoriasis;epidermis;59;male;> 20 y;phototherapy;mid-UV

plaque type psoriasis;epidermis;67;male;< 1 y;phototherapy;mid-UV

plaque type psoriasis;epidermis;40;male;> 20 y;phototherapy;mid-UV

plaque type psoriasis;epidermis;73;female;Unknown;phototherapy;mid-UV

plaque type psoriasis;epidermis;47;female;> 10 y;phototherapy;mid-UV

plaque type psoriasis;epidermis;43;male;> 10 y;phototherapy;mid-UV

plaque type psoriasis;epidermis;17;male;> 10 y;phototherapy;mid-UV

plaque type psoriasis;epidermis;46;female;> 10 y;phototherapy;mid-UV

plaque type psoriasis;epidermis;74;female;2 y;phototherapy;mid-UV

Transgenic ATF6-MER mouse;C57 BL/6;male;~30wk;heart LV;tamoxifen

A YOKE_B061

A HID U_B004

A HID U_B007

A HID B_B010

A HID U_B015

A YOKE_B025

A SIT_B035

A SIT_B036

Y HID_B037

Y HID_B040

KO - knock-out Untreated - 0 hrs - repeat 1 - Cy3 - mAdbID:61726

KO - knock-out Untreated - 0 hrs - repeat 2 - Cy5 - mAdbID:61725

KO - knock-out Untreated - 0 hrs - repeat 1 - Cy5 - mAdbID:61724

C57BL;male;9-10 weeks;liver;adult;Primary hepatocytes;C57BL;male;9-10 weeks;liver;adult;Primary hepatocytes;Genotype/Genetic variation Alb-Cre +/-;Transgenic-heterozygous for Cre recombinase

Treatment time: 24 hour

KO - knock-out Untreated - 0 hrs - repeat 2 - Cy3 - mAdbID:61727

Cells were treated with 10nM 4-hydroxytamoxifen or ethanol vehicle

Cells were grown at 37 degrees and 5% carbon dioxide in RPMI + 20% FBS with glutamine, non-essential amino acids, sodium pyruvate, penicillin/streptomycin additives plus IL-3, IL-6 at 10ng/mL and SCF at 20ng/mL

Sample name: CSB_HFD_3_(4)

Sample name: CSB_HFD_5_(6)

male;grape extract (B);day 0 (basal);Isolated peripheral blood mononuclear cells (PBMCs)

Isolated PBMCs from diabetic male patient_Grape extract group_basal expression level

Sample name: CSB_CR_6

Sample name: CSB_HFD_6_(3)

Moderate Asthma;Fresh Bronchial Epithelial Cells;female;28.88767

Moderate Asthma;Fresh Bronchial Epithelial Cells;female;40.17808

Moderate Asthma;Fresh Bronchial Epithelial Cells;female;54.90137

Moderate Asthma;Fresh Bronchial Epithelial Cells;female;36.00274

male;CABG patient, atrial tissue;sevoflurane anesthesia, after CABG surgery

Stably-infected control or Sox2shRNA cells cells were grown in triplicate plates to 80% confluence.

Mouse osteosarcoma cells 482 expressing either scrambled or Sox2shRNA900 (A)  were selected in DMEM and 10%FBS + 200ug/ml hygromycin.  These cells are described in BasuRoy et al,S Oncogene 2010: http://www.ncbi.nlm.nih.gov/pubmed/21927024

Gene Array Scanner (Affymetrix) at NYU School of Medicine Genome Technology Center according to manufacturer's protocol.

CEL files were generated using GCOS 1.4 software (Affymetrix) and normalized using GeneSpring GX11 software (Agilent, Santa Clara, CA).  Probe level  normalization was by RMA (Robust Mutichip Average) algorithm and principal component analysis was used to examine variances in the data.
Gene expression changes >1.66 fold were determined to be statistically significant by t test (p<=0.05) of relative intensity signal values of triplicate samples using GeneSpring software.

Total cellular RNA from OS 482 scrambled and OS-482 Sox2shRNA cells  was extracted by RNEASY. RNA quality was assessed using an Agilent 2100 Bioanalyzer and Nanodrop ND-1000.  cRNA was prepared from 100 ng RNA using the Affymetrix 3’ IVT Express labeling kit and array processing protocol (Affymetrix).   cRNAs were hybridized to mouse genome  430A 2.0 arrays (Affymetrix) which contain 22690 gene probes.  Arrays were processed and scanned according to procedures recommended by the manufacturer (Affymetrix)

2.5 ug cRNA samples were hybridized to mouse A430-2 Affymetrix chips which contain 22,290 entities.

Fragmented, biotinylated cRNA was prepared from 100 ng RNA using Affymetrix 3' IVT Express labelling kit and array prcessing protocol (Affymetrix).

GeneChips were scanned using the The Affymetrix GeneChip Scanner 3000.

Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Global scaling was applied to allow comparison of gene Signals across multiple microarrays: after exclusion of the highest and lowest 2%, the average total chip Signal was calculated and used to determine what scaling factor was required to adjust the chip average to an arbitrary target of 150. All Signal values from one microarray were then multiplied by the appropriate scaling factor.

Trizol extraction of total RNA was performed according to the manufacturer's protocol.

Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

Gene expression data during developmental stage of palatal shelves at E14.5

C57BL/6 X SV129, Age: Embryonic Day 14.5, Tissue: Palatal Shelves

Colonic biopsy was collected during endoscopy from unaffected area of a patient with indeterminate colitis (IC). The standard Affymetrix protocols were followed to prepare target from 5ug of total RNA. The expression profiles generated from normal individuals were compared to that from patients with different types of disease.

disease unaffected colon of an adult with indeterminate colitis (IC).

colonoscopic biopsy from adult with unaffected colon from adult with IC

Colonic biopsy was collected during endoscopy from affected area of a patient with indeterminate colitis (IC). The standard Affymetrix protocols were followed to prepare target from 5ug of total RNA. The expression profiles generated from normal individuals were compared to that from patients with different types of disease.

disease affected colon of an adult with indeterminate colitis (IC).

colonoscopic biopsy from adult with affected colon from adult with IC

Colonic biopsy was collected during endoscopy from unaffected area of a patient with ulcerative colitis (UC). The standard Affymetrix protocols were followed to prepare target from 5ug of total RNA. The expression profiles generated from normal individuals were compared to that from patients with different types of disease.

disease unaffected colon of a adult with ulcerative colitis (UC).

colonoscopic biopsy from adult with unaffected colon from adult with UC

Colonic biopsy was collected during endoscopy from affected area of a patient with bacterial infectious colitis (INF). The standard Affymetrix protocols were followed to prepare target from 5ug of total RNA. The expression profiles generated from normal individuals were compared to that from patients with different types of disease.

disease affected colon of an adult with bacterial infectious colitis (INF).

colonoscopic biopsy from adult with affected colon from adult with INF

M454 + QV RNA

M474 + QV RNA

FVB;transformed by ha-ras gene;Primary prostate epithelial cell culture, oncogene-transduced

FVB;transformed by neuT gene;Primary prostate epithelial cell culture, oncogene-transduced

Study of rat femur fracture healing in adult rats (26 weeks old at fracture) at 4 weeks after fracture.  RNA from two rats were pooled for each array

Study of rat femur fracture healing in adult rats (26 weeks old at fracture) at 6 weeks after fracture.  RNA from two rats were pooled for each array.

Study of rat femur fracture healing in adult rats (26 weeks old at fracture) at 1 week after fracture.  RNA from two rats were pooled for each array

Study of rat femur fracture healing in adult rats (26 weeks old at fracture) at 2 weeks after fracture.  RNA from two rats were pooled for each array.

Study of rat femur fracture healing in older rats (52 weeks old at fracture) at the time of fracture.  RNA from two rats were pooled for each array.

Study of rat femur fracture healing in older rats (52 weeks old at fracture) at 3 days after fracture.  RNA from two rats were pooled for each array.

Study of rat femur fracture healing in older rats (52 weeks of age at fracture) at 4 weeks after fracture.  RNA from two rats were pooled for each array.

Study of rat femur fracture healing in older rats (52 weeks of age at fracture) at 6 weeks after fracture.  RNA from two rats were pooled for each array.

Macrophages were extacted from the peritoneal cavity of mutated mice (IL-4--) infected with the nematode Brugya Malayi. AAM were extracted and treated for RNA extraction.

RNA was extracted from a pool of two spleens taken from three month old C57BL/10 derived B10.NOD H2g7 Idd3 congenic mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.

RNA was extracted from a pool of three spleens taken from three month old C57BL/10 derived B10.NOD H2g7 mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.

reduction mammoplasty histologically normal breast epithlieum patient 347

reduction mammoplasty histologically normal breast epithlieum patient 352

RNA was extracted from a pool of three spleens taken from three month old nonobese diabetic (NOD) derived NOD.B10 Idd5 R444 congenic mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.

RNA was extracted from a pool of three spleens taken from three month old nonobese diabetic (NOD) derived NOD.B6 Idd3 R450 congenic mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.

RNA was extracted from a pool of three spleens taken from three month old nonobese diabetic (NOD) derived NOD.B10 Idd9 R28 congenic mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.

RNA was extracted from a pool of three spleens taken from three month old nonobese diabetic (NOD) derived NOD.B6 Idd3 R450 B10 Idd5 R8 congenic mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.

reduction mammoplasty histologically normal breast epithlieum patient 310

reduction mammoplasty histologically normal breast epithlieum patient 314

reduction mammoplasty histologically normal breast epithlieum patient 278

reduction mammoplasty histologically normal breast epithlieum patient 309

reduction mammoplasty histologically normal breast epithlieum patient 350

RNA was extracted from a pool of three thymi taken from four week old nonobese diabetic (NOD) derived NOD.B10 Idd5 R444 congenic mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.

reduction mammoplasty histologically normal breast epithlieum patient 334

reduction mammoplasty histologically normal breast epithlieum patient 340

Comparisons: Hyperoxia effects on wild type/1 day treatment, Genotype effects on daily hyperoxia/1 day treatment

Comparisons: Hyperoxia effects on wild type/2 day treatment, Genotype effects on daily hyperoxia/2 day treatment

A673 treated with Puromycin for 3 days with concentration of 0.09 uM (EC50), biological rep2

Gene expression data from A673 cell line that has been treated with Puromycin for 3 days with concentration of 0.09 uM (EC50).

A673 cell line that has been treated with Puromycin for 3 days with concentration of 0.09 uM (EC50).

A673 treated with Puromycin for 3 days with concentration of 0.09 uM (EC50), biological rep3

A673 treated with Puromycin for 24 hours with concentration of 0.09 uM (EC50), biological rep3

Gene expression data from A673 cell line that has been treated with Puromycin for 24 hours with concentration of 0.09 uM (EC50).

A673 cell line that has been treated with Puromycin for 24 hours with concentration of 0.09 uM (EC50).

A673 treated with Puromycin for 3 days with concentration of 0.09 uM (EC50), biological rep1

A673 treated with Puromycin for 24 hours with concentration of 0.09 uM (EC50), biological rep1

A673 treated with Puromycin for 24 hours with concentration of 0.09 uM (EC50), biological rep2

A673 treated with Doxorubicin for 5 days with concentration of 119.76 nM (2 x EC50), biological rep1

Gene expression data from A673 cell line that has been treated with Doxorubicin for 5 days with concentration of 119.76 nM (2 x EC50).

A673 cell line that has been treated with Doxorubicin for 5 days with concentration of 119.76 nM (2 x EC50).

A673 treated with Doxorubicin for 5 days with concentration of 119.76 nM (2 x EC50), biological rep3

C2C12 myoblasts differentiated with 2% horse serum for 5 days.  Treated for 16 hrs with 1% BSA.  RNA collected using Rneasy (Qiagen) protocol.

A673 treated with Puromycin for 5 days with concentration of 0.09 uM (EC50), biological rep1

Gene expression data from A673 cell line that has been treated with Puromycin for 5 days with concentration of 0.09 uM (EC50).

A673 cell line that has been treated with Puromycin for 5 days with concentration of 0.09 uM (EC50).

A673 treated with Puromycin for 5 days with concentration of 0.09 uM (EC50), biological rep2

Treatment: 0.70 mM HOCl in medium

Whole lung total RNA was purified by RNeasy Mini Kit according to the manufacturers protocol (Cat. 74104, Qiagen, Valencia, CA).

Osteoblastic lineage cell;C57BL/6;Control;5-6 weeks post doxycylcin withdrawal

Control osteoblastic lineage cells 5-6 weeks post doxycylin withdrawal

MCI-019 is from a premenopausal high BMD women.

MCI-005 is the sample from a premenopausal high BMD subjects.

MCI-010 was from a postmenopausal high BMD women.

MCI-007 is from a postmenopausal high BMD women.

MCI-014 was from a postmenopausal high BMD women.

MCI-013 was from a postmenopausal high BMD woman.

MCI-020 was from a postmenopausal high BMD woman.

Sample was pooled on basis of total-RNA extracted from CD3+ T cells derived from peripheral blood of both SAA patients in remission. Sample was compared to the same two patients prior therapy (PB_preTherapy_IIa).

Pool of two samples (n=2);;one female/one male;;70/64 years old;;CD3+ T cells, peripheral blood;;(severe) aplastic anemia (SAA) post therapy / in hematological remission

CD3+ T cells, peripheral blood, SAA patients post therapy / in hematological remission

Sample was pooled on basis of total-RNA extracted from CD3+ T cells derived from peripheral blood of both SAA patients.

Pool of two samples (n=2);;one female/one male;;70/64 years old;;CD3+ T cells, peripheral blood;;(severe) aplastic anemia (SAA)

Sample was pooled on basis of total-RNA extracted from CD3+ T cells derived from bone marrow of both SAA patients in remission. Sample was compared to the same two patients prior therapy (BM_preTherapy_IIb).

Pool of two samples (n=2);;one female/one male;;70/64 years old;;CD3+ T cells, bone marrow;;(severe) aplastic anemia (SAA) post therapy / in hematological remission

CD3+ T cells, bone marrow, SAA patients post therapy / in hematological remission

Sample was pooled on basis of total-RNA extracted from CD3+ T cells derived from bone marrow of both SAA patients..

Pool of two samples (n=2);;one female/one male;;70/64 years old;;CD3+ T cells, bone marrow;;(severe) aplastic anemia (SAA)

Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).

Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method.  To obtain detection calls consistent with those produced by Affymetrix' 5.0 software, we used the mas5calls function from the Bioconductor affy package.

RNA was extracted from 5 ml AF supernatant with use of the QIAamp Circulating Nucleic Acid Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol under the section “Purification of circulating RNA from 5 ml serum or plasma” and as described in Dietz et al., 2011 [12].  Samples were stored at -80ºC until further analysis.

Samples were labeled using the Encore Biotin Module (NuGEN, San Carlos, CA)

uterus - Proliferative endometrium from patient with  endometriosis

Cells were transfected with 50 nM Claudin 1 siRNAs using the oligofectamine reagent (Invitrogen). The medium containing siRNA was replaced with a fresh medium with or without TNFa 24 h after transfection. The siSTABLE V2 non-targeting siRNA#1 from Dharmacon (Lafayette, CO) was used as a negative control.

Human lung adenocarcinoma A549 cells were grown in DMEM medium supplied with 10% fetal bovine serum, 1% penicillin-streptomycin, and 1% glutamine. Cells were cultured in a standard humidified incubator at 37°C with 5% CO2.

Affymetrix CEL files were imported into Partek software (Partek Inc., St. Louis, MO) using the default Partek parameters for RMA pre-processing of the probe-level data.

Total RNA was extracted using RNeasy kit (Qiagen, Valencia, CA), and cDNA was synthesized with High-Capacity cDNA Reverse Transcription kits (Applied Biosystems, Foster City, CA) on a PTC-100 Programmable Thermal controller (MJ Research Inc., Watertown, MA).

Human lung adenocarcinoma A549 cells treated without TNFα, in presence of control siRNA

Human lung adenocarcinoma A549 cells treated with TNFα, in presence of control siRNA

BT474-J4;breast cancer;acquired lapatinib-resistant;HER2-positive;lapatinib and foretinib

BT474-J4;breast cancer;acquired lapatinib-resistant;HER2-positive;lapatinib

pancreatic ductal adenocarcinoma tumor;Pdx1-Cre; Ink4a/Arffl/fl; LSL-KrasG12D;Male;7 weeks-old

pancreatic ductal adenocarcinoma tumor;Pdx1-Cre; Ink4a/Arffl/fl; LSL-KrasG12D;Male;10 weeks-old

pancreatic ductal adenocarcinoma tumor;Pdx1-Cre; Ink4a/Arffl/fl; LSL-KrasG12D;Male;8.5 weeks-old

Blood; Fetal Day 14 Liver Hematopoietic

Female; Uterus - pregnant day4.5

This is Nrl-ko-Gfp 4 weeks sample.

For binding assays mature osteoclasts were incubated for 2 hours with 10-11 M 125I-salmon calcitonin (CT) in the absence or presence of 10-8 M salmon CT.

Osteoclast precursor cells were isolated from the bone marrow of 12 weeks old mice and differentiated for 4 days in α-MEM containing 10 nM 1,25(OH)2 Vitamin D3. For the next 6 days they additionally received M-CSF (20 ng/ml) and RANKL (40 ng/ml) to allow terminal differentiation. The conditioned medium was collected from day 1-4 of culture (osteoclast precursor cells) or from day 7-10 of culture (mature osteoclasts).

The data were analyzed with Affymetrix GeneChip Operating Software GCOS 1.4 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 200.

Following fragmentation the cRNA were hybridized for 16 hr at 45C on the arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix IVT labeling protocol from 5 µg total RNA (Expression Analysis Technical Manual, Affymetrix).

Pregnant Wistar rats were orally treated with TCDD (1 mg/kg in corn oil) at GD15.

The data were normalized by quantile normalization using lumi and preprocess package in R. This series includes two dataset; hypothalamic and pituitary samples (each case; N=3x2). The normalization applied each dataset.

The total RNA was extracted from the pituitary and hypothalamus of PND70 male pups according to the manufacturer's protocol (RNeasy Mini Kits).

The biotinylated-cRNA (total amount, 1,500 ng) prepared from each sample was overlaid onto an individual array spot of the rat microarray chip (RatRef12-v1 BeadChip; Illumina), according to the hybridization protocol. The chip was hybridized at 58°C for 19 hours.

The total RNA (250 ng) was converted to its biotinylated-cRNA according to the manufacturer’s procedures (Illumina TotalPrep RNA Amplification Kit). Briefly, reverse transcription to synthesize the first-strand cDNA was performed for 2 hours at 42°C, using an oligo (dT) primer bearing a T7 promoter and reverse transcriptase (ArrayScript; Ambion). The second strand cDNA was synthesized by incubating the first strand for 2 hours at 16°C in the presence of DNA polymerase I and ribonuclease H. After cDNA purification by a short column, the eluted cDNA was used for in vitro transcription with T7 RNA polymerase. In vitro transcription was performed at 37°C for 14 hours, yielding the multiple copies of the biotinylated antisense RNA originated from respective mRNAs in the sample.

This is Nrl-ko-Gfp P10 replicate 2.

Agilent Feature Extraction file: Liver_Keap1 Control_rep1.txt
Gene expression in the liver of  Keap1 Control mice_rep1.

Agilent Feature Extraction file: Liver_Keap1 Control_rep2.txt
Gene expression in the liver of  Keap1 Control mice_rep2.

Agilent Feature Extraction file: Liver_Keap1 Control_rep3.txt
Gene expression in the liver of  Keap1 Control mice_rep3.

Agilent Feature Extraction file: Liver_Keap1 KD_rep1.txt
Gene expression in the liver of  Keap1 KD mice_rep1.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12812 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12763 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12762 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12761 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12763 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12762 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12760 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12751 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12761 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12760 treated with DMSO 8 hours.

Gene expression data from a highly purified inv(14)-negative T-PLL blood sample

CD3-purified cells from T-PLL peripheral blood sample. >95% purity

Gene expression data from a highly purified inv(14)-positive T-PLL blood sample

Gene expression data from PBMC sample of  hepatocellular carcinoma patient
HCC-PBMC-09

HCC-PBMC-08

HCC-PBMC-07

HCC-PBMC-06

HCC-PBMC-05

HCC-PBMC-04

HCC-PBMC-03

HCC-PBMC-02

CHB-PBMC-01

HCC-PBMC-10

Cells were cultured for 48h in the original IVF plate, washed 3 times with DMEM/Ham's F12 (1:1) supplemented with penicillin, streptomycin and amphotericin and resuspended in the same medium supplemented with 10% Fetal calf serum. Cells were incubated for 48h at 37°C with 5% CO2, medium was replaced after 24h.

GeneChips were scanned using the Agilent GeneArray Scanner (Affymetrix)

Data was preprocessed using Robust Multiarray Average (RMA) with default parameters, through the Affy package of bioconductor.

Total RNA was extracted using Trizol (Molecular Research) according to the manufacturer's instructions

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA were prepared according to the Small Sample Target Labeling Assay v.2' protocol from 50 ng total RNA from Affymetrix, (Santa Clara, CA)

All the participants included in the study were women undergoing In-Vitro Fertilization with intracytoplasmatic sperm injection (IVF-ICSI) at the IVF unit. The IVF-ICSI cycles included in the study were conducted according to the long mid luteal GnRH agonist (Diphereline 3.75 mg PharmaBiotech, France) protocol. Controlled ovarian hyperstimulation was conducted with either recombinant follicular stimulating hormone (rFSH- Follitropin Alfa, Serono, UK) or human menopausal gonadotropin (hMG - Menotropin, Ferring, Germany). Following oocyte retrieval, cumulus cells were stripped from the oocyte, in preparation for the ICSI process, with a micropipette.

luteinized human cumulus cells, cultured 48h, nonPCOS, Lean, rep2

S4PosPls
US80900103_251486826534_S01_GE1_105_Dec08_1_2

C56B/6 and CD-1 mixed;wild type;E9.5;E9.5 embryos;posterior second heart field

S3PosPls
slide barcode: 251486826533
US80900103_251486826533_S01_GE1_105_Dec08_1_2

S2PosMns
slide barcode: 251486826532
US80900103_251486826532_S01_GE1_105_Dec08_1_1
Possibally leaked on tecan during hybridization.

S3PosMns
US80900103_251486826533_S01_GE1_105_Dec08_1_1

S1PosMns
slide barcode: 251486826811
US80900103_251486826811_S01_GE1_105_Dec08_1_1

S1PosPls
US80900103_251486826811_S01_GE1_105_Dec08_1_2

Transduction with gammaretroviral supernatants 48h after isolation; transplantation into syngenic mice. FACS-isolation 4 weeks after transplantation

C57BL/6J  bone marrow cells were harvested from mice treated for 4 days with 150 mg 5-fluorouracil/kg  and stimulated for 48 hours in DMEM supplemented with 15% FBS, 10 ng/mL hIL6, 6ng/mL mIL3, and 20ng/mL mSCF

amplified, fragmented, biotin labeled aRNA was hybridized for 18 hr at 45C on Affymetrix GeneChip Mouse 430 2.0. Chips were washed and stained in the Affymetrix Fluidics Station 450 according to manufacturers instructions

Affymetrix GeneChip 3' IVT Express Kit according to manufacturers instructions

GFP+ one marrow cells transduced with pSF91-MN1VP16-IRES-GFP 4  weeks after Tx

TRAF3flox/flox-CD19+/cre (B-TRAF3-/-) and TRAF3flox/flox (littermate control) mice were generated as described previously (Xie et al., 2007, Immunity 27:253)

Data extracted with Illumina Inc. BeadStudio version 3.2.3 without normalization, then processed in R using the lumi package with lumiExpresso and nuID annotation

GFP+ one marrow cells transduced with pSF91-MN1-IRES-GFP 4  weeks after Tx

MC3T3 cells were grown in 50 µg/ml ascorbic acid, 10 mM ß-glycerol phosphate and one of the following compounds: 20 nM TSA (Sigma, St. Louis, MO), 500 nM MS-275 (Calbiochem, San Diego, CA), 500 mM VPA (Sigma), or DMSO (vehicle) for 18 hours.

MC3T3-E1 preosteoblasts were plated at 4x104 cells per well of a 12-well plate and differentiated in Minimal Essential Medium (Invitrogen, Carlsbad, CA) containing 10% FBS (Invitrogen and Cambrex Bioscience/Lonza, Basel. Switzerland), 100 U/ml penicillin, 100 μg/ml streptomycin, 50 µg/ml ascorbic acid, 10 mM ß-glycerol phosphate and one of the following compounds: 20 nM TSA (Sigma, St. Louis, MO), 500 nM MS-275 (Calbiochem, San Diego, CA), 500 mM VPA (Sigma), or DMSO (vehicle) for 18 hours.

Raw data measurements were imported into Genedata Expressionist® Refiner (EPro1.0.32) for overall chip hybridization quality assessment, correction and condensation of probe sets intensity values. Robust Multichip Average (RMA) method was applied for global background subtraction and cross array normalization.  Processed expression data were imported into Genedata Expressionist Analyst.  General assessment of the data distribution was performed with Principle Component Analysis, boxplot and log-log data plots.  Following LOESS normalization, differential expression measures were calculated by Welch test comparisons of control DMSO (vehicle) versus each HDAC inhibitor.

Total RNA was isolated from MC3T3-E1 osteoblasts with Trizol reagent (Invitrogen).

Hybridization of the biotinylated-cRNA to the Affymetrix GeneChip Mouse Genome 430 2.0 Array was performed by the BioMedical Genomics Center’s microarray facility at the University of Minnesota using Affymetrix Genechip® Hybridization Oven 640 and Fluidics Station 450.

Biotin-labeled cRNA was prepared from each culture according to the Affymetrix protocol.  Briefly, RNA was denatured at 70oC with T7-oligo (dT) primer and reverse transcribed using Superscript II at 42oC for 1 hour.  Second strand cDNA synthesis was performed by incubating first strand cDNA with Escherichia coli DNA polymerase I, E. coli. DNA ligase, RNase H, and dNTPs for 2 hours at 16oC.  Biotin-labeled cRNA was prepared from double-stranded cDNA using the Affymetrix GeneChip IVT Labeling kit (Affymetrix, Santa Clara, CA), then purified and fragmented using the Affymetrix Sample Cleanup Module.

Comparison of control mice and mice treated with HDAC inhibitors.

breast cancer derived cell line treated with 0.3 mM of 5-Fluorouracil for 12 hours

breast cancer derived cell line treated with 0.9 uM of Doxorubicin for 36hours

6816115008_H

6816115033_A

6816115033_G

6816115033_H

6816115033_E

6816115033_F

Sample 42
The sample used on the array called sample 25 was also used on this array as sample 42 due to the intended sample not meeting QC standards. This sample was used as a technical replicate and not included in downstream analysis.

MISSION™ shRNA Lentiviral Transduction Particles (Sigma Aldrich) were used to achieve stable NET1 knockdown. 5 NET1 specific shRNA constructs, and one non target construct were transduced separately into AGS cells. Briefly, AGS cells were incubated with the Net1-specific shRNA lentiviral particles at a ratio of 2 particles : 1 cell, in the presence of hexadimethrine bromide to improve transduction efficiency. Non-target shRNA lentiviral particles were used to control for the effects of the transduction process itself. Successfully transduced cells included a puromycin resistance tag, and these cells were selected using 1μg/ml puromycin.    Net 1 knockdown was confirmed using quantitative RTPCR and western blot analysis.  For the remainder of this study, two distinct cell types were used: NET1 knockdown cells and non-target shRNA cells.

Human Caucasian gastric adenocarcinoma cells (AGS cells) were purchased from the European Collection of Cell Cultures (ECACC) and cultured in Hams F12 medium (Sigma Aldrich), supplemented with 10% fetal bovine serum, L-glutamine and Penicillin-Streptomycin (Sigma Aldrich), as per ECACC recommendations and incubated at 37ºC and 5%CO2.

Scanned images, obtained using Affymetrix Software (MAS5), were normalized using robust multichip average (RMA) express analysis

RNA was extraction by Trizol™ (Sigma Aldrich) following the manufacturers instructions.

Following fragmentation,  cRNA was hybridized for 16 hr at 45C on Affymetrix U133 plus 2.0 genechips. GeneChips were washed and stained in the Automated fluidics 450 station.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 μg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix) using the Affymetrix IVT labeling kit.

Gene expression in NET1 knockdown AGS cells treated with LPA.
GB 4 65B +LPA.CEL

gastric adenocarcinoma AGS cells;non targetting shRNA (control);A;NET1 present;LPA

Control AGS cells (transduced with non targetting shRNA) treated with 10 microM LPA for 4 hr

GB 1 63A +LPA.CEL

GB 2 63B +LPA.CEL

GB 3 65A +LPA.CEL

shRNAmir-mediated knockdown of Geminin was induced in GemKD cells by doxycycline addition

mouse ES cells were induced to undergo neural fate commitment by culture in N2B27 medium for 2 days

Raw CEL and DAT files were analyzed with dChip software (http://biosun1.harvard.edu/complab/dchip/)(2) after normalization to exclude probesets that did not meet the following preliminary cutoff values: i) expression, represented by model-based expression indices (MBEI), was changed more than 1.3-fold in treated versus untreated samples (E/B >1.3) groups, ii) MBEI differences were larger than 30 (E-B > 30), iii) expression was claimed as “present (P)” in at least one sample in each experiment. Probe sets that showed a change in expression upon Geminin knockdown that met cutoff values in at least 2 of the 3 experiments were considered for further single gene validation.

Total RNA was isolated from GemKD cells differentiated in N2B27 medium for two days with or without 500ng Dox and used for microarray analysis with the Affymetrix GeneChip Mouse Genome 430 2.0 Array.

neurectoderm derived from embryonic stem cells;Geminin knockdown, shRNAmir #11;derivative of ES-E14TG2a (ATCC);129P2 (formerly 129/Ola)

Gene expression data of RSG-treated bone marrow-derived macrophages derived from STAT6KO mouse
22_(Mouse430_2).CEL

6;C57Bl/6;STAT6 KO;bone marrow-derived macrophage;Control;Rosiglitazone;10 days

Rats were sacrificed 330 minutes or 5.5 hours after the injection with methylprednisolone

Rats were sacrificed 45 minutes after the injection with methylprednisolone

Rats were sacrificed forty-eight hours after the injection with methylprednisolone

liver from a 42 day old male mouse, GHR-/- mouse was dissected out. Total RNA was extracted using an Ambion RNaqueous RNA extraction kit. Targets were produced using modified Affymetrix procedure from 5ug of total RNA. 3 biological replicates were analysed per each group of animals.Sample also known as D2.

liver from a 42 day old male mouse, GHR-/- mouse was dissected out. Total RNA was extracted using an Ambion RNaqueous RNA extraction kit. Targets were produced using modified Affymetrix procedure from 5ug of total RNA. 3 biological replicates were analysed per each group of animals.Sample also known as D3.

liver from a 42 day old male mouse,wild type was dissected out. Total RNA was extracted using an Ambion RNaqueous RNA extraction kit. Targets were produced using modified Affymetrix procedure from 5ug of total RNA. 3 biological replicates were analysed per each group of animals.Sample also known as B1.

LaserPower: 2.5;; 1.31
Temperature: 36.03

Raw data were normalized by RMA method at gene level using Affymetrix Expression Console.

Ambio WT expression kit and geneChip WT terminal labeling and control kit ( Affimetrix, Ca)

Kyoto Rat liver tissue following animal exposure to orotic acid for 3 days

• The origin of biological samples (In vitro infection of HCT-8 cells with Cryptosporidium parvum)

Cryptosporidium parvum-infected HCT-8 cells, time course 2, mock

Cryptosporidium parvum-infected HCT-8 cells, time course 2, mock (24h post-infection)

WT1(-KTS) expression was induced for 12 hrs and the expression profile of each time-points was compared to the uninduced sample (0 hr)

3224_H1299_VEH_1.CHP
H1299 VEH
3224_H1299_VEH_1.CEL

3223_A549_3uM-Dac_2.CHP
A549 3D
3223_A549_3uM-Dac_2.CEL

WT1(-KTS) expression was induced for 4hrs and the expression profile of each time-points was compared to the uninduced sample (0 hr).

2OS cell line(osteosarcoma;female),Tetracycline-repressible WT1(-KTS) expression, time-course induction of WT1(-KTS) expression

3214_A549_3uM_Aza_1.CHP
A549 3A
3214_A549_3uM_Aza_1.CEL

3213_A549_1uM_Aza_2.CHP
A549 1A
3213_A549_1uM_Aza_2.CEL

3218_A549_0.3uM-Dac_1.CHP
A549 0.3D
3218_A549_0.3uM-Dac_1.CEL

3215_A549_3uM_Aza_2.CHP
A549 3A
3215_A549_3uM_Aza_2.CEL

3220_A549_1uM-Dac_1.CHP
A549 1D
3220_A549_1uM-Dac_1.CEL

3219_A549_0.3uM-Dac_2.CHP
A549 0.3D
3219_A549_0.3uM-Dac_2.CEL

3222_A549_3 uM Dac_1_REPEAT.CHP
A549 3D
3222_A549_3 uM Dac_1_REPEAT.CEL

3221_A549_1uM-Dac_2.CHP
A549 1D
3221_A549_1uM-Dac_2.CEL

TP082505-19_HG-U133A_2_IMFGN0023: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

Sample Type: Cells, Cell Line: HeLa, ATCC Number: CCL-2, Number of Cells Seeded: 2.20E+05, Cell Type: Cervical Carcinoma, Separation Type: Trypsin, Harvest Time Point: 0, Units of Harvest Time Point: hr

Three independent replicates of 4 groups of immature (19/20 days of age) Alpk:APfCD-1 mice were treated with arachis oil (AO) vehicle, 2.5ug/kg 17beta-estradiol (E2), 2ug/kg diethylstilbestrol (DES), or 50mg/kg genistein (GEN), via 3 daily subcutaneous injection, and sacrificed 72hr after initial dose.

The data were processed and anlayzed by the Array Pipe software.

Total RNA was isolated using the TRIzol reagent according to the manufacturer's instructinos.

Biotinylated cRNA was prepared with the Ambion MessageAmp kit for Illumina array.

Lentiviral infection and incubation in hormone depleted medium for 48 hours.

Background correction and normalization of microarray data was performed using the Robust Multichip Average method implemented in the rma function of R/BioConductor. The differential expression was assessed using the empirical Bayes method implemented in BioConductor Limma package. The criteria for selecting differentially expressed genes was a false discovery rate (FDR)-corrected p-value of less than 0.05.

Trizol reagent was used to prepare the RNA followed by additional purification using RNeasy from Qiagen.

1.  The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution is then removed.
2.  The chips are transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
3.  Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

1.  RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out.
2.  The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.
3.  The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using magnetic particles. The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA's that fall outside of an acceptable range will not routinely be carried forward in the analysis. Should this occur, investigators would be notified and asked how they would like to proceed.
4.  The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.

Control fetal heart (vehicle treated with corn oil via oral gavage on gd14.5, collected on gd17.5)

T1.5 fetal heart (treated on gd1.45 via oral gavage, collected on gd17.5)

T3 fetal heart (treated on gd14.5 via oral gavage, collected on gd 17.5)

MCI-006 was from a postmenopausal low BMD woman.

The microarray data were normalized using the Robust Multichip Average (RMA) method.

The Affymetrix arrays were hybridized and washed using the manufacturer's protocol.

cDNA synthesis (SuperScript, Invitrogen) was performed from 10 μg total RNA with a T7-oligo(24)dT primer. The DNA was transcribed into biotin-labeled RNA (Bioarray RNA Labeling Kit, ENZO)

IS patient;male;52;48;Mirandela;Hypercholesterolemia;ever smoker, ever drinker

To obtain stable miR-210 over-expressing cells, HUVEC were infected by retroviral vectors bearing pre-miR-210 sequence or a control scramble sequence. To inhibit miR-210, Locked Nucleic Acid (LNA) oligonucleotides against miR-210 or a control scramble sequence (Exiqon) were transfected by siRNA Transfection Reagent (Santa Cruz), following manufacturer instructions, in 40% confluent HUVEC (4X103/cm2) at the final concentration of 40 nM.

Summarized signal intensities were generated in BRB ArrayTools using justRMA

Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNAeasy mini kit following standard RNA cleanup protocol

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on  HG-U133_Plus_2.1sq. GeneChip.  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Gene expression data from HUVEC over-expressing a scramble control sequence

HUVEC infected by retroviral vectors bearing a control scramble sequence

Small Intestine; d1 small intestine

Small Intestine; Ileum

Diabetic (STZ) rats were treated with sodium tunsgtate at a dose of 0.7g/L during one week, and at 2g/L during the next 4-5 weeks until his glycemia was reduced to a level near to the normoglycemia

GeneChip Scanner 3000 (Affymetrix 00-0074) GeneChip Operating Software ver.1.4 (Affymetrix 690036)

Data Processing GeneChip Operating Software ver.1.4 (Affymetrix 690036)

GeneChip Expression Analysis Technical Mannual, 701021 Rev.5 Hybridization Oven 640 110V (Affymetrix 800138) Wash and staining: Fluidics Station 450 (Affymetrix 00-0079)

One-cycle Target Labeling GeneChip Expression Analysis Technical Mannual, 701021 Rev.5 Section 2 Eukaryotic Sample and Array processing Chapter 1 Eukaryotic Target Prepartion

NSC from neurospheres were enzymatically dissociated for 5-10 minutes at 37ºC with Accutase (Chemicon), then mechanically dissociated and seeded at a density of 5x104 cells/ml.

Mouse forebrains were finely minced, digested for 30 minutes at 37ºC in HBSS media containing 2.5 U/ml Papain (Worthington), 1U/ml Dispase (Roche or Stem Cell Technologies), and 250 U/ml DNase I (Sigma) and mechanically dissociated. NSC/progenitors were purified using two successive Percoll gradients (25% then 65%) (Amersham) and plated on uncoated tissue culture dishes at a density of 105 cells/cm2 in NeuroBasal-A medium supplemented with penicillin (100 U/ml)-streptomycin (100 mg/ml)-glutamine (292 µg/ml), serum-free B27 supplement without vitamin A (2%), bFGF (20 ng/ml), and EGF (20 ng/ml) (self-renewal/proliferation media). Cells were incubated at 37ºC.  Secondary neurospheres were collected 6 days   after initial plating at 50000 cells/ml.

Microarray results were pre-processed by performing a background adjustment and normalization with RMA (robust multi-array analysis) using Bioconductor.

Total RNA was extracted using the mirVana isolation kit following the manufacturer’s protocol (Ambion)

Microarray hybridization was performed at the Stanford PAN facility. RNA was reverse-transcribed to cDNA followed by in vitro transcription and biotinylation. Biotinylated cRNAs were then fragmented, mixed with control cRNA fragments, and hybridized to Affymetrix oligonucleotide arrays (Mouse Genome 430 2.0 Array).

The right ventricle and the interventricular septum of five wild type (Ezh2f/f) and four Ezh2-deficient (Ezh2f/f;Mef2cAHF::Cre) mice were isolated in cold PBS and homogenized in Trizol reagent (Invitrogen).

Affymetrix mouse Gene ST 1.0 arrays were scanned according to manufacturer recommendations.

Raw intensities from CEL files were analyzed using Affymetrix Power Tools (APT, version 1.10.1) to generate RMA (robust multi-array average) expression intensities on a log2 scale for each probe set.

Total RNA was isolated using TRIzol reagent following the manufacturer's instructions.

Affymetrix mouse Gene ST 1.0 arrays were hybridized according to manufacturer recommendations.

70;Adenocarcinoma of breast, ductal, mucinous;G1;IIB;T2;N1a;1;1;37;0;0

Needle biopsies were obtained from the vastus lateralis muscle of 6 healthy, sedentary, 67±2.5 year-old males before and after 3 months of training.  RNA was extracted using Trizol. Targets were produced using standard Affymetrix procedures from about 4ug of total RNA.
Keywords = microarray, exercise, fitness, elderly, training effect

Cells were treated with 2.5 uM CdCl2 in the complete medium for 16 hours.

Cells were treated with 2.5 uM CdCl2 in the complete medium for 32 hours.

Cells were treated with 2.5 uM CdCl2 in the complete medium for 8 hours.

Cells were treated with 2.5 uM CdCl2 in the complete medium for 4 hours.

Control animals (Con) were uninstrumented and were not hemorrhaged or manipulated in any way. Sham (Sh) rats were instrumented, but not hemorrhaged, and physiologic measures were taken for 4 – 23 hrs 6 hrs prior to euthanasia. At 1, 3, 6, 16, 24, 48, or 72 hours after hemorrhage animals were deeply anesthetized with Nembutal (50 mg/kg), and the post hemorrhage blood sample was collected by cardiac puncture and the animals were euthanized by exsanguination.  All tissues were collected within 10 minutes of death and 100 mg amounts of the following tissues were removed and placed in RNALater™  (Ambion, Austin, TX):  intestine, liver, lung, kidney, spleen, heart, skeletal muscle (gastrocnemius) skin, and brain.
Total RNA was isolated from each tissue from each animal with 2 rounds of TRI Reagent® (MRC, Cincinnati, OH) and its quality analyzed by gel electrophoresis.  A reference preparation consisting of equal amounts of RNA pooled from 10 organs (liver, lung, kidney, spleen, heart, skeletal muscle, skin, jejunum, and brain) of untreated control animals was used as reference RNA.  Five-µg samples exhibiting undegraded RNA from each rat lung were reverse transcribed with Superscript II™ (Invitrogen Corp., Carlsbad, CA) in the presence of a C-6 amine modified random hexamer and aminoallodeoxyuridine to produce fluorescent labeled cDNA.  RNA from the reference preparation was all labeled together.  Following reverse transcription, RNA was degraded with 0.1 M NaOH and neutralized with ph 7.0 Hepes buffer.  Following isolation on Qiaquick columns (Qiagen), elution and lyophilization, the lung-sample was labeled with Cy5 ester and reference cDNA samples with Cy3 ester (Amersham Biotech, Piscataway, NJ) After separation from unbound dye, the samples were again lyophilized and then reconstituted in hybridization solution (32% formamide, 5 X Denhardt's solutions, 3X SSC, 20 mM Hepes buffer, ph 7.0)  for 20 hrs at 42 degree. Following hybridization on a microarray (one per rat) and washing to remove unhybridized cDNA and scanning with an Axon 4000B (Axon Instruments, Union City, CA) at 10 micron resolution, the resulting 16-bit TIFF images were analyzed with GenePix 4.1 software (Axon Instruments) for calculation of Cy5 and Cy3 fluorescence intensities at each spot.

MO-Tg U3

MO-Tg U2

MO-WT U4

MO-WT U3

MO-WT U2

Cells were treated with either DMSO (vehicle) or 10μM ATRA for 1, 3, and 6 hours.

Cells were grown in Iscove's Modified Dulbecco's Modified Eagle Medium (IMDM) supplemented with 10% fetal bovine serum(FBS)

Gene specific bead intensities were background corrected and quantile normalized using the variance-stabilizing transformation (VST) from the R package limma.   Log2 expression levels were calculated using the R package limma.

Total RNA was isolated using RNA-Stat 60 (Tel-Test; Friendswood, TX), resuspended in DNase, RNase free water, and stored at -80 C until use.  Two step quality control was performed using an Agilent Bioanalyzer and Quant-IT RiboGreen RNA Assay according to manufacturer's instructions.

Biotinylated cRNA was generated using the Illumina TotalPrep RNA Amplification Kit.

ME180;cervix; derived from metastatic site: omentum;epidermoid carcinoma;Homo sapiens, human;10μM ATRA;6 hours

ME180;cervix; derived from metastatic site: omentum;epidermoid carcinoma;Homo sapiens, human;10μM ATRA;3 hours

Confluent monolayer of HUVEC was treated with a vehicle-control for 24 hours.

Rb-/- prostate epithelial cell line maintained in RPMI-1640 medium without fetal bovine serum for 48 hours

control wild-type prostate epithelial cell line maintained in RPMI-1640 medium without fetal bovine serum for 48 hours

Three different clones from TL3 and HTH 83 cell lines stably expressing scramble shRNA and LAMC2 shRNA were used

The data were analyzed using RMA in the bioconductor and normalized using the Cross Correlation method.  The trimmed mean target intensity of each array was set to 8.

Total RNA was isolated from cultured cells with RNeasy mini kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer’s protocol.

Bitinylated cRNA were fragmented and hybridised to an illumina whole genome expression chip, Human HT-12 v4.0 for 18 h at 58°C. Beadchips were then washed and stained and subsequently scanned to obtain fluorescence intensities.

cRNA were synthesized using Illumina Total Prep RNA Amplification Kit (Illumina)

Littermate were allowed to develop normally in utero until age E14, when they were harvested from the pregnant dam.

SMhu143

SMhu144

SMhu145

SMhu146

SMhu147

SMhu148

SMhu149

SMhu150

SMhu151

SMhu152

A catalytic antioxidant (AEOL 10150) atenuates expression of inflammatory genes in stroke.

White and grey matter in the distribution of the middle cerebral artery after one hour of ischemia followed by 6 hours of reperfusion; first replicate; pooled mRNA from 6 brains.

JLI_62

JLI_58

Total RNA was prepared from the entire small intestine of one 40 day old CFTR null male mouse, CFTR(-/-), congenic on the black6 background, using TRIzol reagent. Mice were fed Peptamen from age 10 days to prevent intestinal obstruction.

JLI_59

JLI_56

JLI_57

JLI_54

JLI_55

Bronchoalveolar lavage cells from a patient with an ISHLT biopsy score of A=1 and B=1 (Acute rejection)

Probe arrays were scanned at 3-μm resolution using the Affymetrix GeneChip System confocal scanner 3000.

Raw data were analyzed with the Affymetrix GeneChip Operating Software (GCOS) version 1.4.

Trizol extraction of total RNA according to the manufacturers instructions.

Following fragmentation, 10 µg of cRNA were hybridized hybridized for 16 hours at 45°C to an Affymetrix mouse 430A 2.0 GeneChip array.

Biotynylated cRNA were prepared according to standard Affymetrix protocol from 3 µg total RNA

BALB/c WT, gender:male, age:8wks, tissue: whole lung, condition: 8DPI

BALB/c WT, gender:male, age:8wks, tissue: whole lung, condition: 4DPI

BALB/c scid, gender:male, age:8wks, tissue: whole lung, condition: 4DPI

When cell confluency reached 50-60% (1 day) the cells were treated with NSC319726 (1 µM) for 24 hours before harvested for RNA extraction.

Biotinylated cRNA was generated using standard Affymetrix protocols.

Drug3_B1_HG-U133_Plus_2
Gene expression data from TOV112 treated with NSC319726

TOV112D;epithelial ovarian cancer cell;NSC319726 (1 µM) for 24 hrs

CTL_A3_HG-U133_Plus_2
Gene expression data from TOV112 cells without treatment

CTL_A2_HG-U133_Plus_2

CTL_A1_HG-U133_Plus_2

Drug3_B3_HG-U133_Plus_2

Drug3_B2_HG-U133_Plus_2

age	55;gender	male;disease	CML;disease phase	chronic phase;previous therapy	no;bcr-abl/G6PDH ratio (%)	25.8;leukocyte count (/nl)	206;hemoglobin (g/dl)	10.1;platelet count (/nl)	331

age	54;gender	male;disease	CML;disease phase	chronic phase;previous therapy	no;bcr-abl/G6PDH ratio (%)	5.7;leukocyte count (/nl)	52.2;hemoglobin (g/dl)	9.3;platelet count (/nl)	388

age	64;gender	male;disease	CML;disease phase	chronic phase;previous therapy	no;bcr-abl/G6PDH ratio (%)	7.1;leukocyte count (/nl)	38.3;hemoglobin (g/dl)	14.1;platelet count (/nl)	212

age	28;gender	female;disease	CML;disease phase	chronic phase;previous therapy	no;bcr-abl/G6PDH ratio (%)	11.2;leukocyte count (/nl)	164;hemoglobin (g/dl)	9.5;platelet count (/nl)	842

age	52;gender	male;disease	CML;disease phase	chronic phase;previous therapy	no;bcr-abl/G6PDH ratio (%)	4.4;leukocyte count (/nl)	30.5;hemoglobin (g/dl)	12.8;platelet count (/nl)	359

age	69;gender	female;disease	CML;disease phase	chronic phase;previous therapy	no;bcr-abl/G6PDH ratio (%)	8.2;leukocyte count (/nl)	9;hemoglobin (g/dl)	14.3;platelet count (/nl)	283

age	42;gender	female;disease	CML;disease phase	chronic phase;previous therapy	no;bcr-abl/G6PDH ratio (%)	5.4;leukocyte count (/nl)	180;hemoglobin (g/dl)	12.1;platelet count (/nl)	476

age	40;gender	female;disease	CML;disease phase	chronic phase;previous therapy	no;bcr-abl/G6PDH ratio (%)	9.5;leukocyte count (/nl)	129;hemoglobin (g/dl)	9.4;platelet count (/nl)	261

neuron progenitor cells (NPC);healthy control;human induced pluripotent stem cells (hiPSC);healthy control

Self-self control.

human induced pluripotent stem cells (hiPSC);schizophrenia;human induced pluripotent stem cells (hiPSC);schizophrenia

21-day-old felmale C57BL/6 mice from Harlan (Indianapolis, IN) were ovariectomized on day 26 and fed with phytoestrogen-free diet two days later (AIN-93G purified rodent diet, Dyets, In., Bethlehem, PA). Experimental treatments began on day 30. Animals received daily subcutaneous injections of 125 ng of E2 (Signma-Aldrich, St. Louis, MO) in 0.02 ml corn oil. RNA were extracted at day 2 after experiment started. Total 6 animals were treated. RNA samples were pooled from 3 animals, resulting two independent biological replicates.

21-day-old felmale C57BL/6 mice from Harlan (Indianapolis, IN) were ovariectomized on day 26 and fed with phytoestrogen-free diet two days later (AIN-93G purified rodent diet, Dyets, In., Bethlehem, PA). Experimental treatments began on day 30. RNA samples were extracted at day0 without any treatment. Total 6 animals were used. RNA from 3 animals were pooled together as one sample, resulting in two independent biological replicates.

Gene expression data from  3 uM EPZ004777 treated, DAY 2, biological rep.1, MV4-11 cells

MV4-11;biphenotypic B myelomonocytic leukemia (MLL-AF4 rearragenment);IMDM with 10% FBS;EPZ004777;day 2;1

Gene expression data from  3 uM EPZ004777 treated, DAY 2, biological rep.2, MV4-11 cells

MV4-11;biphenotypic B myelomonocytic leukemia (MLL-AF4 rearragenment);IMDM with 10% FBS;EPZ004777;day 2;2

Mouse Lung AIN Diet 8hr 1mg/kg As Injection, biological replicate F
AN080906_Sample 40.CEL

Sodium arsenite added to food: None; Injection: IP 8hr 1 mg/kg sodium arsenite in saline; Diet: AIN-76A; Sodium arsenite added to drinking water: None

Mouse Lung AIN Diet 5wk 10ppb As Food Exposure, biological replicate E
AN080206_Sample 41 Lung.CEL

Mouse Lung LRD Diet 5wk 10ppb As Food Exposure, biological replicate B
AN080806_Sample 30.CEL

Mouse Lung AIN Diet 5wk 100ppb As Drinking Water Expousre, biological replicate D
AN080406_Sample 32.CEL

Sodium arsenite added to food: None; Injection: None; Diet: AIN-76A; Sodium arsenite added to drinking water: 100 ppb, 5wk

Mouse Lung AIN Diet 8hr 1mg/kg As Injection, biological replicate E
AN080206_Sample 24 Lung.CEL

Mouse Lung AIN Diet 8hr 1mg/kg Dex and 1mg/kg As Injection, biological replicate C
AN080806_Sample 27.CEL

Mouse Lung LRD Diet 5wk 10ppb As Drinking Water Exposure, biological replicate B
AN080406_Sample 36.CEL

Mouse Lung AIN Diet 8hr 1mg/kg Dex Injection, biological replicate E
AN080806_Sample 38.CEL

Mouse Lung LRD Diet 5wk 10ppb As Food Exposure, biological replicate C
AN080306_Sample 33.CEL

Mouse Lung AIN Diet 8hr 1mg/kg As Injection, biological replicate B
AN080806_Sample 35.CEL

HCT116 cells with enforced miR-34a expression, technical replicate 1

Gene expression data from HCT116 cells with enforced expression of miR-34a.  Described in:

Eeyore mouse is a mixed strain (C57BL/6, NOD-SCID) from a N-ethyl-N-nitrosourea (ENU)-treated C57BL/6 founder line. It carries a unique missense mutation (T2996C, Accession AJ511873) resulting in a serine to proline substitution in the C-terminal D4-domain of Mucin 2 (Muc2).

C57BL/6, NOD-SCID;Male;8 weeks;Large Intestine (Distal and Proximal);C57BL/6, NOD-SCID Eeyore T2996C

21B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

F9 cells were treated with TSA (0.07uM) for 24 hrs.  RNA was isolated using tri-reagent followed up with DNAse treatment and purified using an RNeasy spin column.  RNA was submitted to an Affymetrix core Microarray facility (Renselaer, NY) and was further processed according to Affymetrix protocol.

F9 cells were treated with RA (5 x 10-7 M) for 24 hrs.  RNA was isolated using tri-reagent followed up with DNAse treatment and purified using an RNeasy spin column.  RNA was submitted to an Affymetrix core Microarray facility (Renselaer, NY) and was further processed according to Affymetrix protocol.

The data were analyzed with Gene Chip Operating System (GCOS) using Affymetrix default analysis settings and global scaling as normalization method

12 weeks of RTX therapy;F;64;synovial knee biopsy;rheumatoid arthritis;EULAR Good-responder;synovium

Mc3T3-E1_T0-2
MOE4302_042809H_RH3_Ctl2

Mc3T3-E1_T1-2
MOE4302_042809H_RH4_AA2

baseline;F;64;synovial knee biopsy;rheumatoid arthritis;EULAR Good-responder;synovium

12 weeks of RTX therapy;M;44;synovial knee biopsy;rheumatoid arthritis;EULAR Moderate-responder;synovium

Mc3T3-E1_T1-3
MOE4302_042809H_RH6_AA3

12 weeks of RTX therapy;F;68;synovial knee biopsy;rheumatoid arthritis;EULAR Good-responder;synovium

baseline;M;44;synovial knee biopsy;rheumatoid arthritis;EULAR Moderate-responder;synovium

12 weeks of RTX therapy;F;33;synovial knee biopsy;rheumatoid arthritis;EULAR Moderate-responder;synovium

Data were analyzed by the Robust Multi-array Average (RMA) algorithm using the Affymetrix Expression Console. An unpaired t test was performed with log2-transformed data to identify significantly differentially expressed transcripts. Fold change was calculated using DNAStar ArrayStar 11.0 software

Total RNA from E18.5 lungs was isolated with RNeasy® plus mini kit (Qiagen)

Following fragmentation, 1 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Gene 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Gene expression data from embryonic lungs at day E18.5 Wild type
Lungs of timed-pregnant C57BL/6 wild type (+/+) and Hmga2 ( -/-) were dissected from the embryos at E18.5

Mice were administered 4mg of 20mg/mL tamoxifen dissolved in corn oil via oral gavage, mice were then sacrificed 36 hours post-tamoxifen administration via CO2 euthanasia.

Partek was used to generate RMA.RMA signals were generated for the core probe sets using the RMA background correction, Quantile normalization and summarization by Median Polish. Summarized signals for each probe set were log2 transformed.

Extraction of total RNA was performed using the Qiagen Rneasy Midi Kit with 20-30 mg of pancreatic tissue according to the manufacturer's instructions.

Hybridization was done using Affymetrix standard hybridization protocol for Gene ST 1.0 arrays

RNA was labeled using Affymetrix standard WT protocol (non-Ambion) from 100ng total RNA.

SK03M012
Gene expression data from MIST1-null pancreatic RNA with inducible MIST1 transgene 36 hours post-tamoxifen

MIST1-null pancreatic RNA with inducible MIST1 transgene 36 hours post-tamoxifen

SK03M011

SK03M010

SK03M009

SK03M008
Gene expression data from MIST1-null pancreatic RNA 36 hours post-tamoxifen

SK03M007

SK03M006

cels were treated for 12 hours with tamoxifen to induce overexpression of Gfi1b (Gfi1b fused to estrogen receptor domain)

AMuLV pro-B cell line expressing Gfi1b-estrogen receptor fusion protein

E2F-1 gene expression profiling by adenovirus-mediated gene transfer in SKMEL-2 melanoma cell line.
Keywords = E2F-1
Keywords = apoptosis
Keywords = adenovirus
Keywords = cell cycle
Keywords = ASK-1
Keywords = melanoma
Keywords = gene therapy

human immortalized mesenchymal stem cells;RNF40;5 days adipocyte differentiation

human immortalized mesenchymal stem cells;RNF40;2 days adipocyte differentiation

5991413039_B
Euploid Down's Syndrome;induced pluripotent stem cell;CCL54 C87;rep2

euploid induced pluripotent stem cell;Down's Syndrome;CCL54;male;P20;C87

5991413039_C
Euploid Down's Syndrome;induced pluripotent stem cell;CCL54 C87;rep3

5445316039_L
Down's Syndrome;induced pluripotent stem cell;CCL54 C18;rep3

induced pluripotent stem cell;Down's Syndrome;CCL54;male;P11;C18

5991413039_A
Euploid Down's Syndrome;induced pluripotent stem cell;CCL54 C87;rep1

5445316039_J
Down's Syndrome;induced pluripotent stem cell;CCL54 C18;rep1

5445316039_K
Down's Syndrome;induced pluripotent stem cell;CCL54 C18;rep2

Johns Hopkins Microarray Core Facility
http://www.microarray.jhmi.edu/

amnion mesenchymal cells, 8h interleukin-1-beta, biological rep3

amnion mesenchymal cells, 8h interleukin-1-beta, biological rep2

MCI-016 was from a premenopausal low BMD woman.

Mice and diets.  One-month-old male mice of the long-lived B6C3F1 strain were purchased from Harlan (Indianapolis, IN) and maintained as described after weaning (15).  Mice were housed in groups of 4 per cage and fed a non-purified diet, PMI Nutrition International Product #5001 (Purina Mills, Richmond, IN).  At 5 months of age, the mice were individually housed, and randomly assigned to one of two groups, control (CON) or long-term CR (LTCR).  CON mice were fed 93 kcal per week of a defined control diet (AIN-93M, Diet No. F05312, BIO-SERV).  LTCR mice were fed 52.2 kcal per week of a defined CR diet (AIN-93M 40% Restricted, Diet No. F05314, BIO-SERV).  The LTCR mice consumed approximately 40% fewer calories than mice in the CON mice.  The CR diet was enriched so that the CR mice consumed approximately the same amount of protein, vitamins, and minerals per gram body weight as the control mice.

Experimental design.  At 20 months of age, cohorts of mice in the CON group were randomly assigned to one of 7 experimental groups (Fig. 1).  A CON group continued to be fed 93 kcal per week of control diet for 8 weeks.  A CR8 group was fed 77 kcal per week of CR diet for 2 weeks, followed by 52.2 kcal per week of CR diet for 6 weeks.  The remaining dietary groups were fed the control diets containing, respectively, metformin (MET; Sigma, St. Louis, MO), glipizide (GLIP; Sigma), MET plus GLIP, rosiglitazone (ROS; Avandia, SmithKline Beecham) or soy isoflavone extract (SOY; NOVASOY 400, Life Extension Foundation) for 8 weeks at the dosages indicated in Table 1.  The drugs were mixed with powdered control diet and cold-pressed into one gram pellets (BIO-SERV Inc.).  At 0900, all mice were fed 2/7 of the weekly allotment of food on Monday and Wednesday and 3/7 on Friday.  The mice had free access to acidified tap water.  They were fasted for 48 hours and killed by cervical dislocation at 22 months of age.  No signs of pathology were detected in the animals used for the studies reported (n=4 per group).  Organs were removed rapidly, flash frozen, and stored in liquid nitrogen.  The weights of the mice were monitored bi-weekly.  Mouse weights are given in Table 1.

One-month-old male mice of the long-lived B6C3F1 strain were purchased from Harlan (Indianapolis, IN) and maintained as described after weaning (15).  Mice were housed in groups of 4 per cage and fed a non-purified diet, PMI Nutrition International Product #5001 (Purina Mills, Richmond, IN).  At 5 months of age, the mice were individually housed, and randomly assigned to one of two groups, control (CON) or long-term CR (LTCR).  CON mice were fed 93 kcal per week of a defined control diet (AIN-93M, Diet No. F05312, BIO-SERV).  LTCR mice were fed 52.2 kcal per week of a defined CR diet (AIN-93M 40% Restricted, Diet No. F05314, BIO-SERV).  The LTCR mice consumed approximately 40% fewer calories than mice in the CON mice.  The CR diet was enriched so that the CR mice consumed approximately the same amount of protein, vitamins, and minerals per gram body weight as the control mice.

date: 2001

Peripheral blood cells, taken at ER hours after trauma exposure (Control sample).

Peripheral blood cells, taken 4 months after trauma exposure (PTSD sample). date: 2002

14 days hindlimb suspended, 5 day reloaded

Array data were analyzed with the dChip software. After smoothing spline normalization, expression values were calculated applying the perfect-match/mismatch difference model algorithm (dChip).

Amplification of RNA by two rounds of reverse transcription followed by T7 promoter-dependent in-vitro transcription. Then standard labeling according to Affymetrix protocols.

Total RNA from FACS-sorted HSC was amplified by two rounds of RT and T7 promoter-based in-vitro transcription and the resultant biotinylated cRNA was then hybridized to Affymetrix Mouse Genome 430 2.0 arrays.

FACS-sorted Lin-, c-kit+, Sca-1+ HSC from the bone marrow of PU.1 knockdown mice with targeted disruption of the distal enhancer (URE) –14kb upstream of the PU.1 gene.

GI_dev, small bowel fetal day 16.5

Large Intestine; Distal Colon

Small Intestine; d14 small intestine

Small Intestine; Duodenum

HUVEC infected by retroviral vectors bearing pre-miR-210 sequence

Gene expression data from HUVEC in which miR-210 activity was blocked by a complementary anti-miR-210-LNA

Raji cells (1×10^6 cells/well in 6-well plates) were electroporated on an Amaxa Nucleofector using the Amaxa kit V (Lonza, Cologne, Germany) following manufacturer’s recommendations with 1.5µg of meridian Mimic for miR-142-3p or control (Dharmacon-ThermoFisher, Lafayette, CO).

Raji cells were cultured in 6-well plates in RPMI 1640 medium supplemented with penicillin (100 U/ml), streptomycin (100 μg/ml), sodium pyruvate (1 mM), and 10% heat-inactivated fetal calf serum (FCS) (Gibco, Cergy-Pontoise, France) at 37 ºC in a humidified incubator with 5% CO2.

Scanned with an Agilent Technologies Microarray Scanner using default parameters.

Data extraction of median feature intensity without background subtraction was peformed with Feature Extraction software v9.1.3.1 (Agilent Technologies). In order to remove systemic signal intensity bias between each array, median feature intensity were normalized with the function lowess (Locally weighted scatterplot smoothing) method, and then spots with half of the samples exhibiting signal less than the mean of all median signals were removed.

24 hours after transfection, cells were centrifuged and lysed with 1mL TRIzol (Invitrogen, Cergy Pontoise, France). RNA extraction was performed following manufacturer’s recommendations. RNA was quantified using a NanoDrop ND-1000 spectrophotometer, and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

The labeled cRNA samples were fragmented in fragmentation buffer at 60°C for 30 min before the microarray hybridization. Samples were hybridized to a whole human genome 4x44K Agilent microarrays during 14 hours at 65°C in a rotating hybridization oven (Agilent Technologies). The hybridization slides were washed, stabilized, dried, and immediately scanned.

Cyanine-3 (Cy3) and cyanine-5 (Cy-5) labeled cRNA was prepared from 100ng using the Agilent Quick Amp Labeling Kit (Agilent Technologies, Palo Alto, CA) following the two-colour manufacturer’s protocol. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

Raji_Mi_3p_24h_2_56779_1
Each sample represents one channel of a dual-channel array.

Raji;human Burkitt's lymphoma;male;expression of miR-142-3p mimic;24 hrs

Raji_Mi_3p_24h_4_56779_2

LC-MA10

JLI_60

White and grey matter in the distribution of the middle cerebral artery after one hour of ischemia followed by 6 hours of reperfusion; third replicate; pooled mRNA from 6 brains.

White and grey matter in the distribution of the middle cerebral artery after one hour of ischemia followed by 6 hours of reperfusion; second replicate; pooled mRNA from 6 brains.

White and grey matter in the distribution of the middle cerebral artery after one hour of ischemia followed by treatment (IV) with the catalytic antioxidant AEOL 10150 and then 6 hours of reperfusion; mRNA from a single brain #12.

White and grey matter in the distribution of the middle cerebral artery after one hour of ischemia followed by treatment (IV) with the catalytic antioxidant AEOL 10150 and then 6 hours of reperfusion; mRNA from a single brain #11.

White and grey matter in the distribution of the middle cerebral artery after one hour of ischemia followed by treatment (IV) with the catalytic antioxidant AEOL 10150 and then 6 hours of reperfusion; third replicate; pooled mRNA from 6 brains.

White and grey matter in the distribution of the middle cerebral artery after one hour of ischemia followed by treatment (IV) with the catalytic antioxidant AEOL 10150 and then 6 hours of reperfusion; first replicate; pooled mRNA from 6 brains.

White and grey matter in the distribution of the middle cerebral artery after one hour of ischemia followed by treatment (IV) with the catalytic antioxidant AEOL 10150 and then 6 hours of reperfusion; mRNA from a single brain #14.

White and grey matter in the distribution of the middle cerebral artery after one hour of ischemia followed by treatment (IV) with the catalytic antioxidant AEOL 10150 and then 6 hours of reperfusion; mRNA from a single brain #13.

JLI_63

JLI_64

control and Snai1 knockout ESCs were cultured in standard ESC culture condition with LIF and feeder.

Data was analyzed using the limma and affy bioconductor packages implemented in the R-statistical environment version 2.12.2. RMA was used to normalize the data and fit log2 transformed expression values.

Total RNA of ESCs was collected and purified using RNeasy Mini Kits (QIAGEN)

Following fragmentation, 16 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated aRNA were prepared according to the Affymetrix GeneChip 3’ IVT Express kit protocol from 250 ng total RNA (Affymetrix GeneChip 3’ IVT Express kit Instruction Manual, P/N 702646 Rev. 5)

RNA was extracted with QIAGEN RNeasy mini kit (DNase I treated) in accordance with the protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

The 13 data sets were first processed by Affymetrix GCOS V.1.4.0.036 software which computed present/absent calls for each probe set and the signal values were adjusted to an overall target intensity of 1500.  Data was then normalized in Genespring version 7.3.1 in 3 steps.  1. Data trasnformation: set measurements less than 0.01 to 0.01.  2. per chip: Normalization to 50th percentile.  3.  Per Gene: Normalize to median.

Tri-reagent extraction of total RNA was performed according to the manufacturer's instructions.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133A 2.0 arrrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

A circumferential piece of tissue was obtained at the distal aspect of each specimen.  The tissue was flash frozen at -80 degrees for later processing.  Frozen specimens were homogenized into TriReagent  and RNA was isolated according to the manufacturer’s instruction.  RNA was processed and hybridized to Affymetrix microarray.

appendix sample removed from patient who went to the operating room with the diagnosis of acute appendicitis

SC-1;diffuse large B-cell lymphoma (DLBCL) cells stably transfected with a tetracycline-inducible LITAF expression vector;none

DLBCL cell line SC-1 stably transfected with a tetracycline-inducible LITAF expression vector, absence of doxycycline

RL;diffuse large B-cell lymphoma (DLBCL) cells stably transfected with a tetracycline-inducible LITAF expression vector;doxycycline

DLBCL cell line RL stably transfected with a tetracycline-inducible LITAF expression vector, presence of doxycycline

RL;diffuse large B-cell lymphoma (DLBCL) cells stably transfected with a tetracycline-inducible LITAF expression vector;none

DLBCL cell line RL stably transfected with a tetracycline-inducible LITAF expression vector, absence of doxycycline

A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factor can be identified. This entry corresponds to the RNA isolated from uninduced INS-1 cell line #5a containing MODY5 mutant P328L329delCCTCT of hepatocyte nuclear factor-1b (HNF1b).
Keywords = P328L329

CGC_KO3.CEL

A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factors can be identified. This entry corresponds to the RNA isolated from tet-induced INS-1 cell line #5a containing MODY5 mutant P328L329delCCTCT of hepatocyte nuclear factor-1b (HNF1b).

A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factors can be identified. This entry corresponds to the RNA isolated from uninduced INS-1 cell line #6a containing MODY5 mutant P328L329delCCTCT of hepatocyte nuclear factor-1b (HNF1b).

A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factors can be identified. This entry corresponds to the RNA isolated from tet-induced INS-1 cell line #6a containing MODY5 mutant P328L329delCCTCT of hepatocyte nuclear factor-1b (HNF1b).

heart from beta1-Gly389 transgenic mice at 90 days of age. The alpha-myosin heavy chain promoter was utilized to direct expression of the human beta1-Gly389 cDNAs to cardiac myocytes.

C57BL/6J;129S5/Brd mixed hybrid;Cre knockout of Dicer;uterine;15 days

For AOM/DSS group of mice, a single intraperitoneal injection of AOM was given at Day 1, followed by three cycles of DSS administration (cycle 1: 2%, Day 8~14; cycle 2: 1.5%, Day 29~33; cycle 3: 1.5%, Day 50~54) in the drinking water. For control group, AOM was replaced by saline, and DSS was replaced by distilled water.

6-week-old male ICR mice were maintained in Central Sourth University Animal Facility according to the Institutional Animal Care Guidelines. All animals were housed in plastic cages (4 or 5 mice/cage) with free access to distilled water and a standard diet under specific-pathogen free (SPF) conditions of humidity (50±10%), lightning (12-h light/dark cycle) and temperature (24±0.5℃).

Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Gene expression data from inflamed colorectal mucosa of the experimental group at the end of 2 weeks after intraperitoneal injection of AOM.

Gene expression data from normal colorectal mucosa of the control group at the end of 2 weeks after intraperitoneal injection of saline.

Gene expression data from low grade dysplasia lesion in the colorectum of the experimental group at the end of 4 weeks after intraperitoneal injection of AOM.

CD1;A2AR KO;male;14 weeks;ventricular myocardium;20 mg/kg LPS isolated from E. coli

8-10 weeks old male Villin-Claudin-2 transgenic mice and WT littermates were provided either normal drinking water (control) or Dextran Sodium Sulfate (DSS: 4% w/v) for 10 days.

The data were analyzed with Affymetrix's Expression Console using Affymetrix default analysis settings and RMA normalization method.

RNA was prepared using the RNeasy mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Gene 1.0 ST Array. Cartridges were washed and stained in the Affymetrix Fluidics Station 400.

Villin-Claudin-2 transgenic (Cl-2TG);colon epithelial cells;male;dextran sulfate sodium

Villin-Claudin-2 transgenic (Cl-2TG);colon epithelial cells;male;water

Peripheral blood mononuclear cells;TTF=70min;Race=White;Sex=Female

Peripheral blood mononuclear cells;oligoarticular JIA;LT6;132min;White;Female

Diabetic Male Wistar rat  after 28 days of diabetes induced with streptozotocin

Peripheral blood mononuclear cells;oligoarticular JIA;LT6;110min;Black/African American;Male

siRNA experiments (siEGFP; siEGR4), using Lipofectamin (Invitrogen), follwing the manufacturer's protocol.

Dried microarray slides were scanned immediately on the Agilent DNA Microarray Scanner using one color scan setting for 4x44K array formats (Scan area: 61x21.6 mm; Scan resolution: 5μm; Dye channel: Green; Green PMT: 100%).

Features of the scanned images were extract with Feature Extraction version 10.7 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid template: 014850_D_F_20080627) to obtain background subtracted and spatially detrended Processed signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The output files were processed for analysis of gene expression using GeneSpring version 11.5 and Microsoft Excel 2007.

RNA was prepared using the Qiagen RNeasy mini kit. DNase digestion were performed on-column. RNA was quantified using the NanoDrop-1000 Spectrophotometer and RNA quality was monitored using the Agilent 2100 Bioanalyzer (Agilent).

1.65 μg of Cy3-labelled cRNA (specific activity in the range of 13-25 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's protocol. When the fragmentation reaction completed, 55 μl of 2x Agilent's GEx hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to 4x44K Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed one minute at room temperature with  Agilent's GE Wash Buffer 1 (addition of Triton X-102 at 0.005%) and one minute with 37°C GE Wash buffer 2 (pre-warmed overnight at 37°C), dried the array slides at room temperature about 10 seconds, then scanned immediately using Tecan scanner. The procedures were performed in the ozone - protection hood as recommendation by Agilent manufacturer.

Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng of total RNA using the Agilent's Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (Qiagen).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer. cRNA was used for hybridization immediately without freezing and thawing.

SBC-5 cells, siEGFP (control), 48 hr after siRNA, duplicate sample 2

SBC-5 cells, siEGR4 (target), 48 hr after siRNA, duplicate sample 1

SBC-5 cells, siEGR4 (target), 48 hr after siRNA, duplicate sample 2

SBC-5 cells, siEGFP (control), 72 hr after siRNA, duplicate sample 1

SBC-5 cells, siEGFP (control), 72 hr after siRNA, duplicate sample 2

SBC-5 cells, siEGR4 (target), 72 hr after siRNA, duplicate sample 1

SBC-5 cells, siEGR4 (target), 72 hr after siRNA, duplicate sample 2

cKO females were injected intraperitoneally with vehicle (saline) or E2 (0.25 ug of 17beta-estradiol) for 2 h or 24 h.

cKO females at the age of 8 to 10 weeks were ovariectomized and housed for 10 days before the treatment.

Uterine samples were collected at 2 or 24 h after the injection. Tissues were immediately frozen in liquid nitrogen. RNA was extracted by using RNeasy Mini Kit (Qiagen, Valencia, CA) and treated with DNaseI (Qiagen) according to the manufacturer's protocol.

Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer's protocol.

Gene expression after 24h E2 treatment in cKO female mouse uterine tissue.
Replicate 1

C57BL/6;Wnt7aCre+;Esr1f/f (uterine epithelial ERα conditional knockout);8-10 weeks;female;uterus;17beta-estradiol;24h

Gene expression after 2h E2 treatment in cKO female mouse uterine tissue.
Replicate 3

C57BL/6;Wnt7aCre+;Esr1f/f (uterine epithelial ERα conditional knockout);8-10 weeks;female;uterus;17beta-estradiol;2h

MLL_00267;PBMC;no Multilineage dysplasia, acute myeloid leukemia, biallelic

MLL_00265;PBMC;no Multilineage dysplasia, acute myeloid leukemia, biallelic

MLL_00269;PBMC;no Multilineage dysplasia, acute myeloid leukemia, biallelic

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20597.gif
name: 20597_Infection

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20598.gif
name: 20598_Infection

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20578.gif
name: 20578_Infection

Common Reference 2 round amplification 2 ug;Mening UNSTIM WB SW 3a

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20595.gif
name: 20595_Infection

Common Reference 2 round amplification 2 ug;Mening UNSTIM WB SW 0b

Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/20790.gif
name: 20790_Infection

Common Reference 2 round amplification 2 ug;Mening SWB WB SW 24a

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20596.gif
name: 20596_Infection

Common Reference 2 round amplification 2 ug;Mening UNSTIM WB NP 3a

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20576.gif
name: 20576_Infection

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20592.gif
name: 20592_Infection

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20593.gif
name: 20593_Infection

Common Reference 2 round amplification 2 ug;Mening UNSTIM WB SW 1b

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20594.gif
name: 20594_Infection

C57Bl/6;wt;Cells cultured 96h with allogenic APC and anti CD3 antibody

Normal and PCOS women were treated with FSH after pituitary downregulation until E2 levels reached 300 pg/mL per dominant follicles. hCG  was then administered followed by transvaginal oocyte retrieval.

Ovarian aspirates were collected after oocyte retrieval from the consented normal and PCOS patients in the operating room and processed immediately for granulosa cell isolation and RNA extraction to minimize RNA degradation. RNA was stored at -80°C until use.

GeneChips were scanned using GeneChip® Scanner 7G by Affymetrix.

The CEL files from the two Affymetrix series were combined using the matchprobes package in the R programming environment. Thereafter, the RMA method in the R affy package was used to obtain probe set expression summaries.

Trizol extraction of total RNA was performed according to the manufacturer's instructions.The precipitated product was further purified using RNeasy Mini Kit (Qiagen, CA).

Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45 C on the HG-133 Plus 2 Affymetrix GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Control (TRE-Ovol2-Flag, or wild type 2 mice/array) and Ovol2 overexpression in epidermis (TRE-Ovol2-Flag;K5-tTA (Ovol2 BT), 2 mice/array)

Gene expression data from isolated skin
TRE-Ovol2-Flag or TRE-Ovol2-Flag;K5-tTA

C57BL/6-129Sv hybrid background;Setdb1 2lox/1lox/Cre;embryonic stem cell

C57BL/6-129Sv hybrid background;Setdb1 2lox/1lox;tamoxifen;embryonic stem cell

NSC were plated in 6-well polyornithine/laminin coated plates and treated 5h after plating with DMSO or X5050 during 24h.

NSCs were grown in medium containing Neurobasal, D-MEM/F-12, N-2 and B-27

the data were RMA normalized  and  analysed with Partek Genomic Suit

Extraction of total RNA with RNeasy Mini kit with DNase I digestion according to the manufacturer's instructions.

Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip human Gene from Affymetrix GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix)

Gene expression data from NSC SA-01 treated with X5050 (100 µM final)

blast count: 80

Sample_ID:t09 // Patient:J-128 // Histology:Intestinal // Metastasis:- // p53_mut:+ // E-cadherin_mut:+ // beta-Catenin_mut:+

Within 6 hours of collection, blood was processed by density gradient centrifugation using Ficoll-Paque PLUS (GE Healthcare, Sweden). Residual red blood cells were lysed and washed with phosphate-buffered saline (PBS). The isolated peripheral blood mononuclear cells (PBMCs) were stored at -80 oC.

Patients with primary pancreatic, gastric or HCC were recruited at diagnosis. Informed consent was obtained from all subjects before blood samples were collected. A total of 10 ml of blood was collected into BD Vacutainer® Plus K2EDTA tubes (Becton-Dickinson, USA).

The data was analysed using Partek Genomics Suite version 6.6. CEL files were imported into Partek with GCRMA background correction, quantile normalisation and log2 transformation.

Total RNA was extracted from PBMC and WBC using TRIzol reagent (Invitrogen, USA) according to the manufacturer's protocol.

Gene expression data from PBMC sample of hepatocellular carcinoma patient.

peripheral blood mononuclear cell (PBMC);hepatocellular carcinoma (HCC)

non tumorigenic human breast epithelial MCF10A cell line: Keap1 siNA_rep4

non tumorigenic human breast epithelial MCF10A cell line: Keap1 siNA_rep3

non tumorigenic human breast epithelial MCF10A cell line: Keap1 siNA_rep2

COP rats were obtained from Charles River Laboratories (Wilmington, MA). At 9 weeks of age, a silastic tubing implant containing 5mg of the synthetic estrogen diethylstilbestrol (DES) was surgically implanted subcutaneously in the interscapular region of male rats. Each animal received an intraperitoneal injection of BrdU (50mg/kg) 4 hours prior to sacrifice. Animals were sacrificed at 21 weeks of age by decapitation and pituitary glands were immediately harvested, weighed and flash-frozen in liquid nitrogen. Tissues were homogenized through a 22-gauge needle and total RNA was extracted using the Absolutely RNA Kit (Stratagene). A total of 4 DES-treated males were used, resulting in three independent biological replicates.

COP strain, male, age 21 weeks, treated with the synthetic estrogen diethylstilbestrol (DES) for 12 weeks

BN rats were obtained from Harlan (Indianapolis, IN). Empty silastic tubing implants were surgically inserted into control animals’ interscapular regions, as sham treatment, at 9 weeks of age. Each animal received an intraperitoneal injection of BrdU (50mg/kg) 4 hours prior to sacrifice. Animals were sacrificed at 21 weeks of age by decapitation and pituitary glands were immediately harvested, weighed and flash-frozen in liquid nitrogen. Tissues were homogenized through a 22-gauge needle and total RNA was extracted using the Absolutely RNA Kit (Stratagene). A total of 3 control males were used, resulting in two independent biological replicates.

C57BL/6N;Stat1 KO (ko);Bone marrow derived macrophages (BMMs);6h IFNg

PBMC were immediately isolated from 20 ml of whole blood by Ficoll–Hypaque (Flow Laboratories, Irvine, UK) density gradient centrifugation. Isolated cells were stored at –80°C in FBS+10% DMSO until use.

Before RNA extraction, cells were thaw, counted and their viability determined by Trypan Blue exclusion (>90% PBMC were viable). A minimum of 5 milion cryopreserved PBMC were centrifuged, and immediately lysed for RNA extraction.

We used the default settings of Affymetrix Microarray Suite software version 5 (MAS 5.0; Affymetrix) to calculate scaled gene expression values.

Total RNA was extracted by RNeasy mini kit (QIAGEN Inc., Valencia, CA) according to the manufacturer’s instructions and resuspended in DEPC-treated Rnase-free distilled water. RNA concentration was determined by NanoDrop® ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) and its integrity was assessed by electrophoresis using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

Affymetrix GeneChips Human Genome U133 Array Set HG-U133A (Affymetrix) were hybridizated with 15 micrograms of fragmented cRNA, according to manufacturer’s instructions

The One-Cycle cDNA Synthesis Kit (Affymetrix) was used. Starting from 1.5 micrograms of total RNA we performed the in vitro transcription (IVT) reaction for complementary RNA (cRNA) amplification and biotin labeling, according to the manufacturer’s instructions. The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip brand expression arrays.

Patient SE, stable renal transplant recipients, male, 31 years old, T0 (time of enrollment)

Patient SE, stable renal transplant recipients, male, 31 years old, T1 (3 months after the switching of the therapy)

Patient CV, stable renal transplant recipients, male, 58 years old, T0 (time of enrollment)

Patient CV, stable renal transplant recipients, male, 58 years old, T1 (3 months after the switching of the therapy)

Patient GM, stable renal transplant recipients, female, 53 years old, T0 (time of enrollment)

Patient GM, stable renal transplant recipients, female, 53 years old, T1 (3 months after the switching of the therapy)

Cells expressing IkBa dominant negative cultured in absence of dox, TNF stimulation for 1h

Cells expressing IkBa dominant negative cultured in absence of dox, TNF stimulation for 3h

sample of squamous cell carcinoma of the skin (scc_07):

sample of squamous cell carcinoma of the skin (scc_11):

sample of squamous cell carcinoma of the skin (scc_14):

Jurkat cells were cultured in RPMI 1640 + 10% fetal bovine serum.

sample of normal skin (no_21):

sample of normal skin (no_22):

sample of squamous cell carcinoma of the skin (scc_01):

sample of squamous cell carcinoma of the skin (scc_06):

Dox treatment (E6.5 to E14.5) induced tumors in CCSP-rtTA/TetO-Cretg/-/LSL-KrasG12D/PtenΔ/Δ mice between 10-12 weeks of age

Compound-transgenic mice harboring Pten gene with loxP-flanked exon-V (Ptenflox/flox), SP-C–rtTAtg/−; and TetO-Cretg/- were generated. Mice harboring SPC-rtTA/Ptenflox/flox, TetO-Cretg/-/Ptenflox/flox, SPC-rtTA, or TetO-Cretg/- as controls

Affymetrix Microarray Suite 5.0 was used to scan and quantitate the gene chips under default settings.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on mouse MOE430 chips Array. GeneChips were washed and stained in the Affymetrix

Male;77;3h;6.1;schizophrenic;superior temporal cortex (Brodmann Area 22, BA22)

Male;41;8h;6.3;schizophrenic;superior temporal cortex (Brodmann Area 22, BA22)

Two 90 minute exposures (3 hr recovery in between) to 1.0% isoflurane every day for 2.5 days, for a total of 5 exposures

Two 90 minute exposures (3 hr recovery in between) to 0.8% halothane every day for 2.5 days, for a total of 5 exposures

Two 90 minute exposures (3 hr recovery in between) to 1.0% isoflurane every day for 5 days, for a total of 10 exposures

MDA-MB-231 were transduced with a lentivirus expressing eGFP alone or GATA3 and eGFP and cells were sorted for GFP expression

MDA-MB-231 expressing control GFP or GATA3 were grown in DMEM/high glucose supplemented with 10% FBS, sodium pyruvate and pen/strep. 1.5 million cells were seeded into 100 mm dishes and RNA collected after 2 days.

Scanned on an Affymetrix GeneChip scanner 3000 and data collected using Affymetrix GCOS software

Data was processed into log base 2 gene expression measures with gcRMA algorithm and quantile normalization.  The data were processed in BRB-ArrayTools developed by Richard Simon and BRB-ArrayTools Development Team (http://linus.nci.nih.gov/BRB-ArrayTools.html).

RNA was isolated by Trizol® according to the manufacturer's instructions.  All samples used for microarray analysis had a high quality score (RIN >9).

RNA (1 ug) was reverse transcribed with a T7-oligo(dT) primer and biotin labeled using the Affymetrix One Cycle Target Labeling kit (Affymetrix) following the manufacturer’s protocol.

Gene expression data from IRAK1/IRAK2 KO macrophages stimulated with MALP-2 for 4h

Gene expression data from IRAK1/IRAK2 KO macrophages stimulated with MALP-2 for 8h

C3H-HeOuJ mice exposed to filterd air  for 72hrs- lungs were removed-frozen in liquid nitrogen-RNA extraction.
Lot batch =

C3H-HeJ mice were exposed to ozone. Lungs were removed-frozen in liquid nitrogen-RNA extraction.
Lot batch =

T127;Normal cortex;Male;35;Clear-cell renal cell carcinoma;wild type;wild type;wild type

T127;Clear-cell renal cell carcinoma (ccRCC) tumor;Male;35;Clear-cell renal cell carcinoma;T3NxM0;n/a;3;wild type;wild type;mutant

Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient T127

1393;Clear-cell renal cell carcinoma (ccRCC) tumor;Male;83;Clear-cell renal cell carcinoma;T1NxMx;n/a;1;wild type;wild type;mutant

Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 1393

1524;Normal cortex;Male;70;Clear-cell renal cell carcinoma;wild type;wild type;wild type

1524;Clear-cell renal cell carcinoma (ccRCC) tumor;Male;70;Clear-cell renal cell carcinoma;T1NxMx;n/a;2;wild type;mutant;mutant

Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 1524

T22;Clear-cell renal cell carcinoma (ccRCC) tumor;Male;67;Clear-cell renal cell carcinoma;T3N0M0;III;3;wild type;wild type;mutant

Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient T22

T26;Clear-cell renal cell carcinoma (ccRCC) tumor;Male;73;Clear-cell renal cell carcinoma;T3NxM1;IV;4;mutant;wild type;mutant

Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient T26

T79;Normal cortex;Male;59;Clear-cell renal cell carcinoma;wild type;wild type;wild type

T79;Clear-cell renal cell carcinoma (ccRCC) tumor;Male;59;Clear-cell renal cell carcinoma;T3NxM0;n/a;4;wild type;mutant;mutant

Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient T79

T84;Clear-cell renal cell carcinoma (ccRCC) tumor;Male;52;Clear-cell renal cell carcinoma;T4N1M1;IV;4;wild type;mutant;mutant

Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient T84

p53-null NSCs were infected with retrovirus expressing either control vector or PlagL2, and cultured in 1% FBS for 24 hr.

lung tissue;CD-1_Nrf2 -/-;13 weeks + 5 month + 13 days;2R4F whole mainstream smoke 750 µg/ml, treatment over 5 month + 15 days recovery, 3x1h exposure per day

First strand cDNA was synthesized from 1 ug total RNA by incubation (42C, 1 hr) in a 20 ml reaction volume containing 2.5 mM T7-(dT)24 primer, 50 mM Tris-HCl pH 8.3, 75 mM KCL, 3 mM MgCl2, 10 mM DTT and 500 mM dNTP, 10 U/ml Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA, USA).Second strand cDNA was synthesized directly by adding 91 ml RNase free water, 30 ml 5 times second strand reaction buffer (Invitrogen), 3 ml 10 mM dNTP, 1 ml Escherichia coli DNA ligase (10 U/ml), 4 ml E. coli DNA polymerase I (10 U/ml), 1 ml E. coli RNase H (2 U/ml) followed by incubation (2 hr, 16C). The ends of the double-stranded cDNA were polished using T4 DNA polymerase (20 U, 5 min, 16C). The cDNA was purified and concentrated by phenol/ chloroform extraction and ethanol precipitation.

Female (age range 33-49), skin biopsy from upper nates. No nickel exposure

Female (age range 33-49), skin biopsy taken from upper nates no nickel exposure

134;None;12/21/50;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;7/12/05;Abdominal pain;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;11-15-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

135;none;8/14/59;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;7/28/05;bloody diahorrea;0;TRUE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;11-15-01;descending colon;Uninflamed;total RNA from 10 human cell lines

133;Omeprazole 20mg;4/23/65;M;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;5/13/05;FH Colon Cancer;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;11-15-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

Trasnsformed Lymphocytes Unaffected (Unaffected pateint of MZ twin pair 1)

Melan-Ink4a cells stimulated with 10 nM NRG1-b1 (NRG1) (No. 377-HB; R&D Systems, Minneapolis, MN, USA) for 21 days.

All cells were grown at 37°C with 10% CO2 in RPMI medium 1640 supplemented with 10% FBS (Gibco, Scotland, UK), 200 nM 12-O-Tetradecanoylphorbol 13-acetate (TPA) (Sigma- Aldrich, St Louis, MO, USA) and 200 pM cholera toxin (CT) (Sigma- Aldrich). Medium was changed thrice a week. Total RNA was isolated from 90% confluent cells.

Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays. Gene expression intensities were calculated using the Gene Chip Operating software 1.2 (GCOS 1.2; Affymetrix).

Cel files generated by the Affymetrix GCOS program were imported in the Affymetrix Expression Consol program and RMA (Robust Microarray Analysis) normalization was performed to generate the .Chp files.

Total RNA was isolated from 90% confluent cells as reported by Loftus et al. (2002) with one modification: following the Trizol reagent (Invitrogen, Carlsbad, CA, USA) lysis of the cell, a 5 min, 65°C incubation was added.

Hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix Mouse GeneChipÒ 1.0 ST chips according to Affymetrix protocols.Chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described by Affymetrix.

200 ng of total RNA was used in conjunction with the Affymetrix recommended protocol for the GeneChip 1.0 ST chips.

Biological replicates were collected from consecutive passages, no additional treatment was performed.

Prdm14-null and wild-type control cells were grown in 2i culture conditions as described by Ying et al. (Nature, 2008)

The data were normalised using quantile normalisation with the lumi package in Bioconductor
not detected probes omitted (detection p-value where a probe is not detected in a sample if the p-value is above 0.01)

RNA was extracted with the RNeasy kit from Qiagen, followed by clean-up and DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

The Illumina Total-prep 96-RNA amplification kit from Ambion was used.

Mouse bone marrow-derived mast cells treated with IL3+SCF, rep 6

Gene expression data from mouse bone marrow-derived mast cells treated with IL3+SCF, rep 6 of 6.

reduction mammoplasty histologically normal breast epithlieum patient 368

reduction mammoplasty histologically normal breast epithlieum patient 360

RNA was extracted from a pool of three spleens taken from three month old C57BL/10 derived B10.NOD H2g7 Idd3 congenic mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.

RNA was extracted from a pool of three spleens taken from three month old nonobese diabetic (NOD) mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.

skeletal muscle (gastrocnemius);male;Zucker;fatty (fa/fa);Troglitazone

skeletal muscle (gastrocnemius);male;Zucker;fatty (fa/fa);Pioglitazone

skeletal muscle (gastrocnemius);male;Zucker;lean (fa/+);normal chow

skeletal muscle (gastrocnemius);male;Zucker;fatty (fa/fa);Rosiglitazone

Subject Age : 48

Wt Mouse_cerebellum_Standard diet supplemented with resveratrol_Ad Lib_Replicate-3

Sample name: WT_Resv_4

C57BL/6;WT;male;cerebellum;1 year;SD supplemented with 100 mg/kgchow resveratrol ad libitum

Wt mouse, cerebellum, standard diet supplemented with resveratrol ad lib

Wt Mouse_cerebellum_Standard diet supplemented with resveratrol_Ad Lib_Replicate-4

Sample name: WT_Resv_5

Wt Mouse_cerebellum_Standard diet supplemented with resveratrol_Ad Lib_Replicate-1

Sample name: WT_Resv_2

Wt Mouse_cerebellum_Standard diet supplemented with resveratrol_Ad Lib_Replicate-2

Sample name: WT_Resv_3

Sample name: WT_SD_3

C57BL/6;WT;male;cerebellum;1 year;standard AIN-93G diet (SD; carbohydrate:protein:fat ratio of 64:19:17 percent of kcal) ad libitum for 8 months

Sample name: WT_SD_4

Wt Mouse_cerebellum_Standard diet supplemented with resveratrol_Ad Lib_Replicate-5

Sample name: WT_Resv_6

Sample name: WT_SD_2

Sample name: WT_SD_5

Csbm/m Mouse_cerebellum_Old_nicotinamide riboside treatment_Replicate-1

Sample name: OLD-CSB_NR-15

Peripheral blood mononuclear cells;oligoarticular JIA;GTE6;230min;White;Female

Dicer Knockout 1

Peripheral blood mononuclear cells;oligoarticular JIA;GTE6;210min;White;Male

Peripheral blood mononuclear cells;oligoarticular JIA;GTE6;225min;White;Male

Peripheral blood mononuclear cells;oligoarticular JIA;LT6;120min;White;Female

Peripheral blood mononuclear cells;oligoarticular JIA;GTE6;90min;White;Female

Cells were plated on collagen-coated six-well plates. Viability was determined by Trypan Blue exclusion, and was at least 75%. Hepatocytes were suspended in William's E medium (Lonza Bioscience, Verviers, Belgium) supplemented with 10% (v/v) fetal calf serum, 20 m-units/mL insulin, 10 nM dexamethasone, 100 U/mL penicillin, 100 μg/mL of streptomycin, 0.25 μg/mL fungizone and 50 μg/mL gentamycin. After four hours the medium was discarded and replaced with fresh medium. The next day, cells were incubated in fresh medium in the presence or absence of Wy14643 (10 uM) dissolved in DMSO for 6 and 24 hours, followed by RNA isolation.

Mouse hepatocytes were isolated by two-step collagenase perfusion from 6 different strains of mouse; NMRI, SV129, FVB, DBA, BALB/C and C57BL/6J.

Total RNA was prepared from mouse primary hepatocytes using TRIzol reagent and whereafter Purified total RNA was isolated using Qiagen RNEasy columns.

Primary hepatocytes isolated from SV129 mouse strain treated with DMSO for 6h

Primary hepatocytes isolated from SV129 mouse strain treated with Wy14643 for 24h

Primary hepatocytes isolated from SV129 mouse strain treated with DMSO for 24h

Primary hepatocytes isolated from FVB mouse strain treated with Wy14643 for 6h

Primary hepatocytes isolated from BL6 mouse strain treated with DMSO for 6h

Primary hepatocytes isolated from BL6 mouse strain treated with Wy14643 for 24h

Primary hepatocytes isolated from BL6 mouse strain treated with DMSO for 24h

Primary hepatocytes isolated from SV129 mouse strain treated with Wy14643 for 6h

Primary hepatocytes isolated from FVB mouse strain treated with DMSO for 6h

Primary hepatocytes isolated from FVB mouse strain treated with Wy14643 for 24h

luteinized human cumulus cells, cultured 48h, nonPCOS, Lean, rep5

luteinized human cumulus cells, cultured 48h, nonPCOS, Lean, rep6

luteinized human cumulus cells, cultured 48h, nonPCOS, Lean, rep3

luteinized human cumulus cells, cultured 48h, nonPCOS, Lean, rep4

luteinized human cumulus cells, cultured 48h, nonPCOS, Obese, rep3

luteinized human cumulus cells, cultured 48h, nonPCOS, Obese, rep4

luteinized human cumulus cells, cultured 48h, nonPCOS, Obese, rep1

luteinized human cumulus cells, cultured 48h, nonPCOS, Obese, rep2

luteinized human cumulus cells, cultured 48h, nonPCOS, Obese, rep5

Monolayers of HUVECs in 9 cm Petri dishes were washed and collected into Trizol by cell-scraper

Confluent monolayers of HUVECs in 9 cm Petri dishes were cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 4 hours

bone marrow mesenchymal stromal cells (BM-MSCs);multiple myeloma;IIIa;F;47

bone marrow mesenchymal stromal cells (BM-MSCs);multiple myeloma;IIIb;F;52

bone-marrow mesenchymal stromal cells extracted from healthy donor

Control rats 72h after injection with PBS
Treatment, type=time_course, description=Control animals are treated with PBS, measurement=72.0 h

Gene expression was quantified by robust multi-array analysis (RMA)

Total RNA was extracted from individual yolk sacs (n = 4 per group) using RNAzol (Campro Scientific, Veenendaal, The Netherlands) and glass beads according to the manufacturer's instructions.
biotin

The One-Cycle Target Labeling and Control Reagent kit (Affymetrix #900493) and the protocols optimized by Affymetrix were used to prepare biotinylated cRNA (from 5μg of total RNA) for microarray hybridization.

total RNA from mouse embryo yolk sacs, 4 individual yolk sacs of each genotype were pooled as sample.

Gene expression after 24h vehicle treatment in cKO female mouse uterine tissue.

C57BL/6;Wnt7aCre+;Esr1f/f (uterine epithelial ERα conditional knockout);8-10 weeks;female;uterus;saline;24h

Replicate 2

Rats 24h after injection with dose kainate.
Treatment, type=time_course, description=KA animals are treated with kainate., measurement=24.0 h

Control rats 24h after injection with PBS
Treatment, type=time_course, description=Control animals are treated with PBS, measurement=24.0 h

Gene expression data from mouse CD3+ Itk knockout T-cells with anti-CD3 stimulation

Gene expression data from mouse CD3+ Wt T-cells with anti-CD3 stimulation

Rats 72h after injection with dose kainate.
Treatment, type=time_course, description=KA animals are treated with kainate., measurement=72.0 h

MOLM-14 cell line, transduced with shSYK_2 and selected with  1 µg/ml puromycin 48 hours post-infection

MOLM-14 cell line, transduced with shSYK_1 and selected with  1 µg/ml puromycin 48 hours post-infection

Raw data were processed using the RMA method.  Values are in Log base 2.

GeneChip Expression 3'Amplification One-Cycle Target Labeling (Affymetrix)

This sample is part of three biological replicates of WT genotype

MOLM-14 cell line, transduced with a control luciferase and selected with  1 µg/ml puromycin 48 hours post-infection

This sample is part of three biological replicates of FHL-/- genotype

U937 cell line, transduced with a control luciferase and selected with  1 µg/ml puromycin 48 hours post-infection

LaserPower: 2.53;; 1.26
Temperature: 38.23

Stimulations were done with plate-coated anti-CD3(1mg/ml) and anti-CD28 (1mg/ml)for 13 hours.

Mice were maintained under specific pathogen-free conditions according to institutional guidelines under approved protocols in Kyoto University.

Slide were washed and then scanned with an Agilent G2505B scanner

Data were obtained and processed with the Agilent Feature Extraction Software(v9.5).  The resulting data were imported into Expressionist and quantile normalized intensities were exported.

Total RNAs were extracted with Qiagen RNeasy mini kit with on-column DNaseI treatment.  RNA quality was assessed using Agilent 2100 Bioanalyzer according to manufacturer's instructions.

Cy3 labeled cRNA was produced using Agilent Low Input QuickAmp Labeling Kit according to manufacturer's protocol.

C57BL/6;Female;7 weeks old;CD4 positive T cell;TCR-stimulated;WT

C57BL/6;Female;6 weeks old;CD4 positive T cell;unstimulated;Trim28CKO

Trim28 conditional KO mice naïve CD4 positive cell, unstimulated, replicate 1

Trim28 conditional KO mice naïve CD4 positive cell, unstimulated, replicate 2

Trim28 conditional KO mice naïve CD4 positive cell, unstimulated, replicate 3

C57BL/6;Female;6 weeks old;CD4 positive T cell;TCR-stimulated;WT

LaserPower: 2.51;; 1.34
Temperature: 34.68

C57BL/6;Female;7 weeks old;CD4 positive T cell;unstimulated;Trim28CKO

Trim28 conditional KO mice naïve CD4 positive cell, unstimulated, replicate 4

C57BL/6;Female;7 weeks old;CD4 positive T cell;TCR-stimulated;Trim28CKO

Trim28 conditional KO mice naïve CD4 positive cell, TCR-stimulated, replicate 1

E9.5 yolk sacs tissues were rinsed once in 1:1 20% sucrose PBS:Optimal Cutting Temperature freezing media (OCT, Tissue-Tek), then OCT alone and frozen. A small portion of the embryo tail was used for PCR genotyping. Eight micron E9.5 sections were stained with the LCM frozen section staining kit (Molecular Devices, Mountain View, CA, USA) and used for laser capture dissection experiments. The ArcturusXT™ laser capture microdissection (LCM) instrument (Applied Biosystems, Inc.) was used to isolate erythroid cells from yolk sac cryosections obtained from WT, KLF1-/-, and KLF1-/-KLF2-/- embryos. The manufacturer’s protocol was followed for preparing the instrument, isolating the cells, and visually inspecting the isolated erythroid cells on the LCM cap.

Timed-pregnant mice were anesthetized and sacrificed. E9.5 yolk sacs were dissected from the embryo and cryoprotected in PBS with 20% sucrose.

Image analysis was performed on the E9.5 WT, KLF1-/-, and KLF1-/-KLF2-/- erythroid yolk sac data set using the GeneChip Operating System version 1.4 (GCOS1.1, Affymetrix Inc.). The image of the scanned array was stored as a DAT file using the Affymetrix software.

Quality control parameters such as scaling factors used to normalize the chips, average background and noise were also analyzed. The raw intensities for each probe set were stored in electronic formats by the GCOS software. Scaling factors used to normalize the chips to a target value (TGT), and in this study, the TGT was set at 100. Probe set expression summaries were calculated with the Probe set expression summaries were calculated with the Robust Multi-average (RMA) algorithm (Irizarry et al., 2003). RMA expression summaries were obtained for wildtype,  KLF1-/-, and KLF1-/-KLF2-/- erythroid GeneChips using the rma function in the affy package in R/Bioconductor. Thereafter control probe sets were removed leaving 22,626 probe sets for statistical analysis. A moderated t-test was used to compare the 8 WT and 3 KLF1-/- samples using the limma Bioconductor package (Gentleman et al., 2004; Smyth et al., 2004) in the R programming environment (http://www.R-project.org), and to identify the probe sets that were significantly differentially expressed. The Jonckheere-Terpstra test for trend was performed to identify probe sets having significantly decreasing expression across the 8 wild-type, 3 KLF1-/-, and 3 KLF1-/-KLF2-/- samples.

Total RNA was isolated from WT, KLF1-/-, and KLF1-/-KLF2-/- erythroid cells using reagents from the (ToTALLY RNA isolation kit; Ambion Inc., Austin, TX, USA) and quality assessment by capillary electrophoresis were performed as previously described (Redmond et al., Blood Cells Molecules and Diseases 2006, 37:27).

Fifteen μg of labeled erythroid RNA was fragmented and 10 μg was hybridized to Affymetrix GeneChip Mouse Genome 430A 2.0 arrays for 18 hours (Affymetrix Inc.). The 8 microarrays were washed and stained with streptavidin–phycoerythrin as described (Redmond et al., Blood Cells Molecules and Diseases 2006, 37:27).

Ten to 20 ng of WT, KLF1-/-, and KLF1-/-KLF2-/- erythroid RNA was used to generate double stranded cDNA with the T7-oligo (dT) primer according to the Affymetrix GeneChip Two cycle target labeling protocol (Affymetrix Inc., Santa Clara, CA, USA). Labeled cRNA yield and purity was determined as described (Redmond et al., 2006).

Comparison between mouse embryonic day 9.5 (E9.5) wild-type, KLF1-/-, KLF1-/- KLF2-/- yolk sac microdissected erythroid precursors

Following washing and staining, the BeadChips were imaged using the Illumina iScan Reader to measure fluorescence intensity at each probe.

BeadChip data files were analyzed with Illumina’s GenomeStudio gene expression module (v1.8.0)

Total RNA from 10-20 mg fresh frozen tissues were prepared using the RNeasy mini kits (Qiagen, Valencia, CA) following manufacturer’s instructions. After elution, RNA samples were concentrated by EtOH precipitation at –20oC overnight, and resuspended in nuclease-free water.  Before labeling, RNA samples were quantitated using a ND-1000 spectrophotometer (NanoDrop Wilmington, DE) and evaluated for degradation using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Samples were required to have a RIN >6.5, an OD 260:280 of 1.9-2.1, an OD 260/230 >1.5 and >1.5 28S:18S ratio of the ribosomal bands for gene expression array analysis.

750ng of the biotin labeled cRNA probes were mixed with hybridization reagents and hybridized overnight to the HumanHT-12 v4 BeadChips.

Initially, 500ng total RNA was converted to cDNA, followed by an in vitro transcription step to generate biotin labeled cRNA using the Ambion Illumina Total Prep RNA Amplification Kit (Ambion, Austin, TX) as per manufacturer’s instructions.

U87;20 uM Temozolomide + 10 uM Y15;glioblastoma cancer cell line

human cellular RNA_primary airway epithelial cells_tracheobronchial _H465_6h_Con_HG-U133A_2_YCHSUP501

H465_6h_Con_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;24.450;2.11

human cellular RNA_primary airway epithelial cells_tracheobronchial _H510_2h_0.4mM_HG-U133A_2_YCHSUP501

H510_2h_0.4mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;24.116;2.13

human cellular RNA_primary airway epithelial cells_tracheobronchial _H511_6h_Con_HG-U133A_2_YCHSUP501

H511_6h_Con_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;23.783;2.13

human cellular RNA_primary airway epithelial cells_tracheobronchial _H465_6h_4mM_HG-U133A_2_YCHSUP501

H465_6h_4mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;21.753;2.10

human cellular RNA_primary airway epithelial cells_tracheobronchial _H510_2h_Con_HG-U133A_2_YCHSUP501

H510_2h_Con_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;28.105;2.13

human cellular RNA_primary airway epithelial cells_tracheobronchial _H510_6h_0.4mM_HG-U133A_2_YCHSUP501

H510_6h_0.4mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;29.459;2.10

human cellular RNA_primary airway epithelial cells_tracheobronchial _H510_2h_1mM_HG-U133A_2_YCHSUP501

H510_2h_1mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;19.666;2.14

human cellular RNA_primary airway epithelial cells_tracheobronchial _H510_2h_4mM_HG-U133A_2_YCHSUP501

H510_2h_4mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;23.69;2.13

human cellular RNA_primary airway epithelial cells_tracheobronchial _H510_6h_1mM_HG-U133A_2_YCHSUP501

H510_6h_1mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;30.888;2.10

human cellular RNA_primary airway epithelial cells_tracheobronchial _H510_6h_4mM_HG-U133A_2_YCHSUP501

H510_6h_4mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;25.208;2.10

VX was added to cell culture at the specified concentrations and maintained for 1 h. Then VX was removed and the culture was washed 3X with fresh medium. The culture was then maintained at 37 °C with 5% CO2 until the indicated time points.

Human hNHEPS hepatocytes were seeded in 6-well plates in media formulated by the manufacturer (Lonza, Walkersville, MD) and cultured at 37 °C under humidified 5% CO2 for 48 h before VX exposure.

The chips were scanned using an Affymetrix GeneChip Instrument System and the image (.DAT) files were processed using the Affymetrix GeneChip Operating Software (GCOS) to generate cell intensity (.CEL) files.

The data were averaged and normalized in Partek Genomics Suite 6.5 (Partek, St. Louis, MO) using the robust multiarray analysis (RMA) algorithm.

Total RNA was isolated using the RNeasy Plus Mini Kit from Qiagen (Valencia, CA) following the manufacturer’s protocol, including an on-column DNase digestion.

Hybridization was carried out using the Affymetrix GeneChip Hybridization, Wash, and Stain Kit following the manufacturer’s protocols.

~0.1 μg of total RNA were labeled using the Affymetrix (Santa Clara, CA) GeneChip 3’ IVT Express Kit following the manufacturer’s protocol.

gene expression data of hNHEPS human hepatocytes not exposed to VX at the beginning of experiment

Normal human primary hepatocytes isolated from non-transplantable donor tissue;0;0;none

hNHEPS human hepatocytes not exposed to VX at the beginning of experiment

gene expression data of hNHEPS human hepatocytes not exposed to VX at 6 h

Normal human primary hepatocytes isolated from non-transplantable donor tissue;6 h;0;none

blast count: 92

blast count: 30

blast count: 16

blast count: 51

blast count: 61

Air
1
24

Air
1
24

Synovium; acute arthritis

Nervous Sysem; Peripheral, Sensory-dorsal root ganglion

Skin;  Skin postnatal Day 2-3

Skin; Fetal Skin Day 16

Tissue dissection and immediate immersion/homogenization in TRIzol.  Aqueous phase transferred to QIAgen RNeasy Mini column for RNA prep.

See Affymetrix GeneChip® Expression Analysis Technical Manual.  Used the GeneChip® Fluidics Station 450.

C57BL-6J mice were given intratracheal saline control and sacrificed at 24 hrs.

C57BL-6J  were given intratracheal saline control.  Lungs were harvested and frozen at 14d.
Lot batch =

C57BL-6J were given intratracheal bleomycin (1.5U per kg).  Lungs were harvested and frozen at 72h.
Lot batch =

C57BL-6J were given intratracheal bleomycin (1.5U per kg) and sacrificed at 24hrs.
Lot batch =

Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. At P18, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.

Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. At P21, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.

Mice used were in a mixed background between 129/SvEv and C57BL/6. They were Rp1 knockout mice (Rp1-/-). At P7, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.

Oral Squamous cell Epithelium Tissue-Normal;OSCC-9;Tongue;66;M;T2N0M0;TNM,Tumor-node-metastasis

A549 human lung cancer cells (1X10^5 per T-25 flask in 7 mL complete RPMI 1640 medium) were seeded eights days prior to treatment of non-cycling plateau phase cultures with drug.  At four hours prior to RNA isolation, mannitol (5% final concentration) was added to the culture.  After incubation for four hours, the culture was washed twice with HBSS supplemented with 0.5% BSA and total RNA was isolated.

Mannitol control treated A549 human lung cancer cell cultures replicate A

Actinomycin D treated A549 human lung cancer cell cultures replicate C

Mannitol control treated A549 human lung cancer cell cultures replicate C

Mannitol control treated A549 human lung cancer cell cultures replicate B

Actinomycin D treated A549 human lung cancer cell cultures replicate B

1.25uM sapphyrin PCI-2050 treated A549 human lung cancer cell cultures replicate B

1.25uM sapphyrin PCI-2050 treated A549 human lung cancer cell cultures replicate A

Gene expression data under ER stress from lymphoblastoid cells of twin 1735:1 treated with 500nM thapsigargin.

lymphoblastoid cell line;1735;GM14506;Twin number 1;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1735:1 treated with DMSO.

lymphoblastoid cell line;1735;GM14506;Twin number 1;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1726:2 treated with 500nM thapsigargin.

lymphoblastoid cell line;1726;GM14479;Twin number 2;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1726:2 treated with DMSO.

lymphoblastoid cell line;1726;GM14479;Twin number 2;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1726:1 treated with 500nM thapsigargin.

lymphoblastoid cell line;1726;GM14478;Twin number 1;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1726:1 treated with DMSO.

lymphoblastoid cell line;1726;GM14478;Twin number 1;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1721:2 treated with 500nM thapsigargin.

lymphoblastoid cell line;1721;GM14468;Twin number 2;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1721:2 treated with DMSO.

lymphoblastoid cell line;1721;GM14468;Twin number 2;DMSO;4 hours

Gene expression data from atherosclerotic aortas isolated from APOE-deficient mice.
APOE-2

APOE-1

Gene expression data under ER stress from lymphoblastoid cells of twin 1735:2 treated with 500nM thapsigargin.

lymphoblastoid cell line;1735;GM14507;Twin number 2;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1735:2 treated with DMSO.

lymphoblastoid cell line;1735;GM14507;Twin number 2;DMSO;4 hours

gavage with D3T (3H-1, 2-dithiole-3-thione) for 0.3 mmol/kg body weight, disolved in vehicle (saturated sucrose); 1st, 3rd and 5th day, once per day

gavage with 0.2 ml vehicle (saturated sucrose); 1st, 3rd and 5th day, once per day

IA, IB, II, IIIA, IIIB, or IV=IV;67;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=IV;63;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=IV;NA;female, male:NA;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=not determined;normal

IA, IB, II, IIIA, IIIB, or IV=IV;65;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=IV;63;female, male:female;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=IV;73;female, male:female;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=IV;52;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=IV;39;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=mixed type;normal

normal;IA, IB, II, IIIA, IIIB, or IV=IA;73;female, male:male;early gastric cancer or advanced gastric cancer=early gastric cancer;moderately differentiated or poorly differentiated=moderately differentiated;intestinal type, diffuse type, mixed type, or not determined=intestinal type

normal;IA, IB, II, IIIA, IIIB, or IV=IA;60;female, male:male;early gastric cancer or advanced gastric cancer=early gastric cancer;moderately differentiated or poorly differentiated=moderately differentiated;intestinal type, diffuse type, mixed type, or not determined=intestinal type

brain (frontal cortex);healthy control;45 yr;white;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);healthy control;40 yr;white;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);healthy control;31 yr;white;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);healthy control;39 yr;white;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);schizophrenia;59 yr;white;295.9;14 yr;male;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);healthy control;53 yr;white;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);healthy control;38 yr;white;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);healthy control;60 yr;white;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

"female subject, 18-45 yrs, peripheral blood mononuclear cells prior to 30 min intravenous saline challenge"

"female subject, 18-45 yrs, peripheral blood mononuclear cells 6 h after intravenous saline challenge"

"female subject, 18-45 yrs, peripheral blood mononuclear cells prior to (baseline - 0 h) intravenous saline challenge"

Mice were treated with either PBS or heart-passaged CVB3 intraperitoneally. Mice were harvested at 10 days post infection and hearts were flash frozen in liquid nitrogen for RNA extraction.

Gene expression data of female hearts after a 10 day treatment of CVB3

Gene expression data of male hearts after a 10 day treatment of PBS

Gene expression data of female hearts after a 10 day treatment of PBS

Cells were grown in suitable growth media (Cascade Biologics Medium 254 for melanocytes and DMEM F12 with 5% serum for all cell lines)

Microarray Suite 5.0 (MAS 5.0; Affymetrix) software was used to analyze the HG-U133A arrays. All the arrays were normalized to a target signal intensity value of 500.

Total RNA was isolated using Qiagen Rneasy kit according to manufacturers' recommendations

Biotinylated cRNA was prepared according to Affymetrix instructions

image acquisition and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit (P/N 4342142) and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer (P/N 4338036) following the manufacturer’s protocol (P/N 4339629).

Images were auto-gridded and the chemiluminescent signals were quantified, corrected for background, and finally, spot- and spatially-normalized using the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer software v 1.1 (P/N 4336391).

RNA was extracted from the cell lines using our standard procedures using an Invitrogen RNA purification kit (Invitrogen, Carlsbad, CA) according to the instructions provided by the manufacturer and stored in Ambion RNA storage solution at –80o

Array hybridization was performed for 16 hrs at 55 oC. Chemiluminescence detection, image acquisition and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit (P/N 4342142) and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer (P/N 4338036) following the manufacturer’s protocol (P/N 4339629).

Digoxigenin-UTP labeled cRNA was generated and amplified from 2 μg of total RNA from each sample using Applied Biosystems Chemiluminescent RT-IVT Labeling Kit v 1.0 (P/N 4340472) according to the manufacturer’s protocol (P/N 4339629).

Animals were injected i.p. vehicle (5% DMSO in corn oil). After 10 h they were sacrificed.

Raw data were first normalized using log2-transformed expression measure summaries of the probe sets which were computed and normalized using the Robust Multichip Average (RMA) algorithm as described. After transformation to non-logarithmic data, the expression estimates were scaled to the average expression levels in the control group and transcript levels further analyzed using Gene Spring Software (Silicon Genetics, Redwood, USA).

All was done according to the Affymetrix recommendations. Briefly, double-stranded cDNA was synthesised using 10μg of total RNA with a (dT)24-T7 primer and amplified with T7 RNA polymerase in the presence of biotinylated nucleotides to cRNA.

primary unilateral non-metastatic postmenopausal ERα-positive breast tumor;woman;62 years

primary unilateral non-metastatic postmenopausal ERα-positive breast tumor;woman;74 years

primary unilateral non-metastatic postmenopausal ERα-positive breast tumor;woman;72 years

Primary culture of dermal fibroblasts from keloid, treated with 1.5uM hydrocortisone

Cirrhosis was induced by inhalation of CCl4 administered twice weekly. Control and cirrhotic rats were fed ad libitum with standard feed and water containing Phenobarbital (0.3 g/L) as drinking fluid

Scanning was performed with an Agilent Microarray Scanner (Agilent Technologies)

GeneChip analysis was performed with libraries from the Bioconductor project. The starting point for all the analysis was the CEL files generated by the Affymetrix software. Each CEL file contains data on the intensity at each probe on the GeneChip. To import CEL file data into the Bioconductor system, we used the ReadAffy function of the “affy” package. Next, we used the RMA approximation for background adjustment, normalization, and summarization using the median polish algorithm . The RMA measures were computed using the RMA function from the affy package.

Total RNA was extracted from frozen liver with Trizol reagent (Life Technologies, Rockville, MD). The extracted total RNA was purified with the RNeasy kit (Qiagen).

The fragmented cRNA was hybridized to the oligonucleotide microarray, which was washed and stained with streptavidin-phycoerythrin  as described in the Affymetrix GeneChip Expression Analysis Manual (Affymetrix, Santa Clara, CA)

Twenty µg of total RNA was used to synthesize double-strand cDNA with SuperScript II reverse transcriptase (Life Technologies) and a T7-(dT)24 primer (Metabion, Germany). Then, biotinylated cRNA was synthesized from the double-stranded cDNA using the RNA Transcript Labeling kit (Enzo Life Sciences) and was purified and fragmented.

Wistar, Gender: male, Tissue: cirrhotic liver, Induction of cirrhosis: CCl4

Cirrhosis was induced by inhalation of CCl4 administered twice weekly. Control and cirrhotic rats were fed ad libitum with standard feed and water containing Phenobarbital (0.3 g/L) as drinking fluid .

Osteocytes/-blasts in P2 from human bone chips of patients with OA

Mouse Prmt6 was cloned into pCAGIP.puro and transfected into HM1 cells with Lipofectamine 2000 (Invitrogen). Cells were subjected to 3 days of selection by puromycin (1μg/ml).

HM1 mouse ES cells were cultured in GMEM (GIBCO) supplemented with 15% ES qualified fetal bovine serum (FBS; Hyclone), 1mM sodium pyruvate (GIBCO), 0.1mM β-mercaptoethanol, 0.1mM MEM non-essential amino acids (NEAA; GIBCO) and 1000U/ml of leukemia inhibitory factor (LIF; Millipore) at 37°C and 5% CO2.

The data were analyzed with Robust Multi-array Analysis (RMA) as normalization method.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Gene expression data from control embryonic stem cells
Control RNA 01

MO-B10-WT 4

4 NPC cells, including two from NESG1-negative C6-Ctr cells and two from NESG1-expressing 2F4 cells were cultured by 10% newborn calf serum (NBCS)

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at -80℃ on GeneChip U133_Plus_2 (GPL570 platform)Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

2F4-2
Gene expression data from NESG1-overexpressed NPC 5-8F cells

C6-1
Gene expression data from NESG1-negative expression NPC 5-8F cells

C6-2

ko_7_Cy3

raw data file: US22502676_251486810270_S01_GE2-v5_95_Feb07_1_2.txt
ko_2_Cy5

wt_6_Cy3

raw data file: US22502676_251486810270_S01_GE2-v5_95_Feb07_1_1.txt
wt_1_Cy5

ko_5_Cy3

Pooled Total Prefrontal cortex RNA from 4 female mice overexpressing the human synaptic AChE.

Male;15 months;additional patient information found in Series supplementary file

Male;20 months;additional patient information found in Series supplementary file

Male;28 months;additional patient information found in Series supplementary file

Male;22 months;additional patient information found in Series supplementary file

Male;61 months;additional patient information found in Series supplementary file

Male;47 months;additional patient information found in Series supplementary file

Bone marrow-derived macrophages, MyD88 -/-, unstimulated, 0 minutes

Primary Human Hepatocyte;Female;In Vitro Technologies;Celebral Vascular Accident;1st technical replicate

Primary Human Hepatocyte;Female;In Vitro Technologies;Celebral Vascular Accident;No;1st technical replicate

gene expression data from human embryonic stem cells (lineage H1)

Primary Human Hepatocyte;Female;In Vitro Technologies;Celebral Vascular Accident;Yes

Gene expression data from HDAC1 knock out mouse embryonic stem cells

Mus musculus embryonic stem cells derived from HDAC1 knock out embryos

75;Clear-cell renal cell carcinoma (ccRCC) tumor;Female;48;Clear-cell renal cell carcinoma;T2N0M0;II;2;wild type;mutant;mutant

Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 75

Keywords = Mus musculus,  SJL/J, skeletal muscle, quadriceps, effect of deleted gene dysferlin

Keywords = Mus musculus,  SJL/J,  skeletal muscle, quadriceps, effect of deleted gene dysferlin

Cell strain 7 of cyclin D1KO 3T3 cells obtained by serial passaging MEFs from E14 embryos, stably infected with MSCV murine stem cell virus expressing cyclin D1a.

Sample from retroviral MSCV-D1a infected cyclin D1 knockout 3T3 cells (line 7).

Gene expression data from cyclin D1 knockout 3T3s (cell line 7) infected with full length cyclin D1 (variant D1a) using Murine Stem Cell Virus (MSCV) system.

Cyclophosphamide-treated bone marrow 1 day - Biological Replicate 1 - Technical Replicate 1

Biological replicate 1 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day1

Cyclophosphamide-treated bone marrow 1 day - Biological Replicate 1 - Technical Replicate 2

Biological replicate 1 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated bone marrow cells, day1

Cyclophosphamide-treated bone marrow 1 day - Biological Replicate 2 - Technical Replicate 1

Biological replicate 2 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day1

Cyclophosphamide-treated bone marrow 1 day - Biological Replicate 2 - Technical Replicate 2

Biological replicate 2 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated bone marrow cells, day1

Cyclophosphamide-treated bone marrow 1 day - Biological Replicate 3 - Technical Replicate 1

Biological replicate 3 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day1

Cyclophosphamide-treated bone marrow 1 day - Biological Replicate 3 - Technical Replicate 2

Biological replicate 3 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated bone marrow cells, day1

Cyclophosphamide-treated bone marrow 1 day - Biological Replicate 4 - Technical Replicate 1

Biological replicate 4 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day1

Cyclophosphamide-treated bone marrow 1 day - Biological Replicate 4 - Technical Replicate 2

Biological replicate 4 of 5. Technical Replicate 2 of 2.Cyclophosphamide-treated bone marrow cells, day1

Cyclophosphamide-treated bone marrow 1 day - Biological Replicate 5 - Technical Replicate 1

Biological replicate 5 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day1

Cyclophosphamide-treated bone marrow 1 day - Biological Replicate 5 - Technical Replicate 2

Biological replicate 5 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated bone marrow cells, day1

Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16226.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16227.gif

in vitro Treatment: siHSF1_#2 (Sense 5’-rArCrArGrCUUrCrCrArCrGUrGUUrCrGrGTT-3’ Antisense 5’-UrCrGrArArCrArCrGUrGrGrArArGrCUrGUTT-3’), Treatment Repeat: 1, Units of Treatment Repeat: dose, Treatment Duration: 48.5, Units of Duration: hours, Treatment Time: -48, Units of Treatment Time: hrs, Vehicle for Chemical: Lipofectamine 2000, Amount of Vehicle: 0.44, Route of Exposure: transfection, Units of Amount of Vehicle: ul, Dose or Concentration: 3.3, Units of Dose or Concentration: nM

01-04-05 TP6_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2: These samples were previously hybridized on HG-U133A version 1 chips.  This experiment repeats these samples on HG-133A version 2 chips.  HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

3 months, Sex: Female, Retina: left, Final IOP (mm Hg): 18.2, Strain:DBA/2J

3 months, Sex: Female, Retina: left, Final IOP (mm Hg): 15.3, Strain:DBA/2J

3 months, Sex: Female, Retina: left, Final IOP (mm Hg): 19.1, Strain:DBA/2J

8 months, Sex: Female, Retina: right, Final IOP (mm Hg): 30.4, Strain:DBA/2J

Gfi1bfl/fl and MxCretg gfi1bfl/fl mice were injected 5 times with 500 µg pIpC every other day for a total of 5 injections.

Array scanning was performed according to the manufacturer's instruction (Affymetrix)

Data was processed using the Affymetrix Expression Console software. algorithm-name: rma-gene-default

Samples were hybridized with [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Arrays and scanned using a GeneArray Scanner at the Génome Québec INNOVATION centre of the McGill University, Montréal, QC, Canada

Target RNA was reverse transcribed into cDNA using a NuGEN Ovation Pico RNA Kit and in-vitro transcription was performed to generate biotin-labeled cRNA. cRNA was labeled with streptavidin-phycoerythrin.

DBA/2J Chronic morphine treated, striatum, biological replicate 2

DBA/2J Chronic morphine treated, striatum, biological replicate 3

SWR/J Chronic morphine treated, striatum, biological replicate 1

SWR/J Chronic morphine treated, striatum, biological replicate 2

HEK293 were transfected with human SNRK-pEGFPN3 or pEGFPN3 using Lipofectamine with Plus Reagent at a Lipofectamine:DNA ratio of 2:1, then incubated for 48 hours prior to RNA exraction

HEK293 cells were grown in ATCC MEM media supplemented with 10% FBS, 0.01% sodium pyruvate, 100 units/mL penicillin, and 100 μg/mL streptomycin

The data were processed using the Bioconductor lumi package to conduct variance stabilization and robust spline normalization.

RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent 2100 Bioanalyser.

SMhu120

SMhu119

SMhu122

SMhu121

MCF-7 human cell lines were grown as described previously (Neve et al. 2006, Cancer Cell 10:515–527).

The bead-level data were preprocessed using BASH (Cairns et al. (2008) Bioinformatics 24(24):2921-2), a function from the beadarray package (Dunning et al (2007) Bioinformatics 23(16):2183-4) in Bioconductor, and also log base 2 transformed and quantile normalised using the beadarray package. Detection p-val not provided.

Total RNA was extracted using the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. A DNase I digestion was included. Quality control was performed with Agilent Bioanalyser.

MCF-7 cell line treated with control siRNA and vehicle (control)

normal;IA, IB, II, IIIA, IIIB, or IV=IIIB;61;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

in vitro Treatment: control, Treatment Time: 1, Units of Treatment Time: hour

cells_ATCC 16Lu_human lung fibroblasts_JCB_0_1_1_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014

JCB_0_1_1_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

cells_ATCC 16Lu_human lung fibroblasts_JCB_0_1_31_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014

JCB_0_1_31_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

in vitro Treatment: control, Treatment Time: 24, Units of Treatment Time: hour

cells_ATCC 16Lu_human lung fibroblasts_JCB_0_24_20_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014

JCB_0_24_20_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

cells_ATCC 16Lu_human lung fibroblasts_JCB_0_24_35_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014

JCB_0_24_35_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

in vitro Treatment: untreated, Treatment Time: 12, Units of Treatment Time: hours

Growth Media: DMEM 10%FBS,  Pen/Strep, Fungizone, Growth Conditions: 5% CO2, 37iC

cells_ATCC 16 Lu _human lung fibroblasts_JCB_0_12_19_Lung_Fibroblast_Rcontrol_HG-U133A_2_IMFRT0014

JCB_0_12_19_Lung_Fibroblast_Rcontrol_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

Sample Type: cells, Cell Line: ATCC 16 Lu , Cell Type: human lung fibroblasts, Harvest Time Point: 12 hours

in vitro Treatment: control, Treatment Time: 12, Units of Treatment Time: hour

cells_ATCC 16Lu_human lung fibroblasts_JCB_0_12_34_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014

JCB_0_12_34_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

cells_ATCC 16Lu_human lung fibroblasts_JCB_0_12_4_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014

JCB_0_12_4_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

cells_ATCC 16Lu_human lung fibroblasts_JCB_0_1_16_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014

JCB_0_1_16_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

cells_ATCC 16Lu_human lung fibroblasts_JCB_0_24_5_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014

JCB_0_24_5_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

cells_ATCC 16Lu_human lung fibroblasts_JCB_0_4_17_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014

JCB_0_4_17_Lung_Fibroblast_control_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

corresponds to sample Hu4 in table 1

SMhu086b

corresponds to sample UC1 in table 1

normal;IA, IB, II, IIIA, IIIB, or IV=IV;68;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

Gene expression data from HSCs isolated from male mice treated with oil
MO3 HSC

Human melanoma cell line;M249_R4;V600E BRAF mutant;1 uM PLX4032 for 6h

MO1 HSC

Human melanoma cell line;M229;V600E BRAF mutant;1 uM PLX4032 for 6h

Gene expression data from HSCs isolated from female mice treated with oil
FO1 HSC

FO3 HSC

FE1 HSC

Neuroblastoma SH-SY5Y cells_cloneG_stably transfected with RNAi against DJ-1_replicate2

human neuroblastoma cells;SH-SY5Y;G;stably transfected with RNAi against DJ-1

human neuroblastoma cells;SH-SY5Y;H;stably transfected with scramble control

Signal intensities across microarrays were normalized using the trimmed means scale (Spotfire DecisionSite for Functional Genomics, Somerville, MA).

Tissues were quickly removed and frozen in liquid nitrogen and stored at -80C for subsequent preparation of total RNA. Total RNA was isolated using TRI-Reagent (Molecular Research Center Inc. Cincinnati, Ohio) with modifications to remove DNA using the Qiagen RNAeasy columns and DNaseI Kit (Qiagen, Valencia, CA). RNA was stored at –70C in RNase-free H2O supplemented with the RNase inhibitor Superasin (Ambion, Austin, TX) as per manufacturers directions. Quality and quantity of RNA was determined using a Agilent Bioanalyzer as per manufacturers procedures (Agilent Technologies, Palo Alto, CA).

Pooled hypothalamus RNA samples from 20 C57BL/6J mice with 'high' weight gain after 6 weeks on a high fat diet (D12331;Research Diets, New Brunswick, NJ), followed by 2 weeks of low fat diet, and 6 weeks on a high fat diet. Microarrays were performed in quadruplicate, H1, H2, H3, H4.

Pooled hypothalamus RNA samples from 20 C57BL/6J mice with 'low' weight gain after 6 weeks on a high fat diet (D12331;Research Diets, New Brunswick, NJ), followed by 2 weeks of low fat diet, and 6 weeks on a high fat diet. Microarrays were performed in quadruplicate, L1, L2, L3, L4.

RNA extraction kit “Nucleospin RNA II” (Macherey-Nagel, Dueren, Germany) was used

MDA-MB-231 cells_siRhoGDIbeta transfected_3 days post-tranfection

kidney epithelial proximal tubule cells;NRK-52E;Osborne-Mendel;monuron 6 hr

E12.5 fetal liver (FL) cells from wild type embryos were cultured ex vivo in the presence of Tpo for three days. FL-derived megakaryocytes and their progenitors in the culture were separated by BSA density gradient. Megakaryocyte progenitors (“P” population) were further purified by fluorescence-activated cell sorting (FACS) for cells expressing low levels of CD41. Megakaryocytes (“M” population) were further enriched by CD41 antibody coupled with magnetic beads. Total RNA was isolated from either enriched megakaryocyte or progenitor fractions. ~5-15microgram RNA from each sample was submitted to the Dana Farber Cancer Institute Microarray Core Facility for cDNA and cRNA synthesis, labeling, and hybridization with Affymetrix Mouse Genome 430 2.0 chips according to manufacturer’s instructions. All arrays were normalized and analyzed using the dChip program.

Human hepatoma cell line (HepG2) transduced with recombinant Adenovirus expressing LacZ (Beta-galactosidase control)

Gene expression data from Human hepatoma cell line (HepG2) transduced with recombinant Adenovirus expressing LacZ and cultured for 6 hours. Targets were produced using standard Affymetrix procedures from 10ug of total RNA.

U-87 glioma cell line with shcontrol and TMZ treatment, biological rep3

Gene expression data from U-87 MG cells after stable transfection with sh-control RNA and 16 hours of TMZ treatment

U-87 cells transfected with sh-control RNA  and treated with 100uM TMZ for 16 hours

U-87 glioma cell line with shcontrol and TMZ treatment, biological rep1

U-87 glioma cell line with shcontrol and TMZ treatment, biological rep2

Confluent monolayers of HUVECs in 9 cm Petri dishes were cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 1 hour

Confluent monolayers of HUVECs in 9 cm Petri dishes were cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 6 hours

Gene expression data from mouse organ of Corti apex, Dicer1 conditional knockout

Dicer1tm1Bdh (MGI:3589208) X Tg(Atoh1-cre)1Bfri (MGI:3775845);Dicer1 conditional knockout, Atoh1-Cre;Dicer1(flox/flox);organ of Corti from cochlea, apical half;postnatal day 16

Mouse organ of Corti from cochlea, apical half, Dicer1 conditional knockout

AML blasts from bone marrow;training;mutated;M4;internal tandem duplication (ITD)

I-c671T

I-c532T

primary unilateral non-metastatic postmenopausal ERα-positive breast tumor;woman;55 years

C-c215T

H-s115T

I-c1034T

C-c691T

I-c396T

I-c226T

I-c451T

I-c406T

Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 2 uM Cadmium chloride 2.5-hydrate for 6h at  37 °C.

Triazol extraction of total RNA was performed according to the manufecturer's protocol.

Gene expression data during developmental stage of heart at E17.5

C57BL/6 X SV129, Age: Embryonic Day 17.5, Tissue: Heart Venticle

Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 20 uM Arsenic (III) oxide for 6h at  37 °C

C57BL/6 X SV129, Age: Embryonic Day 17.5, Tissue: Heart Venticlee

primary fibroblasts expressing a shRNA construct targeting KDM4C, construct 2, clone 1

lung tissue;CD-1;13 weeks + 5 month;2R4F whole mainstream smoke 750 µg/ml, treatment over 5 month, 2x1h exposure per day

lung tissue;CD-1;13 weeks + 5 month;2R4F whole mainstream smoke 750 µg/ml, treatment over 5 month, 3x1h exposure per day

Spleens were isolated from WT and KO mice (age around 8 weeks). Spleen was minced and digested with Liberase TM (0.02mg/ml; Roche) and Dnase I recombinant (0.01 U/µl; Roche) for 30 min at 37°C in HBSS followed by lysis of red blood cells. CD3+ and CD19+ cells were depleted using anti-CD3 FITC and anti-CD19 FITC antibodies and anti-FITC microbeads (Miltenyi Biotec). T- and B-depleted splenocytes were stained with CD11c-PE Texas red, CD8a-PeCy5, CD11b-PeCy7, MHCII-APC-Cy7, CD24-Pacific blue and live/dead marker conjugated to Amcyan. CD8+ cDCs were isolated by cell sorting gating on FSC/SSC/singlets/alive/FITC-/ MHCII+/ CD24hi/ CD8+/ CD11cint-hi whereas CD11b+ cDCs were isolated by gating on FSC/ SSC/ singlets/ alive/FITC-/ MHCII+/ CD24lo-int/ CD11b+/ CD11chi. Cell sorting was performed on a FACSAria (BD Biosciences).

Data were processed using Bioconductor. Normalisation was done by RMA.
probe_group_file: MoGene-1_0-st-v1.r4.pgf
meta-probeset_file: MoGene-1_0-st-v1.r4.mps

Standard Affymetrix protocol. cDNA was hybrised on Affymetrix GeneChip Mouse Gene 1.0 ST Arrays (GPL6246).

untreated embryos
fetal liver dissected and disaggregated in PBS

short access to cocaine ,medial prefrontal cortex, 1 hr/day access to cocaine

Male, Wistar, 1 hr/day access to cocaine, medial prefrontal cortex

long access to cocaine ,medial prefrontal cortex, 6 hrs/day access to cocaine

Male, Wistar, 6 hrs/day access to cocaine, medial prefrontal cortex

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Tibolone treated. Patient 30.

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Tibolone treated. Patient 16.

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Tibolone treated. Patient 26.

Swiss;Ovary;4-Vinylcyclohexene Diepoxide (50uM);1;Post natal day 3-7

Neonatal mouse ovaries cultured in4-Vinylcyclohexene Diepoxide (50uM)

Swiss;Ovary;4-Vinylcyclohexene Diepoxide (50uM);2;Post natal day 3-8

Swiss;Ovary;4-Vinylcyclohexene Diepoxide (50uM);3;Post natal day 3-9

WT3; Wild type-3
Gene expression data from wild type yolk sac at E 9.5 day

mixed (SV 129/C57BL/6);wild type (Rnh1 +/+);embryonic day E9.5;yolk sac

HET1; Rnh1 Heterozygous-1

WT1; Wild type-1

WT2; Wild type-2

"female subject, 18-45 yrs, peripheral blood mononuclear cells 24 h after intravenous endotoxin challenge"

Plated 2x10e4 cells/well in 6-well dishes for 24h in RPMI 1640 containing 5% hormone striped fetal bovine serum. Cells were transfected with 10nM non-specific siRNA or Hic-5 specific siRNA using LTX-plus transfection reagent in phenol red-free RPMI 1640. Twenty-four hours following transfection, media was replaced with  fresh hormone stripped 5% FBS. Fourtyeight hours post transfection cells were treated with 10nM hormone or equivalent vehicle (ethanol)

PShTert-AR cells were maintained in RPMI 1640 medium containing 5% fetal bovine serum.

Raw data was processed in in R using Bioconductior and Limma. Array data was normalized using RMA, filtered by mapped probes and an arbitary minimum threshold.

RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

Biotinylated cRNA were prepared from 300ng RNA according to the standard Affymetrix protocol

Detailed methods for the labeling and subsequent hybridizations to the arrays are described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual, Revision 3, from Affymetrix (Santa Clara, CA).

Total RNA was isolated from small intestinal samples using TRIzol reagent (Invitrogen, Breda, the Netherlands) according to the manufacturer’s instructions. RNA was treated with DNAse and purified using the SV total RNA isolation system (Promega, Leiden, the Netherlands).

(129S4/SvJae) (PPARalpha knockout);male;14 weeks;small intestine

E12.5 fetal liver (FL) cells from GATA-1deltaN mutant  embryos were cultured ex vivo in the presence of Tpo for three days. FL-derived megakaryocytes and their progenitors in the culture were separated by BSA density gradient. Megakaryocyte progenitors (“P” population) were further purified by fluorescence-activated cell sorting (FACS) for cells expressing low levels of CD41. Megakaryocytes (“M” population) were further enriched by CD41 antibody coupled with magnetic beads. Total RNA was isolated from either enriched megakaryocyte or progenitor fractions. ~5-15microgram RNA from each sample was submitted to the Dana Farber Cancer Institute Microarray Core Facility for cDNA and cRNA synthesis, labeling, and hybridization with Affymetrix Mouse Genome 430 2.0 chips according to manufacturer’s instructions. All arrays were normalized and analyzed using the dChip program.

GATA-1deltaN mutant E12.5 fetal liver derived megakaryocyte progenitors

E12.5 fetal liver (FL) cells from GATA-1deltaNeodeltaHS mutant  embryos were cultured ex vivo in the presence of Tpo for three days. FL-derived megakaryocytes and their progenitors in the culture were separated by BSA density gradient. Megakaryocyte progenitors (“P” population) were further purified by fluorescence-activated cell sorting (FACS) for cells expressing low levels of CD41. Megakaryocytes (“M” population) were further enriched by CD41 antibody coupled with magnetic beads. Total RNA was isolated from either enriched megakaryocyte or progenitor fractions. ~5-15microgram RNA from each sample was submitted to the Dana Farber Cancer Institute Microarray Core Facility for cDNA and cRNA synthesis, labeling, and hybridization with Affymetrix Mouse Genome 430 2.0 chips according to manufacturer’s instructions. All arrays were normalized and analyzed using the dChip program.

GATA-1deltaNeodeltaHS mutant E12.5 fetal liver derived megakaryocytes

Sample name: TM-37-13R

FORKO (FSH Recptor Knock Out). FORKO mice was generated by deleting all variants of FSH-Receptor

46, XX;Stratagene® QPCR Human Reference Total RNA Cell Line Derivations;Adenocarcinoma, mammary gland;Hepatoblastoma, liver;Adenocarcinoma, cervix;Embryonal carcinoma, testis;Glioblastoma, brain;Melanoma, skin;Liposarcoma;Histiocytic lymphoma; macrophage; histocyte;Lymphoblastic leukemia, T lymphoblast;Plasmacytoma; myeloma; B lymphocyte

STAT3-deficient naïve T cells stimulated for 3 hours with IL-27 1

Gene expression data from STAT3KO naïve CD4+ T cells stimulated for 3 hours with IL-27

CD4+ T;C57BL/6J;Cd4-Cre_C57BL6-STAT3<tm1Dlv> (STAT3KO);stimulated for 3 hours with IL-27 (20 ng/ml)

STAT3-deficient naïve T cells stimulated for 3 hours with IL-27 2

Dulbecco’s Modified Eagle Medium supplemented with 10% (v/v) heat inactivated mycoplasma tested fetal calf serum, 2 mM L-glutamine (6 mM final concentration), 1% (v/v) MEM non-essential amino acids and 50 µg/ml gentamicin. Quercetin in DMEM culture medium was stabilized by 1 mM ascorbate

Dulbecco’s Modified Eagle Medium supplemented with 10% (v/v) heat inactivated mycoplasma tested fetal calf serum, 2 mM L-glutamine (6 mM final concentration), 1% (v/v) MEM non-essential amino acids and 50 µg/ml gentamicin. As quercetin in DMEM culture medium was stabilized by 1 mM ascorbate, control cells were exposed to 1mM ascorbate-only

MDA-MB-231 Breast Cancer Cells Stably Expressing mutant ERa LQ 1 Hr Treatment of 10 nM E2 Sample B

MDA-MB-231 Breast Cancer Cells Stably Expressing Mutant ERa LQ 1 Hr Treatment of 10 nM E2 Sample B

MDA-MB-231 Breast Cancer Cells Stably Expressing mutant ERa LQ 1 Hr Treatment of 10 nM E2 Sample A

MDA-MB-231 Breast Cancer Cells Stably Expressing Mutant ERa LQ 1 Hr Treatment of 10 nM E2 Sample A

Neurons were transduced at 6 DIV using Sindbis virus expressing myc-tagged Hes1 and GFP or GFP alone as control. After 6h viral particles were removed and proteins were allowed to express during 16h.

Neurons were plated for 6 days on 60mm-diameter dishes plates coated with poly-L-lysine at a density of 350,000 neurons/cm2, and they were cultured in Neurobasal supplemented with B-27 and GlutaMAX I.

Microarrays were scanned using the GeneChip® Scanner 3000 7G of Affymetrix

CEL files were processed using the Robust Multichip Average (RMA) normalization
Fold-change (log2) values (M) and their FDR-adjusted p-values were calculated with LIMMA (Linear Models for Microarray Analysis) using the affylmGUI interface. All the statistical analysis was performed using R language and the packages freely available from the “Bioconductor Project” (http://www.bioconductor.org)

Cells were lysed and total RNA was extracted using illustra RNAspin Mini RNA isolation kit from GE Healthcare. RNA quality was analyzed using a BioAnalyzer (Agilent Technologies, Santa Clara, CA).

Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45ºC on GeneChip® Mouse Genome 430_2.0 (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station FS450 according to the GeneChip® Expression Analysis Technical Manual, Affymetrix, 2004

Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1.5 µg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix). The products of reaction were purified and then fragmented at 94ºC during 35 min to obtain fragments between 35 and 200 bp.

FVB;6 DIV cultured hippocampal neurons;Sindbis virus expressing GFP alone

FVB;6 DIV cultured hippocampal neurons;Sindbis virus expressing myc-tagged Hes1 and GFP

This is from a study of femoral fracture healing in female rats 16 weeks old at fracture to compare intramedullary nailing, screw and plate fixation, and sham surgery.  This sample is from the group repaired with a plate and screws (rigid fixation) collected 6 weeks after fracture.  Each sample is a pool of RNA from three rats.  The middle third of the femur was collected with the cortical bone, fracture callus, and marrow elements.  Mid-diaphyseal, simple, transverse fractures were induced by a Gigli saw.

This is from a study of femoral fracture healing in female rats 16 weeks old at fracture to compare intramedullary nailing, screw and plate fixation, and sham surgery.  This sample is from the group receiving sham surgery (no fracture, no plate and no nail) collected 1 day after surgery.  Each sample is a pool of RNA from three rats.  The middle third of the femur was collected with the cortical bone, fracture callus, and marrow elements.

This is from a study of femoral fracture healing in female rats 16 weeks old at fracture to compare intramedullary nailing, screw and plate fixation, and sham surgery.  This sample is from the group repaired with a plate and screws (rigid fixation) collected 4 weeks after fracture.  Each sample is a pool of RNA from three rats.  The middle third of the femur was collected with the cortical bone, fracture callus, and marrow elements.  Mid-diaphyseal, simple, transverse fractures were induced by a Gigli saw.

This is from a study of femoral fracture healing in female rats 16 weeks old at fracture to compare intramedullary nailing, screw and plate fixation, and sham surgery.  This sample is from the group repaired with a plate and screws (rigid fixation) collected 3 days after fracture.  Each sample is a pool of RNA from three rats.  The middle third of the femur was collected with the cortical bone, fracture callus, and marrow elements.  Mid-diaphyseal, simple, transverse fractures were induced by a Gigli saw.

This is from a study of femoral fracture healing in female rats 16 weeks old at fracture to compare intramedullary nailing, screw and plate fixation, and sham surgery.  This sample is from the group repaired with a plate and screws (rigid fixation) collected 1 week after fracture.  Each sample is a pool of RNA from three rats.  The middle third of the femur was collected with the cortical bone, fracture callus, and marrow elements.  Mid-diaphyseal, simple, transverse fractures were induced by a Gigli saw.

siRNAs were transfected into cells in antibiotic-free medium using Lipofectamine RNAiMAX , medium was changed after 4–6 h and cells were harvested after 48 hours .

SNB19 cells were cultured in DMEM media supplemented with 10% FBS and penicillin-streptomycin at 37 °C in 5% CO2. SF539 cells were grown in MEM media with 10% FBX and penicillin-streptomycin at 37 °C in 5% CO2

data was normalized and analyzed using partek software and R packages. Specifically log2 transformation was used for data normalization.

Total RNA was extracted by using Rneasy Plus Mini Kit (Qiagen). RNA quality was determined with the Nanodrop Spectrophotometer (Thermo).

pancreatic acinar cell-specific knockout of the Perk gene; mixed genetic background; postnatal day 32; total pancreas; pooled two mouse cDNA samples equally to generate cRNA.

Human skin biposy (uninvolved) from male patient, 34 years old, 22 years of psoriasis, clear erythema, clear induration, clear scaling.

L;male;34 years;22 years;10 percent;clear;clear (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe);clear (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)

Human skin biposy (lesional) from male patient, 34 years old, 22 years of psoriasis, moderate erythema, mild induration, moderate scaling.

L;male;34 years;22 years;10 percent;moderate;mild (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe);moderate (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)

Human skin biposy (uninvolved) from female patient, 54 years old, 48 years of psoriasis, clear erythema, clear induration, clear scaling.

J;female;54 years;48 years;9 percent;clear;clear (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe);clear (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)

Human skin biposy (lesional) from female patient, 54 years old, 48 years of psoriasis, mild erythema, mild induration, mild scaling.

J;female;54 years;48 years;9 percent;mild;mild (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe);mild (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)

Human skin biposy (uninvolved) from male patient, 40 years old, 20 years of psoriasis, clear erythema, clear induration, clear scaling.

N;male;40 years;20 years;25 percent;clear;clear (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe);clear (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)

Human skin biposy (lesional) from male patient, 40 years old, 20 years of psoriasis, moderate erythema, moderate induration, mild scaling.

N;male;40 years;20 years;25 percent;moderate;moderate (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe);mild (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)

Human skin biposy (uninvolved) from female patient, 42 years old, 36 years of psoriasis, clear erythema, clear induration, clear scaling.

Z;female;42 years;36 years;5 percent;clear;clear (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe);clear (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)

Human skin biposy (lesional) from female patient, 42 years old, 36 years of psoriasis, mild erythema, minimal induration, mild scaling.

Z;female;42 years;36 years;5 percent;mild;minimal (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe);mild (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)

Human skin biposy (uninvolved) from male patient, 76 years old, 56 years of psoriasis, clear erythema, clear induration, clear scaling.

P;male;76 years;56 years;15 percent;clear;clear (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe);clear (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)

Human skin biposy (lesional) from male patient, 76 years old, 56 years of psoriasis, mild erythema, mild induration, minimal scaling.

P;male;76 years;56 years;15 percent;mild;mild (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe);minimal (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)

cells stably expressing the oncogenes c-myc and Ha-ras under the control of the Tet-off regulatable promoter, konstitutive expression of the estradiol activatabel IRF-1hER fusion protein;fibroblast

Origin of sample: Sciatic nerve pooled from 4 to 7 mice, 4 days old (P4) and carrying a Pmp22 transgene (Magyar, J.P., et al., Impaired differentiation of Schwann cells in transgenic mice with increased Pmp22 gene dosage. J. Neurosci. 16, 5351-5360 (1996)).

Origin of sample: Sciatic nerve of 60 day old (P60) wild type mice (mixed background), pooled from 4--7 mice.

Scanning with Affymetrix scanner and MAS 5.0 software. The original images (.dat files) and .cel files are available on request (mantei@cell.biol.ethz.ch) The .cel files produced by MAS 5.0 were normalized using the program dChip (smoothing spline normalization; Li, C. & Wong, W.H. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol. 2, research0032.0031-0032.0011 (2001); http://www.dchip.org). dChip was also used to calculate a probe sensitivity index for each probe on the basis of 18 arrays, and then a "model-based expression index" (MBEI) for each gene on each array (Li, C. & Wong, W.H. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl. Acad. Sci. U.S.A. 98, 31-36 (2001)).

Origin of sample: Sciatic nerve pooled from 4 to 7 mice, 4 days old (P4) and homozygously null for Pmp22 (Adlkofer,K. et al., "Hypermyelination and demyelinating peripheral neuropathy in Pmp22-deficient mice, Nature Genetics 11, 274-280 (1995)).

Gene expression data from HepG2 cell lines after 1.5 hours of PCB153 treatment.

Gene expression data from HepG2 cell lines before PCB153 treatment.

Gene expression data from HepG2 cell lines after 30 minutes of PCB153 treatment.

D5_24h_36
Gene expression data from rat tracheal explants exposed to dexamethasone (treatment) at 24hrs.

D6_24h_19

D3_24h_24

D4_24h_41

D1_24h_40

D2_24h_9

DS5_2h_2

Sprague-Dawley;tracheal explants;dexamethasone & cigarette smoke at 2hrs;5

DS6_2h_35

Sprague-Dawley;tracheal explants;dexamethasone & cigarette smoke at 2hrs;6

DS3_2h_25

Sprague-Dawley;tracheal explants;dexamethasone & cigarette smoke at 2hrs;3

DS4_2h_18

Sprague-Dawley;tracheal explants;dexamethasone & cigarette smoke at 2hrs;4

paraventricular nucleus of the hypothalamus, LPS, 10 micrograms, 3 hours

One of 3 replicates of LDL receptor deficient mice maintained for 12 weeks on low fat diet.

paraventricular nucleus of the hypothalamus, restraint stress, 3 hours

31B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

30B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

2B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

29B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

Sample name: C2
GC1962new.CEL

Sample name: C1
GC1961new.CEL

Standard housing, feeding, and water. Fasted for 5 hours prior to euthanasia.

Slides were scanned by a ScanArray 4000 XL scanner (Packard Biochip Technologies, USA)

Image analysis was carried out using the ImaGene 6.1.0 software (BioDiscovery, Inc., USA)

The hybridization was performed according to the Affymatrix manual using a Tecan HS4800 hybridization station (Tecan, Austria)

100ng of total RNA per sample was amplified and biotinylated using the MessageAmp Premier kit (Ambion)

33B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

gene expression data from Sh2b3 wild type NOTCH1 induced leukemias

Gene expression data from mRNA of substantia nigra from 10mg/kg methylphenidate-treated mouse

mRNA of substantia nigra from 10mg/kg methylphenidate-treated mouse

Gene expression data from mRNA of substantia nigra from 1mg/kg methylphenidate-treated mouse

mRNA of substantia nigra from 1mg/kg methylphenidate-treated mouse

WT Lineage negative, c-Kit and Sca1 (LSK) positive expressing bone marrow progenitors-repeat2
Gene expression data from WT Lineage negative, c-Kit and Sca1 (LSK) positive expressing bone marrow progenitors-repeat2

B6/129;WT;Lineage negative, c-Kit and Sca1 (LSK) positive expressing bone marrow progenitors

negative control inhibitor (mir-30a knockdown control), biological rep2

Peripheral blood mononuclear cells;RF- polyarticular JIA;GTE6;110min;White;Female

Peripheral blood mononuclear cells;RF- polyarticular JIA;GTE6;80min;White;Female

Peripheral blood mononuclear cells;RF- polyarticular JIA;GTE6;140min;White;Male

Peripheral blood mononuclear cells;RF- polyarticular JIA;GTE6;135min;White;Female

Peripheral blood mononuclear cells;RF- polyarticular JIA;GTE6;150min;White;Female

Peripheral blood mononuclear cells;TTF=75min;Race=White;Sex=Male

Fear conditioning in rats leads to long term memory (LTM) formation. A central substrate for this type of LTM is the basolateral amygdala. We sought the expression changes specific to LTM at 6h following pain (a component of conditioning), following anesthesia with isoflurane (a general anesthetic and an effective amnestic agent), and following conditioning during isoflurane. For this also see GSE1779.

Lot batch = rat 9

Total RNA was isolated from wild type C57BL/6 mice treated for 1 day with 4-hydroxytamoxifen (4OHT; Sigma) using Trizol reagent (Gibco BRL). Double stranded cDNA was generated from 10 ug total RNA and used to generate biotinylated cRNA using the Enzo BioArray High Yield Transcription Labelling Kit (Affymetrix). The cRNA was fragmented using the GeneChip Sample Cleanup Module (Affymetrix) and 10 ug were hybridized to GeneChip Mouse Expression Set 430 A oligonucleotide arrays (Affymetrix). Hybridizations were performed according to the manufacturers instructions using an Affymetrix Gene Chip Instrument System. The arrays were scanned on an Affymetrix GeneChip scanner.

Total RNA was isolated from D2 K14deltaNB-cateninER transgenic mice treated for 7 days with 4-hydroxytamoxifen (4OHT; Sigma) using Trizol reagent (Gibco BRL). Double stranded cDNA was generated from 10 ug total RNA and used to generate biotinylated cRNA using the Enzo BioArray High Yield Transcription Labelling Kit (Affymetrix). The cRNA was fragmented using the GeneChip Sample Cleanup Module (Affymetrix) and 10 ug were hybridized to GeneChip Mouse Expression Set 430 A oligonucleotide arrays (Affymetrix). Hybridizations were performed according to the manufacturers instructions using an Affymetrix Gene Chip Instrument System. The arrays were scanned on an Affymetrix GeneChip scanner.

Total RNA was isolated from wild type C57BL/6 mice treated for 0 days with 4-hydroxytamoxifen (4OHT; Sigma) using Trizol reagent (Gibco BRL). Double stranded cDNA was generated from 10 ug total RNA and used to generate biotinylated cRNA using the Enzo BioArray High Yield Transcription Labelling Kit (Affymetrix). The cRNA was fragmented using the GeneChip Sample Cleanup Module (Affymetrix) and 10 ug were hybridized to GeneChip Mouse Expression Set 430 A oligonucleotide arrays (Affymetrix). Hybridizations were performed according to the manufacturers instructions using an Affymetrix Gene Chip Instrument System. The arrays were scanned on an Affymetrix GeneChip scanner.

L3

dead;Hispanic;F;59;HCV;1.4;41;38;0;1;1;1;96;POS;0;POS;6.4;14;POS;Nodular glomerulosclerosis, Diabetic Nephropathy;1;0;1;1;1;0;1;1;1;1;2;1;P;P;P;P;6;0;0.9;duplication;IGG+IGM++IGA+C3+C1q+ capillary wall linear;O;Kidney_Biopsy_Liver_disease

L7

Wild-type myeloid-derived suppressor cell from colon tumor, rep1

MDSC WT-colon tumor

Differentially expressed genes of CD11b+Gr-1+ IMCs in the colonic tumors of HDC-EGFP mice.

C57BL/6J;HDC-EGFP;7 months;colon tumor;CD11b+Gr-1+ myeloid cells in the tumor stroma

CD11b+Gr-1+ myeloid cells sorted from the colon tumors of HDC-EGFP transgenic mice induced with AOM/DSS

Wild-type myeloid-derived suppressor cell from colon tumor, rep2

MDSC WT-colon tumor-R

L8

alive;White;M;38;ETOH;1.4;60;57;0;0;1;0;30;NEG;0;NEG;5.2;11;NEG;normal parenchyma by LM and IF, limited sample;0;0;0;0;0;0;0;0;0;0;1;1;1;1;0;P;3;0;1;normal;IGM+ mesangial;M;Kidney_Biopsy_Liver_disease

L9

D3;PRMT1 knockdown (siPRMT);4d_old aggregated embrioid bodies;ATRA (5 mikromol final conc.) for 12hr

rat hippocampus (combined dorsal and ventral aspects), aged PIO, subject 4

rat hippocampus (combined dorsal and ventral aspects), aged PIO, subject 2

rat hippocampus (combined dorsal and ventral aspects), aged control, subject 2

rat hippocampus (combined dorsal and ventral aspects), aged control, subject 1

rat hippocampus (combined dorsal and ventral aspects), aged control, subject 4

rat hippocampus (combined dorsal and ventral aspects), aged control, subject 3

rat hippocampus (combined dorsal and ventral aspects), aged control, subject 7

rat hippocampus (combined dorsal and ventral aspects), aged control, subject 6

rat hippocampus (combined dorsal and ventral aspects), aged PIO, subject 1

rat hippocampus (combined dorsal and ventral aspects), aged control, subject 8

rat hippocampus (combined dorsal and ventral apsects), aged control, subject 8

This is from a study of femoral fracture healing in female rats 16 weeks old at fracture to compare intramedullary nailing, screw and plate fixation, and sham surgery.  This sample is from the group receiving sham surgery (no fracture, no plate and no nail) and collected 6 weeks after surgery.  Each sample is a pool of RNA from three rats.  The middle third of the femur was collected with the cortical bone, fracture callus, and marrow elements.

This is from a study of femoral fracture healing in female rats 16 weeks old at fracture to compare intramedullary nailing, screw and plate fixation, and sham surgery.  This sample is from the group receiving sham surgery (no fracture, no plate and no nail) collected 1 week after surgery.  Each sample is a pool of RNA from three rats.  The middle third of the femur was collected with the cortical bone, fracture callus, and marrow elements.

This is from a study of femoral fracture healing in female rats 16 weeks old at fracture to compare intramedullary nailing, screw and plate fixation, and sham surgery.  This sample is from the group receiving sham surgery (no fracture, no plate and no nail) and collected 4 weeks after surgery.  Each sample is a pool of RNA from three rats.  The middle third of the femur was collected with the cortical bone, fracture callus, and marrow elements.

This is from a study of femoral fracture healing in female rats 16 weeks old at fracture to compare intramedullary nailing, screw and plate fixation, and sham surgery.  This sample is from the group receiving sham surgery (no fracture, no plate and no nail) and collected 2 weeks after surgery.  Each sample is a pool of RNA from three rats.  The middle third of the femur was collected with the cortical bone, fracture callus, and marrow elements.

Wistar rat liver following animal exposure to orotic acid for 14 days

Wistar rat liver tissue following animal no exposure to orotic acid  (control)

24_DBP

23_VEH

testis;20 weeks;castrated male athymic nude mouse hosts;corn oil vehicle

26_VEH

testis;16 weeks;castrated male athymic nude mouse hosts;corn oil vehicle

25_NON

testis;16 weeks;control (unimplanted samples were snap-frozen immediately);N/A

28_NON

29_VEH

2652_E_12_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siERK2 treatment 60h, 10 nM E2 for 4h

2658_E_13_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siERK1 treatment 60h, 0.1%EtOH for 4h

2655_E_4_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siCtrl treatment 60h, 10 nM E2 for 4h

2661_E_5_(HG-U133A_2).CEL

2656_E_6_(HG-U133A_2).CEL

2650_E_7_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siERK2 treatment 60h, 0.1%EtOH for 4h

2660_E_8_(HG-U133A_2).CEL

2654_E_9_(HG-U133A_2).CEL

2662_E_10_(HG-U133A_2).CEL

2648_E_11_(HG-U133A_2).CEL

C57BL/6N;Sta1 Wildtype (wt);Bone marrow derived macrophages (BMMs);6h IFNg + Listeria monocytogenes (Lis)

MEFs were cultured under normoxia (21% O2) in the standard tissue culture incubator (37C, 5% CO2) with growth medium (high glucose DMEM supplemented with 10% FBS and antibiotics).

Hybridization was performed in Hybridization Oven 320. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

Gene expression data from brain of Npc1+/- mouse1 of age 25 days

Gene expression data from brain of Npc1+/- mouse1 of age 20 days

Gene expression data from brain of Npc1-/- mouse1 of age 25 days

Gene expression data from brain of Npc1-/- mouse1 of age 20 days

Gene expression data from brain of Npc1+/- mouse1 of age 40 days

Gene expression data from brain of Npc1+/- mouse1 of age 37 days

Gene expression data from brain of Npc1-/- mouse1 of age 40 days

Gene expression data from brain of Npc1-/- mouse1 of age 37 days

Gene expression data from brain of Npc1+/- mouse1 of age 55 days

Gene expression data from brain of Npc1+/- mouse1 of age 54 days

The hES cell lines were maintained on a feeder layer of mitomycin C-inactivated murine embryonic fibroblast (MEF) cells. The culture media (DMEM/F12 supllemented with 20% KRS and 4ng/ml bFGF) was changed daily and routine passages were performed by mechanical cutting of hES cells on a fresh feeder layer every 4-5 days.

human ES cells line from Cellartis, Sweden; commercial line derived from normal embryos;X,Y

human embryonic stem (hES) cells line SA01, biological replicate  1

human ES cells line from AZ-VUB laboratory, Belgium; derived from normal embryos;X,Y

human embryonic stem (hES) cells line VUB01, biological replicate  3

Differentiation of hES cells line VUB03_DM1 towards neural rosettes;Neural precursor phenotype

Neural precursor cells derived from hES cells line VUB03_DM1, biological replicate  1

Neural precursor cells derived from hES cells line SA01, biological replicate  3

Neural precursor cells derived from hES cells line VUB03_DM1, biological replicate  3

Neural precursor cells derived from hES cells line VUB03_DM1, biological replicate  2

Cells were grown in three-dimensional cultures in DMEM/F12 medium supplemented with heregulin, horse serum, epidermal growth factor, hydrocortisone, cholera toxin, insulin, penicillin and streptomycin.

MCF10A cells expressing empty vector, HER2, HER3 or HER2/HER3 were grown in three-dimensional cultures for 15 days in the presence of heregulin.

Arrays were scanning using an Affymetrix GeneChip Scanner 3000 and Affymetrix AGCC software.

Raw data was normalized and probeset-level values calculated using the rma() function of the R/bioconductor (R version version 2.8) package affy using the Bioconductor annotation packages.

Total RNA was isolated from the three-dimensional structures with a standard TRIZOL extraction method.

2 ug of fragmented and labeled ssDNA was hybridized to Affymetrix Human Gene 1.0 ST arrays for 16h according to the manufacturers instructions. Washing prior to scanning was done with the Affymetrix Fluidic Station protocol FS450_0007.

200 ng total RNA were amplified using the GeneChipWT cDNA Synthesis Kit (Affymetrix) and 5.5ug of the resulting single-stranded cDNA (ssDNA) were fragmented and labeled with the GeneChip WT Terminal Labeling Kit (Affymetrix).

Mouse was housed individually in a separate cage under a 12-h light–dark cycle and permitted food and water ad libitum. A period of acclimatization for two weeks was allowed prior to any experimental procedure. No treatment was added to the animal’s drinking water .The weight and water consumption was measured weekly. At the end of 4 weeks animal was sacrificed by cervical dislocation and the brain was removed, dissected into left and right hemispheres and cerebellum, flash frozen in liquid nitrogen and stored at -80 C for future use.

Gene expression data from the right forebrain of C57BL mouse received no treatment for four weeks.

Forebrain (left hemisphere), Strain: C57BL, Gender: Male, Age: 4weeks, Drug treatment: Untreated-Control, Period of treatment: 4 weeks, Method of sacrificing: cervical dislocation.

Right brain hemisphere ,C57BL male mouse,Un-treated Control,4 weeks

100pmol siRNA was transfected to 5X10^5 HEK293 cells, and 24hours after sparse cells were moved onto 100mm dish, and confluent cells were moved onto 35mm dish. Cells were harvested after additional 24hours.

Total RNA was purified with an RNeasy Kit (Qiagen, Valencia, CA) and was amplified using a TotalPrep RNA Amplification Kit (Ambion, Austin, TX).

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;HA1077;24h;2;4421339046

Trizol standard protocol Total RNA (TRNA) was isolated utilizing Trizol Reagent (GIBCO/BRL) following the manufacturer's protocol. The quality of TRNA was assessed using the Agilent 2100 Bioanalyzer (version A.02.01S1232, Agilent Technologies). Only RNA with the OD ratio of 1.99-2.0 at 260/280 was used for microarray analysis.

Labeling was performed according to standard Affymetrix instructions at the Genomic Core Facility at the Hospital for Sick Children. Affymetrix standard protocol

Murine 3T3-L1 progenitor adipocytes cell cultures,T3 (treated with resveratrol)

Murine 3T3-L1 progenitor adipocytes cell cultures, T2 (treated with resveratrol)

Murine 3T3-L1 progenitor adipocytes cell cultures, Control 3 (untreated with resveratrol)

Murine 3T3-L1 progenitor adipocytes cell cultures, T1 (treated with resveratrol)

Murine 3T3-L1 progenitor adipocytes cell cultures, Control 2 (untreated with resveratrol)

Healthy rats were maintained during 5-6 weeks, without observing any variation in its normoglycaemia

Diabetic (STZ) rats were maintained during 5-6 weeks, without observing any variation in its hyperglycaemia

Suspension growing cells were pelleted by centifugation and RNA extracted by RNeasy Kit (Qiagen).

SW480, stable line of treatment of ezrin RNAi. Incubate in L15 medium, 37.0°C, air 100%

SW480, stable line of treatment of luciferase RNAi. Incubate in L15 medium, 37.0°C, air 100%

Unaffected MZ twin pair 2 (Unaffected patient of MZ twin pair CCN2)

baseline;F;51;synovial knee biopsy;rheumatoid arthritis;EULAR Good-responder;synovium

12 weeks of RTX therapy;F;51;synovial knee biopsy;rheumatoid arthritis;EULAR Good-responder;synovium

Autoimmune pancreatic islets, day 1 cyclophosphamide treatment, rep 4

Lot batch = jos1172

Autoimmune pancreatic islets, day 2 cyclophosphamide treatment, rep 3

Lot batch = jos1217

Autoimmune pancreatic islets, day 2 cyclophosphamide treatment, rep 2

Lot batch = jos1075

Autoimmune pancreatic islets, day 3 cyclophosphamide treatment, rep 1

Lot batch = m2

Human skin biposy (uninvolved) from male patient, 56 years old, 16 years of psoriasis, clear erythema, clear induration, clear scaling.

R;male;56 years;16 years;30 percent;clear;clear (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe);clear (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)

Human skin biposy (lesional) from male patient, 47 years old, 27 years of psoriasis, moderate erythema, moderate induration, moderate scaling.

W;male;47 years;27 years;6 percent;moderate;moderate (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe);moderate (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)

Human skin biposy (uninvolved) from male patient, 47 years old, 27 years of psoriasis, clear erythema, clear induration, clear scaling.

W;male;47 years;27 years;6 percent;clear;clear (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe);clear (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)

6x107 PBMCs were separated from 6 CIS patients at baseline and after 12 months of IFNb-1a (44 ug s.q. tiw) treatment.

The arrays were scanned with the Hewlett Packard GeneArray Scanner.

Total RNA was extracted using a Rneasy kit according to the manufacturer's instructions.

15 ug of cRNA was used for gene array hybridization. Arrays were hybridized for 16 hours at 45oC in the GeneChip® Hybridization Oven 640.The arrays were washed and stained with R-phycoerythrin streptavidin in the GeneChip® Fluidics Station 400.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7 ug total RNA.

Tumours were digested in collagenase I (Sigma) for 2 h at 37°C on a rocking plate. Collagenase I activity was blocked by addition of EDTA (5mM) and then rinsed in PBS supplemented with 2% FCS. After tumour digestion, cells were blocked for 15 min at room temperature in PBS supplemented with 30% FCS. Immunostaining was performed  by incubation for 30 min on ice. Living tumour cells were selected by forward scatter, side scatter, doublet discrimination and by Hoechst dye exclusion. Tumour epithelial cells (TECs) were selected based on the expression of Epcam (Epcam+) and exclusion of CD45, CD31, CD140a (Lin-). Sorted cells were collected into lysis buffer for RNA extraction.

Mouse colonies were maintained in a certified animal facility in accordance with the European guidelines.

To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

The data were analyzed with R (version 2.14.0) Bioconductor fRMA (version 1.6) package with default analysis settings.

RNA extraction was performed using the RNeasy micro kit (Qiagen) according to the manufacturer’s recommendations and DNAase treatment.

A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix Mouse430 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.

Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).

K14CREER:SOX2fl/fl mice treated with tamoxifen for 1 week;Benign tumour

Chemically-induced skin papillomas in K14CREER:SOX2fl/fl mice treated with tamoxifen for 1 week

Chemically-induced skin papillomas in control mice treated with tamoxifen for 1 week

Moderate Asthma;Fresh Bronchial Epithelial Cells;female;46.16712

Moderate Asthma;Fresh Bronchial Epithelial Cells;female;20.29041

Moderate Asthma;Fresh Bronchial Epithelial Cells;female;20.38904

Moderate Asthma;Fresh Bronchial Epithelial Cells;female;19.67397

Moderate Asthma;Fresh Bronchial Epithelial Cells;female;33.34247

Moderate Asthma;Fresh Bronchial Epithelial Cells;female;43.41918

HepG2 cells stably expressing wild-type THRA and treated with 100 nM T3 for 6h

HepG2 cells stably expressing wild-type THRA and treated with vehicle for 6h.

famale Sprague-Dawley rat, 4-hydroxyphenylretinamide, 782 mg/kg diet for seven days, tissue: liver

famale Sprague-Dawley rat, 4-hydroxyphenylretinamide, 782 mg/kg diet for seven days, tissue: lung

famale Sprague-Dawley rat, 4-hydroxyphenylretinamide, 782 mg/kg diet for seven days, tissue: mammary gland

endothelial, age:32, gender:male, diagnostic group: control, PMI:13h

endothelial, age:42, gender:male, diagnostic group: schizophrenia, PMI:37h

endothelial, age:54, gender:male, diagnostic group: schizophrenia, PMI:38h

endothelial, age:44, gender:male, diagnostic group: schizophrenia, PMI:9h

endothelial, age:37, gender:male, diagnostic group: schizophrenia, PMI:30h

endothelial, age:45, gender:male, diagnostic group: schizophrenia, PMI:35h

neuronal, age:37, gender:male, diagnostic group: schizophrenia, PMI:30h

neuronal, age:45, gender:male, diagnostic group: schizophrenia, PMI:35h

glioblastoma stem cells were differentiated in the presence of FCS for 4 days

Tumor cells were then resuspended in serum-free DMEM/F12 medium (Invitrogen, Carlsbad, CA) containing human recombinant EGF (20 ng/ml; Sigma, St. Louis, MO), bFGF (20 ng/ml; Sigma), B-27 (20 ml per ml of medium; Invitrogen) and heparin (2 mg/ml), and plated at a density of 3x106 live cells/60-mm plate

Data analysis performed using R (2.8.1) and Bioconductor packages. The function rma of package affy (1.20.2) was used for normalization.

Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133A 2.0 chip according to the protocols provided by the manufacturer.

The cDNA was prepared from 5 microg total RNA using the One –Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthezising the cRNA using the IVT labeling kit (Affimetrix). The synthezised cRNA was purified with the GeneChip Sample Cleanup Module (Affimetrix).

vastus lateralis biopsy, 71 year-old sedentary COPD patient (male #1).

vastus lateralis biopsy, 80 year-old trained COPD patient (male #42).

vastus lateralis biopsy, 80 year-old sedentary COPD patient (male #24).

vastus lateralis biopsy, 76* year-old sedentary COPD patient (male #7).

vastus lateralis biopsy, 76 year-old trained COPD patient (male #40).

vastus lateralis biopsy, 76 year-old sedentary COPD patient (male #13).

vastus lateralis biopsy, 71 year-old trained COPD patient (male #35).

vastus lateralis biopsy, 76* year-old trained COPD patient (male #38).

Gene expression data under ER stress from lymphoblastoid cells of individual GM12234 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12236 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data from MCF7 (BUS stock) hormone starved for 0 day.

Gene expression in NET1 knockdown AGS cells.
GB 7 63A NO LPA.CEL

gastric adenocarcinoma AGS cells;63 shRNA;A;NET1 knockdown;no LPA (control)

SMhu176

SMhu175

SMhu174

gastric adenocarcinoma AGS cells;non targetting shRNA (control);B;NET1 present;LPA

Cells were infected with 1 plaque forming unit per cell of West Nile Virus

Primary cells were extracted from cadaveric eyes and ARPE19 cells were obtained from the ATCC. Cells were then grown at 30ºC with 5% CO2 in DMEM + 10%FCS

GeneChips were scanned with the Affymetrix GeneChip Scanner 3000

Data was analysed with the GeneSping Gx11 program using RMA function

After 24h post infection, cells were lysed with Trizol and RNA was extracted using Rneasy kit (Qiagen)

Following fragmentation,  cRNA was hybridized onto Human Exon 1.0 ST chips for 16h. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

SMhu178

SMhu177

gastric adenocarcinoma AGS cells;non targetting shRNA (control);B;NET1 present;no LPA (control)

gastric adenocarcinoma AGS cells;non targetting shRNA (control);A;NET1 present;no LPA (control)

GC sensitive clone C7H2-S11 treated for 6 hours with 100nM dexamethasone (a glucocorticoid).

Csbm/m Mouse_cerebellum_Standard diet supplemented with resveratrol_Ad Lib_Replicate-4

Sample name: CSB_Resv_4

Treatment: 2.1 mM HOCl in medium

SMhu064

SMhu063

SMhu066

SMhu065

SMhu054

SMhu053

SMhu062

SMhu061

SMhu068

SMhu067

Beta4 nAChR subunit null mice following nicotine-induced seizures

non-cancerous, cirrhotic liver tissues surrounding hepatocellular carcinoma from male Fischer344 rat fed choline-deficient, L-amino acid-defined diet for 70 w

Gene expression data from CUTLL1 cells treated with compound E for 3days and washouted compound E for 2 hours

B6;Eos (Ikzf4) knockout;8 weeks;female;spleen;regulatory T cells (Tregs);CD4+CD25hi;CD19, CD8a, CD11b, CD11c, NK1.1;MoFlo Sorter

Freshly isolated mouse placental trophoblast was CD9 enriched with an immunomagnetic column

CEL files were normalised using RMA method using affy package from Bioconductor version 2.8

RNA from BM from 4 different individuals was extracted using Minikit (Qiagen, Valencia California)

the fourth run of normal bladder cell treated with APF. Membrane B is used

BioBreeding DR+/+ rat, day 65, mast cells derived from pancreatic lymph node.

BB Rat day 65 female diabetic resistant mast cells from pancreatic lymph node

THP-1 cell line infected with GSK3A Construct 6 shRNA, biological rep1
Sample name: THP1_GSK3A_6-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B06_596642.CEL

THP-1 cell line infected with GSK3A Construct 6 shRNA, biological rep2
Sample name: THP1_GSK3A_6-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B11_596554.CEL

THP-1 cell line infected with GSK3A Construct 5 shRNA, biological rep1
Sample name: THP1_GSK3A_5-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B05_596730.CEL

Five days after initial plating, cultures were inoculated with SeV (MOI 20) or an equivalent amount of UV-inactivated SeV for 4 d.

BioBreeding DRlyp/lyp rat, day65, mast cells derived form pancreatic lymph node

BB Rat day 65 female diabetic prone mast cells from pancreatic lymph node

hsa-mir-30a/30d inhibitor (mir-30a knockdown in OVSAYO), biological rep2

Healthy control;44;Female;N/A;N/A;6.20;10;Right;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 0

Healthy control;50;Male;N/A;N/A;6.75;49;Right;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 1

Healthy control;38;Female;N/A;N/A;6.00;33;Right;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 3

Healthy control;46;Male;N/A;N/A;6.67;31;Left;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 1

Healthy control;34;Female;N/A;N/A;6.87;24;Right;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 0

Healthy control;44;Female;N/A;N/A;6.59;28;Right;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 3

Healthy control;31;Male;N/A;N/A;6.13;11;Right;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 1;0 (no use) to 6 (heavy use)): 1

Healthy control;42;Male;N/A;N/A;6.91;37;Left;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 3;0 (no use) to 6 (heavy use)): 4

Healthy control;38;Female;N/A;N/A;6.70;28;Right;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 0

Healthy control;48;Male;N/A;N/A;6.91;24;Right;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 1;0 (no use) to 6 (heavy use)): 1

Study of rat femur fracture healing in old rats (52 weeks old at fracture) at 1 week after fracture.  RNA from 2 rats was pooled for each array.  Sample is middle third of femur with external callus, cortical bone and marrow elements.

Study of rat femur fracture healing in old rats (52 weeks old at fracture) at 2 weeks after fracture.  RNA from 2 rats was pooled for each array.  Sample is middle third of femur with external callus, cortical bone and marrow elements.

Study of rat femur fracture healing in old rats (52 weeks old at fracture) at 3 days after fracture.  RNA from 2 rats was pooled for each array.  Sample is middle third of femur with external callus, cortical bone and marrow elements.

Study of rat femur fracture healing in adult rats (26 weeks old at fracture) at 6 weeks after fracture.  RNA from 2 rats was pooled for each array.  Sample is middle third of femur with external callus, cortical bone and marrow elements.

Study of rat femur fracture healing in old rats (52 weeks old at collection) as intact femur.  RNA from 2 rats was pooled for each array.  Sample is middle third of femur with cortical bone and marrow elements.

Study of rat femur fracture healing in adult rats (26 weeks old at fracture) at 2 weeks after fracture.  RNA from 2 rats was pooled for each array.  Sample is middle third of femur with external callus, cortical bone and marrow elements.

Study of rat femur fracture healing in adult rats (26 weeks old at fracture) at 4 weeks after fracture.  RNA from 2 rats was pooled for each array.  Sample is middle third of femur with external callus, cortical bone and marrow elements.

Study of rat femur fracture healing in old rats (52 weeks old at fracture) at 4 weeks after fracture.  RNA from 2 rats was pooled for each array.  Sample is middle third of femur with external callus, cortical bone and marrow elements.

mouse embryonic fibroblasts retrovirally transfected with pBabePuro containing the catalytic subunit of mouse telomerase (mTert)

mouse embryonic fibroblasts retrovirally transfected with pBabePuro (empty virus)

C57BL/6 BMDM stimulated overnight with 50 IU/ml IFN-g and infected with WA(pTTS,pP60)

Pooled diaphragm RNA samples from five 8 wk old male mdx5cv mice

Pooled diaphragm RNA samples from five 8 wk old male C57BL10 mice

Cyclophosphamide-treated spleen 5 days - Biological Replicate 1 - Technical Replicate 1

Biological replicate 1 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated splenocytes, day 5

Cyclophosphamide-treated spleen 5 days - Biological Replicate 1 - Technical Replicate 2

Biological replicate 1 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated splenocytes, day 5

Cyclophosphamide-treated spleen 2 days - Biological Replicate 2 - Technical Replicate 2

Biological replicate 2 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated splenocytes, day 2

Cyclophosphamide-treated spleen 2 days - Biological Replicate 3 - Technical Replicate 1

Biological replicate 3 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated splenocytes, day 2

Cyclophosphamide-treated spleen 2 days - Biological Replicate 3 - Technical Replicate 2

Biological replicate 3 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated splenocytes, day 2

Cyclophosphamide-treated spleen 2 days - Biological Replicate 4 - Technical Replicate 1

Biological replicate 4 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated splenocytes, day 2

Cyclophosphamide-treated spleen 2 days - Biological Replicate 4 - Technical Replicate 2

Biological replicate 4 of 5. Technical Replicate 2 of 2.Cyclophosphamide-treated splenocytes, day 2

Cyclophosphamide-treated spleen 2 days - Biological Replicate 5 - Technical Replicate 1

Biological replicate 5 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated splenocytes, day 2

Cyclophosphamide-treated spleen 2 days - Biological Replicate 5 - Technical Replicate 2

Biological replicate 5 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated splenocytes, day 2

Filter	570
Scan Date	Dec 14 2005 01:24PM

Station	1
Module	3

Filter	570
Scan Date	Dec 16 2005 11:34AM

Station	1
Module	4
Hybridize Date	Dec 16 2005 11:11AM

hair follicles from embryo-deleted area (absence of functional Notch1)

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56953
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.45; Parameter Scan Time = 22:42:33; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 13245; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.45; Parameter Scan Time = 22:42:33; Parameter PMT Volts = 670; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 186850; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.57; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56937
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.97; Parameter Scan Time = 18:05:38; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 11934; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.97; Parameter Scan Time = 18:05:38; Parameter PMT Volts = 670; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 185539; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.55; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56951
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.27; Parameter Scan Time = 21:41:32; Parameter PMT Volts = 550; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 13184; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.27; Parameter Scan Time = 21:41:32; Parameter PMT Volts = 770; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 186789; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.58; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56952
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.48; Parameter Scan Time = 22:54:56; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 13258; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.48; Parameter Scan Time = 22:54:56; Parameter PMT Volts = 670; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 186863; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.58; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56934
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.24; Parameter Scan Time = 18:54:53; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 11984; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.24; Parameter Scan Time = 18:54:53; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 185588; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56919
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.48; Parameter Scan Time = 20:40:47; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 11128; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.48; Parameter Scan Time = 20:40:47; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 184733; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56917
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.63; Parameter Scan Time = 18:22:58; Parameter PMT Volts = 550; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 10991; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.63; Parameter Scan Time = 18:22:58; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 184596; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56950
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.45; Parameter Scan Time = 22:30:27; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 13233; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.45; Parameter Scan Time = 22:30:27; Parameter PMT Volts = 670; Parameter Scan Date = 2004-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 186838; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.58; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56916
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.78; Parameter Scan Time = 18:36:15; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 11003; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.78; Parameter Scan Time = 18:36:15; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 184608; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.55; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56933
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.64; Parameter Scan Time = 20:51:02; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 12099; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.64; Parameter Scan Time = 20:51:02; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-08; Parameter Pixel Size = 10; Parameter Laser on time = 185703; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

non-small cell lung carcinoma cell line H1299;Lipofection-mediated siRNA delivery;12hr

non-small cell lung carcinoma cell line H1299;PTD-DRBD-mediated siRNA delivery;12hr

Cervical cancer, squamous cell carcinoma, microdissected, age 59, stage IIB, HPV 18

Cervical cancer, squamous cell carcinoma, microdissected, age 33, stage IV, HPV 16

Cervical cancer, squamous cell carcinoma, microdissected, age 57, stage IIB, HPV 18

Cervical cancer, squamous cell carcinoma, microdissected, age 64, stage IIB, HPV 18

Cervical cancer, squamous cell carcinoma, microdissected, age 69, stage IIB, HPV 16

Whole genome transcriptome profile of murine anterior palatal tissue, collected at E15.5, from control mice.

A HID B_B013

A HID B_B012

A HID B_B011

A HID B_B009

A VIS _B097

A HID B_B091

A HID B_B090

Y SIT_B076

A HID B_B017

A HID B_B014

Fresh Atypical ductal hyperplasia (ADH) tissue collected from breast of a women who had cancer before ADH, or had cancer at the time as ADH or developed cancer after ADH diagnosis

C57Bl6;4 weeks;BCR-ABL1 transformed pre-B cells;BCR-ABL1-driven ALL;Wild-type;Imatinib (2uM for 16h)

2nd Run - Muscle biopsy (vastus laterlis) from morbidly obese patient (sample name: JGB-5) before gastric bypass surgery (2nd staining)

2nd Run - Muscle biopsy (vastus laterlis) from morbidly obese patient (sample name: JGB-1) before gastric bypass (2nd staining)

2nd Run - Muscle biopsy (vastus laterlis) from morbidly obese patient (sample# JGB-4) after gastric bypass surgery (2nd staining)

2nd Run - Muscle biopsy (vastus laterlis) from morbidly obese patient (sample# JGB-3) before gastric bypass surgery (2nd staining)

2nd Run - Muscle biopsy (vastus laterlis) from morbidly obese patient (sample# JGB-6) after gastric bypass surgery (2nd staining)

128;Pentaza;3/19/81;M;JEWISH;FALSE;FALSE;FALSE;FALSE;FALSE;4/1/05;IBS Type symptoms;0;TRUE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

126;None;4/4/87;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;3/1/05;FH of Crohn's disease, Symtom free at procedure;0;TRUE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

135;none;8/14/59;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;7/28/05;bloody diahorrea;0;TRUE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;11-15-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

136;metranidazole 400mg TDS Prednisolone;5/21/51;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;7/20/05;Diarrhoea PR bleeding;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;11-15-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

205;Pentaza 3g/d;6/8/79;M;CAUCASIAN;10/1/03;8/30/04;FALSE;TRUE;FALSE;NO;FALSE;FALSE;10/8/04;4;0;15;19;110;5;3;43;FALSE;0;BOTH;BOTH;BOTH;unknown;unknown;10/8/04;BOTH;BOTH;BOTH;unknown;unknown;12/9/04;NEW;ex;1/1/85;3/1/03;15-24;None;UC;1-25-01;terminal ileum;Inflamed;total RNA from 10 human cell lines

MS brain lesions were characterized histologically according to disease activity as AP (active plaque), CAP (chronic active plaque), CP (chronic plaque). Control brain samples were analyzed to rule out neurological disorders.

Fresh-frozen autopsy brain samples from MS and control subjects were studied

GeneChips were scanned using the Affymatrix Genechip Scanner 3000 7G.

The data were analyzed with Affymatrix Gene Expression Console using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

Total RNA from MS and control brain samples were extracted utilizing RNAEasy kit from Qiagen.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 2.0 array (Affymatrix). GeneChips were washed and stained in the GeneChip Hybridization Oven 640.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ug total RNA (3'IVT protocol from Affymatrix ).

Fresh-frozen autopsy brain samples
Gene expression data from active MS brain lesions -following demyelination with active inflammation

chronice active plaque;multiple sclerosis following demyelination-active inflammation;multiple sclerosis brain lesion

Gene expression data from chronic MS brain lesions - after inflammation has subsided and gliosis has set in

chronic plaque;multiple sclerosis after inflammation has subsided-late stage;multiple sclerosis brain lesion

Gene expresssion data from active MS brain lesions - early stage before demyelination

active plaque;multiple sclerosis early stage-active inflammation;multiple sclerosis brain lesion

Gene expression data from healthy control brain samples

Moderate Asthma;Fresh Bronchial Epithelial Cells;female;52.78082

Moderate Asthma;Fresh Bronchial Epithelial Cells;female;22.31507

Moderate Asthma;Fresh Bronchial Epithelial Cells;female;22.80822

Moderate Asthma;Fresh Bronchial Epithelial Cells;female;19.40822

Moderate Asthma;Fresh Bronchial Epithelial Cells;female;27.08767

Moderate Asthma;Fresh Bronchial Epithelial Cells;female;48.50137

We used the Human Genome U133 Plus 2.0 Array (Affymetrix) containing 54,675 probe sets to determine global impacts of A. phagocytophilum infection in NB4 cells at four hours post-infection.  The mRNA was isolated using the TRI reagent extraction protocol (Molecular Research Center, Cincinnati) followed by RNeasy cleanup. cRNA production, labeling reactions, hybridization, staining and washing were performed according to the Gene Chip Expression Analysis Technical Manual (Affymetrix, Santa Clara) at the W.M. Keck Facility (Yale University).  Image data were quantified by using genechip/suite microarray suite 5.0 (MAS 5.0) and default parameters were used for identification of informative probes.

PC from WM patient, isolated using Kappa or Lambda-fluorescein isothiocyanate, CD10-PE,CD38-PerCPCy5.5,CD19-PE-Cy7, CD34-APC and CD45-APC-Cy7.

control;no glaucoma;No radiation treatment;DBA/2J-Gpnmb+;Female;10.5

Gene expression data from MCF7 (BUS stock) exposed to 0 pM 17beta-estradiol for 48 hours.

A mouse testicular Sertoli cell line, TTE3, derived from transgenic mice harboring a temperature-sensitive simian virus 40 large T-antigen was used. TTE3 cells were treated with 0.2 mM bisphenol A (BPA) for 0 h.

A mouse testicular Sertoli cell line, TTE3, derived from transgenic mice harboring a temperature-sensitive simian virus 40 large T-antigen was used. TTE3 cells were treated with 0.2 mM bisphenol A (BPA) for 3 h.

A mouse testicular Sertoli cell line, TTE3, derived from transgenic mice harboring a temperature-sensitive simian virus 40 large T-antigen was used. TTE3 cells were treated with 0.2 mM bisphenol A (BPA) for 6 h.

human peripheral blood derived monocytes, 8 hour LPS stimulation, biological rep2

human peripheral blood derived monocytes, 8 hour LPS stimulation, biological rep1

human peripheral blood derived monocytes, no stimulation, biological rep2

human peripheral blood derived monocytes, 4 hour LPS stimulation, biological rep2

human peripheral blood derived monocytes, 4 hour LPS stimulation, biological rep1

human peripheral blood derived monocytes, 2 hour LPS stimulation, biological rep2

human peripheral blood derived monocytes, 2 hour LPS stimulation, biological rep3

mouse embryonic fibroblasts (MEFs);KSR1 -/-;H-RasV12, KSR1, and GFP;DBA

Primary culture of type II cells collected from SPC WT lung (adult);adult;type II lung epithelial;Surfactant Proteiin C WT;129S6/SvEvTac

Primary culture of typeII cells collected from SPC WT lung (adult);adult;type II lung epithelial;Surfactant Proteiin C WT;129S6/SvEvTac

Gene expression data from mouse CD8+ Itk knockout T-cells without stimulation

Ovaries dissected from 4-day old female rat pups were maintained in a whole organ culture system on floating filters (0.4 µm Millicell-CM; Millipore Corp., Billerica, MA, USA) in 0.5 ml DMEM-Ham's F-12 medium (1:1, vol/vol; Life Technologies, Inc.) containing 0.1% BSA (Sigma), 0.1% albumax (Life Technologies, Inc.), 0.05 mg/ml L-ascorbic acid (Sigma), and 27.5 µg/ml transferrin (Sigma) in a 4-well culture plate (Nunc plate; Applied Scientific, South San Francisco, CA, USA). Medium was supplemented with final concentration 5 µg/ml gentamicin, 3.25 µg/ml streptomycin, and 3.25 units/ml penicillin to prevent bacterial contamination. Ovaries were treated with no factor (control) or NT3 (rh NT3, 50 ng/ml; R&D Systems, Minneapolis, MN, USA).

Four-day old female Sprague-Dawley rats (Harlan Laboratories, Inc., USA) were euthanized according to Washington State University IACUC approved protocols and the ovaries removed and cultured whole as described previously

The data were analyzed with GeneSpring GX7 (Agilent Technologies, Santa Clara, CA) software using MAS5.0 algorithm for pre-processing  and global scaling as normalization method.  The trimmed mean target intensity of each array was set to 210.

RNA was isolated from whole rat ovaries (2-3 ovaries per each sample) after homogenization in 1 ml Trizol™ reagent (Sigma-Aldritch, USA), according to manufacturer’s instructions.

Following fragmentation, cRNA were hybridized  on Affymetrix GeneChip Rat Genome 230 2.0 Array according to standard Affymetrix protocol. Chips were washed and stained in the   Affymetrix Fluidics Station 4500.

Biotin-labeled cRNA were prepared according to the standard Affymetrix protocol from at least 3 ug total RNA  (Expression Analysis Technical Manual, 2001, Affymetrix).

Gene expression data from rat P4 Ovary cultured for 48 hours with NT3

Epididymal adipose;GPR120 KO;normal diet ND;mixed 129/Sv and C57BL/6;mouse 719

24 hrs tetracycline (1000 ng/ml) to induce expression of the transcription factor.

Whole genome transcriptome profile of tongue mesenchyme from embryonic day 14.5 control mice .

Sample is skeletal muscle from morbidly obese patient undergoing elective abdominal surgery

European-American (EA);Female;healthy control;Peripheral blood;CD14-PerCP;CD14 positive monocytes

African-American (AA);Female;healthy control;Peripheral blood;CD14-PerCP;CD14 positive monocytes

TIG3 diploid fibroblasts were were grown in DMEM media supplemented with 10% (v/v) fetal calf serum. For siRNA experiments cells were transfected with siRNA oligonucleotides specific for EZH2 and harvested for preparation of RNA after 44 hours.

The Identification of gene expression changes in human embryonic fibroblast cells depleted of EZH2. Sample B

TIG3 diploid lung embryonic fibroblasts were transfected with siRNA oligos specific for the Polycomb protein EZH2. After 44 hours expression analysis was performed.

The Identification of gene expression changes in human embryonic fibroblast cells depleted of EZH2. Sample C

The Identification of gene expression changes in human embryonic fibroblast cells depleted of BMI-1. Sample C

TIG3 diploid fibroblasts were were grown in DMEM media supplemented with 10% (v/v) fetal calf serum. For siRNA experiments cells were transfected with siRNA oligonucleotides specific for EED and harvested for preparation of RNA after 44 hours.

The Identification of gene expression changes in human embryonic fibroblast cells depleted of EED. Sample A

TIG3 diploid lung embryonic fibroblasts were transfected with siRNA oligos specific for the Polycomb protein EED. After 44 hours expression analysis was performed.

The Identification of gene expression changes in human embryonic fibroblast cells depleted of EZH2. Sample A

The Identification of gene expression changes in human embryonic fibroblast cells depleted of EED. Sample B

The Identification of gene expression changes in human embryonic fibroblast cells depleted of EED. Sample C

ApoE-/-;C57BL/6;Jackson labs (backcrossed >10 generations against C57BL/6 background).;Male;9 weeks;Total aorta from root to bifurcation.;non-diabetic

Aorta from ApoE-/- mouse without diabetes sacrificed at 9 weeks.

Cell strain 12 of cyclin D1KO 3T3 cells obtained by serial passaging MEFs from E14 embryos, stably infected with MSCV-GFP control Murine Stem Cell Virus.

Sample from retroviral MSCV-GFP control infected cyclin D1 knockout 3T3 cells (line 12).

Gene expression data from cyclin D1 knockout 3T3s (cell line 12) infected with MSCV-GFP control using Murine Stem Cell Virus (MSCV) system.

Cell strain 1 of cyclin D1KO 3T3 cells obtained by serial passaging MEFs from E14 embryos, stably infected with MSCV murine stem cell virus expressing cyclin D1b.

Sample from retroviral MSCV-D1b infected cyclin D1 knockout 3T3 cells (line 1).

Gene expression data from cyclin D1 knockout 3T3s (cell line 1) infected with a splice variant of cyclin D1 (variant D1b) using Murine Stem Cell Virus (MSCV) system.

Gene expression analysis of the kidney of mouse treated with 7 repeat daily doses of vancomycin at 200 mg/kg administered via the intravenous route (iv)

Kidney from mice treated with 7 daily iv injections of vancomycin at 200 mg/kg

Total RNA was extracted from lymphoblastoid cells of AU1348302 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;AU1348302 is a control male without autism.

Total RNA was extracted from lymphoblastoid cells of AU1327303 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;AU1327303 is a control male without autism.

Cervical cancer, squamous cell carcinoma, microdissected, age 28, stage IIIB, HPV 45

Cervical cancer, squamous cell carcinoma, microdissected, age 55, stage IIIB, HPV 16

Cervical cancer, squamous cell carcinoma, microdissected, age 41, stage IIIB, HPV 16

Cervical cancer, squamous cell carcinoma, microdissected, age 62, stage IIIB, HPV 45

Cervical cancer, squamous cell carcinoma, microdissected, age 45, stage IIIB, HPV 16

Cervical cancer, squamous cell carcinoma, microdissected, age 54, stage IIIB, HPV 16

Cervical cancer, squamous cell carcinoma, microdissected, age 43, stage IIB, HPV 16

Cervical cancer, squamous cell carcinoma, microdissected, age 40, stage IIIB, HPV 16

Cervical cancer, squamous cell carcinoma, microdissected, age 32, stage IIIB, HPV 16

Total RNA was extracted from lymphoblastoid cells of AU1038304 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;AU1038304 is a control male without autism.

Total RNA was extracted from lymphoblastoid cells of AU1157302 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;AU1157302 is a control male without autism.

Total RNA was extracted from lymphoblastoid cells of AU1086301 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;AU1086301 is a control male without autism.

human prostate cancer cells; clone 2-1

Total RNA was extracted from lymphoblastoid cells of AU1165305 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;AU1165305 is a control male without autism.

human prostate cancer cells; scrambled control-1

human prostate cancer cells; scrambled control-2

human prostate cancer cells; clone 3-1

Total RNA was extracted from lymphoblastoid cells of AU1165303 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;AU1165303 is a control male without autism.

Total RNA was extracted from lymphoblastoid cells of AU1215303 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;AU1215303 is a control male without autism.

Gene expression from Dex-treated wild-type liver

Gene expression from untreated wild-type liver

Doxocycline was used to induce expression of integrated FTO copy. siRNA transfection was performed using Lipofectamine 2000 reagent following manufacture's instruction

The data were analyzed with MAS5 using Affymetrix default analysis settings and global scaling to a target intensity of 1000 as normalization method.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip HG-U133Plus_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Affymetrix Hybridization, Wash and Stain Kit..

Biotinylated cRNA were prepared according to the Affymetrix ExpressKit protocol starting from 200 ng total RNA.

Gene expression data from Flp-In™ 293 T-Rex cells treated with scrambled siRNA, after 48h

Gene expression data from Flp-In™ 293 T-Rex cells after 48h of depletion from FTO

Gene expression data from generated FTO2_D4 clone, 48h after induced espression of integrated copy of the FTO gene

FTO;48h after induced espression of integrated copy of the FTO gene

Gene expression data from generated FTO2_D4 clone, 24h after induced espression of integrated copy of the FTO gene

FTO;24h after induced espression of integrated copy of the FTO gene

pancreatic acinar cell-specific knockout of the Perk gene; mixed genetic background; postnatal day 16; total pancreas; replicate mouse #1.

CCL3-injected Ccl3-/-, replicate 2

Hereditary gingival fibromatosis(HGF) patient Gingiva replicate1

normal gingiva tissue removed during surgical procedures and stored in liquid nitrogen immediately

CHB-PBMC-10

CHB-PBMC-11

CHB-PBMC-08

CHB-PBMC-09

CHB-PBMC-06

CHB-PBMC-07

CHB-PBMC-04

CHB-PBMC-05

CHB-PBMC-02

CHB-PBMC-03

Mouse was housed individually in a separate cage under a 12-h light–dark cycle and permitted food and water ad libitum. A period of acclimatization for two weeks was allowed prior to any experimental procedure. Clozapine was added to the animal’s drinking water in a concentration equivalent to the highest human clinical dosage (i.e. 12mg/kg/day for Clozapine) and delivered through light protected bottles. The weight and water consumption was measured weekly and the drug concentration in water was adjusted accordingly .At the end of 12 weeks animal was sacrificed by cervical dislocation and the brain was removed, dissected into left and right hemispheres and cerebellum, flash frozen in liquid nitrogen and stored at -80 C for future use.

Gene expression data from the right forebrain of C57BL mouse received Clozapine oral treatment for twelve weeks..

Forebrain (left hemisphere), Strain: C57BL, Gender: Male, Age: 4weeks, Drug treatment: Atypical antipsychotic Clozapine, Dose: 12mg/kg/day, Route of treatment: Oral treatment-Drug added to drinking water, Period of treatment: 12 weeks, Method of sacrificing: cervical dislocation.

Right brain hemisphere ,C57BL male mouse,Clozapine treated,Orally,12 weeks

Gene expression data from the right forebrain of C57BL mouse received Clozapine oral treatment for twelve weeks.

75% C57BL/6, 25% CBAJ;Male;9 weeks (Moderate stage);Mutant huntingtin

Station	1
Module 3

Station	1
Module 2

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Module	4

Station	1
Module 4

Gene expression of H441 cells transfected with control siRNA-biological replicate 3

Gene expression of H441 cells transfected with control siRNA-biological replicate 2

Gene expression of H441 cells transfected with control siRNA-biological replicate 1

Gene expression of H441 cells transfected with siRNA against the ETS2 gene- biological replicate 2

Gene expression of H441 cells transfected with siRNA against the ETS2 gene- biological replicate 1

medullary thymic epithelial cells from wild type mice were FACS-sorted

thymic macrophages from wild type mice were FACS-sorted
Keywords = macrophage

thymic dendritic cells from wild type mice were FACS-sorted
Keywords = DC

Cells were treated with 2.5 uM rosiglitazone (RSG). Ligands or vehicle were added to the cell culture starting from the first day.

GC sensitive clone C7H2-S12 treated for 6 hours with 0.1% ethanol (carrier control).

GC sensitive clone C7H2-S11 treated for 6 hours with 0.1% ethanol (carrier control).

GC resistant clone C7H2-R19E5 treated for 6 hours with 0.1% ethanol (carrier control).

GC resistant clone C7H2-R10E7 treated for 6 hours with 0.1% ethanol (carrier control).

GC resistant clone C7H2-R3B5 treated for 6 hours with 0.1% ethanol (carrier control).

GC resistant clone C7H2-R9C10 treated for 6 hours with 0.1% ethanol (carrier control).

GC resistant clone C7H2-R19E7 treated for 6 hours with 0.1% ethanol (carrier control).

GC resistant clone C7H2-R19F2 treated for 6 hours with 0.1% ethanol (carrier control).

100pmol of gene-specific siRNAs or negative control siRNAs (Invitrogen Stealth) were transfected into 2x105 ES or MEF cells in six-well plates using a standard reverse transfection protocol with Lipofectamine RNAiMax (Invitrogen).  Cells were harvested after 48h of RNAi treatment. For the double RNAi knockdown of Kdm6a, after 48h of RNAi treatment 8 x105 cells were re-incubated with 400pmol of siRNAs in 100mm plates followed by a 24h culture before harvest.

ES cells were maintained in standard ES medium with 1000 U/ml leukemia inhibitory factor (LIF) (Millipore) on MEF feeders. ES cells were incubated on 1% gelatin coated dishes for 30min to deplete MEF feeders and transferred to fresh gelatin coated plates for culture for RNAi experiments and cell collection.

Array hybridizations were done at the Microarray Facility at CHDD (University of Washington, Seattle WA).

Raw data files from paired RNAi experiments were analyzed with Affymetrix® Expression Console™ Software using the RMA gene default.

Total RNA was prepared by the Qiagen RNeasy kit with on-column DNaseI digestion

Hybridization and washing were performed according to the standard Affymetrix protocol.

Gene expression data from mouse undifferentiated male ES cells WD44 after 48h treatment of 100pmol of Kdm6a siRNAs. Kdm6a single-RNAi experiment 1 in WD44.

Mouse male ES cells WD44 after single RNAi treatment of Kdm6a siRNAs. Kdm6a RNAi experiment-1 in WD44.

Gene expression data from mouse undifferentiated male ES cells WD44 after 48h treatment of 100pmol of negative control siRNAs (Invitrogen Stealth control). Kdm6a single-RNAi experiment 1 in WD44.

Mouse male ES cells WD44 after single RNAi treatment of negative control siRNAs. Kdm6a RNAi experiment-1 in WD44.

Gene expression data from mouse undifferentiated male ES cells WD44 after 48h treatment of 100pmol of Kdm6a siRNAs. Kdm6a single-RNAi experiment 2 in WD44.

Mouse male ES cells WD44 after single RNAi treatment of Kdm6a siRNAs. Kdm6a RNAi experiment-2 in WD44.

Gene expression data from mouse undifferentiated male ES cells WD44 after 48h treatment of 100pmol of negative control siRNAs (Invitrogen Stealth control). Kdm6a single-RNAi experiment 2 in WD44.

Mouse male ES cells WD44 after single RNAi treatment of negative control siRNAs. Kdm6a RNAi experiment-2 in WD44.

peripheral blood from 8-10 E12.5 embryos;Cbfb-/-;Cbfb+/- x Cbfb+/-

peripheral blood from 8-10 E12.5 embryos;Cbfb+/+;Cbfb+/MYH11 x C57/Bl6

Runx1KO_2
Gene expression data from KSL cells from Runx1-knockout mice

C57BL/6;Runx1-knockout mice (Runx1floxed/floxedMxCre+/-);bone marrow;sorted c-Kit+/Sca-1+/Lin-/IL7Ra- (KSL) cells;3 months after poly IC treatment

Runx1KO_3

Runx1KO_1

RUNX1(41-214)_3
Gene expression data from KSL cells from RUNX1(41-214)-expressing mice

C57BL/6;RUNX1(41-214)-expressing mice;RUNX1(41-214)-expressing retroviral vector;bone marrow;sorted c-Kit+/Sca-1+/Lin-/IL7Ra- (KSL) cells;4 months after transduction/transplantation with RUNX1(41-214)-expressing retroviral vector

RUNX1(41-214)_1

RUNX1(41-214)_2

A549 a pulmonary alveolar epithelial cell line was used in mechanical stretch and parenchymal cell activation experiments. Cells were grown in flexercell plates coated with collagen I, and allowed to grow O/N. Cells were then exposed to TNF alpha 20ng/ml stimulation for 1hr or 4hrs. Two replicates for each time point were performed. This is the first replicate for the 4hr time point. Experiemnt was carried out Nov 21 2002

A549 a pulmonary alveolar epithelial cell line was used in mechanical stretch and parenchymal cell activation experiments. Cells were grown in flexercell plates coated with collagen I, and allowed to grow O/N. Cells were then exposed to TNF alpha 20ng/ml stimulation + cyclic stretch (20% elongation) for 1hr or 4hrs. Two replicates for each time point were performed. This is the second replicate for the 1hr time point. Experiemnt was carried out Jan 31 2003

Alveolar epithelial cells exposed to both TNF (20ng/ml) and cyclic stretch (20% elongation) for 1hr

A549 a pulmonary alveolar epithelial cell line was used in mechanical stretch and parenchymal cell activation experiments. Cells were grown in flexercell plates coated with collagen I, and allowed to grow O/N. Cells were then exposed to TNF alpha 20ng/ml stimulation for 1hr or 4hrs. Two replicates for each time point were performed. This is the first replicate for the 1hr time point. Experiemnt was carried out Oct 20 2002

A549 a pulmonary alveolar epithelial cell line was used in mechanical stretch and parenchymal cell activation experiments. Cells were grown in flexercell plates coated with collagen I, and allowed to grow O/N. Cells were then exposed to TNF alpha 20ng/ml stimulation for 1hr or 4hrs. Two replicates for each time point were performed. This is the second replicate for the 4hr time point. Experiemnt was carried out Jan 31 2003

A549 a pulmonary alveolar epithelial cell line was used in mechanical stretch and parenchymal cell activation experiments. Cells were grown in flexercell plates coated with collagen I, and allowed to grow O/N. Cells were then exposed to TNF alpha 20ng/ml stimulation + cyclic stretch (20% elongation) for 1hr or 4hrs. Two replicates for each time point were performed. This is the First replicate for the 4hr time point. Experiemnt was carried out Nov 21 2002

alveolar epithelial cells exposed to TNF (20ng/ml) and cyclic stretch (20% elongation) for 4hrs

A549 a pulmonary alveolar epithelial cell line was used in mechanical stretch and parenchymal cell activation experiments. Cells were grown in flexercell plates coated with collagen I, and allowed to grow O/N. Cells were then exposed to TNF alpha 20ng/ml stimulation + cyclic stretch (20% elongation) for 1hr or 4hrs. Two replicates for each time point were performed. This is the first replicate for the 1hr time point. Experiemnt was carried out Oct 20 2002

alveolar epithelial cell line exposed to TNF (20ng/ml) and cyclic stretch (20% elongation) for 1hr

A549 a pulmonary alveolar epithelial cell line was used in mechanical stretch and parenchymal cell activation experiments. Cells were grown in flexercell plates coated with collagen I, and allowed to grow O/N. Cells were then exposed to TNF alpha 20ng/ml stimulation + cyclic stretch (20% elongation) for 1hr or 4hrs. Two replicates for each time point were performed. This is the second replicate for the 4hr time point. Experiemnt was carried out Jan 31 2003

Inducible stable HEK 293 Flp-In T-REx Ero1alpha-WT cells, expression induced with doxycycline for 24 h

Inducible stable HEK 293 Flp-In T-REx Ero1alpha-C104A/C131A cells, expression not induced

Inducible stable HEK 293 Flp-In T-REx Ero1alpha-WT cells, expression not induced

Transgenic for alpha tropomyosin slow, snap frozen, gastrocnemus muscle, 10 month age animal

Transgenic, snap frozen, gastrocnemus muscle, 10 month age animal

Transgenic for alpha tropomyosin slow, snap frozen, gastrocnemus muscle, 7month age animal

Wild type, snap frozen, gastrocnemus muscle, 10 month age animal

Transgenic for alpha tropomyosin slow, snap frozen, extensor digitorum longus muscle, 10 month age animal

The CEL file for this submission could not be fully recovered; the linked supplementary file is approximately 75% complete

Transgenic, snap frozen, extensor digitorum longus muscle, 10 month age animal

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_6-sp3

CD8 T cells isolated from spleen; transduced with shRNA targeting: Alk; Sample name: 6-sp3

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_1-tu2

CD8 T cells isolated from tumor; transduced with shRNA targeting: Lacz; Sample name: 1-tu2

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_1-tu3

CD8 T cells isolated from tumor; transduced with shRNA targeting: Lacz; Sample name: 1-tu3

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_2-tu1

CD8 T cells isolated from tumor; transduced with shRNA targeting: Ppp2r2d; Sample name: 2-tu1

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_2-tu2

CD8 T cells isolated from tumor; transduced with shRNA targeting: Ppp2r2d; Sample name: 2-tu2

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_2-tu3

CD8 T cells isolated from tumor; transduced with shRNA targeting: Ppp2r2d; Sample name: 2-tu3

clinically localized prostate cancer tissue pool extracted from sample P1, P2, P3, P4 and P5

clinically localized prostate cancer tissue pool extracted from sample P1, P2, P3, P4 and P5, replicates of PX1.

U-33 cells stably transfected with a PPARg2 expression construct (U-33/g2 cells);24 hrs;Rosiglitazone present

PPARg2 expression construct, 24 hrs, No Rosiglitazone (PPAR_24_1)

U-33 cells stably transfected with a PPARg2 expression construct (U-33/g2 cells);24 hrs;No Rosiglitazone present

U-33 cells stably transfected with a PPARg2 expression construct (U-33/g2 cells);72 hrs;Rosiglitazone present

PPARg2 expression construct, 72 hrs, No Rosiglitazone (PPAR_72_1)

U-33 cells stably transfected with a PPARg2 expression construct (U-33/g2 cells);72 hrs;No Rosiglitazone present

PPARg2 expression construct, 24 hrs, No Rosiglitazone (PPAR_24_2)

PPARg2 expression construct, 72 hrs, No Rosiglitazone (PPAR_72_2)

SFMC isolated by Ficoll gradient centrifugation from pauciarticular JRA patient
Keywords = Pauciarticular course, juvenile rheumatoid arthritis (JRA), synovial fluid mononuclear cells (SFMC)

TH cells from LC, wild type control, young time point, biological replicate 3

TH_LCY_WT_3

C57BL6/J;No;Aug-11;63;male;LC (locus coeruleus);P22;Y/X;TH/-;brain;tyrosine hydroxylase (TH)-positive locus coeruleus (LC) neurons

Primary mouse microglia from WT and TLR4 knockout WT and TLR4 knockout were exposed to hypoxic or hypoglycemic (ischemic) or normoxic or normoglycemic (control) conditions for 24 h in triplicate. All cells were then exposed to 24 h of normoxic or normoglycemic (reperfusion) conditions.

GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Functional Genomics Laboratory at the Center for Ecogenetics and Environmental Health (http://depts.washington.edu/ceeh/ServiceCores/FC1/FC1.html).

RNA was isolated from cultured myocytes by extraction with a commercially available kit (Qiagen) according to the manufacturer’s instructions.

For microarray hybridization, RNA was processed for hybridization to Affymetrix GeneChip® Mouse Gene 1.0 ST Arrays through a core facility in the Functional Genomics Laboratory at the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer’s instructions.

52B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

51B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

50B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

4B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; not assessable

53B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

C57BL/6 mice were bred with mice heterozygous for Nf1.  Their male pups were euthanized at P18 and  brains quickly dissected and flash-frozen.  Their livers were also removed and frozen for the purpose of genotyping.  Hippocampi from two wild-type mice were pooled and RNA extracted for expression profiling.
Lot batch =

C57BL/6 mice were bred with mice heterozygous for Nf1.  Their male pups were euthanized at P15 and  brains quickly dissected and flash-frozen.  Their livers were also removed and frozen for the purpose of genotyping.  Hippocampi from two NF+/- mice were pooled and RNA extracted for expression profiling.na
Lot batch =

To achieve somatic deletion of Lkb1 in mouse, we generated Lkb1 L/L, rosa26CreERT2 mice. In this model, the treatment of adult Lkb1 L/L, rosa26CreERT2 mice with tamoxifen results in efficient deletion of Lkb1 (Lkb1 KO mice) in hematopoietic organs and cells, including HSC-enriched LSK cells. At 1 day post completing tamoxifen injection (DPI), we prepared single cell suspensions form bone marrow (from femoral and tibial bones), and stained and sorted LSK populations using FACSAria (Becton Dickinson, Mountain View, CA).

MAS5.0 was used to normalize arrays and to compute expression indices. Briefly, raw probe intensities were normalized across profiles. Expression values for each probe set were summarized. Differentially expressed probe sets were selected based on fold change as well as modified t-statistics after adjusting for multiple tests.

Bone marrow LSK cells were sorted from mice at 1 DPI (15,000-20,000 cells/sample). RNA from sorted LSK cells was extracted using PicoPure RNA Isolation Kit (Molecular Devices) per manufacturer's instructions, and cDNA was prepared utilizing Superscript II Rnase H-Reverse transcriptase (Invitrogen).

Approximately 10 ng of total RNA was first amplified by The RiboAmp® HS PLUS RNA Amplification Kit (Arcturus) and then processed to produce biotinylated cRNA targets.

Gene expression profiles on Affymetrix mouse 430 2.0 chips for Lkb1 KO #6 HSCs.

C57BL/Ka-CD45.2:Thy-1.1;Lkb1 knockout;bone marrow from femoral and tibial bones;LSK (Lin-, Sca-1+, c-Kit+) cells

LSK (Lin-, Sca-1+, c-Kit+) cells sorted from Lkb1 KO bone marrow cells

Gene expression profiles on Affymetrix mouse 430 2.0 chips for Lkb1 KO #7 HSCs.

Gene expression profiles on Affymetrix mouse 430 2.0 chips for Lkb1 KO #4 HSCs.

Gene expression profiles on Affymetrix mouse 430 2.0 chips for Lkb1 KO #5 HSCs.

Here Lkb1 L/L mice treated with tamoxifen were used as Lkb1 WT mice. At 1 day post completing tamoxifen injection (DPI), we prepared single cell suspensions form bone marrow (from femoral and tibial bones), and stained and sorted LSK populations using FACSAria (Becton Dickinson, Mountain View, CA).

Gene expression profiles on Affymetrix mouse 430 2.0 chips for Lkb1 WT 7 HSCs.

C57BL/Ka-CD45.2:Thy-1.1;wild-type;bone marrow from femoral and tibial bones;LSK (Lin-, Sca-1+, c-Kit+) cells

LSK (Lin-, Sca-1+, c-Kit+) cells sorted from Lkb1 WT bone marrow cells

Gene expression profiles on Affymetrix mouse 430 2.0 chips for Lkb1 WT 5 HSCs.

Gene expression profiles on Affymetrix mouse 430 2.0 chips for Lkb1 WT 6 HSCs.

2F4-1

mRNA extracted from  lung fibroblasts derived from open lung biopsies of a patient (FASSc2) with fibrosing alveolitis associated with systemic sclerosis. Lung fibroblasts were grown to confluence in DMEM with 10% fetal calf serum. At confluence, lung fibroblasts were serum-deprived overnight, and exposed to  serum-free culture-medium with the addition of 0.1% BSA for 4 hours. At the end of treatment period total RNA was harvested, quantified, and integrity was verified by denaturing gel electrophoresis.

mRNA extracted from  lung fibroblasts derived from open lung biopsies of a patient (FASSc1) with fibrosing alveolitis associated with systemic sclerosis. Lung fibroblasts were grown to confluence in DMEM with 10% fetal calf serum. At confluence, lung fibroblasts were serum-deprived overnight, and exposed to 4 ng/ml of activated TGF-ß1 (R&D Systems) in serum-free culture-medium with the addition of 0.1% BSA for 4 hours. At the end of treatment period total RNA was harvested, quantified, and integrity was verified by denaturing gel electrophoresis.

lung fibroblasts from patients with fibrosing alveolitis associated with systemic sclerosis

mRNA extracted from  lung fibroblasts derived from open lung biopsies of a patient (FASSc1) with fibrosing alveolitis associated with systemic sclerosis. Lung fibroblasts were grown to confluence in DMEM with 10% fetal calf serum. At confluence, lung fibroblasts were serum-deprived overnight, and exposed to serum-free culture-medium with the addition of 0.1% BSA for 4 hours. At the end of treatment period total RNA was harvested, quantified, and integrity was verified by denaturing gel electrophoresis.

lung fibroblasts from patient with fibrosing alveolitis associated with systemic sclerosis

SK03M003
Gene expression data from wildtype pancreatic RNA 36 hours post-tamoxifen

SK03M002

SK03M001

SK03M005

SK03M004

All fibroblasts were cultured in 5% CO2 and at 37°C in DMEM containing 15% FBS, 2 mM L-glutamine, 0.1 mM non-essential aminoacids, sodium Pyruvate, and 55 μM b-mercaptoethanol.

Expression signals were scanned on an Affymetrix GeneChip Scanner (7G upgrade). The data extraction was done by the Affymetrix GCOS software v.1.4.

The statistical analysis of the data was performed using ArrayStar 3. Briefly, raw CEL files were imported together with gene annotation from NetAffix (from 11/13/2009) and normalized using RMA algorithm and quantile normalization. As both H9 ESC and HGPS-iPSC originate from female samples, and in order to check for any possible bias introduced by the X and Y chromosome-coded genes, we performed the same analysis with only autosome genes.

Total RNA was isolated using Trizol (Invitrogen) followed by cDNA synthesis using High capability RNA-to-cDNA Mater Mix (Invitrogen).

The GeneChip microarray processing was performed by the Functional Genomica Core in the Institute for Research in Biomedicine (Barcelona, Spain) according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA). The amplification and labeling were processed as indicated in Nugen protocol with 25ng starting RNA. For each sample, 3.75ug ssDNA were labeled and hybridized to the Affymetrix HG-U133 Plus 2.0 chips.

hgps-fib_2: Human HGPS fibroblasts AG01972, AG11498, AG06297, and normal fibroblasts GM00038 (9 year), AG05247 (87 year), AG09602 (92 year) were purchased from Coriell Cell Repository

hgps-fib_1: Human HGPS fibroblasts AG01972, AG11498, AG06297, and normal fibroblasts GM00038 (9 year), AG05247 (87 year), AG09602 (92 year) were purchased from Coriell Cell Repository

E14.5;Prmt5F/FNes;mixed C57BL/6 X 129S1/SvlmJ;NPC;Prmt5 depletion

Erythroid progenitors on day 6 of differentiation;transduced with control empty vector

Normal cervix, age 27 years, micordissected squamous epitheilium

Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56595.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56594.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56610.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56602.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56593.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56592.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56600.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56608.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56587.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56604.gif

Setleis Syndrome Patient described in Al-Gazali and Al-Talabani (1996) Clin Dysmorphol 5(3):249-53.

Pool of RNAs from cells in passages 14 and 15 of Coriell cell line GM03377

female;Homozygous for the Q119X mutation in the TWIST2 gene;Puerto Rican

1:1 Pool of RNAs from two siblings, female and male, affected with Setleis Syndrome

mixed;Homozygous for the Q119X mutation in the TWIST2 gene;Puerto Rican

The just.gcRMA normalization with normalize.ExpressionSet.lvs function from FLUSH.LVS.bundle package of the Bioconductor project was used. Low signal probesets were filtered out according to expression of probesets assigned to Y chromosome in female samples (expression lower than 95 percentile of Y-chromosome probesets in at least 20 samples), differential probesets were selected with Kruskal-Wallis test..

Gene expression data from untreated NZM15 metastatic melanoma cells

Gene expression data from NZM15 metastatic melanoma cells treated with non-targeting negative control siRNA (luciferase)

skin;NZM15;metastatic melanoma;neck nodule;luciferase siRNA negative control

NZM15 metastatic melanoma cells treated with luciferase negative control siRNA

Gene expression data from NZM15 metastatic melanoma cells treated with siRNA targeting MITF

Gene expression data from NZM15 metastatic melanoma cells treated with siRNA targeting PAX3

SMhu017

Total RNAs were extracted using RNAzol . 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).

Confluent HUVECs were stimulated with COMP-Ang1 (more potent Angiopoietin-1 than native Angiopoietin-1) for 1 hour after starvation overnight

ASC at passage 1 were cryopreserved until subcultivation. Cells were growth under hypoxic conditions. ASC at passage 3 were used for RNA extraction.

Human subcutaneous adipose tissue was washed, minced and digested with collagenase I-A. The digested tissue was sequentially filtered and centrifuged. The pellet was resuspended in culture medium, seeded and incubated overnight under hypoxic (1% O2) conditions. Adherent cells were referred as ASC. Cells were growth under hypoxic conditions, and culture medium was change every 2-3 days, as described previously (Oñate et al., FASEB J, 2012; 26:4327-36).

The raw data (.CEL files) was processed using Robust Multi-array Average (RMA) algorithm, implemented by Expression Console 1.1.1. software (Affymetrix default settings).

Total cell RNA was extracted using silica-membrane columns (RNesasy Mini Kit, Qiagen) according to the manufacturer's instructions.

Labeled and fragmented samples were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0ST Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

After preprocessation of 200 ng of RNA, for each sample, with Ambion WT Expression kit (User Guide  P/N 4425209 Rev.C 09/2009, Ambion), biotinylated DNA were prepared using the Affymetrix GeneChip Terminal Labeling kit from 5,5 ug of ssDNA  (GeneChip WT Terminal, Labeling and Hibridization User Manual , P/N 702808 Rev.7 2009, Affymetrix) according to manufacturers' guidelines.

Gene expression data from ASC isolated from subcutaneous WAT of lean individual 3

Gene expression data from ASC isolated from subcutaneous WAT of lean individual 2

Gene expression data from ASC isolated from subcutaneous WAT of lean individual 1

Gene expression data from ASC isolated from subcutaneous WAT of morbidly obese patient 3

Gene expression data from ASC isolated from subcutaneous WAT of morbidly obese patient 2

Gene expression data from ASC isolated from subcutaneous WAT of morbidly obese patient 1

ME180;cervix; derived from metastatic site: omentum;epidermoid carcinoma;Homo sapiens, human;10μM ATRA;1 hour

ME180;cervix; derived from metastatic site: omentum;epidermoid carcinoma;Homo sapiens, human;DMSO (Vehicle);NA

C57BL/6J;129S5/SvEvBrd;Inha-/-;granulosa cell;44-46hr PMSG, 6hr hCG

pancreatic acinar cell-specific knockout of the Perk gene; mixed genetic background; postnatal day 16; total pancreas; replicate mouse #2.

wild-type control (littermates) of "P19_exPKO_pancreas"; mixed genetic background; postnatal day 19; total pancreas; pooled two mouse cDNA samples equally to generate cRNA.

male mice (8 wks) were treated (oral gavage) with niacin bound chromium (nbc; 10 mg/kg wt) in water for 10 weeks (5d per wk). At the end of study subcutaneous fat was harvested for microarray analysis.

pancreatic acinar cell-specific knockout of the Perk gene; mixed genetic background; postnatal day 19; total pancreas; pooled two mouse cDNA samples equally to generate cRNA.

C57BL/6x129Sv;female;hCAR transgenic in mCAR knockout background;phenobarbitol

Gene expression data from male F344 rats treated with a single dose of vehicle, i.e. control, 0mg/kg, for 96 hours

Brain tissue from Fisher 344 male rat, Animal #246, control (0mg/kg) D-Serine

Brain tissue from Fisher 344 male rat, Animal #244, control (0mg/kg) D-Serine

Brain tissue from Fisher 344 male rat, Animal #245, control (0mg/kg) D-Serine

Brain tissue from Fisher 344 male rat, Animal #243, control (0mg/kg) D-Serine

C57BL/6;male;ESC-like cells;Prdm14 Knockout, pPyCAG-AGP14 transgene;2i

SMhu102

SMhu101

SMhu096

SMhu095

SMhu094

SMhu093

SMhu100

SMhu099

SMhu098

SMhu097

raw data processing was performed using ArrayMagic (Buness et al., 2005) and VSN normalization method; two independent array hybridization from every sample were merged; after removal of bad quality clones (marked as - and 0 on array, generalized log2 ratios from 26618 cDNA clones were given in the data table

cell line HCT-116, Ki-RAS-mutation, DNMT1 knockout, U0126-treated;common reference sample

cell line HCT-116, Ki-RAS-mutation, DNMT1 knockout, DMSO-treated;common reference sample

cell line HCT-116, Ki-RAS-mutation, DNMT wildtype, DMSO-treated;common reference sample

cell line HCT-116, Ki-RAS-mutation, DNMT wildtype, non-treated;common reference sample

cell line HCT-116, Ki-RAS-mutation, DNMT wildtype, Aza-treated;common reference sample

cell line HCT-116, Ki-RAS-mutation, DNMT wildtype, U0126-treated;common reference sample

cell line HCT-116, Ki-RAS-mutation, DNMT1 knockout, non-treated;common reference sample

in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 24, Units of Duration: hrs, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 6, Units of Dose or Concentration: ppm

nasal epithelium, formaldehyde inhalation exposure, 6 ppm, 6 hrs per day, 24 h time point

Rat230_2;15;ul;2.242;1.1;1.97;1:5;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;288;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.088;0.579;1.8;1:5;8.6;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;289;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.853;0.955;1.88;1:5;8.2;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;290;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.326;0.691;1.83;1:5;8.3;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;292;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.04;0.53;1.97;1:5;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;286;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.448;0.781;1.85;1:5;8.2;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;309;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;0.881;0.457;1.95;1:5;8.2;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;310;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.315;0.668;1.95;1:5;8.8;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;312;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;2.539;1.303;1.91;1:5;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;221;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.381;0.716;1.91;1:5;8.1;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;222;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

CD14+ monocytes were isolated by density centrifugation (LymphoPrep) and successive positive selection with magnetic beads (Miltenyi).

CD14+ after 2 wk quercetin supplementation, biological replicate 2

The data was analysed with Bioconductor software package for R using the simpleaffy package (2.16.0-1) and normalisation method was gcrma (slow) with the gcrma package (2.12.1).

Total RNA isolation including an on-column DNA-digestion step was performed with RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

Human Genome U133+ 2.0 GeneChip® microarrays were hybridized for 16h at 45°C with 15µg fragmented, biotin-labeled cRNA. Arrays were washed and stained using the GeneChip Hybridization, Wash and Stain Kit (Affymetrix) and the Fluidics Station 450 (FS450_0004 script) .

Biotinylated cRNA was prepared from 2µg total RNA with MessageAmp™ II-Biotin Enhanced Kit (Ambion).

gene expression data from peripheral blood mononuclear cells (PBMC) isolated from (fasting) blood samples before and after a 2 wk supplementation of 150mg quercetin per day

CD14+ after 2 wk quercetin supplementation, biological replicate 3

CD14+ after 2 wk quercetin supplementation, biological replicate 1

Technical replicate #3 of ATF2 knockout. These mice are mixed background of FVB and C57bl6 and the age when they got the papillomas was about 9 months.

Technical replicate #2 of ATF2 knockout. These mice are mixed background of FVB and C57bl6 and the age when they got the papillomas was about 9 months.

Gene expression data from CAPAN2 cells transduced with control lentivirus

The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.

Total RNA was purified with Trizol and additional purification with Rneasy column.

Mutant tet2

Naïve T- cells isolated from spleen were cultured on a-CD3 coated plates with 2.5 mg/ml a-CD28, 20 ng/ml IL-6, 20 ng/ml IL-23, 1 ng/ml hTGFb, 10 mg/ml a-IL4 and 10 mg/ml a-IFNg for 42 hrs

The matrix data table was created by first log transforming the raw data and then filtering out all probes that showed a standard deviation of <0.25  across all samples as well as probes that do not have an associated entrez id. Agilent Feature Extraction software version 10.7 was used for background subtraction and LOWESS normalization.
The normalized data was then analyzed further using Partek Genomic Suite Version 6.6 by performing a 1-way ANOVA test between the IRF4 KO vs IRF4 Het samples. Data for the probes which showed a > 2-fold change (up or down) with a p-value <0.05 is presented in the 'Analyzed_data.txt' file (available on Series records). It is presented in ascending order of differential expression (Fold-Change) between the IRF4 KO vs IRF4 Het samples. The probeset ID, Gene Symbol, p-value of differential expression and Fold-Change between the IRF4 KO and IRF4 Het samples are indicated. Negative fold changes indicate down-regulation in IRF4 KO samples and positive fold changes indicate up-regulation.

Total RNA was isolated using Qiagen RNeasy kit following manufacturer's protocol and including on-column DNase-digestion. RNA was quantified using UV-spec Nanodrop and then profiled on Agilent Bioanalyzer.

Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Agilent’s Quick Amp Labeling Kit. 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal mouse reference (Stratagene, La Jolla, CA).

C57BL/6J;IRF4 +/-;spleen;Naïve CD4+, CD62L hi, CD25 - T cells;Th17;42 hrs;Reference: pooled RNA from 11 tissues

C57BL/6J;IRF4 -/-;spleen;Naïve CD4+, CD62L hi, CD25 - T cells;Th17;42 hrs;Reference: pooled RNA from 11 tissues

PGC-1alpha -/- differentiated brown fat cells expressing a siRNA specific for PGC-1beta knockdown (rep1)

immortalized cells derived from brown fat tissue of PGC-1alpha KO mouse (mixed background), expressing a siRNA specific for PGC-1beta knockdown.

PGC-1alpha -/- differentiated brown fat cells expressing a control siRNA (rep2)

immortalized cells derived from brown fat tissue of PGC-1alpha KO mouse (mixed background), expressing a control siRNA.

PGC-1alpha -/- differentiated brown fat cells expressing a control siRNA (rep1)

PGC-1alpha -/- differentiated brown fat cells treated 4h cAMP (rep2)

PGC-1alpha -/- differentiated brown fat cells expressing a siRNA specific for PGC-1beta knockdown (rep2)

WT mouse skin treated once with acetone and collected 24 hr later, replicate 2

WT mouse skin treated once with acetone and collected 24 hr later, replicate 1

DKO mouse skin treated once with acetone and collected 24 hr later

DKO mouse skin treated once with acetone and collected 24 hr later, replicate 2

DKO mouse skin treated once with acetone and collected 24 hr later, replicate 1

DKO mouse skin treated once with TPA (phorbol ester 12-O-tetradecanoylphorbol-13 acetate, 6.8 nmol in 200 μl acetone) and collected 24 hr later

DKO mouse skin treated once with TPA and collected 24 hr later, replicate 2

DKO mouse skin treated once with TPA and collected 24 hr later, replicate 1

DKO mouse skin treated daily with TPA (phorbol ester 12-O-tetradecanoylphorbol-13 acetate, 6.8 nmol in 200 μl acetone) during 4 days and collected 24 hr later

DKO mouse skin treated daily with TPA during 4 days and collected 24 hr later, replicate 1

DKO mouse skin treated daily with TPA during 4 days and collected 24 hr later

DKO mouse skin treated once with TPA and collected 24 hr later, replicate 3

DKO mouse skin treated daily with TPA during 4 days and collected 24 hr later, replicate 3

DKO mouse skin treated daily with TPA during 4 days and collected 24 hr later, replicate 2

LOX-1:221302;LOX1_oxLDL_6hr:221302;Classification:Bad;Gradient Severity:0.06;Distortion Severity:0.14;Defective Area (%):0.01;Outlier Area (%):0.04;3'/5' Mean:1.42;Background Mean Dev.:2.84;Absent (%):62.16;Absent (%) Dev.:3.03;Scaling Factor:0.63;Scaling Factor Dev.:0.12;LOX1;6 hours;Oxidized LDL;221302;HAECT;50 ug/ml;Endothelial;Human:Homo sapiens;LOX1_oxLDL_6hr;282295693

LOX-1:221201;LOX1_oxLDL_2hr:221201;Classification:Good;Gradient Severity:0.03;Distortion Severity:0.06;Defective Area (%):0.01;Outlier Area (%):0;3'/5' Mean:1.47;Background Mean Dev.:1.61;Absent (%):57.99;Absent (%) Dev.:0.2;Scaling Factor:0.58;Scaling Factor Dev.:0.28;LOX1;2 hours;Oxidized LDL;221201;HAECT;50 ug/ml;Endothelial;Human:Homo sapiens;LOX1_oxLDL_2hr;282295563

LOX-1:213402;LOX1_Untreated_12hr:213402;Classification:Good;Gradient Severity:0.05;Distortion Severity:0.02;Defective Area (%):0;Outlier Area (%):0;3'/5' Mean:1.55;Background Mean Dev.:0.39;Absent (%):57.62;Absent (%) Dev.:0.49;Scaling Factor:0.55;Scaling Factor Dev.:0.52;LOX1;12 hours;(Not applicable);213402;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;LOX1_Untreated_12hr;282295783

LOX-1:113101;GFP_0hr:113101;Classification:Bad;Gradient Severity:0.05;Distortion Severity:0.12;Defective Area (%):0.08;Outlier Area (%):0;3'/5' Mean:1.61;Background Mean Dev.:6.14;Absent (%):61.21;Absent (%) Dev.:2.29;Scaling Factor:0.45;Scaling Factor Dev.:1.4;GFP;0 hours;(Not applicable);113101;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;GFP_0hr;282295413

LOX-1:221503;LOX1_oxLDL_24hr:221503;Classification:Good;Gradient Severity:0.04;Distortion Severity:0.09;Defective Area (%):0.01;Outlier Area (%):0.01;3'/5' Mean:1.54;Background Mean Dev.:0.02;Absent (%):56.45;Absent (%) Dev.:1.4;Scaling Factor:0.45;Scaling Factor Dev.:1.36;LOX1;24 hours;Oxidized LDL;221503;HAECT;50 ug/ml;Endothelial;Human:Homo sapiens;LOX1_oxLDL_24hr;282295943

LOX-1:221202;LOX1_oxLDL_2hr:221202;Classification:Bad;Gradient Severity:0.02;Distortion Severity:0.01;Defective Area (%):0;Outlier Area (%):0.01;3'/5' Mean:1.68;Background Mean Dev.:2.61;Absent (%):57.66;Absent (%) Dev.:0.45;Scaling Factor:0.4;Scaling Factor Dev.:1.8;LOX1;2 hours;Oxidized LDL;221202;HAECT;50 ug/ml;Endothelial;Human:Homo sapiens;LOX1_oxLDL_2hr;282295573

LOX-1:213103;LOX1_0hr:213103;Classification:Good;Gradient Severity:0.04;Distortion Severity:0.03;Defective Area (%):0;Outlier Area (%):0.01;3'/5' Mean:1.53;Background Mean Dev.:1.32;Absent (%):58.85;Absent (%) Dev.:0.46;Scaling Factor:0.54;Scaling Factor Dev.:0.6;LOX1;0 hours;(Not applicable);213103;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;LOX1_0hr;282295463

LOX-1:213201;LOX1_Untreated_2hr:213201;Classification:Good;Gradient Severity:0.04;Distortion Severity:0.07;Defective Area (%):0;Outlier Area (%):0.01;3'/5' Mean:1.67;Background Mean Dev.:0.2;Absent (%):57.28;Absent (%) Dev.:0.75;Scaling Factor:0.54;Scaling Factor Dev.:0.59;LOX1;2 hours;(Not applicable);213201;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;LOX1_Untreated_2hr;282295533

LOX-1:213401;LOX1_Untreated_12hr:213401;Classification:Medium;Gradient Severity:0.12;Distortion Severity:0.05;Defective Area (%):0.27;Outlier Area (%):0.01;3'/5' Mean:1.51;Background Mean Dev.:0.52;Absent (%):56.98;Absent (%) Dev.:0.98;Scaling Factor:0.6;Scaling Factor Dev.:0.12;LOX1;12 hours;(Not applicable);213401;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;LOX1_Untreated_12hr;282295773

female;juvenile, 8 weeks (P58);Sv129 / C57BL/6N mixed background;Cldn16 -/-;renal tissue

Total RNA was extracted using the Micro-to-Midi Total RNA Purification System (Invitrogen)

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

QK-knockdown U87 transduced with a scrambled non-targeting microRNA (miR-NT)

female;juvenile, 8 weeks (P59);Sv129 / C57BL/6N mixed background;Cldn16 -/-;renal tissue

JAK2V617F-mutant AML cell line HEL;JAK2 knockdown (Jak2-9 shRNA)

We used two established transgenic mouse lines: transgenic mice expressing Cre recombinase under the control of the AMH gene promoter selectively in Sertoli cells (Lecureuil C, Genesis 2002) and the floxed Rb mice were generously provided by Dr Anton Berns, of The Netherlands Cancer Institute (Vooijs M, Oncogene 1998). To generate the Sertoli cell-specific Rb conditional knockouts, transgenic Amh-Cre male mice were bred with female mice containing two floxed copies of Rb. These matings yielded SC-RbKO mice, along with other genotypes.

The arrays were scanned with the Illumina BeadArray Reader. Normalization and statistical analyses of the microarray data were performed using the statistical software R package limma (http://www.R-project.org) or Sigma Stat 3.1 (SPSS Inc., Chicago, IL, USA).

Data are normalized to remove variation between samples caused by non-biological reasons. This data set has been normalized using the quantile normalization method which is a standard method used for normalizing Illumina data.

RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. The RNA concentrations were measured with Nanodrop ND-1000 (Thermo Fisher Scientific, Waltham, MA, USA) and RNA quality was controlled by Experion analysis (Bio-Rad Laboratories, Hercules, CA, USA). The microarray analysis were carried out at the Finnish DNA-Microarray Centre utilizing the MouseWG-6 v2 Expression BeadChips (Illumina, San Diego, CA, USA).

The labelled cRNA was purified and hybridized to the BeadChip at 58 deg.C, for 17 hours following the Illumina Whole-Genome Gene Expression Protocol for BeadStation. Hybridization was detected with Cyanine3-streptavidine (GE Healthcare, Little Chalfont, UK)

Biotinylated cRNA were prepared with the Illumina RNA TotalPrep Amplification Kit (Ambion Inc., Austin, TX, USA).

0KD2
Gene expression data from undifferentiated TG2 knockout NB4.

0KD1

2N1
Gene expression data from 48 hour ATRA-differentiated wild-type NB4.

0KD3

2N3

2N2

2KD2
Gene expression data from 48 hour ATRA-differentiated TG2 knockout NB4.

2KD1

3N1

2KD3

FOXA1 overexpressing LNCaP prostate cancer cell line replicate 1

Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67348.gif; format: GIF

Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67347.gif; format: GIF

Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67346.gif; format: GIF

Embryo dissections:
All procedures involving animals have been approved previously by the Animal Care and Use Committee Tel Aviv University. ADNP heterozygous mice were housed in a 12-h light and 12-h dark cycle facility and free access to rodent chow and water was available. Mice were checked for plug every three hours. Plug day was assigned as day 0 (E0). A definitive determination of the developmental stage of each embryo at the time of harvesting was also based on anatomical analysis. E9 whole embryos were separated from the extra embryonic tissue (yolk sac and amnion), immersed in ice-cold magnesium- and calcium-free phosphate-buffered saline, snap-frozen in liquid nitrogen, and stored at -80°C until analysis. The extra embryonic tissue was stored separately and used for genotyping.
Genotyping:

Genomic DNA was extracted from embryonic yolk sacs. Lysis buffer (100 mM Tris HCl pH 8.5, 5mM EDTA, 0.2% SDS, 200 mM NaCl, proteinase K 0.35 mg/ml) was added to each sample (0.5ml) followed by a 16hr incubation period at 37°C with gentle shaking. Isopropanol (0.5 ml) was then added and samples were mixed. Precipitated DNA was then transferred to a new tube containing 1ml ethanol, subjected to centrifugation at 20,000g and the resulting DNA pellet was air-dried and dissolved in 50 microLl 10 mM Tris-HCl, pH 8, 1 mM EDTA (TE) buffer. The resulting DNA was then subjected to polymerase chain reaction (PCR) amplification to check for the existence of ADNP and/or neomycin resistance gene in the embryonic genome. The PCR mixtures contained 0.5μg genomic DNA, 0.25 μM of each primer (sense and antisense), 1.5 mM MgCl2 and 3 units Taq polymerase in a final volume of 50 μl. (Buffers and enzyme were obtained from Life Technology Gibco BRL, Paisley, Scotland). PCR was performed using the following cycle parameters: 94 °C for 4 min, followed by 30 cycles, each including 94 °C for 30 s, specific annealing temperature for 40 s and elongation at 72 °C for 40 s. Reactions were terminated at 72 °C for 10 min. Control reactions containing water instead of DNA template for each primer used (PCR-) were included.

RNA extraction:
Two embryos from the same genotype and gestational time were pooled and RNA was isolated using Qiagene RNeasy mini kit (Quiagene, Hilden, Germany). Because of the small amounts of RNA extracted from one embryo at age E9 (~1.5μg) a two embryo pool comprised of littermates possessing the same genotype was used. For comparative experiments all embryos were at approximately the same age.

Gene array:

All experiments were performed using Affymetrix MOE430A oligonucleotide arrays, as described at http://www.affymetrix.com/products/arrays/specific/mouse430a_2.affx. Total RNA from each sample was used to prepare biotinylated target RNA, with minor modifications from the manufacturer's recommendations (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).
Briefly, 3-5 µg of mRNA was used to generate first-strand cDNA by using a T7-linked oligo(dT) primer. After second-strand synthesis, in vitro transcription was performed with biotinylated UTP and CTP (Enzo Diagnostics), resulting in approximately 100-fold amplification of RNA. A complete description of procedures is available at: http://bioinf.picr.man.ac.uk/mbcf/downloads/GeneChip_Target_Prep_Protocol_CRUK_v_2.pdf.
The target cDNA generated from each sample was processed according to manufacturer's recommendation using an Affymetrix GeneChip Instrument System
(http://www.affymetrix.com/support/technical/manual/expression_manual.affx). Briefly, spike controls were added to 10 µg fragmented cDNA before overnight hybridization. Arrays were then washed and stained with streptavidin-phycoerythrin, before being scanned on an Affymetrix Gene Chip scanner. A complete description of these procedures is available at
http://bioinf.picr.man.ac.uk/mbcf/downloads/GeneChip_Hyb_Wash_Scan_Protocol_v_2_web.pdf Additionally, quality and amount of starting RNA was confirmed using an agarose gel. After scanning, array images were assessed by eye to confirm scanner alignment and the absence of significant bubbles or scratches on the chip surface. 3'/5' ratios for GAPDH and beta-actin were confirmed to be within acceptable limits (0.8-0.88), and BioB spike controls were found to be present on all the arrays, with BioC, BioD and CreX also present in increasing intensity.

TP082505_22_HG-U133A_2_IMFGN0023: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

261;Asacol 800mg BD;1/7/57;M;CAUCASIAN;1/1/98;1/1/98;FALSE;FALSE;TRUE;NO;FALSE;FALSE;6/14/05;2;0;0;0;0;0;0;0;TRUE;2;BOTH;BOTH;unknown;unknown;unknown;6/14/05;BOTH;BOTH;BOTH;BOTH;BOTH;8/15/05;DISEASE IN REMISSION;never;unknown;none;UC;11-15-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

261;Asacol 800mg BD;1/7/57;M;CAUCASIAN;1/1/98;1/1/98;FALSE;FALSE;TRUE;NO;FALSE;FALSE;6/14/05;2;0;0;0;0;0;0;0;TRUE;2;BOTH;BOTH;unknown;unknown;unknown;6/14/05;BOTH;BOTH;BOTH;BOTH;BOTH;8/15/05;DISEASE IN REMISSION;never;unknown;none;UC;11-15-01;descending colon;Inflamed;total RNA from 10 human cell lines

263;Azathioprine 75mg Fosomax 70mg;11/9/58;F;CAUCASIAN;3/1/00;6/1/00;FALSE;FALSE;FALSE;YES;FALSE;TRUE;7/8/05;1;0;0;0;0;0;0;0;TRUE;0;BOTH;unknown;unknown;unknown;unknown;7/8/05;BOTH;BOTH;unknown;unknown;unknown;8/15/05;DISEASE IN REMISSION;never;unknown;none;UC;11-15-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

263;Azathioprine 75mg Fosomax 70mg;11/9/58;F;CAUCASIAN;3/1/00;6/1/00;FALSE;FALSE;FALSE;YES;FALSE;TRUE;7/8/05;1;0;0;0;0;0;0;0;TRUE;0;BOTH;unknown;unknown;unknown;unknown;7/8/05;BOTH;BOTH;unknown;unknown;unknown;8/15/05;DISEASE IN REMISSION;never;unknown;none;UC;11-15-01;descending colon;Inflamed;total RNA from 10 human cell lines

265;Pentaza 500mg TDS;8/17/71;M;CAUCASIAN;2/5/04;3/22/04;FALSE;FALSE;FALSE;NO;FALSE;FALSE;7/19/05;1;0;0;0;0;0;0;0;TRUE;0;BOTH;BOTH;BOTH;BOTH;BOTH;7/19/05;BOTH;BOTH;BOTH;BOTH;BOTH;8/15/05;DISEASE IN REMISSION;current;0-4;none;UC;11-15-01;descending colon;Inflamed;total RNA from 10 human cell lines

265;Pentaza 500mg TDS;8/17/71;M;CAUCASIAN;2/5/04;3/22/04;FALSE;FALSE;FALSE;NO;FALSE;FALSE;7/19/05;1;0;0;0;0;0;0;0;TRUE;0;BOTH;BOTH;BOTH;BOTH;BOTH;7/19/05;BOTH;BOTH;BOTH;BOTH;BOTH;8/15/05;DISEASE IN REMISSION;current;0-4;none;UC;11-15-01;ascending colon;Inflamed;total RNA from 10 human cell lines

267;Mesalazine 800mg TDS;8/16/74;M;CAUCASIAN;5/1/05;5/10/05;FALSE;FALSE;FALSE;NO;FALSE;FALSE;8/15/05;1;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;unknown;unknown;unknown;9/20/05;BOTH;BOTH;BOTH;BOTH;BOTH;9/30/05;DISEASE IN REMISSION;ex;5/1/03;5-14;None;UC;11-15-01;ascending colon;Inflamed;total RNA from 10 human cell lines

265;Pentaza 500mg TDS;8/17/71;M;CAUCASIAN;2/5/04;3/22/04;FALSE;FALSE;FALSE;NO;FALSE;FALSE;7/19/05;1;0;0;0;0;0;0;0;TRUE;0;BOTH;BOTH;BOTH;BOTH;BOTH;7/19/05;BOTH;BOTH;BOTH;BOTH;BOTH;8/15/05;DISEASE IN REMISSION;current;0-4;none;UC;11-15-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

249;Azathioprine 150mg Salazopyrine;1/12/60;M;CAUCASIAN;3/1/90;3/24/90;FALSE;FALSE;FALSE;YES;FALSE;FALSE;4/8/05;3;0;0;0;0;0;0;0;FALSE;0;12;12;12;12;12;11;11;11;12;BOTH;BOTH;BOTH;BOTH;BOTH;4/8/05;BOTH;BOTH;BOTH;BOTH;BOTH;5/30/05;FAILURE OF THERAPY;never;unknown;None;UC;11-15-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

267;Mesalazine 800mg TDS;8/16/74;M;CAUCASIAN;5/1/05;5/10/05;FALSE;FALSE;FALSE;NO;FALSE;FALSE;8/15/05;1;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;unknown;unknown;unknown;9/20/05;BOTH;BOTH;BOTH;BOTH;BOTH;9/30/05;DISEASE IN REMISSION;ex;5/1/03;5-14;None;UC;11-15-01;descending colon;Inflamed;total RNA from 10 human cell lines

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_1-sp3

CD8 T cells isolated from spleen; transduced with shRNA targeting: Lacz; Sample name: 1-sp3

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_2-sp1

CD8 T cells isolated from spleen; transduced with shRNA targeting: Ppp2r2d; Sample name: 2-sp1

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_1-sp1

CD8 T cells isolated from spleen; transduced with shRNA targeting: Lacz; Sample name: 1-sp1

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_1-sp2

CD8 T cells isolated from spleen; transduced with shRNA targeting: Lacz; Sample name: 1-sp2

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_2-sp2

CD8 T cells isolated from spleen; transduced with shRNA targeting: Ppp2r2d; Sample name: 2-sp2

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_2-sp3

CD8 T cells isolated from spleen; transduced with shRNA targeting: Ppp2r2d; Sample name: 2-sp3

Cells were mock transduced and 2 x 105 cells were plated onto 60 mm dishes in triplicates and harvested 4 days later.

Cells were grown in DMEM/10% fetal bovine serum in the presence of antibiotics.

Gene expression data from DAOY cells stably expressing Bmi1 and Mel18 shRNA

Gene expression data from DAOY cells stably expressing Alk shRNA

hair follicles from anagen-deleted area (presence of functional Notch1)

Normalized against other samples in series by log regression on signal obtained with control spots (first 64 samples). For this sample VALUE=RAW_SIGNAL * 100/(103.8 -4.3937*LN(RAW_SIGNAL))

mixed genetic background, predominantly (>87.5%) C57BL/6 with some CD1. Genotype: PTEN mutant = Mx1-Cre positive: PTENfx/fx. Sex: Male. Age: Eight and a half weeks (at tissue isolation). Tissue: Intestinal Polyp (from jejunun/ileum).

Normalized against other samples in series by log regression on signal obtained with control spots (first 64 samples). For this sample VALUE=RAW_SIGNAL * 100/(97.194 + 4.2422*LN(RAW_SIGNAL))

mixed genetic background, predominantly (>87.5%) C57BL/6 with some CD1. Genotype: Mx1-Cre negative: PTENfx/+. Sex: Female. Age:;small intestine (jejunum/ileum).

Normalized against other samples in series by log regression on signal obtained with control spots (first 64 samples). For this sample VALUE=RAW SIGNAL * 100/(2.5416*LN(RAW SIGNAL) + 77.834)

mixed genetic background, predominantly (>87.5%) C57BL/6 with some CD1. Genotype: PTEN mutant = Mx1-Cre positive: PTENfx/fx. Sex: Female. Age: Eight and a half weeks (at tissue isolation). Tissue: Intestinal polyp from small intestine (jejunum/ileum region).

MCI-009 was from a postmenopausal low BMD woman.

Normalized against other samples in series by log regression on signal obtained with control spots (first 64 samples). For this sample VALUE= RAW SIGNAL * 100/(105.83+ 4.6698*LN(RAW_SIGNAL))

Angiotensin II dissolved in PBS was continuously and subcutaneously infused in mice at a rate of 432 microg/kg/day using Alzet osmotic minipumps implanted dorsally under isofluorane anesthesia as reported

Extraction of total RNA was performed with RNeasy Qiagen Kit according to the manufacturer's instructions.

Littermate wild-type and PKCz -/- male mice (32 weeks of age) were subjected to continuous infusion of angiotensin II (or PBS as a control) for 14 days, a well established model for the induction of cardiac hypertrohy

Gene expression data under ER stress from lymphoblastoid cells of individual GM11992 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM11993 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM11882 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM11992 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM11994 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM11995 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM11993 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM11994 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM11995 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12003 treated with 4 ug/ml tunicamycin 8 hours.

Fluorescence intensities were captured with a an Affimetrix GeneArray 2500 Scanner, and quantified with Affymetrix Microarray Suite 5.0.

Samples were hybridized to MG U74Av2 arrays (Affymetrix) and stained with streptavidin-phycoerythrin.

RNA was isolated using TRIzol (Invitrogen) and RNeasy reagents (Qiagen).

Rats 6h after injection with dose kainate.
Treatment, type=time_course, description=KA animals are treated with kainate., measurement=6.0 h

Control rats 6h after injection with PBS
Treatment, type=time_course, description=Control animals are treated with PBS, measurement=6.0 h

Control rats 1h after injection with PBS
Treatment, type=time_course, description=Control animals are treated with PBS, measurement=1.0 h

HaCaT cells at day 12 of calcium induced in-vitro differentiation;ZNF750 gene silencing

FVB/N;Wild-type;pulmonary vascular microendothelial cells (PMVEC)

PMVEC isolated from mice carrying immortomouse and Rosa26-rtTA transgenes

FVB/N;Bmpr2-delx4+ mutation;pulmonary vascular microendothelial cells (PMVEC)

PMVEC isolated from mice carrying TetO7-Bmpr2-delx4, immortomouse and Rosa26-rtTA transgenes

Sample_ID:t22 // Patient:J-287 // Histology:Intestinal // Metastasis:+ // p53_mut:++ // E-cadherin_mut:+ // beta-Catenin_mut:-

Lot batch = Joslin core 931

Lot batch = Joslin core 954

Lot batch = Joslin core 929

Lot batch = Joslin core 952

Lot batch = Joslin core 1527

Brown preadipocyte cell lines derived from newborn IRS-3 KO mice. Preadipocytes were grown to confluence (day 0) in differentiation medium (Dulbeco’s modified Earle’s medium containing 10% fetal bovine serum supplemented with 20 nM insulin and 1 nM T3). Brown preadipocytes were synchronized by overnight serum starvation. Total RNA was isolated with ULTRASPEC RNA Isolation System (Biotecx Laboratories, Inc., Houston, TX) following the manufacture’s instruction. 28 ug of total RNA were subjected to cDNA and cRNA preparations as previously described. 15 ug of adjusted cRNA were hybridised to Affymetrix U74A-v2 arrays (Santa Clara, CA). Intensity values were quantitated by MAS 5.0 software (Affymetrix). All chips were subjected to global scaling to a target intensity of 1,500 to take into account the inherent differences between the chips and their hybridization efficiencies.
Lot batch = Joslin core 699

Lot batch = Joslin core 930

Lot batch = Joslin core 953

Lot batch = Joslin core 1528

Lot batch = Joslin core 700

Levitiracetam hippocampus 6

Levitiracetam hippocampus 7

Crohn's Disease subject (20 year old black male, SAK_1259851809)

Subject Age : 20

Crohn's Disease subject (39 year old caucasian male, SAK_1275567445)

Crohn's Disease subject (46 year old black female, SAK_1259829456)

Crohn's Disease subject (22 year old black female, SAK_1259740044)

Ulcerative Colitis (63 year old caucasian female, SAK_1318991541)

Subject Age : 63

Subject Age : 73

Ulcerative Colitis (29 year old caucasian female, SAK_1305780306)

Levitiracetam brainstem 7

ACRL_CBM__Treated_B

ACRL_CBM__Control_B

1 µg/ml doxycycline or mock (H2O) was used to induce expression of the integrated NPAP1 copy.

Gene expression data from cell line T-REx293-NPAP1, 24 h after induced expression of the integrated NPAP1 gene, technical replicate 1

1 µg/ml doxycycline was used to induce expression of the integrated NPAP1 copy.

Gene expression data from cell line T-REx293-NPAP1, 24 h after induced expression of the integrated NPAP1 gene, technical replicate 2

Gene expression data from cell line T-REx293-NPAP1, 24 h after induced expression of the integrated NPAP1 gene, technical replicate 3

Peripheral blood mononuclear cells;TTF=150min;Race=Black/African American;Sex=Male

Peripheral blood mononuclear cells;TTF=90min;Race=White;Sex=Male

Peripheral blood mononuclear cells;healthy control;GTE6;104min;White;Female

Peripheral blood mononuclear cells;healthy control;LT6;77min;White;Female

Peripheral blood mononuclear cells;TTF=105min;Race=White;Sex=Female

Peripheral blood mononuclear cells;healthy control;GTE6;95min;UK;Male

Peripheral blood mononuclear cells;TTF=125min;Race=Black/African American;Sex=Male

C57BL/6;C-DGCR8 KO (D4-cre/DGCR8 KO/Ai9 tdTomato);retina;cone photoreceptors;postnatal day 40

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20553.gif
name: 20553_Infection

Common Reference 2 round amplification 2 ug;Mening SWB WB SW 12b

Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23207.gif
name: 23207_Infection

Common Reference 2 round amplification 2 ug;Mening UNSTIM WB NP 0b

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20550.gif
name: 20550_Infection

Common Reference 2 round amplification 2 ug;Mening SWB WB SW 12a

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20530.gif
name: 20530_Infection

Common Reference 2 round amplification 2 ug;Mening UNSTIM WB SW 24b

Gene expression data from WT, YFP+ muscle stem cells isolated from a noninjured animal

mixed C57BL6;Pax7CreER/+;Rosa26REYFP/+;3-5 months old;noninjured;hindlimb muscle;QSC;control

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20554.gif
name: 20554_Infection

Common Reference 2 round amplification 2 ug;Mening UNSTIM WB SW 12a

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20570.gif
name: 20570_Infection

Common Reference 2 round amplification 2 ug;Mening UNSTIM WB SW 12b

CR_D1

Neural precursor cells derived from hES cells line SA01, biological replicate  1

Gene expression data from brain of Npc1+/- mouse1 of age 62 days

Gene expression data from brain of Npc1+/- mouse1 of age 67 days

Mesodermal Precursor Cells derived from hES cells line VUB01, biological replicate 1

All data analyses were based on the use of “internal standards” as presented elsewhere (1).
Two-step normalization procedure (1). The first step is the determination of the parameters of the background of the array – average (Av) and standard deviation (SD) using a special iteration procedure. Data in each array are normalized making these parameters equal zero and one correspondingly. After this normalization the gene expressions are presented in the units of the SD of background. We accept S =3 SDs above the mean background level as the preliminary criterion for distinguishing expressed from non-expressed genes. Only genes expressed above background are used for the second step “adjustment”.     The second step is the adjustment of the normalized profiles to each other by robust regression analysis of genes expressed above background. This procedure is based on the selection of equally expressed genes as a homogenous family of genes with normally distributed residuals defined as deviations from the regression line. The parameters of this distribution are obtained by the iterative procedure similar to the one used before for the selection of the kernel part of normally distributed background noise. Outliers are thereafter determined as having deviations n associated with this internal standard of equality of expression including thousands members. The functions used for normalization were implemented in Matlab and in Bioconductor package diffGeneAnalysis.
1.Dozmorov, I. M., and I. Lefkovits. 2010. Internal standard-based analysis of microarray data.1. Analysis of differential gene expressions. Nucl. Acid Res. Epub ahead of print.

cDNA was synthesized and labeled with the Ovation Biotin RNA Amplification and Labeling System (NuGEN Technologies, Inc.)

MCF7 pre-treated for 1h with cycloheximide, treated with E2 for 24h

MAT1A_wt15_5

MAT1A knockout at 15 month age, peritumoral tissues, biological replicate 2

MAT1A_NT2
Gene expression data from MAT1A knockout at 15 month, peritumoral tissue.

C57B6SJL;MAT1A knockout;15 months;liver, peritumoral tissue;hepatocellular carcinoma

Mouse liver peritumoral tissue, MAT1A knockout, hepatocellular carcinoma, 15 months

MAT1A knockout at 15 month age, peritumoral tissues, biological replicate 1

MAT1A_NT1

MAT1A knockout at 15 month age, peritumoral tissues, biological replicate 4

MAT1A_NT4

MAT1A knockout at 15 month age, peritumoral tissues, biological replicate 3

MAT1A_NT3

MAT1A knockout at 15 month age, tumoral tissue, biological replicate 1

MAT1A_T1

MAT1A knockout at 15 month age, peritumoral tissues, biological replicate 5

MAT1A_NT5

MAT1A knockout at 15 month age, tumoral tissue, biological replicate 3

MAT1A_T3

MAT1A knockout at 15 month age, tumoral tissue, biological replicate 2

MAT1A_T2

lung;;Familial IIP;;Nonspecific Interstitial Pneumonia;Stratagene;;740000

Stratagene;;740000;lung;;Sporadic IIP;;Nonspecific Interstitial Pneumonia

Lung, Sporadic Idiopathic Interstitial Pneumonia (S-IIP), Nonspecific Interstitial Pneumonia (NSIP)

Stratagene;;740000;lung;;Familial IIP;;Nonspecific Interstitial Pneumonia

Gene expression data from cochleas of  nicotinic cholinergic receptor alpha9 subunit knockout mice at P13.
P13_a9knockout_rep3

P60_wildtype_rep1

P60_wildtype_rep3

Gene expression data from cochleas of wild type mice at P13.
P13_wildtype_rep2

P13_wildtype_rep3

P13_a9knockout_rep1

P13_a9knockout_rep2

P60_a9knockout_rep1

P60_a9knockout_rep2

primary unilateral non-metastatic postmenopausal ERα-positive breast tumor;woman;64 years

primary unilateral non-metastatic postmenopausal ERα-positive breast tumor;woman;69 years

primary unilateral non-metastatic postmenopausal ERα-positive breast tumor;woman;52 years

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-09/55562
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.23; Parameter Scan Time = 18:22:25; Parameter PMT Volts = 550; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 6528; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.23; Parameter Scan Time = 18:22:25; Parameter PMT Volts = 660; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 180069; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.53; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-09/55561
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.51; Parameter Scan Time = 18:46:28; Parameter PMT Volts = 550; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 6551; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.51; Parameter Scan Time = 18:46:28; Parameter PMT Volts = 660; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 180092; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.55; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56900
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.00; Parameter Scan Time = 19:02:39; Parameter PMT Volts = 550; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 11030; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.45; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.00; Parameter Scan Time = 19:02:39; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 184635; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-09/55563
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.05; Parameter Scan Time = 18:10:11; Parameter PMT Volts = 550; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 6515; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.05; Parameter Scan Time = 18:10:11; Parameter PMT Volts = 660; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 180056; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.53; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-09/55549
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.65; Parameter Scan Time = 17:43:11; Parameter PMT Volts = 560; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 6488; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.65; Parameter Scan Time = 17:43:11; Parameter PMT Volts = 660; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 180030; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.52; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-09/55564
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.48; Parameter Scan Time = 20:12:13; Parameter PMT Volts = 550; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 6637; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.48; Parameter Scan Time = 20:12:13; Parameter PMT Volts = 660; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 180178; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-09/55565
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.19; Parameter Scan Time = 20:41:14; Parameter PMT Volts = 560; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 6665; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.19; Parameter Scan Time = 20:41:14; Parameter PMT Volts = 690; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 180206; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.55; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56901
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.42; Parameter Scan Time = 20:16:41; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 11104; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.42; Parameter Scan Time = 20:16:41; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 184708; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-09/55566
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.82; Parameter Scan Time = 20:24:39; Parameter PMT Volts = 550; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 6648; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.82; Parameter Scan Time = 20:24:39; Parameter PMT Volts = 660; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 180189; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-10/56902
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.18; Parameter Scan Time = 19:27:42; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 11056; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.45; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.18; Parameter Scan Time = 19:27:42; Parameter PMT Volts = 670; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 184660; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel

lung tissue;CD-1_Nrf2 -/-;13 weeks + 5 month + 1 day;2R4F whole mainstream smoke 750 µg/ml, treatment over 5 month + 1 day recovery, 4x1h exposure per day

Keywords = cardiomyopathy

Male mice from fiona transgenic line (dystrophin-deficient with a transgene expressing high level of full length utrophin) were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.

Male mice from mdx (C57BL/10ScSn-Dmdmdx/J) line were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.

Cerebellum_transgenic nuclear exclusion signal Htt exon1 142Q A61_8 months_replicate 2

A61 NES 142Q TG2	F6/22	A61	NES Htt exon 1 142Q	Mouse	8 months	Cerebellum	Male

Cerebellum_transgenic nuclear exclusion signal Htt exon1 142Q A61_8 months_replicate 1

A61 NES 142Q TG1	F6/13	A61	NES Htt exon 1 142Q	Mouse	8 months	Cerebellum	Male

Cerebellum_transgenic nuclear localization signal Htt exon1 142Q S46_3 months_replicate 2

S46 NLS 142Q TG2	F5/9	S46	NLS Htt exon 1 142Q	Mouse	3.5 months	Cerebellum	Female

Cerebellum_transgenic nuclear exclusion signal Htt exon1 142Q A39_4 months_replicate 2

A39 NES 142Q TG2	F5/52	A39	NES Htt exon 1 142Q	Mouse	4 months	Cerebellum	Female

0.107142857;wildtype;GIST Tumor;Universal Human Reference RNA (Stratagene)

-0.06;exon 11;GIST Tumor;Universal Human Reference RNA (Stratagene)

0.461538462;exon 11;GIST Tumor;Universal Human Reference RNA (Stratagene)

0.388888889;exon 11;GIST Tumor;Universal Human Reference RNA (Stratagene)

0.34;exon 11;GIST Tumor;Universal Human Reference RNA (Stratagene)

Gene expression data under ER stress from lymphoblastoid cells of twin 1734:2 treated with 500nM thapsigargin.

lymphoblastoid cell line;1734;GM14504;Twin number 2;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1734:2 treated with DMSO.

lymphoblastoid cell line;1734;GM14504;Twin number 2;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1734:1 treated with 500nM thapsigargin.

lymphoblastoid cell line;1734;GM14503;Twin number 1;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1734:1 treated with DMSO.

lymphoblastoid cell line;1734;GM14503;Twin number 1;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1736:2 treated with 500nM thapsigargin.

lymphoblastoid cell line;1736;GM14509;Twin number 2;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1736:2 treated with DMSO.

lymphoblastoid cell line;1736;GM14509;Twin number 2;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1736:1 treated with 500nM thapsigargin.

lymphoblastoid cell line;1736;GM14508;Twin number 1;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1736:1 treated with DMSO.

lymphoblastoid cell line;1736;GM14508;Twin number 1;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1743:1 treated with 500nM thapsigargin.

lymphoblastoid cell line;1743;GM14532;Twin number 1;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1743:1 treated with DMSO.

lymphoblastoid cell line;1743;GM14532;Twin number 1;DMSO;4 hours

Total RNA was extracted from lymphoblastoid cells of AU066703 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;AU066703 is a male with autism and full mutation of FMR1.

Total RNA was extracted from lymphoblastoid cells of AU066704 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;AU066704 is a male with autism and full mutation of FMR1.

9_JQ1-3_(Mouse430_2)

10_MLN8237-1_(Mouse430_2)

12_MLN8237-3_(Mouse430_2)

JLI_75

6_DMSO-6_(Mouse430_2)

7_JQ1-1_(Mouse430_2)

Gene expression profile of an adrenocortical adenoma  with a T41A CTNNB1 mutation

265;Normal cortex;Female;43;Clear-cell renal cell carcinoma;wild type;wild type;wild type

324;Normal cortex;Male;60;Clear-cell renal cell carcinoma;wild type;wild type;wild type

265;Clear-cell renal cell carcinoma (ccRCC) tumor;Female;43;Clear-cell renal cell carcinoma;T1N0M0;I;2;wild type;mutant;mutant

Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 265

324;Clear-cell renal cell carcinoma (ccRCC) tumor;Male;60;Clear-cell renal cell carcinoma;T1NxMx;n/a;2;wild type;wild type;mutant

Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 324

325;Clear-cell renal cell carcinoma (ccRCC) tumor;Female;80;Clear-cell renal cell carcinoma;T1NxMx;n/a;1;wild type;wild type;wild type

Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 325

325;Normal cortex;Female;80;Clear-cell renal cell carcinoma;wild type;wild type;wild type

1393;Normal cortex;Male;83;Clear-cell renal cell carcinoma;wild type;wild type;wild type

KO - knock-out Treated - 0.5 hrs - repeat 2 - Cy5 - mAdbID:62539

There is cardiac dysfunction in male eNOS (-/-) with age and 50% mortality at 21M. It was of interest to investigate the gene expression profile of aged eNOS (-/-) male in comparison to (+/+) in order to explore the genetic markers and molecular mechanisms leading to heart failure. RNA was extracted from the left ventricle from male (-/-) (n=3) and (+/+) (n=4) at the age of 21M.
Keywords = eNOS knockout
Keywords = exercise

Gene expression profile of high grade serous carcinoma of fallopian tube

Cryptosporidium parvum-infected HCT-8 cells, time course 3, mock

Cryptosporidium parvum-infected HCT-8 cells, time course 3, mock (24h post-infection)

Gene expression data from Human hepatoma cell line (HepG2) transduced with recombinant Adenovirus expressing LacZ and cultured for 12 hours. Targets were produced using standard Affymetrix procedures from 10ug of total RNA.

Gene expression data from mouse CD8+ Wt T-cells with anti-CD3 stimulation

Gene expression data from mouse CD4+ Itk knockout T-cells with anti-CD3 stimulation

Gene expression data from mouse CD8+ Itk knockout T-cells with anti-CD3 stimulation

Expression data were extracted from image files produced on Affymetrix® GeneChip Operating Software 1.0® (GCOS®).

RNA was extracted from sorted cells using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instruction.

Following fragmentation, Biotin-labeled cDNA was hybridized to the Mouse Genome 430 2.0 Array® (Affymetrix®) for 16 h at 45°C as recommended by the manufacturer. Washing was performed using an automated fluidics workstation, and the array was immediately scanned with GeneChip Scanner 3000 7G.

Biotin-labeled cDNA probes were prepared using the NuGen Ovation Biotin labeling system (NuGEN Technologies, Inc.), according to the manufacturer's protocol.

Lineage(-), Sca-1(+), c-Kit(+) cells derived from Evi-1(flox/flox) mice were transduced with GFP (control) or Cre-GFP expressing retroviruses. Total RNA was prepared from sorted GFP(+) cells.

TGCT cell line NTera2/clone D1, untreated, undifferentiated and pluripotent

Testicular germ cell tumor (embryonal carcinoma) cell line NTera2 (clone D1). Embryonal carcinoma cell lines, and especially NTera2, are generally pluripotent and share features with embryonic stem cells. Time point 0 days (untreated) in a time series of 0, 3, and 7 days of culturing with retinoic acid which stimulates these cells to differentiation. Maintained at high cell density (>5 000 000 cells per 75 cm2 tissue culture flask) in Dulbecco Modified Eagles Medium (DMEM high glucose formulation; GIBCO LifeTechnologies, UK) supplemented with 10% fetal calf serum.
Keywords = cell line
Keywords = differentiation
Keywords = embryonic stem cell
Keywords = NT2
Keywords = NTera2
Keywords = pluripotent
Keywords = retinoic acid
Keywords = teratocarcinoma
Keywords = totipotency
Keywords = undifferentiated

c57bl6 female mice were challenged with saline.  Mice were euthanized 4 hours after and bladders removed for cDNA array analysis
Lot batch = 2/2

c57bl6 female mice were challenged with saline.  Mice were euthanized 24 hours after and bladders removed for cDNA array analysis

c57bl6 female mice were challenged with Substance P 1 micromolar.  Mice were euthanized 1 hour after and bladders removed for cDNA array analysis.

c57bl6 female mice were challenged with Substance P 1 micromolar.  Mice were euthanized 4 hours after and bladders removed for cDNA array analysis

c57bl6 female mice were challenged with Substance P 1 micromolar.  Mice were euthanized 24 hours after and bladders removed for cDNA array analysis
Lot batch = 2/3

c57bl6 female mice were challenged with LPS 100 milligrams/ml.  Mice were euthanized 1 hour after and bladders removed for cDNA array analysis

c57bl6 female mice were challenged with LPS 100 milligrams/ml.  Mice were euthanized 4 hours after and bladders removed for cDNA array analysis

c57bl6 female mice were challenged with LPS 100 milligrams/ml.  Mice were euthanized 24 hours after and bladders removed for cDNA array analysis

AP-2 gamma targetting siRNA 3: CCACACUGGAGUCGCCGAAUA Technical Replicate 3

Non-silencing control siRNA: AAUUCUCCGAACGUGUCACGU Technical Replicate 1

AP-2 gamma targetting siRNA 3: CCACACUGGAGUCGCCGAAUA Technical Replicate 1

AP-2 gamma targetting siRNA 3: CCACACUGGAGUCGCCGAAUA Technical Replicate 2

Non-silencing control siRNA: AAUUCUCCGAACGUGUCACGU Technical Replicate 2

Non-silencing control siRNA: AAUUCUCCGAACGUGUCACGU Technical Replicate 3

136;metranidazole 400mg TDS Prednisolone;5/21/51;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;7/20/05;Diarrhoea PR bleeding;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;11-15-01;descending colon;Inflamed;total RNA from 10 human cell lines

Lot batch = 5296

Gene expression data from NZM12 metastatic melanoma cells treated with non-targeting negative control siRNA (luciferase)

skin;NZM12;metastatic melanoma;small intestine;luciferase siRNA negative control

NZM12 metastatic melanoma cells treated with luciferase negative control siRNA

whole right lung, 3 weeks after a bleomycin dose of 125mg/kg, given by osmotic minipump.

whole right lung, 6 weeks after a bleomycin dose of 125mg/kg, given by osmotic minipump.

whole right lung, 6 weeks after a bleomycin dose of 100mg/kg, given by osmotic minipump.

Primary hepatocytes isolated from BL6 mouse strain treated with Wy14643 for 6h

Primary hepatocytes isolated from NMRI mouse strain treated with DMSO for 24h

Primary hepatocytes isolated from NMRI mouse strain treated with Wy14643 for 6h

Primary hepatocytes isolated from NMRI mouse strain treated with Wy14643 for 24h

Primary hepatocytes isolated from NMRI mouse strain treated with DMSO for 6h

TP19;DCE2.1;Childhood Absence Epilepsy + Febrile Seizures;-4;42;45;FEMALE;None

Left ventricular myocardium in patients with Dilated cardiomyopathty (16)

Left ventricular myocardium in patients with Dilated cardiomyopathty (30)

Rat liver, treated with DMN, 15 mg/kg in water per orally, extrated 48 hours after treatment, biological rep2

Rat liver, treated with DMN, 15 mg/kg in water per orally, extrated 48 hours after treatment, biological rep3

Rat liver, treated with DMN, 15 mg/kg in water per orally, extrated 48 hours after treatment, biological rep4

Rat liver, treated with DMN, 15 mg/kg in water per orally, extrated 48 hours after treatment, biological rep5

Rat liver, treated with DNP, 15 mg/kg in water per orally, extrated 48 hours after treatment, biological rep1

Rat liver, treated with DNP, 15 mg/kg in water per orally, extrated 48 hours after treatment, biological rep2

Rat liver, treated with DNP, 15 mg/kg in water per orally, extrated 48 hours after treatment, biological rep3

Rat liver, treated with DNP, 15 mg/kg in water per orally, extrated 48 hours after treatment, biological rep4

transcripts expression data from Igf1 -/- mouse vestibular organ at P90

CGC_WT8.CEL

CGC_WT7.CEL

Gene expression data from WT mouse cortex tissue at post-natal day 29

37;Adenocarcinoma of breast, ductal, medullary features;G3;IIA;T2;N0 (i-);0;0;51;0;0

54;Adenocarcinoma of breast, ductal, lobular features;G3;IIIA;T3;N2a;1;1;15;0;0

GNMT_8WT5

GNMT_8WT4

GNMT_8ko2
Gene expression data from GNMT knockout at 8 month, when the tissue has been histopathologically determined to be hepatocellular carcinoma.

GNMT_8ko1

GNMT_8ko4

GNMT_8ko3

MAT1A_3_2
Gene expression data from MAT1A knockout at 3 month, when the tissue has been histopathologically determined to be steatosis.

MAT1A_3_1

MAT1A_3_4

MAT1A_3_3

Ebola-infected macrophages harvested at 1h post-treatment from donor 3

Mock infected macrophages harvested at 1h post-treatment from donor 3

Ebola-infected macrophages harvested at 6h post-treatment from donor 1

Mock infected macrophages harvested at 6h post-treatment from donor 1

Ebola-infected macrophages harvested at 1h post-treatment from donor 1

Mock infected macrophages harvested at 1h post-treatment from donor 1

Ebola-infected macrophages harvested at 6h post-treatment from donor 2

Mock infected macrophages harvested at 6h post-treatment from donor 2

Ebola-infected macrophages harvested at 1h post-treatment from donor 2

Mock infected macrophages harvested at 1h post-treatment from donor 2

Primary human erythroid progenitor cells expressing HDAC2 H6 shRNA biological replicate 1

Primary human erythroid progenitor cells expressing HDAC2 H6 shRNA

Primary human erythroid progenitor cells expressing HDAC2 H6 shRNA biological replicate 2

Primary human erythroid progenitor cells expressing HDAC2 H6 shRNA biological replicate 3

FBN+/+.TGFBRIIko_4
Gene expression data from Tgfbr2 knockout mice

Mouse bone marrow-derived mast cells treated with IL3+SCF, rep 1

Gene expression data from mouse bone marrow-derived mast cells treated with IL3+SCF, rep 1 of 6.

Mouse bone marrow-derived mast cells treated with IL3+SCF, rep 3

Gene expression data from mouse bone marrow-derived mast cells treated with IL3+SCF, rep 3 of 6.

Mouse bone marrow-derived mast cells treated with IL3+SCF, rep 2

Gene expression data from mouse bone marrow-derived mast cells treated with IL3+SCF, rep 2 of 6.

Transfection was conducted using Lipofectamine 2000 (Invitrogen) according to the manual provided.  For shRNA, cells were selected in 6-well culture plate for 3 d using puromycin.  The cells were then harvested for either extraction of protein or RNA.

Murine ES cells (E14) were cultured in ES cell medium consisting of Glasgow Minimum Essential Medium (GMEM; Invitrogen), 15% ES cell qualified fetal bovine serum (FBS; Invitrogen), 0.055 mM β-mercaptoethanol (Sigma), 100 mM sodium pyruvate (Invitrogen), 0.1 mM MEM nonessential amino acid (NEAA, Invitrogen) and 1,000 units/ml of LIF (Millipore).

The data were analyzed using RMA in the bioconducter and normalized using cross correlation.

Gene expression data from Zfp322a RNAi ( selected by puromycin for 3 days).

lung, upper lobe;surgical biopsy;early idiopathic pulmonary fibrosis (IPF);male;58

lung, upper lobe;surgical biopsy;early idiopathic pulmonary fibrosis (IPF);male;70

lung, upper lobe;surgical biopsy;early idiopathic pulmonary fibrosis (IPF);female;56

lung, lower lobe;explant;advanced idiopathic pulmonary fibrosis (IPF);male;64

lung, upper lobe;surgical biopsy;early idiopathic pulmonary fibrosis (IPF);male;54

lung, lower lobe;surgical biopsy;early idiopathic pulmonary fibrosis (IPF);male;58

AFGE1068-10.CEL

AFGE1068-8.CEL

AFGE1068-4.CEL

AFGE1068-3.CEL

AFGE1068-7.CEL

AFGE1068-6.CEL

CG
32 mg
4

CG
32 mg
4

CG
32 mg
8

The filters were exposed for approx. 6 hours on Fuji BAS screens and signal intensities were read out using a Fuji Bas-1800 reader (Fuji Photo Film).

Signal intensities for every cDNA clone and background spots were determined using the Visual Grid software (GPC-Biotech, Munich). Raw intensities were background corrected by subtracting the local background (estimated block-wise) and normalised.

The radioactive cDNA was purified using Sephadex columns, denatured and added to denatured salmon sperm and human placenta DNA as blocking reagents. To aid grid positioning during image analysis radioactively labelled 1 ng kanamycin cDNA was added to the complex probe. This mixture was added to 10 ml hybridisation buffer (1M NaCl, 1% SDS, 0.1xSSC) and hybridised overnight at 65°C and then washed three times for 20 min at 65°C (0.1% SDS, 0.1X SSC).

20 microgram of tota RNA was primed with oligodT(12-18) and reverse transcribed with AMV (Roche) in the presence of alpha 33P-dCTP (Amersham Pharmacia Biotech).

sample 1:
non-steroidal anti-inflammatory drugs (NSAID), disease modifying antirheumatic drugs (DMARD), steroids
sample 2:
steroids
sample 3:
no treatment

disease modifying antirheumatic drugs (DMARD), non-steroidal anti-inflammatory drugs (NSAID)

sample 1:
non-steroidal anti-inflammatory drugs (NSAID), disease modifying antirheumatic drugs (DMARD)
sample 2:
disease modifying antirheumatic drugs (DMARD), steroids

20 microgram of tota RNA was primed with oligodT(12-18) and reverse transcribed with AMV (Roche) in the presence of alpha 33P-dCTP (Amersham Pharmacia Biotech)

sample 1;68;male;sample 2;77;female;sample 3;72;male;sample 4;unknown;unknown

Muscle; Smooth - Bladder- day 1 postnatal male

Muscle; Smooth-Bladder_adult

Nasal; Olfactory Epithelium

Oral Squamous cell Epithelium Tissue-Tumor;OSCC-12;Maxilla;46;Male;T4N0M0;TNM,Tumor-node-metastasis

Oral Squamous cell Epithelium Tissue-Tumor;OSCC-11;Tongue;32;M;T3N2bM0;TNM,Tumor-node-metastasis

Oral Squamous cell Epithelium Tissue-Tumor;OSCC-10;Tongue;64;M;T4N2bM0;TNM,Tumor-node-metastasis

Oral Squamous cell Epithelium Tissue-Tumor;OSCC-9;Tongue;66;M;T2N0M0;TNM,Tumor-node-metastasis

Oral Squamous cell Epithelium Tissue-Tumor;OSCC-8;Tongue;77;M;T2N0M0;TNM,Tumor-node-metastasis

Oral Squamous cell Epithelium Tissue-Tumor;OSCC-7;Floor of mouth;48;M;TNM,Tumor-node-metastasis

Oral Squamous cell Epithelium Tissue-Tumor;OSCC-5;Tongue;64;M;T1N2bM0;TNM,Tumor-node-metastasis

Oral Squamous cell Epithelium Tissue-Tumor;OSCC-6;Vestibule;72;M;T2N0M0;TNM,Tumor-node-metastasis

Oral Squamous cell Epithelium Tissue-Tumor;OSCC-4;Floor of the mouth;60;M;T4N1M0;TNM,Tumor-node-metastasis

The initial analysis of generated Affymetrix data was performed with their MAS 5.0 software.The chip data were scaled to 500,then exported as text files to be loaded into the Genespring 6.0 program(Silicon Genetics,Redwood City,CA).The prescaled data were normalized by using the normalization steps

Oral Squamous cell epithelium tissue;OSCC-2;58;F;T2N0M0;TNM,TUMOR-NODE-METASTASIS

reduction mammoplasty histologically normal breast epithlieum patient 288

16_PC

16_BM

16_Bsl

15_Bsl

15_PC

long access to cocaine, nucleus accumbens, 6 hrs/day access to cocaine

glioblastoma cells;42MGBA cells;STAG2 knock-in post-Cre clone 53-1 (STAG2 corrected)

glioblastoma cells;42MGBA cells;STAG2 knock-in post-Cre clone 53-7 (STAG2 corrected)

glioblastoma cells;42MGBA cells;STAG2 knock-in post-Cre clone 92-6 (STAG2 corrected)

colorectal cancer cells;HCT116 cells;non-recombinant clone 24 (STAG2 wild-type)

colorectal cancer cells;HCT116 cells;non-recombinant clone 27 (STAG2 wild-type)

colorectal cancer cells;HCT116 cells;STAG2 knockout clone 7 (STAG2 deficient)

colorectal cancer cells;HCT116 cells;STAG2 knockout clone 21 (STAG2 deficient)

14;Normal cortex;Female;64;Clear-cell renal cell carcinoma;wild type;wild type;wild type

14;Clear-cell renal cell carcinoma (ccRCC) tumor;Female;64;Clear-cell renal cell carcinoma;T1N0M0;I;3;wild type;mutant;wild type

Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 14

26;Normal cortex;Female;77;Clear-cell renal cell carcinoma;wild type;wild type;wild type

26;Clear-cell renal cell carcinoma (ccRCC) tumor;Female;77;Clear-cell renal cell carcinoma;T2N0Mx;n/a;2;wild type;wild type;mutant

Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient 26

Tsc1-deficient CD4 naïve cells with CD3-CD28 stimulation for 4h KAI277

Tsc1-deficient;CD4 naive cells;CD3-CD28 stimulation for 4h;C57BL\6

Tsc1-deficient CD4 naïve cells with aCD3-CD28 stimulation for 4h

Tsc1-deficient CD4 naïve cells with CD3-CD28 stimulation for 4h KAI274

wild-type naïve CD4 T cells with CD3-CD28 stimulation for 4h KAI271

normal;IA, IB, II, IIIA, IIIB, or IV=IIIB;50;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

normal;IA, IB, II, IIIA, IIIB, or IV=IIIB;37;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

normal;IA, IB, II, IIIA, IIIB, or IV=II;53;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

normal;IA, IB, II, IIIA, IIIB, or IV=II;59;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

normal;IA, IB, II, IIIA, IIIB, or IV=II;34;female, male:female;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

normal;IA, IB, II, IIIA, IIIB, or IV=IIIA;74;female, male:female;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

normal;IA, IB, II, IIIA, IIIB, or IV=IIIA;54;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

normal;IA, IB, II, IIIA, IIIB, or IV=IIIA;77;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

normal;IA, IB, II, IIIA, IIIB, or IV=IIIA;60;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

brain (frontal cortex);bipolar disorder;49 yr;white;296.54;20 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);bipolar disorder;51 yr;white;296.44;23 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);bipolar disorder;59 yr;white;296.53;25 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);bipolar disorder;64 yr;white;295.7;19 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);bipolar disorder;45 yr;white;296.44;35 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);bipolar disorder;47 yr;white;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);bipolar disorder;48 yr;white;296.53;31 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);bipolar disorder;41 yr;white;296.72;14 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);bipolar disorder;29 yr;white;296.44;18 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);bipolar disorder;41 yr;Native American;296.53;22 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

Gene expression data from ICR MEF infected  with pMX-Oct4 and pMX-jhdm1b(jmjc) retrovirus

HepG2 cells stably expressing HCC-THRA mutant bN treated with 100 nM T3 for 6h

HepG2 cells stably expressing RCCC-THRA mutant 15b treated with vehicle for 6h.

HepG2 cells stably expressing RCCC-THRA mutant 15b treated with 100 nM T3 for 6h

WT;E2;24h;C57bl6/Jx129;adult (10+ weeks);ovariectomized female;uterus

MCF-7,  cells were maintained in DMEM containing 10% fetal bovine serum (FBS). For experiments involving estrogen depletion, media was replaced by phenol-free DMEM containing 5% charcoal/dextran-treated FBS.

The data were analyzed with Expression Console software (1.3.1.187). Gene level analysis, PLIER summarization method, PM-GCBG background correction, sketch-quantile normalized.

10 ug of cRNA was used for second-cycle cDNA synthesis and was purified, fragmented, labeled, and hybridized to GeneChip Human Gene 1.0 ST Arrays at 45C for 16.5 hours per manufacturer's instructions.  GeneChips were washed and stained per manufacturer's instructions in the Affymetrix Fluidics Station 400.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

OV-90;eukaryotic expression vector pcDNA3.1 containing the full-length cDNA for CD157;eukaryotic expression vector pcDNA3.1 containing no insert;OV-90

OV-90;eukaryotic expression vector pcDNA3.1 containing no insert;eukaryotic expression vector pcDNA3.1 containing the full-length cDNA for CD157;OV-90

Female;54;4h;6.5;control;superior temporal cortex (Brodmann Area 22, BA22)

"female subject, 18-45 yrs, peripheral blood mononuclear cells 30 min after intravenous endotoxin challenge"

Male;81;5h;6.1;control;superior temporal cortex (Brodmann Area 22, BA22)

Male;76;6h;6;control;superior temporal cortex (Brodmann Area 22, BA22)

Male;82;11h;6;schizophrenic;superior temporal cortex (Brodmann Area 22, BA22)

Female;75;3h;6;schizophrenic;superior temporal cortex (Brodmann Area 22, BA22)

Female;88;7h;5.7;schizophrenic;superior temporal cortex (Brodmann Area 22, BA22)

Female;89;8h;6.3;schizophrenic;superior temporal cortex (Brodmann Area 22, BA22)

Male;82;11h;6.4;schizophrenic;superior temporal cortex (Brodmann Area 22, BA22)

"female subject, 18-45 yrs, peripheral blood mononuclear cells prior to (baseline - 0 h) intravenous endotoxin challenge"

neocortex-30 months of age-resveratrol diet-biological replicate2

neocortex-30 months of age-resveratrol diet-biological replicate1

neocortex-30 months of age-resveratrol diet-biological replicate4

neocortex-30 months of age-resveratrol diet-biological replicate3

neocortex-30 months of age, resveratrol diet-biological replicate5

Prostate-specific Pten and Lrf deletion anterior prostate tumor 1

whole brain;C57BL/6J;Sarm1-/-;8 weeks, 5 days;107 pfu of VSV-Indiana strain

Gene expression data from aortas isolated from captopril-treated APOE-deficient mice.
Capto-2

Capto-1

Gene expression data from Deltoid, control, cohort 07, subject 07U

Gene expression data from Biceps, control, cohort 07, subject 07U

Gene expression data from Biceps, control, cohort 03, subject 03U

Gene expression data from Deltoid, control, cohort 03, subject 03U

Mouse Lung AIN Diet 8hr 1mg/kg Dex Injection, biological replicate A
AN080306_Sample 15.CEL

Mouse Lung AIN Diet 5wk Control, biological replicate E
AN080306_Sample 14.CEL

Mouse Lung AIN Diet 5wk 100ppb As Drinking Water Expousre, biological replicate A
AN080206_Sample 13 Lung.CEL

Mouse Lung LRD Diet 5wk 10ppb As Food Exposure, biological replicate F
AN080406_Sample 19.CEL

Mouse Lung AIN Diet 8hr 1mg/kg Dex Injection, biological replicate B
AN080906_Sample 18.CEL

Mouse Lung AIN Diet 5wk Control, biological replicate F
AN080906_Sample 17.CEL

Mouse Lung AIN Diet 5wk 10ppb As Drinking Water Exposure, biological replicate C
AN080906_Sample 16.CEL

Aorta;SRF-flex2neo -SM22CreERT2ki/+;smooth muscle specific SRF knockout;4 month-old

SMhu155

SWR/J Chronic morphine treated, striatum, biological replicate 3

rat hippocampus (CA1 region), IntermediateCort, 18 months old, subject 13

rat hippocampus (CA1 region), IntermediateCort, 18 months old, subject 12

rat hippocampus (CA1 region), IntermediateCort, 18 months old, subject 15

rat hippocampus (CA1 region), IntermediateCort, 18 months old, subject 14

rat hippocampus (CA1 region), IntermediateCort, 18 months old, subject 17

rat hippocampus (CA1 region), IntermediateCort, 18 months old, subject 16

rat hippocampus (CA1 region), IntermediateCort, 18 months old, subject 19

rat hippocampus (CA1 region), IntermediateCort, 18 months old, subject 18

rat hippocampus (CA1 region), LowCort, 18 months old, subject 21

rat hippocampus (CA1 region), LowCort, 18 months old, subject 20

Gene expression from MEFs carrying a tet-inducible Pten transgene at 48 hrs after inducing PTEN

Pten-null (Ptenloxp/loxp), with doxycycline-inducible PTEN transgene;embryonic fibroblasts;tet-inducible Pten transgene;48 h;C57BL\6

MEFs carrying a tet-inducible Pten transgene, 48 hrs after inducing PTEN

RWPE-1;Immortalized normal prostate epithelial cells.;100 nM 1,25(OH)2D;24 hours

RWPE-1;Immortalized normal prostate epithelial cells.;Vehicle (0.1% ethanol);24 hours

Medial gastrocnemius removed from 8-month old muscle glycogen synthase WT or overexpressing mouse. RNA was extracted using GibcoBRL TRIzol Reagent and a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA.

Liver;wild-type;high fat diet HFD;mixed 129/Sv and C57BL/6;mouse 546

Epididymal adipose;wild-type;high fat diet HFD;mixed 129/Sv and C57BL/6;mouse 546

Liver;GPR120 KO;high fat diet HFD;mixed 129/Sv and C57BL/6;mouse 428

Gene expression data from rat P4 Ovary cultured for 48 hours with no treatment

Flow sorted transduced and untransduced Lin- hematopoietic progenitors were pelleted and total RNA extracted with Qiagen Rneasy Micro Kit

S3F11 medium:  murine stem cell factor (mSCF) 50 ng/ml, murine interleukin 3 (mIL-3) 20 ng/ml, human FMS like tyrosine kinase 3 ligand (hFlt-3) 50 ng/ml, and human interleukin 11 (hIL-11) 50 ng/ml

CEL files were background corrected, quantile normalized and summarized using the RMA package (Bioconductor). QC was performed with ArrayQualityMetrics (Bioconductor)

Qiagen Rneasy Micro Kit followed by linear RNA amplification with GeneChip 3 IVT Express Kit (Affymetrix)

12.5 ug of fragmented and biotin labeled aRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Gene expression data from untransduced Lin- hematopoietic progenitors cultured in S3F11 medium

peripheral blood;sickle-cell patient;PBMC;RNA extracted from PBMC

Control subject, biopsy taken from the sigmoideum, no macroscopic signs of inflammation.

RNA was extracted from a pool of three thymi taken from four week old nonobese diabetic (NOD) derived NOD.B6 Idd3 R450 congenic mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.

LC-MA1

LC-MA2

LC-MA3

LC-MA4

LC-MA5

LC-MA6

LC-MA7

Trizol extraction of total RNA was performed according to the manufacturer's instructions followed by Qiagen's Rneasy kit purification

gene expression data from rat testis 8 h after cadmium treatment

gene expression data from rat testis 20 h after cadmium treatment

JLI_85

Cyclophosphamide-treated bone marrow 2 days - Biological Replicate 5 - Technical Replicate 2

Biological replicate 5 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated bone marrow cells, day 2

Cyclophosphamide-treated bone marrow 2 days - Biological Replicate 1 - Technical Replicate 2

Biological replicate 1 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated bone marrow cells, day 2

Cyclophosphamide-treated bone marrow 2 days - Biological Replicate 1 - Technical Replicate 1

Biological replicate 1 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day 2

Cyclophosphamide-treated bone marrow 2 days - Biological Replicate 2 - Technical Replicate 2

Biological replicate 2 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated bone marrow cells, day 2

Cyclophosphamide-treated bone marrow 2 days - Biological Replicate 2 - Technical Replicate 1

Biological replicate 2 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day 2

Cyclophosphamide-treated bone marrow 2 days - Biological Replicate 3 - Technical Replicate 2

Biological replicate 3 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated bone marrow cells, day 2

Cyclophosphamide-treated bone marrow 2 days - Biological Replicate 3 - Technical Replicate 1

Biological replicate 3 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day 2

Cyclophosphamide-treated bone marrow 2 days - Biological Replicate 4 - Technical Replicate 2

Biological replicate 4 of 5. Technical Replicate 2 of 2.Cyclophosphamide-treated bone marrow cells, day 2

Cyclophosphamide-treated bone marrow 2 days - Biological Replicate 4 - Technical Replicate 1

Biological replicate 4 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated bone marrow cells, day 2

Total RNA was prepared from the entire small intestine of one 40 day old CFTR control male mouse, CFTR(+/+), congenic on the black6 background, using TRIzol reagent. Mice were fed Peptamen from age 10 days to prevent intestinal obstruction.

A3WTS703

A4WTS804

A1WTS101

A2WTS202

MAS 5 global scaling at default values; normalization factor=1, target value=500

Cerebellum_transgenic nuclear exclusion signal Htt exon1 142Q A39_10 months_replicate 1

A39 NES 142Q TG5	F1/2	A39	NES Htt exon 1 142Q	Mouse	10.5 months	Cerebellum	Male

Cerebellum_transgenic nuclear exclusion signal Htt exon1 142Q A39_10 months_replicate 2

A39 NES 142Q TG6	F1/4	A39	NES Htt exon 1 142Q	Mouse	10.5 months	Cerebellum	Female

MCF-7;human breast adenocarcinoma cells;1 nM final conc. E2 + 1 uM 27-Hydroxycholesterol (27HC) for 24hr;1

129P3/J Acute morphine treated, striatum, biological replicate 2

129P3/J Acute morphine treated, striatum, biological replicate 1

MCF-7;human breast adenocarcinoma cells;1 nM final conc. vehicle (ethanol) + 1 uM 27-Hydroxycholesterol (27HC) for 24hr;2

MCF-7;human breast adenocarcinoma cells;1 nM final conc. vehicle (ethanol) + 1 uM 27-Hydroxycholesterol (27HC) for 24hr;1

sorted CML CD34+CD38- cells treated with the combination of IM and LBH

RNA was extracted from a pool of three thymi taken from four week old nonobese diabetic (NOD) derived NOD.B6 Idd3 R450 B10 Idd5 R8 congenic mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000). Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution. These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set. The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977). These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.

LM2 cells cultured with HMVEC-L and then purified by FACS;Purchased from Stratagene, Inc.

Peritoneal MF were stimulated with recombinant IFNg (10 ng/ml) for 6hrs.

Peritoneal MF were isolated from naïve euthanized mouse and plated in 24-well TC dishes into complete RPMI media, with 10% FBS and 15% L929 conditional sup containing MCSF o/n to allow MF adherence. Floaters (B cells, T cells etc) were discarded, fresh pre-warmed media was added over MF and cells stimulated with IFNg for 6hrs before RNA collection

Total RNA from stimulated or control peritoneal MF was isolated using Qiagen RNEasy Kit. DNA was removed using Qiagen Dnase protocol.

Biotinylated cRNA was prepared using the Ambion Illumina® TotalPrepTM RNA Amplification Kit

Epidydimal white adipose tissue from WT after 16 weeks of high fat diet feeding, replicate 3

Epidydimal white adipose tissue from WT after 16 weeks of high fat diet feeding, replicate 2

Epidydimal white adipose tissue from ASC-/- after 16 weeks of high fat diet feeding, replicate 1

Epidydimal white adipose tissue from WT after 16 weeks of high fat diet feeding, replicate 4

Epidydimal white adipose tissue from ASC-/- after 16 weeks of high fat diet feeding, replicate 3

Epidydimal white adipose tissue from ASC-/- after 16 weeks of high fat diet feeding, replicate 2

FBN+/-.TGFBRIIko_10
Gene expression data from fibrillin-1 mutant with Tgfbr2 knockout mice

Gene expression data from WT, YFP+ muscle stem cells, isolated from hindlimb that was contralateral to an hindlimb were we induced a muscle injury, 28 days post injury

mixed C57BL6;Pax7CreER/+;Rosa26REYFP/+;3-5 months old;BaCl2 muscle injury;hindlimb muscle contralateral to BaCl2 muscle injury;CSC;28 days post injury

Data were analyzed using Expression Console version 1.1 (Affymetrix) using the default RMA algorithm.

Labeled cDNA was hybridized on the Mouse Gene ST array for 18 hours at 45C. Arrays were washed and stained on an Affymetrix Fluidics Station 450 using protocol FS_450_0007.

Biotinylated cDNA was prepared using the NuGEN Technologies Ovation Pico WTA System, WT Ovation Exon Module, and Biotin Module according to the manufacturer's instructions.

B6EiC3SnF1/J (mix of B6 and C3H background);wild-type;skeletal muscle;male;5 months

TH cells from LC, Mecp2 null, young time point, biological replicate 3

TH_LCY_KO_3

C57BL6/J;No;Aug-11;72;male;LC (locus coeruleus);P22;Y/Mecp2-;TH/-;brain;tyrosine hydroxylase (TH)-positive locus coeruleus (LC) neurons

Gene expression data from WT, YFP+ muscle stem cells, isolated from hindlimb that was contralateral to an hindlimb were we induced a muscle injury, 2.5 days post injury

mixed C57BL6;Pax7CreER/+;Rosa26REYFP/+;3-5 months old;BaCl2 muscle injury;hindlimb muscle contralateral to BaCl2 muscle injury;CSC;2.5 days post injury

breast cancer derived cell line treated with 0.4 uM of Doxorubicin for 24 hours

Cardiac differentiation of hES cells is as described by Laflamme et al Nature Biotechnology 2007

The complete set of microarray data was assessed for quality, followed by quantile normalization using the Bioconductor package lumi.  The dataset was initially filtered by flagging probes that were below a signal 'noise floor,' which was established using the 75th percentile of the negative control probe signals within each array.  We subsequently filtered the dataset by employing a variance filter using the 'shorth' function of the Bioconductor package genefilter.  Pair-wise statistical analyses was performed using Bioconductor v. 2.10, limma v.3.12.3, lumi v.2.8.0.

RUES2;human embryonic stem cells;control shRNA;Day 5 of cardiac differentiation; cardiovascular progenitor cell stage

RUES2;human embryonic stem cells;shRNA targeting TMEM88;Day 5 of cardiac differentiation; cardiovascular progenitor cell stage

immortalized human mammary epithelial cell line treated with 0.01 mM of 5-Fluorouracil for 24 hours

immortalized human mammary epithelial cell line treated with 0.2 uM of Doxorubicin for 36hours

immortalized human mammary epithelial cell line treated with 0.06 mM of 5-Fluorouracil for 24 hours

heart from beta1-Arg389 transgenic mice at 90 days of age. The alpha-myosin heavy chain promoter was utilized to direct expression of the human beta1-Arg389 cDNAs to cardiac myocytes.

Phytohemagglutinin-activated PBMCs enriched for CD8+ cells from normal control subject J (JAcCD8)

Gene expression data from PBMC of normal control subject J followig PHA+IL2 activation for 10 days followed by CD8+ enrichment

phytohemagglutinin-activated PBMCs enriched for CD8+ cells from normal control subject J

PBMCs enriched for CD8+ cells from normal control subject J (JCD8)

Gene expression data from PBMC of normal control subject J enriched for CD8+ T cells

Phytohemagglutinin-activated PBMCs from normal control subject K (KAcPBMC)

Gene expression data from PBMC of normal control subject K followig PHA+IL2 activation for 10 days

phytohemagglutinin-activated PBMCs from normal control subject K

Phytohemagglutinin-activated PBMCs enriched for CD8+ cells from normal control subject C (CAcCD8)

Gene expression data from PBMC of normal control subject C followig PHA+IL2 activation for 10 days followed by CD8+ enrichment

phytohemagglutinin-activated PBMCs enriched for CD8+ cells from normal control subject C

PBMCs enriched for CD8+ cells from normal control subject C (CCD8)

Gene expression data from PBMC of normal control subject C enriched for CD8+ T cells

Phytohemagglutinin-activated PBMCs from normal control subject J (JAcPBMC)

Gene expression data from PBMC of normal control subject J followig PHA+IL2 activation for 10 days

phytohemagglutinin-activated PBMCs from normal control subject J

Phytohemagglutinin-activated PBMCs enriched for CD8+ cells from normal control subject K (KAcCD8)

Gene expression data from PBMC of normal control subject K followig PHA+IL2 activation for 10 days followed by CD8+ enrichment

phytohemagglutinin-activated PBMCs enriched for CD8+ cells from normal control subject K

"female subject, 18-45 yrs, peripheral blood mononuclear cells 24 h after intravenous saline challenge"

"female subject, 18-45 yrs, peripheral blood mononuclear cells 168 h after intravenous saline challenge"

TP15;CCN1.1R;Unaffected;-N/A;37;40;MALE;None;**Note this sample has a Biological replicate- Blood was taken from this patient on two separate occasions and two different transformed lymphocytes were arrayed. The matching sample is CCN1.1**

Unaffected MZ twin pair 1 Repeat (Unaffected patient of MZ twin pair CCN1)

TP14;CCN1.2;Unaffected;-N/A;37;40;MALE;None;**Note this sample has a Biological replicate- Blood was taken from this patient on two separate occasions and two different transformed lymphocytes were arrayed. The matching sample is CCN1.2R**

Unaffected MZ twin pair 1 (Unaffected patient of MZ twin pair CCN1)

ACRL_CBM__Control_A

TP13;CCN1.1;Unaffected;-N/A;37;40;MALE;None;**Note this sample has a Biological replicate- Blood was taken from this patient on two separate occasions and two different transformed lymphocytes were arrayed. The matching sample is CCN1.1R**

Concordant for Epilepsy twin pair 4 (Affected patient of MZ twin pair CCE4)

TP39;CCE4.1;Childhood Absence Epilepsy;-11.5;31;34;MALE;Epilim & Lamictal

cells_ATCC 16Lu_human lung fibroblasts_JCB_10_4_22_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

JCB_10_4_22_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

in vitro Treatment: V2O5, Treatment Time: 24, Units of Treatment Time: hour, Dose or Concentration: 10, Units of Dose or Concentration: ug/cm2

cells_ATCC 16Lu_human lung fibroblasts_JCB_10_24_40_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

JCB_10_24_40_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

in vitro Treatment: V2O5, Treatment Time: 1, Units of Treatment Time: hour, Dose or Concentration: 10, Units of Dose or Concentration: ug/cm2

cells_ATCC 16Lu_human lung fibroblasts_JCB_10_1_6_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

JCB_10_1_6_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

cells_ATCC 16Lu_human lung fibroblasts_JCB_10_1_36_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

JCB_10_1_36_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

cells_ATCC 16Lu_human lung fibroblasts_JCB_10_24_25_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

JCB_10_24_25_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

cells_ATCC 16Lu_human lung fibroblasts_JCB_10_24_10_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

JCB_10_24_10_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

in vitro Treatment: V2O5, Treatment Time: 12, Units of Treatment Time: hour, Dose or Concentration: 10, Units of Dose or Concentration: ug/cm2

cells_ATCC 16Lu_human lung fibroblasts_JCB_10_12_39_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

JCB_10_12_39_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

cells_ATCC 16Lu_human lung fibroblasts_JCB_10_12_24_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

JCB_10_12_24_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

cells_ATCC 16Lu_human lung fibroblasts_JCB_10_1_21_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

JCB_10_1_21_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

cells_ATCC 16Lu_human lung fibroblasts_JCB_10_12_9_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014

JCB_10_12_9_Lung_Fibroblast_V2O5_HG-U133A_2_IMFRT0014: Vanadium and Oxidant-Induced Stress in Human Lung Fibroblasts

ES cells were trypsinized  and separated from MEF cells by placing all cells in culture  with ES media for one hour. During this period MEF cells adhere while ES cells remain in suspension. ES cells in suspension were aspirated and centrifuged to form a pellet used for total RNA extraction.

Embryonic Stem Cells were cultured on gelatin and a MEF feeder layer in the presence 20 percent fetal bovine serum containing LIF, as previously described (Doetschman et al. 1985). Media was changed dialy.

GeneChips were scanned using the Affymetrix GeneArray Scanner 3000

Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix

male;placebo (A);6 months;Isolated peripheral blood mononuclear cells (PBMCs)

male;placebo (A);12 months;Isolated peripheral blood mononuclear cells (PBMCs)

Cultures were maintained in Dulbecco’s modified Eagle’s medium (DMEM;Invitrogen; Carlsbad, CA, USA) with L-glutamine and high glucose plus 10% FBS (Invitrogen) and 100U/mL penicillin streptomycin (Invitrogen) at 37oC and 5% CO 2. Cells were passaged at confluence by 0.25% trypsin EDTA (Invitrogen).

B6; gender: mix; age: 0-2d; tissue: dermis; passage #: 4; treatment: 5-aza-2'-deoxycytidine; biological replicate: 1

B6; gender: mix; age: 0-2d; tissue: dermis; passage #: 4; treatment: control; biological replicate: 1

B6; gender: mix; age: 0-2d; tissue: dermis; passage #: 4; treatment: 5-aza-2'-deoxycytidine; biological replicate: 3

B6; gender: mix; age: 0-2d; tissue: dermis; passage #: 4; treatment: control; biological replicate: 2

B6; gender: mix; age: 0-2d; tissue: dermis; passage #: 4; treatment: control; biological replicate: 3

skeletal muscle;insulin resistant;untreated;0.8;84;70;1210;68.1;40;38.6;2724

skeletal muscle;insulin resistant;untreated;0.94;307;18;1680;83;23.6;60;1958.8

top2b-/- in 129SvEv (minor 129SvJ) background;;E14.5 embryo;;male;;whole brain

24 hrs tetracycline (1000 ng/ml) to induce expression of the transcription factors

Top2b+/+ in 129SvEv (minor 129SvJ) background;;E16.5 embryo;;male;;whole brain

Gene expression data of male hearts after a 10 day treatment of CVB3

top2b-/- in 129SvEv (minor 129SvJ) background;;E16.5 embryo;;female;;whole brain

brain microvessels from WKY treated with vehicle for 4 weeks subcutaneously by osmotic minipump.

12-week-old Wistar Kyoto (WKY), male, brain microvessels, treated with vehicle for 4 weeks subcutaneously by osmotic minipump.

Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos that contain a deletion in the CH1 domain of both alleles of p300 and one allele of CBP (tri-CH1).  Subconfluent MEFs were treated with either 21% oxygen (normoxia) with 5% carbon dioxide at 37 C in a humid chamber for 6hrs.  At the start of treatment, medium was removed and replaced with medium (DMEM+10% FBS+pen-strep+ l-glu) that had been preequilibrated overnight in normoxia.  Immediately after treatment, cells were lysed in Trizol for RNA extraction.
Sample Type: Mouse Total RNA
Project: Brindle
Sample User: jmorris
Experiment User: jmorris
Lot Number: 3002159
Algorithm: Statistical
Corner+ Avg:36, Count:32
Corner- Avg:5956, Count:32
BF: Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0045,Gamma1L:0.0045,Gamma2H:0.006,Gamma2L:0.006,Perturbation:1.1,TGT:500,NF:1.000000,SF:10.301489,SFGene:All
Background:Avg:33.29,Stdev:0.90,Max:35.8,Min:31.8
Noise:Avg:1.58,Stdev:0.10,Max:1.9,Min:1.4
RawQ:1.21

Primary wildtype mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos.   Subconfluent MEFs were treated with 21% oxygen (normoxia) with 5% carbon dioxide at 37 C in a humid chamber for 6hrs.  At the start of treatment, medium was removed and replaced with medium (DMEM+10% FBS+pen-strep+ l-glu) that had been preequilibrated overnight in normoxia.  Immediately after treatment, cells were lysed in Trizol for RNA extraction.
Lot Number: 3002034
Corner+ Avg:88, Count:32
Corner- Avg:13537, Count:32
BF: Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0045,Gamma1L:0.0045,Gamma2H:0.006,Gamma2L:0.006,Perturbation:1.1,TGT:500,NF:1.000000,SF:3.461269,SFGene:All
Background:Avg:40.18,Stdev:1.27,Max:43.6,Min:37.9
Noise:Avg:2.55,Stdev:0.22,Max:3.1,Min:2.2
RawQ:1.58

Primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos that contain a deletion in the CH1 domain of both alleles of p300 and one allele of CBP (tri-CH1). Subconfluent MEFs were treated with 0.1% oxygen (hypoxia), with 5% carbon dioxide at 37 C in a humid chamber for 6hrs.  At the start of treatment, medium was removed and replaced with medium (DMEM+10% FBS+pen-strep+ l-glu) that had been preequilibrated overnight in hypoxia.  Immediately after treatment, cells were lysed in Trizol for RNA extraction.
Corner+ Avg:42, Count:32
Corner- Avg:5181, Count:32
BF: Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0045,Gamma1L:0.0045,Gamma2H:0.006,Gamma2L:0.006,Perturbation:1.1,TGT:500,NF:1.000000,SF:8.697724,SFGene:All
Background:Avg:45.24,Stdev:4.65,Max:58.7,Min:39.5
Noise:Avg:2.21,Stdev:0.30,Max:2.8,Min:1.6
RawQ:1.50

Primary wildtype mouse embryonic fibroblasts (MEFs) were generated from e14.5 embryos.  Subconfluent MEFs were treated with 0.1% oxygen (hypoxia), with 5% carbon dioxide at 37 C in a humid chamber for 6hrs.  At the start of treatment, medium was removed and replaced with medium (DMEM+10% FBS+pen-strep+ l-glu) that had been preequilibrated overnight in hypoxia.  Immediately after treatment, cells were lysed in Trizol for RNA extraction.
Corner+ Avg:51, Count:32
Corner- Avg:6978, Count:32
BF: Alpha1:0.05,Alpha2:0.065,Tau:0.015,Gamma1H:0.0045,Gamma1L:0.0045,Gamma2H:0.006,Gamma2L:0.006,Perturbation:1.1,TGT:500,NF:1.000000,SF:6.730389,SFGene:All
Background:Avg:36.53,Stdev:1.00,Max:38.9,Min:34.8
Noise:Avg:1.90,Stdev:0.14,Max:2.3,Min:1.7
RawQ:1.38

Cells were grown to 70% confluency in 60 mm culture dishes and exposed to 10 mM Phenol for 6h at 37 °C.

Double stranded cDNA was synthesized (GeneChip® Expression 3' Amplification One-Cycle Target Labeling and Control Reagents, 900493) and biotin labeled cRNA was in vitro transcribed (GeneChip® Expression 3' Amplification One-Cycle Target Labeling and Control Reagents, 900493). Cleanup of the cDNA and the fragmented cRNA was carried out with the GeneChip Sample Module (Affymetrix,900371). The integrity of the total RNA and of the subsequent preparation steps was validated using the Agilent 2100 bioanalyzer (Waldbronn, Germany).).

The placenta (E 10.5) of a congenic adra2B-/- mouse embryo (maternal genotype Adra2b+/-) was rapidly dissected and flash frozen.

The whole procedure was carried out according to the Affymetrix standard protocol.

Sample represents the Paraventricular nucleus from 5 dehydrated animals (3 Days)

Sprague Dawley;Male;10-12 weeks;Hypothalamic Paraventricular nucleus

CHARACTERISTICS;Sprague Dawley;Male;10-12 weeks;Hypothalamic Paraventricular nucleus

Sample represents the Paraventricular nucleus from 5 control animals

Additional details provided in accompanying manuscript, BC2 TC_TCR

Additional details provided in accompanying manuscript, BC2 TC_NOC

Additional details provided in accompanying manuscript, BC3 TC_NOC

Additional details provided in accompanying manuscript, BC3 TC_TCR

AML blasts from bone marrow;test;wild-type;M5a;internal tandem duplication (ITD)

AML blasts from bone marrow;test;wild-type;M1;internal tandem duplication (ITD)

AML blasts from bone marrow;test;wild-type;M4;internal tandem duplication (ITD)

Gene expression data from HSF1-/- T cells activated at 37oC for 5h with plate bound anti-CD3.

Gene expression data from HSF1-/- T cells activated at 40oC for 5h with plate bound anti-CD3.

lung tissue;CD-1;13 weeks + 1 day;fresh air, treatment over 1 day, 3x1h exposure per day

U2-OS cells were stably transfected with low levels of ERb 1-530, this sample represents E2 10nM treated cells at 24 hours and was used in a time-course experiment

U2-OS cells were stably transfected with low levels of ERbeta1-530. This sample represents E2 10 nM treated cells for 8 hours.

U2-OS cells were stably transfected with low levels of ERb 1-530, this sample represents E2 10nM treated cells at 8 hours and was used in a time-course experiment

U2-OS cells were stably transfected with low levels of ERb 1-530, this sample represents E2 10nM treated cells at 48 hours and was used in a time-course experiment

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Untreated control. nr 12, replicate (control 12 has been arrayed twice).

ES cells were cultured in the presence or absence of Vitamin C (L-ascorbic acid 2-phosphate, 200 μg/ml) for 72 hours.  Vitamin C was added to ES cells one day after seeding.  Medium with or without Vitamin C supplementation was replaced daily.

ES cells were cultured on 0.1% gelatin coated plates in N2B27 medium supplemented with the MEK inhibitor PD0325901 (1μM, Stemgent), and the GSK3β inhibitor CHIR99021 (3μM, Selleck Chemicals), and LIF (1000U/ml, Millipore).

Arrays were scanned with GCS3000 using the standard procedures recommended by Affymetrix.

Intensities of the Affymetrix CEL files were background subtracted, quantile normalized, and summarized for each probe set into a logarithm base two intensity value using the robust multi-array average method (RMA) implemented in the Affymetrix package AGCC 3.2.2.

Total RNA was extracted with Qiagen RNeasy kit with on-column DNAse digestion

Hybridization was performed by Gladstone Genomics Core facility according to GeneChip Expression Analysis Technical Manual 702232 Rev. 3

Samples were amplified with NuGEN Ovation Pico WTA V2 and labelled with the Encore Biotin Module by the Gladstone Genomics Core facility according to manufacturer's protocol.

uterus - Early secretory endometrium from patient with endometriosis

A673 treated with cytarabine (ARA-C) for 5 days with concentration of 0.34 uM (2 x EC50), biological rep3

A673 treated with Doxorubicin for 3 days with concentration of 59.88 nM (EC50), biological rep2

Gene expression data from A673 cell line that has been treated with Doxorubicin for 3 days with concentration of 59.88 nM (EC50).

A673 cell line that has been treated with Doxorubicin for 3 days with concentration of 59.88 nM (EC50).

A673 treated with Doxorubicin for 3 days with concentration of 59.88 nM (EC50), biological rep1

SMhu018

SMhu021

SMhu022

SMhu023

SMhu024

CD1;wild type; Raldh2 +/+;embryonic brain;Rostral/Anterior;14 somite stage

E14 mESCs were infected with lentivirus containing shRNA targeting Usp22 or control (Luc).  RNA was extracted from both samples and subjected to expression analysis by affymetrix array.

Mouse ESCs were maintained in feeder-free conditions on gelatin-coated plates in 20% defined FBS-DMEM supplemented with 1% L-glutamine, 1% HEPES, 1% NEAA, 0.001% beta-merceptoethanol, and fresh LIF. The MEK inhibitor PD0325901 (1 μM) and GSK3 inhibitor CH99021 (3 μM), together known as 2i, were added fresh along with LIF.

Chips were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software

Background correction and normalization were done using Iterative Plier 16 with GeneSpring V12.0 software (Agilent, Palo Alto, CA, USA). 1.5-fold (p-value<0.12) differentially expressed gene list was generated. The differentially expressed gene list was loaded into Ingenuity Pathway Analysis (IPA) 8.0 software (http://www.ingenuity.com) to perform biological network and functional analyses.

mRNA was harvested using Trizol reagent and cleaned up using Rneasy column from Qiagen

Affymetrix gene chips, Mouse gene 1.0 ST array (Affymetrix, Santa Clara, CA), were hybridized with fragmented and biotin-labeled target (2.5 mg) in 110 μl of hybridization cocktail. Target denaturation was performed at 99°C for 2 min. and then 45°C for 5 min, followed by hybridization for 18 h. Arrays were then washed and stained using Gene chip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG and anti-streptavidin biotinylated antibody.

cDNAs were fragmented and chemically labeled with biotin to generate biotinylated ST-cDNA using FL-Ovation cDNA biotin module V2 (NuGen Technologies, Inc.).

Vehicle treament for human hepatocyte donor A.  Growth media:  In vitro technologies hepatocyte incubation media (cat no. Z90009)

Total RNA was extracted from lymphoblastoid cells of AU010603 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;AU010603 is a male with autism and duplication of 15q11-13.

Primary Human Hepatocyte;Male;In Vitro technologies;Hypoxia;None

Gene expression data from LNCaP cells after transfection with control siRNA
LNCaP-DHT-siCtrl-1

LNCaP prostate cancer cells;transfected with control siRNA;in the presence of DHT

LNCaP cells transfected with control siRNA in the presence of 10 nM DHT

Gene expression data from LNCaP cells after transfection with siRNA against EZH2
LNCaP-DHT-siEZH2-1

LNCaP prostate cancer cells;depleted of EZH2;in the presence of DHT

LNCaP-DHT-siCtrl-0

LNCaP-DHT-siEZH2-0

abl-VEH-siCtrl-2

abl-VEH-siEZH2-2

abl-VEH-siCtrl-1

abl-VEH-siEZH2-1

LNCaP-DHT-siCtrl-2

LNCaP-DHT-siEZH2-2

mIMCD3 cells were treated for 1 hour with vehicle (control) or aldosterone. Total RNA was isolated and used as template to generate the eventual cRNA target. The experiment was repeated a total of three times. Six cRNA samples, three control and three treated, were generated and used in a total of six hybridizations. This data set represents the aldosterone-treated sample for replication 3.

After the 2-day growth, media was changed to 10% charcoal-stripped FBS RPMI and at this time 10 microM of polyamide targeted to the ARE or 10 microM of a control polyamide were added.  Cells were grown for 48 hours more.  Bicalutamide (10 microM) was added to the appropriate cells, incubataed for 2 hours.  DHT was added (1 nM) for 16 hours.

LNCaP cells seeded in 12-well plates at 90-100,000 cells per plate in 10% FBS RPMI for 3 days.

Standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix)

Cells were harvested for RNA using the Qiagen RNEasy kit and protocol.  Control cells that were not treated with DHT were also harvested.

Untreated LNCaP cells stimulated with DHT, biological replicate 2

Untreated LNCaP cells stimulated with DHT, biological replicate 3

Untreated LNCaP cells not stimulated with DHT, biological replicate 2

Untreated LNCaP cells stimulated with DHT, biological replicate 1

Bicalutamide treated LNCaP cells not stimulated with DHT, biological replicate 3

Polyamide 1 treated LNCaP cells not stimulated with DHT, biological replicate 1

Bicalutamide treated LNCaP cells not stimulated with DHT, biological replicate 1

Bicalutamide treated LNCaP cells not stimulated with DHT, biological replicate 2

Polyamide 1 treated LNCaP cells not stimulated with DHT, biological replicate 2

Polyamide 1 treated LNCaP cells not stimulated with DHT, biological replicate 3

226;Azathioprine 150mg Asacol 1.6g Ca Vit D B12;6/15/74;F;CAUCASIAN;1/1/89;1/1/89;FALSE;FALSE;FALSE;YES;FALSE;TRUE;1/11/05;8;0;0;0;0;0;0;0;FALSE;0;BOTH;unknown;unknown;unknown;unknown;1/11/05;BOTH;unknown;unknown;unknown;unknown;3/7/05;FAILURE OF THERAPY;current;15-24;None;UC;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

232;Pentaza 2g BD;1/9/63;F;CAUCASIAN;1/1/95;1/1/95;FALSE;FALSE;FALSE;unknown;FALSE;FALSE;1/31/05;1;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;BOTH;BOTH;BOTH;1/31/05;BOTH;BOTH;BOTH;BOTH;BOTH;3/7/05;FAILURE OF THERAPY;never;unknown;None;UC;8-9-01;descending colon;Inflamed;total RNA from 10 human cell lines

204;AZA 200mg, Insulin, Asprin, Atenolol, Simvastatin;8/15/43;M;CAUCASIAN;7/1/02;8/1/02;FALSE;FALSE;FALSE;YES;FALSE;TRUE;11/1/04;5;0;0;0;0;0;0;0;FALSE;0;11;12;12;12;0;0;0;0;0;BOTH;BOTH;BOTH;unknown;unknown;11/1/04;BOTH;BOTH;BOTH;unknown;unknown;12/16/04;FAILURE OF THERAPY;ex;1/1/58;1/1/01;25+;Type 2 DM 02/2004.-Gout.;UC;8-9-01;descending colon;Inflamed;total RNA from 10 human cell lines

215;Prednisolone 5ng Balsalazide Lansoperazole;5/6/60;M;CAUCASIAN;5/1/02;8/16/02;FALSE;FALSE;FALSE;NO;FALSE;FALSE;11/16/04;3;0;0;0;0;0;0;0;TRUE;0;BOTH;BOTH;BOTH;BOTH;unknown;11/16/04;unknown;unknown;unknown;unknown;unknown;5/31/05;DISEASE IN REMISSION;ex;1/1/03;1/1/04;5-14;None;UC;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

231;prednisolone 40mg heparin clarithromycin;10/29/77;F;CAUCASIAN;10/1/00;11/19/02;FALSE;FALSE;FALSE;unknown;FALSE;FALSE;1/28/05;7;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;BOTH;unknown;unknown;9/14/05;BOTH;BOTH;BOTH;unknown;unknown;9/14/05;FAILURE OF THERAPY;never;unknown;None;UC;6-2-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

232;Pentaza 2g BD;1/9/63;F;CAUCASIAN;1/1/95;1/1/95;FALSE;FALSE;FALSE;unknown;FALSE;FALSE;1/31/05;1;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;BOTH;BOTH;BOTH;1/31/05;BOTH;BOTH;BOTH;BOTH;BOTH;3/7/05;FAILURE OF THERAPY;never;unknown;None;UC;6-2-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

226;Azathioprine 150mg Asacol 1.6g Ca Vit D B12;6/15/74;F;CAUCASIAN;1/1/89;1/1/89;FALSE;FALSE;FALSE;YES;FALSE;TRUE;1/11/05;8;0;0;0;0;0;0;0;FALSE;0;BOTH;unknown;unknown;unknown;unknown;1/11/05;BOTH;unknown;unknown;unknown;unknown;3/7/05;FAILURE OF THERAPY;current;15-24;None;UC;6-2-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

227;Asacol Prednisolone 5 Omeprazole Warfarin Cal VitD;4/17/28;M;CAUCASIAN;1/1/90;1/1/90;FALSE;FALSE;FALSE;NO;FALSE;FALSE;1/14/05;3;0;0;0;0;0;0;0;TRUE;0;BOTH;BOTH;BOTH;BOTH;BOTH;1/14/05;BOTH;BOTH;BOTH;BOTH;BOTH;3/7/05;FAILURE OF THERAPY;ex;1/1/72;5-14;Prostate cancer 1985, Previous DVT's on warfarin;UC;6-2-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

222;Prednisolone 20mg Balsalazide;4/13/52;M;CAUCASIAN;9/1/85;6/20/86;FALSE;FALSE;FALSE;YES;TRUE;FALSE;12/16/04;9;0;0;0;0;0;0;0;FALSE;0;BOTH;unknown;unknown;unknown;unknown;12/16/04;BOTH;BOTH;BOTH;unknown;unknown;3/7/05;FAILURE OF THERAPY;never;unknown;None;UC;5-25-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

215;Prednisolone 5ng Balsalazide Lansoperazole;5/6/60;M;CAUCASIAN;5/1/02;8/16/02;FALSE;FALSE;FALSE;NO;FALSE;FALSE;11/16/04;3;0;0;0;0;0;0;0;TRUE;0;BOTH;BOTH;BOTH;BOTH;unknown;11/16/04;unknown;unknown;unknown;unknown;unknown;5/31/05;DISEASE IN REMISSION;ex;1/1/03;1/1/04;5-14;None;UC;6-2-01;terminal ileum;Uninflamed;total RNA from 10 human cell lines

OA_3_Chon_CHyaff_D14_133P
human chondrocytes isolated from non-weight bearing area of the knee cartilage of patients undergoing ACT treatment, subcultured up to passage 2 (primary cells = passage 0), seeded onto hyaff-11 scaffold, maintained for 14 days in the presence of TGFbeta 1,  chondrocytes obtained from OA donor 3

OA_2_Chon_CHyaff_D14_133P
human chondrocytes isolated from non-weight bearing area of the knee cartilage of patients undergoing ACT treatment, subcultured up to passage 2 (primary cells = passage 0), seeded onto hyaff-11 scaffold, maintained for 14 days in the presence of TGFbeta 1,  chondrocytes obtained from OA donor 2

Gene expression data from Mtb-infected and PZA treated mouse lungs

Mtb infected mouse lungs treated with PZA-42 days post infection

M479 - QV RNA

M465 - QV RNA

M452 + QV RNA

M473 + QV RNA

peripheral CD4+CD25hi cells;Cbfb-flox/flox, Foxp3-ires-Cre;male;16 weeks;purified CD4+CD25hi cells from spleen and lymph nodes

ID = C477
Stage 2A (NED)
Total RNA

ID = C464
Stage 2B (NED)
Total RNA

ID = C451
Total RNA

ID = C437
Total RNA

ID = C405
Stage 2B
Total RNA

ID = C366
Total RNA

ID = C348
Total RNA

ID = C290
Stage 2A
Total RNA

ID = C484
Stage 2A
Total RNA

ID = C482
Stage 1B
Total RNA

Gene expression data from  3 uM EPZ004777 treated, DAY 4, biological rep.2, MV4-11 cells

MV4-11;biphenotypic B myelomonocytic leukemia (MLL-AF4 rearragenment);IMDM with 10% FBS;EPZ004777;day 4;2

LNCaP androgen-sensitive human prostate  adenocarcinoma cell line;SRF Silencing;R1881

LNCaP androgen-sensitive human prostate  adenocarcinoma cell line;control siRNA;R1881

LNCaP androgen-sensitive human prostate  adenocarcinoma cell line;SRF Silencing;EtOH vehicle

Gene expression data from Vehicle treated, DAY 4, biological rep.2, MV4-11 cells

MV4-11;biphenotypic B myelomonocytic leukemia (MLL-AF4 rearragenment);IMDM with 10% FBS;Vehicle;day 4;2

luteinized human cumulus cells, cultured 48h, nonPCOS, Lean, rep1

ko_05.CEL

ko_06.CEL

ko_10.CEL

ko_11.CEL

LC-MA8

Peripheral blood mononuclear cells;systemic JIA;LT6;85min;White;Male

Peripheral blood mononuclear cells;systemic JIA;LT6;120min;White;Male;159

Peripheral blood mononuclear cells;systemic JIA;GTE6;100min;White;Male;118

Peripheral blood mononuclear cells;systemic JIA;GTE6;135min;Black/African American;Male;176

Peripheral blood mononuclear cells;systemic JIA;LT6;120min;White;Male

Peripheral blood mononuclear cells;systemic JIA;LT6;100min;White;Male

Peripheral blood mononuclear cells;systemic JIA;LT6;205min;White;Male

Peripheral blood mononuclear cells;systemic JIA;LT6;185min;Asian;Female

Fourth ventricular choroid plexus from Otx2ko mice at E13, biological replicate 3

Fourth ventricular choroid plexus from Otx2ko mice at E13, biological replicate 2

Fourth ventricular choroid plexus from Otx2ko mice at E13, biological replicate 1

Gene expression data from embryonic lungs at day E18.5 Hmga2 KO

HepG2 cells treated with 2.5 microMolar  5-aza-dC for 4 days, with medium replaced daily; Trichostatin A  at 500 nM was added for the last 24 h

Ambion MessageAmp II Biotin Enhanced single round aRNA amplification protocol

human cellular RNA_primary airway epithelial cells_tracheobronchial _H511_2h_4mM_HG-U133A_2_YCHSUP501

H511_2h_4mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;19.758;2.11

human cellular RNA_primary airway epithelial cells_tracheobronchial _H511_2h_1mM_HG-U133A_2_YCHSUP501

H511_2h_1mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;16.848;2.11

human cellular RNA_primary airway epithelial cells_tracheobronchial _H511_2h_0.4mM_HG-U133A_2_YCHSUP501

H511_2h_0.4mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;25.945;2.12

human cellular RNA_primary airway epithelial cells_tracheobronchial _H510_6h_Con_HG-U133A_2_YCHSUP501

H510_6h_Con_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;29.490;2.12

human cellular RNA_primary airway epithelial cells_tracheobronchial _H421_2h_4mM_HG-U133A_2_YCHSUP501

H421_2h_4mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;11.442;2.08

human cellular RNA_primary airway epithelial cells_tracheobronchial _H421_2h_1mM_HG-U133A_2_YCHSUP501

H421_2h_1mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;12.21;2.08

human cellular RNA_primary airway epithelial cells_tracheobronchial _H421_2h_0.4mM_HG-U133A_2_YCHSUP501

H421_2h_0.4mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;9.883;2.1

human cellular RNA_primary airway epithelial cells_tracheobronchial _H511_2h_Con_HG-U133A_2_YCHSUP501

H511_2h_Con_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;18.378;2.09

human cellular RNA_primary airway epithelial cells_tracheobronchial _H421_6h_0.4mM_HG-U133A_2_YCHSUP501

H421_6h_0.4mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;27.167;2.13

Treatment_2: in vitro Treatment: HCLO, Treatment Duration: 2, Units of Duration: hour

human cellular RNA_primary airway epithelial cells_tracheobronchial _H421_2h_Con_HG-U133A_2_YCHSUP501

H421_2h_Con_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;13.666;2.07

2653_E_15_(HG-U133A_2).CEL

2665_E_14_(HG-U133A_2).CEL

2664_E_17_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siERK1 treatment 60h, 10 nM E2 for 4h

2659_E_16_(HG-U133A_2).CEL

3490_E_20_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siCtrl treatment 60h, 0.1%EtOH for 24h

2651_E_18_(HG-U133A_2).CEL

3497_E_23_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siCtrl treatment 60h, 10 nM E2 for 24h

3501_E_21_(HG-U133A_2).CEL

3495_E_25_(HG-U133A_2).CEL

3494_E_24_(HG-U133A_2).CEL

Sample_ID:t01 // Patient:J-159 // Histology:Diffuse // Metastasis:- // p53_mut:- // E-cadherin_mut:- // beta-Catenin_mut:+

Sample_ID:n24 // Patient:J-n24 // Histology:Normal // Metastasis:NA // p53_mut:NA // E-cadherin_mut:NA // beta-Catenin_mut:NA

Sample_ID:t03 // Patient:J-290 // Histology:Diffuse // Metastasis:+ // p53_mut:- // E-cadherin_mut:+ // beta-Catenin_mut:-

Sample_ID:t02 // Patient:J-258 // Histology:Diffuse // Metastasis:+ // p53_mut:++ // E-cadherin_mut:- // beta-Catenin_mut:-

Sample_ID:t05 // Patient:J-108 // Histology:Diffuse // Metastasis:+ // p53_mut:- // E-cadherin_mut:- // beta-Catenin_mut:+

Sample_ID:t04 // Patient:J-133 // Histology:Diffuse // Metastasis:+ // p53_mut:++ // E-cadherin_mut:+ // beta-Catenin_mut:-

Sample_ID:t07 // Patient:J-199 // Histology:Intestinal // Metastasis:+ // p53_mut:- // E-cadherin_mut:+ // beta-Catenin_mut:-

blast count: 98

Sample_ID:t08 // Patient:J-125 // Histology:Intestinal // Metastasis:+ // p53_mut:++ // E-cadherin_mut:+ // beta-Catenin_mut:++

blast count: 13

blast count: 10

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D1;8

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D14;8

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D7;8

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D42;6

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D21;6

male;non-metastatic prostate cancer;peripheral blood;white blood cells;baseline;8

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D72 (30 days post-EBRT);6

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D42;8

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D21;8

T166;Mouse tumorgraft, cohort 4;Male;56;Clear-cell renal cell carcinoma;mutant;wild type;mutant

Gene expression profiling of mouse tumorgraft, cohort 4 of patient T166

T166;Mouse tumorgraft, cohort 8;Male;56;Clear-cell renal cell carcinoma;mutant;wild type;mutant

Gene expression profiling of mouse tumorgraft, cohort 8 of patient T166

T164;Mouse tumorgraft, cohort 1;Male;75;Clear-cell renal cell carcinoma;wild type;wild type;wild type

Gene expression profiling of mouse tumorgraft, cohort 1 of patient T164

T183;Mouse tumorgraft from metastasis, cohort 1;Male;56;Clear-cell renal cell carcinoma;wild type;mutant;mutant

Gene expression profiling of mouse tumorgraft from metastasis, cohort 1 of patient T183

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;Control;12h;1;4421339046

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;HA1077;6h;2;4421339046

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;Control;6h;2;4421339046

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;HA1077;2h;2;4421339046

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;Control;2h;2;4421339046

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;HA1077;24h;1;4421339033

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;Control;24h;1;4421339033

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;HA1077;12h;2;4421339033

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;Control;24h;2;4421339046

C57 Bk6;1.5 day;forebrain;primary cell culture astrocyte;HA1077;12h;2;4421339046

LaserPower: 2.57;; 1.58
Temperature: 39.73

LaserPower: 2.56;; 1.58
Temperature: 39.19

Two groups of 3 days old mice were treated with oil or retinoic acid. At day 4 one half of each group was treated with saline solution or dexametasone. Lungs were removed snap frozed for RNA extraction

LaserPower: 2.54;; 1.37
Temperature: 36.93

LaserPower: 2.51;; 1.42
Temperature: 36.13

LaserPower: 2.54;; 1.45
Temperature: 35.32

FVB;MMTV-iFGFR1;Female;6 weeks;Mammary gland;not treated (0 hour)

RNA extracted from lymphoblastic cell line derived from normal subject.

72 hours after transduction with Mn1, gfp positive bone marrow cells were sorted and RNA isolated

WAO9 human embryonic stem cells;subjected to a hepatic differentiation protocol;d5

Samples were prepared for laser capture microdissection as per Potter GUDMAP.org protocols

GCOS used to generate expression values, with all probe sets, signal set to 1500.

RNA was purified with QIagen RNeasy Micro kit, as describe in Potter Protocols GUDMAP.org

Target was prepared with Epicentre two round IVT kit as per Potter GUDMAP.org protocol

neuronal, age:34, gender:male, diagnostic group: control, PMI:22h

neuronal, age:49, gender:female, diagnostic group: control, PMI:45h

CFU-PreB colonies grown in M3630 media (Stem Cell Technologies) were collected on Day 7.

Samples were scanned at the Genome Technology Access Center (Washington University in St. Louis)

RMA-summarized gene-level expression values computed using Affymetrix Expression Console.

B220+ cells were sorted directly into TRIzol LS (Life Technologies) and RNA was extracted using standard protocols. cDNA was prepared using the PicoSL Ovation system (NuGen). Samples were hybridized to Mouse Gene 1.0 ST arrays.

Samples were hybridized to Mouse Gene 1.0 ST arrays (Affymetrix) at the Genome Technology Access Center (Washington University in St. Louis)

Sample name: Het_5
Gene-level RMA expression value derived from Expression Console software

Sample name: Het_4

Data was analyzed with Agilent Genespring GX v. 7.3.1 using Affymetrix GCOS generated flag data from scaled CHP files, and RMA-normalized CEL files.

Trizol extraction of total RNA was performed from flash frozed/pulverized samples according to the manufacturer's instructions.

Following fragmentation, 10 micrograms of cRNA wer hybridized for 16 hr at 45C on GeneChip Human Genome U133A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 micrograms total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

Early gene expression data from xenograft tumors following sensitizing and PDT treatment.

Sample tumor (untreated) collected parallel to PDT treated sample

DEX-treated embryonic primary chondrocyte cultures, incubated for 24hr

Microarray data were pre-processed using the GC-RMA algorithm in Genespring GX* Expression values were further filtered by retaining only those  probe sets with expression values of at least 50 in at least 25% of all conditions, thus generating a list of 22 091 probe sets. To assess differential gene expression between treatments at both the 6 and 24 hr time points, a Welch ANOVA test with a p-value cut-off of 0.01 and a 5% false discovery rate (FDR)

DMSO-treated embryonic primary chondrocyte cultures, incubated for 24hr

Reh, transient knockdown of CBFA2T3 and transient expression of IKKb(EE)

Healthy control;51;Male;N/A;N/A;6.70;31;Right;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 1

Healthy control;47;Male;N/A;N/A;6.60;11;Left;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 1;0 (no use) to 6 (heavy use)): 0

Study of rat femur fracture healing in young rats (6 weeks old at fracture) at 2 weeks after fracture.  RNA from 2 rats was pooled for each array

Healthy control;47;Male;N/A;N/A;6.57;36;Left;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 0

Study of rat femur fracture healing in young rats (6 weeks old at fracture) at 6 weeks after fracture.  RNA from 2 rats was pooled for each array.  Sample is middle third of femur with external callus, cortical bone and marrow elements.

The cells were treated with CT16 siRNA or control siRNA for 48 h

The cells were maintained at 5% CO2 and 37°C in Dulbecco's Modified Eagle Medium (DMEM) (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum.

The microarray data were normalized using the quantile normalization method in Bioconductor  (http://www.bioconductor.org)

RNA was extracted with Trizol reagent followed by purification with Qiagen’s RNeasy MiniKit, (cat no74106) according to the manufacturer’s protocol. The DNase treatment was included and done with Qiagen’s RNase free DNase Set (cat no 79254) according to Qiagen’s protocol. cRNA quality was controlled by BioRad’s Experion electrophoresis station.

Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit

Sample name: GFPMYCneg_2G
Gene expression data from MYC negative GC B cell subpopulation, paired to 1G

Sample name: GFPMYCpos_7G
Gene expression data from MYC positive GC B cell subpopulation, paired to 8G

Sample name: GFPMYCpos_11G
Gene expression data from MYC positive GC B cell subpopulation, paired to 12G

Sample name: GFPMYCpos_9G
Gene expression data from MYC positive GC B cell subpopulation, paired to 10G

Sample name: GFPMYCpos_1G
Gene expression data from MYC positive GC B cell subpopulation, paired to 2G

Treatment: 3.5 mM HOCl in medium

Treated with 10uM Motexafin gadolinium and 50uM Zinc for 4 hrs -- replicate #1

Untreated LNCaP cells not stimulated with DHT, biological replicate 1

WT versus knock-out HSCs purified from 6-8 week old mice; KO allele described in Pub Med ID:  22013525

HSCss were extracted from bone marrow and purified using flow cytometry for KSL (lack of lineage marker expression (Lin-) and postive expression for c-Kit and Sca-1), expression of CD150 and included in the side population (Hoechst dye exclusion)

TP16;CCN1.2R;Unaffected;-N/A;37;40;MALE;None;**Note this sample has a Biological replicate- Blood was taken from this patient on two separate occasions and two different transformed lymphocytes were arrayed. The matching sample is CCN1.2**

Adult male mice, age 8-16 weeks old, 129/Black Swiss background were used. Mice are heterozygous for the Na,K-ATPase alpha 1 isoform. Hearts were removed and immediatedly homogenized in Trizol using the procedure by Molecular Research Center (Cincinnati, Ohio) with an additional phenol-chloroform step in the total RNA isolation. A pool of 5 hearts was used in the RNA isolation.

Adult male mice, age 8-16 weeks old, 129/Black Swiss background were used. Mice are wild-type. Hearts were removed and immediatedly homogenized in Trizol using the procedure by Molecular Research Center (Cincinnati, Ohio) with an additional phenol-chloroform step in the total RNA isolation. A pool of 5 hearts was used in the RNA isolation.

/Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual. 2001. Affymetrix).

/Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

Following fragmentation, cRNA was hybridized on Affymetrix Human Gene 1.0 ST array

Gene expression data from TK6 cells treated with cadmium chloride

Gene expression data from TK6 cells treated with inorganic arsenic

RNA pool from MPH-treated LCLs generated from unaffected controls

unaffected;MPH;EBV-transformed lymphoblastoid cell lines;LCLs from 6 unaffected controls

Gene expression data from ovarioectomized mouse aortae 7-8 days after implantation with estrogen (E2) or placebo pellets.

Gene expression data from HEB-deficient double-positive thymocytes

HEB-deficient double positive cells sorted from thymus of 8 week old mouse

Gene expression data from E2A-deficient HEB-deficient double-positive thymocytes

E2A and HEB deficient double positive cells sorted from thymus of 8 week old mouse

RelA (NF-kB subunit) siRNA knocked-down cells, 4 hrs after NCS treatment, replicate C

p53 siRNA knocked-down cells, 4 hrs after NCS treatment, replicate C

p53 siRNA knocked-down cells, 4 hrs after NCS treatment, replicate A

p53 siRNA knocked-down cells, 4 hrs after NCS treatment, replicate B

a time series of ConA injections was administered and  20 mg/kg ConA was injected through the mouse caudal vein at one of 4 time points (0 hr, 1 hr, 3 hr, 6 hr),here is  hepatic gene expression at "1 hr" (rep1)

a time series of ConA injections was administered and  20 mg/kg ConA was injected through the mouse caudal vein at one of 4 time points (0 hr, 1 hr, 3 hr, 6 hr),here is  hepatic gene expression at "1 hr" (rep2)

a time series of ConA injections was administered and  20 mg/kg ConA was injected through the mouse caudal vein at one of 4 time points (0 hr, 1 hr, 3 hr, 6 hr),here is  hepatic gene expression at "1hr" (rep3)

a time series of ConA injections was administered and  20 mg/kg ConA was injected through the mouse caudal vein at one of 4 time points (0 hr, 1 hr, 3 hr, 6 hr),here is  hepatic gene expression at "3 hr" (rep1)

2-4 month old male C57BL6 mice were injected once hourly for four hours with caerulein and sacrificed at the four hour point following which total RNA was isolated using guanadimium isothiocianate

Approximately 10 µg of total RNA was processed to produce fluorescently labeled cRNA targets.

2-4 month old male C57BL6 mice were injected once hourly for four hours with caerulein and sacrificed at the four hour point following which total RNA was isolated using guanadinium isothiocianate

Approximately 10 µg of total RNA was processed to produce fluorescently cRNA targets.

2-4 month old male C57BL6 mice were injected once hourly for four hours with saline and sacrificed at the four hour point following which total RNA was isolated using guanadinium isothiocianate

Approximately 10µg of total RNA was processed to produce fluorescently labeled cRNA targets.

2-4 month old male Mist1KO mice were injected once hourly for four hours with saline and sacrificed at the four hour point following which total RNA was isolated using guanadinium isothiocianate

Approximately10 µg of total RNA was processed to produce fluorescently labeled cRNA targets.

Gene expression data from glomeruli of patient with Nephrosclerosis.

peripheral blood from 8-10 E12.5 embryos;Cbfb+/+;Cbfb+/- x Cbfb+/-

gene expression data from pregnant mouse cervix treated with EtOH

Male mice were sacrificed in the non-fasted state by isoflurane overdose, shaved with electric clippers, and whole dorsal skin removed and flash frozen in liquid nitrogen

Male Lox and SKO mice on a C57BL/6J background were weaned at 3 weeks of age and maintained on a standard rodent diet (Purina Formulab 5008) until 8-9 weeks of age

All AFX 430 2.0 gene chips scanned on AFX GC3000 G7 scanner using Command console. Data extracted from scanned images using Expression console. All recommended AFX control parameters ok.

Expression measurements were pre-processed to provide background correction, normalization and log base 2 transformation using RMA (Robust Multi-array Average) (Irizarry RA, et al. Biostatistics 4: 249-264, 2003). We used two analytical approaches to generate lists of differentially expressed probe sets, loosely referred to as genes. First, we calculated an un-moderated t-statistic for every probe set by applying Welch’s t-test. The resulting p-values were used to calculate q-values, which account for multiple tests and provide thresholds so that lists can be generated for a target false discovery rate (FDR) (Storey JD, and Tibshirani R. Proc Natl Acad Sci U S A 100: 9440-9445, 2003). Using this method, we targeted a FDR of 5% and probe sets with q-values below 0.05 are considered to be of interest. We also applied EBarrays (Kendziorski CM, et al. Stat Med 22: 3899-3914, 2003; Newton MA, et al. J Comput Biol 8: 37-52, 2001), which along with RMA is implemented in R, a publicly available statistical analysis environment (R. Development Core Team. R: A language and environment for statistical computing. http://www.r-project.org. Vienna, Austria: R Foundation for Statistical Computing, 2005) and available at Bioconductor (Gentleman RC, et al Genome Biol 5: R80, 2004.). EBarrays is an empirical Bayes approach which models the probability distribution of a set of expression measurements (Kendziorski CM, et al. Stat Med 22: 3899-3914, 2003, 50). It accounts generally for differences among probe sets in their true underlying expression levels, measurement fluctuations and distinct expression patterns for a given probe set among conditions (Kendziorski CM, et al. Stat Med 22: 3899-3914, 2003). An expression pattern is an arrangement of the true underlying intensities (u1) in each condition. The number of patterns possible depends on the number of conditions from which the expression measurements were obtained. For example, when measurements are taken from two conditions, two patterns of expression are possible: equivalent expression (EE; u1 = u2) and differential expression (DE; u1 ≠ u2). Since we do not know a priori which probe sets are in which patterns, the marginal distribution of the data is a mixture over the possible patterns with model parameters determined by the full set of array data. In this way, the approach utilizes information across a set of arrays to optimize model fit and is thus more efficient than a number of methods that make inferences one probe set at a time (Kendziorski CM, et al. Stat Med 22: 3899-3914, 2003). The approach also naturally controls for both type I and type II errors (Kendziorski CM, et al. Stat Med 22: 3899-3914, 2003). The fitted model parameters provide information on the number of probe sets expected in each expression pattern. Furthermore, the fitted model is used to assign posterior probability distributions to every probe set. Each probe set specific distribution gives the posterior probability of that probe set's individual expression pattern. The posterior expected FDR is controlled by thresholding the posterior probabilities. Two approaches were used as discussed in (Newton MA, et al. Detecting differential gene expression with a semiparametric hierarchical mixture method. Biostatistics 5: 155-176, 2004.). The most conservative approach to control the FDR at 5%, for example, is to only consider probe sets with specific posterior probability of EE less than 0.05 (hard threshold). We also report results from the less conservative approach that determines the exact threshold required (soft threshold) so that the average posterior probability of EE for all probe sets on a list is less than 0.05.

RNA was extracted from skin with TRI reagent (Molecular Research Center), DNase treated with Turbo Dnase (Ambion), and re-extraced with TRI reagent to inactivate Dnase

Hybridization cocktail prepared acording to the protocols and procedures in the AFX Expression Analysis Technical Manual. 10 ug of aRNA applied to AFX array and hybridized overnight at 45C for 16 hours in AFX 640 Hybridization oven. AFX 430 2.0 gene chips were post processed on the AFX 450 Fluidics Station according to all AFX protocols and procedures defined for the array (EukGE_WS2v5_450)

Samples were labeled using the Ambion MessageAMP Biotin II-Enhanced IVT kit using 1.5 ug of RNA for all samples and processed according to kit instruction manual. 14 hour IVT reaction at 37C.

male;C57BL/6J;Scd1flox/flox (Lox) control;Dorsal skin;8-9 wks old

MCF-7;human breast adenocarcinoma cells;1 nM final conc. E2 + 1 uM 27-Hydroxycholesterol (27HC) for 24hr;2

CD4+CD8+ double positive thymocytes were treated with medium and 0.1% PBS for 3 hours

Gene expression data from  primary HCL cell of  patient D treated with DMSO for 48h
ET29

Cells were seeded at a density of 1x106 per 10 cm Petri dish 24 hours before treatment. Cells were then incubated with 8 ml of a freshly prepared cisplatin solution of 50 µM at 37 ºC for 1 hour. At the end of the 1-hour incubation, the media was removed, cells washed twice in warm PBS, and incubated in drug-free media at 37 ºC for 10 hours.

The SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen, Paisley, UK) was used to convert the mRNA in the T-RNA samples into ds-cDNA by reverse transcription with an oligo-dT primer. Initially, first strand cDNA was formed in a reaction containing 15 g of T-RNA and 100 pmol of T7-oligo (dT) primer (5’ – GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG - (dT)24 – 3’) (Proligo, France). This mixture was incubated at 70 °C for 10 minutes and quickly chilled on ice for 5 minutes, after which the following reagents were added: first strand reaction buffer [50 mM Tris-HCl (pH 8.3) 75 mM KCl, 3 mM MgCl2], 10 mM dithiothreitol (DTT) and 500 µM each dNTP. Tubes were placed at 42 °C for 2 minutes to equilibrate the temperature prior to the addition of Superscript II reverse transcriptase (400 U) and further incubated for 1 hour at 42 °C. The second strand cDNA synthesis was performed by adding, to the solution containing the first strand cDNA, 200 µM each dNTP, 10 U of E. coli DNA ligase, 40 U of E. coli DNA polymerase I, 2 U of E. coli RNase H and second strand reaction buffer [20 mM Tris-HCl (pH 6.9), 90 mM KCl, 4.6 MgCl2, 0.15 mM beta–NAD+, 10 mM (NH4)2SO4]. The reaction was incubated for 2 hours at 16 °C. Following this incubation, 10 U of T4 DNA polymerase were added and incubated for 5 minutes at 16 °C. The reaction was stopped by the addition of 31.25 mM EDTA. The resulting ds-cDNA was extracted against an equal volume of phenol:chloroform:isoamyl alcohol (25:24:1) (Sigma, Poole, UK) using phase lock gels (Eppendorf, Cambridge, UK) and centrifuging at 12,000 × g for 2 minutes. The ds-cDNA was then precipitated from the aqueous phase by the addition of 0.5 volumes of 7.5 M ammonium acetate (Sigma, Poole, UK) and 2.5 volumes of absolute ethanol (Sigma, Poole, UK), using Pellet Paint (Novagen, Nottingham, UK) as a carrier. Pellet was washed in ethanol, dried and resuspended in an appropriate volume of RNase/DNase-free water (Sigma, Poole, UK).

Quadriceps muscle;P.q.9;Pompe;rhGAA;12 Weeks;F;1.2m;Walking;Decreased;Positive Clinical Outcome

Quadriceps muscle;P.q.9;Pompe;rhGAA;52 Weeks;F;1.2m;Walking;Decreased;Positive Clinical Outcome

Quadriceps muscle;P.q.8;Pompe;rhGAA;52 Weeks;M;6.4m;Standing;Decreased;Positive Clinical Outcome

Quadriceps muscle;P.q.9;Pompe;rhGAA;00 Weeks;F;1.2m;Walking;Decreased;Positive Clinical Outcome

Quadriceps muscle;P.q.10;Pompe;rhGAA;52 Weeks;M;6.9m;Walking;Decreased;Positive Clinical Outcome

Quadriceps muscle;P.q.11;Pompe;rhGAA;00 Weeks;F;2.1m;No gains;Stable;Poor Clinical Outcome

Quadriceps muscle;P.q.10;Pompe;rhGAA;00 Weeks;M;6.9m;Walking;Decreased;Positive Clinical Outcome

Quadriceps muscle;P.q.10;Pompe;rhGAA;12 Weeks;M;6.9m;Walking;Decreased;Positive Clinical Outcome

Quadriceps muscle;P.q.11;Pompe;rhGAA;12 Weeks;F;2.1m;No gains;Stable;Poor Clinical Outcome

gene expression was measured 24 hours + induction of Cyr61 protein in glioma cells

whole blood;Cutaneous psoriasis without arthritis;Female;3;8.89390828199863;38;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Cutaneous psoriasis without arthritis;Male;2;12.6235455167693;37;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Cutaneous psoriasis without arthritis;Male;1;2.8104038329911;26;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Cutaneous psoriasis without arthritis;Male;2;0.770020533880903;39;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Cutaneous psoriasis without arthritis;Male;3;16.9158110882957;18;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Cutaneous psoriasis without arthritis;Male;1;17.7488021902806;21;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Psoriatic arthritis;Female;2;31.0;23;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Psoriatic arthritis;Female;1;27.0;24;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Cutaneous psoriasis without arthritis;Male;4;18.009582477755;20;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Cutaneous psoriasis without arthritis;Male;4;44.2600958247776;8;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

KO - knock-out Treated - 0.5 hrs - repeat 2 - Cy3 - mAdbID:62530

KO - knock-out Treated - 0.5 hrs - repeat 1 - Cy3 - mAdbID:62496

Synovial biopsies (n = 4 to 6), obtained by needle arthroscopy from the swollen knee of a patient with rheumatoid arthritis

SAM630145;C57BL/6;spr881;IL17RC Knock out;pooled mouse reference RNA

We performed transcriptomic microarrays analysis on control HMEC-TR cells (transfected by scramble si-RNA) and cells inactivated for TIF1γ or Smad4 (SiRNA strategy) and treated or not with TGFβ1 for 24 hours. Inactivation of TIF1γ and Smad4 expression was checked by Western Blot.

Human mammary epithelial cells (HMEC-TR) kindly provided by RA Weinberg have been previously described (Elenbaas B. et al. 2001 and Morel A.P. et al. 2008). These cells were cultured in 1:1 Dulbecco’s Modified Eagle’s Medium DMEM/HAMF12 medium (Invitrogen) complemented with 10% FBS (Cambrex) and 100 U/ml penicillin-streptomycin (Invitrogen), 2 mM L glutamine (Invitrogen), 10 ng/ml human epidermal growth factor (hEGF, PromoCell), 0.5 mg/ml hydrocortisone (Sigma) and 10 mg/ml insulin (Sigma).

The Arrays were scanned using the Gene Chip Scanner 3000. Then CEL files were generated using the Affymetrix GeneChip Operating Software (GCOS)

CHP files were processed using MAS 5.0 analysis algorithm with Affymetrix GeneChip Operating Software (GCOS)

Total RNA from the transfected HMEC-TR cells was isolated by Trizol and miRNeasy Mini extraction kit (Qiagen). RNA quality was assessed by an Agilent Bioanalyzer (model 2100; Agilent Technologies).

Human mammary epithelial cells infected with retrovirus carrying hTERT and the oncogenic allele of H-Ras, H-RasV12 described in (Elenbaas B, Spirio L, Koerner F, Fleming MD, Zimonjic DB, Donaher JL, Popescu NC, Hahn WC, and Weinberg RA (2001) Human breast cancer cells generated by oncogenic transformation of primary mammary epithelial cells. Genes Dev 15: 50-65)

Mtb infected mouse lungs treated with PZA-63 days post infection

Mixed; mostly C57BL/6 with some 129S/SvImJ (from CJ7 ES cells).;Eed KO;9-day old;bone marrow;long-term hematopoietic stem cells (LT-HSC);Lin-Sca1+CD48-CD150+

After washing and staining, the test chip is placed in the Affymetrix GeneChip array scanner and image data is captured and converted to
numerical output using the Microarray Analysis Suite version 4.0.

Acquired experimental data from the chip is analyzed using the GeneChip Microarray Suite version 4.0. For comparison between two chips, the 'baseline chip' intensity values are measured and
normalized to the average signal intensity. Intensity values of the 'experimental chip' are then compared to the baseline chip and a 'difference change' is calculated. Alternatively, hybridization signals may be normalized using the specific expression signals from the set of bacterial control transcripts. The output of the GeneChip software provides a qualitative call: 'increase', 'marginal increase', 'no change',
'decrease', and 'marginal decrease' as well as discrete numerical metrics used to make the call. Expression elements may be ranked based on absolute level of expression or relative change in
expression between a two chip comparison. All numerical data may be exported to a Microsoft Excel spreadsheet for further analysis. Expression elements are identified by a GenBank accession number
and the GeneChip analysis software allows for immediate hyperlink to the GenBank entry for full sequence annotation.

Tissue homogenization in RNAzol B, followed by organic clean-up and isopropanol precipitation.

Fifteen micrograms of fragmented cRNA is delivered to the core facility. A hybridization 'cocktail' is constructed containing the cRNA, 50 pM of control oligonucleotide B2 (Geneset), 1X control cRNA mix, 0.1 mg/ml herring sperm DNA, and 1X MES hybridization buffer in a volume of 300 ml, The control oligonucleotide B2 (5'-biotin:GTCGTCAAGATGCTACCGTTCAGGA-3') is designed to hybridize to structural features on the chip to allow for proper scanning and grid alignment. The control cRNA mix is provided by the core facility and is composed of a second set of four, biotinylated, in vitro antisense transcripts of cDNAs encoding the E. coli biotin synthesis genes bioB, bioC, bioD, and the P1 bacteriophage cre recombinase gene. Probes corresponding to these bacterial transcripts are also represented on all Affymetrix GeneChips (including test chips). Each synthetic transcript is quantitated and represented at a copy number of 2x108 to 2x1010, corresponding roughly to the expected dynamic range of detection for the GeneChip. This set of control cRNAs allows for the monitoring of hybridization, washing, and staining conditions and also provides a second set of reference samples for normalizing between experiments. One hundred microliters of the hybridization cocktail is heated to 95°C, 45°C, and then applied to the a Test2 GeneChip array. The remainder of the cocktail is stored at -70°C and the test chip is hybridized at 45°C for 16 hours. After hybridization, the hybridization cocktail is removed from the chip and stored at -70°C. The chip is immediately placed in the Affymetrix GeneChip Fluidics Station 400 and washed using the preprogrammed steps "mini_euk2". This wash program involves a low stringency wash, high stringency wash, steptavidin/phycoerythrin stain, low stringency wash, anti-streptavidin antibody stain, a secondsteptavidin/phycoerythrin stain, and a final low stringency wash. If the labeled cRNA target passes all metrics of the Test2 chip, it is again heated to 95°C, 45°C,and hybridized to the GeneChip of interest. Hybridization, washing, staining, and scanning is repeated
as described above except the automated fluids program "euk2" is used. The labeled cRNA target maybe repeatedly hybridized on 4-6 chips.

At least ten micrograms of total RNA is isolated from indicated tissues or cell lines using Trizol reagent (Life Technologies) following the supplier's protocol. RNA is then treated with RNase-free, DNase (Life Technologies) and further purified using the RNeasy total RNA clean up protocol (Qiagen). Purified, DNA-free RNA is assessed for integrity by formaldehyde / agarose gel electrophoresis and quantitated by 260 nm absorbence. An aliquot of cRNA control mix is added to ten micrograms of purified total RNA. The cRNA control mix is provided by the core facility and is composed of a set of four, in vitro transcripts generated
by T3 RNA polymerase. These polyadenylated transcripts encode the B. subtilis genes thr, trp, phe, and lys. Probes corresponding to these bacterial transcripts are represented on all Affymetrix GeneChips
(including test chips). Each synthetic transcript is quantitated and represented at a copy number of 5x106 to 5x108, corresponding roughly to the expected dynamic range of detection for the GeneChip
system. This set of control transcripts allows for the monitoring of cDNA synthesis and in vitro transcription of biotinylated targets and also provides a reference sample for normalizing between
experiments. RNA is converted to double stranded cDNA using the SuperScript Choice system (Life Technologies) following the supplier's protocol except that an HPLC-purified T7-dT24 primer (Geneset) is
utilized for first strand synthesis. After synthesis, the double stranded cDNA is purified by phenol/chloroform extraction and ethanol precipitation. The purified cDNA is used to generate the biotinylated cRNA target using the Bioarray High Yield RNA transcript labeling kit (Enzo) and following the supplier's protocol. The labeled cRNA is then
purified using the RNeasy total RNA clean up protocol (Qiagen) and quantitated by 260nm absorbence. Twenty micrograms of cRNA is fragmented by heating at 94°C for 35 minutes in fragmentation
buffer (40 mM Tris-acetate pH 8.1; 125 mM KOAc; 30 mM MgOAc). An aliquot of fragmented and nfragmented cRNA is analyzed by formaldehyde/agarose gel electrophoresis to ensure appropriate size
distribution (average size: 700 bp unfragmented and 100 bp after fragmentation).

For the test chip, the levels of bioB, bioC, bioD, cre, phe, trp, lys, and thr will be assessed. All transcripts should be called 'present' and the average difference values of each should be in approximate
proportion to their absolute copy number. Successful signal from bioB, bioC, bioD, and cre, but suboptimal signal from phe, trp, lys, and thr suggests that cDNA synthesis and in vitro transcription was
inefficient. Poor signal from all controls suggests a hybridization, washing, or staining failure. Normally, the bioB hybridization control (representing 2x108 transcript copies) will be at or slightly above the level of background noise. The relative expression level of GAPDH and b-actin will also be assessed. The test chip contains probes directed at the 5' and 3' end of these genes for human, mouse, and rat species.
In general, the signals from 5' directed probe sets should be no lower than 50% of those from 3' directed probe sets. A 5'/3' ratio of less than 0.5 suggests that cDNA synthesis may have been less than efficient.

Gene expression data from Human hepatoma cell line (HepG2) transduced with recombinant Adenovirus expressing GPI-PLD and cultured for 6 hours. Targets were produced using standard Affymetrix procedures from 10ug of total RNA.

HEK293 human embryonic kidney cell line;MIF depletion, siRNA-mediated;siRNA concentration = 50pmol/ml

For Th17 differentiation: 2ng/mL rhTGF-β1 (Miltenyi Biotec), 25ng/mL rmIl-6 (Miltenyi Biotec), 20ng/ml rmIl-23 (Miltenyi Biotec), and 20ng/ml rmIL-β1 (Miltenyi Biotec). After differentiation, the cells were then rested for 72 h and restimulated with IL-23

Cd4+ T cells were purified from spleen and lymph nodes using anti-CD4 microbeads (Miltenyi Biotech) then stained in PBS with 1% FCS for 20 min at room temperature with anti-Cd4-PerCP, anti-Cd62l-APC, and anti-Cd44-PE antibodies (all Biolegend, CA). Naïve Cd4+ Cd62lhigh Cd44low T cells were sorted using the BD FACSAria cell sorter.  Sorted cells were activated with plate bound anti-Cd3 (2μg/ml) and anti-Cd28 (2μg/ml) in the presence of cytokines.

Expression data was preprocessed using the RMA algorithm followed by quantile normalization, with the parameters in the ExpressionFileCreator module of the GenePattern suite set to default

Extraction of total RNA was performed according to the RNeasy Mini Kit (Qiagen) manufacturer's instructions.

Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse 430 2.0 microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (3' IVT Express Kit, Affymetrix).

Study of rat femur fracture healing in young rats (6 weeks old at fracture) at 4 weeks after fracture.  RNA from two rats were pooled for each array.

Study of rat femur fracture healing in young rats (6 weeks old at fracture) at 6 weeks after fracture.  RNA from two rats were pooled for each array.

Study of rat femur fracture healing in adult rats (26 weeks old at fracture) for intact bone collected on the day of fracture.  RNA for two rats was pooled for each array.

Study of rat femur fracture healing in adult rats (26 weeks old at fracture) at 3 days after fracture.  RNA for two rats were pooled for each array.

Study of rat femur fracture healing in young rats (6 weeks old at fracture) for intact bone at the time of fracture.  RNA from two rats were pooled for each array.

Study of rat femur fracture healing in young rats (6 weeks old at fracture) at 3 days after fracture.  RNA from two rats were pooled for each array.

Study of rat femur fracture healing in young rats (6 weeks old at fracture) at 1 week after fracture.  RNA from two rats were pooled for each array.

Study of rat femur fracture healing in young rats (6 weeks old at fracture) at 2 weeks after fracture.  RNA from two rats were pooled for each array.

Study of rat femur fracture healing in adult rats (26 weeks old at fracture) at 1 week after fracture.  RNA from two rats was pooled for each array.

Gene expression data from MigR1 transduced CUTLL1 cells treated with compound E for 3days

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Tibolone treated. Patient 6.

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Tibolone treated. Patient 6, replicate (patient 6 has been arrayed twice).

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Tibolone treated. Patient 1.

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Estradiol + medroxyprogesterone acetate treated. Patient 29.

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Estradiol + medroxyprogesterone acetate treated. Patient 25.

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Tibolone treated. Patient 11.

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Tibolone treated. Patient 11, replicate (patient 11 has been arrayed twice).

wild-type mouse forebrain

knock-in mouse cerebellum
Treatment, type=time_course, measurement=11.0 weeks

Lesional skin from imiquimod-treated mouse, biological replicate 1

Lesional skin from imiquimod-treated mouse, biological replicate 2

Lesional skin from imiquimod-treated mouse, biological replicate 3

The animals were raised and cared for in accordance with the guidelines established by the Innsbruck Medical University, Austria

The raw signal intensities were proprocessed in R (version 2.9.1) using Bioconductor's gcrma package (version 2.16.0).

Liver samples from 6 week old p14 KO and control mice (gender matched) were homogenized in 1ml of Trizol Reagent using a tissue hand-homogenizer (5 ml, Unilab Politakis OHG). The extraction of total RNA was performed according to the manufacturer's directions, and the RNA was subsequently purified by passage through Rneasy mini-columns (QIAGEN, Valencia, CA).

20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix Mouse Genome 430 2.0 GeneChips.

1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.

Expression profile of liver sample from p14 KO mouse, biological replicate 1.

Six week old male C57BL/6 mouse with conditional liver p14 knock out.

Expression profile of liver sample from p14 KO mouse, biological replicate 2.

Expression profile of liver sample from control mouse, biological replicate 2.

Expression profile of liver sample from control mouse, biological replicate 3.

Expression profile of liver sample from p14 KO mouse, biological replicate 3.

Expression profile of liver sample from control mouse, biological replicate 1.

male, 7.5 months old, floxed myostatin genes, CAGG-CreER transgene, C57BL/6 background

Total RNA was isolated and purified using RNeasy Mini Columns and DNase On-Column digestion (Qiagen, Valencia, CA) according to the manufacturer’s specifications.  RNA quality was assessed by OD reading and 1% formaldehyde agarose gel

gene expression data from the Superior Frontal Gyrus of 2y-old normal girl, RNA labeled and hybridized Dec. 2001

Superior Frontal Gyrus from a 2year-old girl not suffering from Rett Syndrome and therefore considered as a normal subject.

Total RNA from each sample was isolated and purified using RNeasy Mini Columns and DNase On-Column digestion (Qiagen, Valencia, CA) according to the manufacturer’s specifications. RNA quality was assessed by OD reading and 1% formaldehyde agarose gel. Because there was not enough RNA material, samples from the 2 and 4 year-old brains were pooled and used as a single sample.

gene expression data from the Superior Frontal Gyrus of pooled RNA from a 2 and a 4 year-old girl both suffering from Rett Syndrome (RTT) and labeled and hybridized Dec. 2001

Superior Frontal Gyrus from 2 and 4 year-old girls suffering from Rett Syndrome.

gene expression data from the Superior Frontal Gyrus of 5 year-old normal girl, RNA labeled and hybridized Nov. 2001

Superior Frontal Gyrus from a 5 year-old girl not suffering from Rett Syndrome and therefore considered as a normal subject.

Total RNA from each sample was isolated and purified using RNeasy Mini Columns and DNase On-Column digestion (Qiagen, Valencia, CA) according to the manufacturer’s specifications. RNA quality was assessed by OD reading and 1% formaldehyde agarose gel.

gene expression data from brain area 8/9 of a 6 year-old girl suffering from from Rett Syndrome (RTT) 6yr, RNA labeled and hybridized Aug. 2001

Superior Frontal Gyrus from a 6 year-old girl suffering from Rett Syndrome.

non-transgenic;In the non-transgenic control animals no abnormalities in lung tissue was detected with the exception of a single animal which showed a slight focal interstitial mononuclear cell infiltration.

Female;50;PBMC;Patient 999;BETAFERON;24 month of BETAFERON;multiple sclerosis;NAB+

Female;50;PBMC;Patient 999;BETAFERON;12 month of BETAFERON;multiple sclerosis;NAB+

Female;50;PBMC;Patient 999;BETAFERON;3 month of BETAFERON;multiple sclerosis;NAB+

Female;50;PBMC;Patient 999;baseline;baseline;multiple sclerosis;NAB+

Female;50;PBMC;Patient 998;BETAFERON;24 month of BETAFERON;multiple sclerosis;NAB+

Female;50;PBMC;Patient 998;BETAFERON;12 month of BETAFERON;multiple sclerosis;NAB+

Female;50;PBMC;Patient 998;BETAFERON;3 month of BETAFERON;multiple sclerosis;NAB+

Female;50;PBMC;Patient 998;baseline;baseline;multiple sclerosis;NAB+

Female;33;PBMC;Patient 108;BETAFERON;3 month of BETAFERON;multiple sclerosis;NAB-

Female;33;PBMC;Patient 108;baseline;baseline;multiple sclerosis;NAB-

Day: 12; Drug: Methamphetamine; Phase: Drug treatment; Replicate: 3

samples were collected in parallel in 4 biological independent replicates

Chips were processed on an Affymetrix GeneChip Fluidics Station 450 and Scanner 3000

Data were analyzed using the oligo (v1.18.1) R/Biocondutor package and normalized using the RMA algorithm

The labeled ssDNA was hybridized to Affymetrix Mouse Gene 1.0 ST Array (Affymetrix)

Sense ssDNA was fragmented and labeled using the GeneChip® WT Terminal Labeling and Controls Kit.

Gene expression data from mESCs stably expressing a control shRNA

Gene expression data from mESC stably expressing shRNA targeting Kdm2b

rat hippocampus (combined dorsal and ventral aspects), young control, subject 4

230;Asacol 1.6g/ day;12/27/57;F;CAUCASIAN;3/12/02;12/3/03;FALSE;FALSE;FALSE;NO;FALSE;FALSE;1/25/05;1;0;0;0;0;0;0;0;FALSE;0;BOTH;unknown;unknown;unknown;unknown;1/25/05;BOTH;unknown;unknown;unknown;unknown;3/7/05;DISEASE IN REMISSION;never;unknown;? MS never proven;UC;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

rat hippocampus (combined dorsal and ventral aspects), young control, subject 1

10 male Fischer rats, aged 14 months were trained sequentially on two tasks, SWM and OMT; hippocampal tissue collected 24 hours after a 7 day training/testing sequence

Following washing and staining, the BeadChips were imaged using the Illumina BeadArray Reader to measure fluorescence intensity at each probe.

BeadChip data files are analyzed with Illumina’s GenomeStudio gene expression module (V1.6.0)

Total RNA from highly purified splenic CD11b+Gr-1high cells from the different experimental groups was quantified by a ND-1000 spectrophotometer (NanoDrop, Thermo Scientific) and evaluated for degradation using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Samples requirements were as follows: RIN >7, an OD 260:280 of 1.9-2.0, and an OD 260/230 >1.8.

The labeled probes were then mixed with hybridization reagents and hybridized overnight to the MouseWG-6 v2 BeadChips.

Initially, we converted 250-500 ng total RNA to cDNA, followed by in vitro transcription to generate biotin-labeled cRNA (Illumina TotalPrep RNA Amplification Kit, Ambion Inc., Austin, TX).

lymphoid;Splenic CD11b+Gr-1 cells;tumor bearing;wild type w/ AT-3 tumor;H-2b

female;1;42;Severe_8;33;94;Prednisolone 5mg od, Aminophylline 225mg bd,Seretide 500 2pbd,doxycycline, Tiotropium;CD4+ T-cells

male;1;32;Severe_3;98;113;prednisolone 15mg od,Seretide 500mcg 2pbd,Montelukast 10mg nocte,Ventolin prn,Phyllocontin 450mg bd,Flixonase od;CD4+ T-cells

female;1;21;Severe_2;105;101;Prednisolone 8mg - 1mg for 5wks(stopped 30/5/08),seretide 500mcg 1pbd,Singular 10mg bd,Phyllocontin 225mg am 450mg pm,Ventolin prn;CD4+ T-cells

female;1;55;Severe_1;82;105;Flixotide 500mcg 2pbd,Oxis 12 1pbd,Loratadine 1 tab od,Beconase 2pbd;CD4+ T-cells

female;1;45;Severe_7;71;105;Prednisolone 10mg od, Insulin S/C,Seretide 500mcg 2pbd, Metformin,Nexium, Flixonase,Tramacet,Calcium,Valsartan,Amitriptyline;CD4+ T-cells

female;1;54;Severe_6;55;69;Prednisolone 10-20mg od,Combivent neb 2-4/day,Cetirizine 10mg od,Terbutaline 500mcg od,Budesonide 400mcg 2pbd, Aminophylline SR 450mg bd, Formoterol 12mcg 2pbd;CD4+ T-cells

female;1;54;Severe_5;44;61;Prednisolone 5mg od,Montelukast 10mg od,Symbicort 400/12 2pbd,Omeprazole 20mg od,Uniphyllin 400mg bd,Bricanyl prn;CD4+ T-cells

female;1;55;Severe_4;65;81;Prednisolone 10mg od,Spiriva 18mcg od,Methotrexate 12.5mg wkly, Seretode 500 1pbd,Fosamax 70mg once/wk,Folic acid 5mg od,Calchichew,Cocodamol prn;CD4+ T-cells

Heart; HyperdynamicControl

Heart; embryonic_d14.5 wt heart

Heart; tg - hyperdynamic

Gene expression analysis of the kidney of mouse treated with 7 repeat daily doses of vancomycin at 50 mg/kg administered via the intravenous route (iv)

Kidney from mice treated with 7 daily iv injections of vancomycin at 50 mg/kg

H1299 lung cancer cells were grown in RPMI media supplemented with 10% (v/v) fetal calf serum. For siRNA experiments cells were infected with lentivirus which carry shRNAs specific for RBP2 and harvested for preparation of RNA after 72 hours.

H1299 lung cancer cells were grown in RPMI media supplemented with 10% (v/v) fetal calf serum.

Images were scanned using an Affymetrix GeneArray Scanner, using default oarameters. The resulting images were analyzed using Affymetrix Genechip Command Console 2.0 software.

Biotinylated cRNA were prepared from the purified total RNA equivalent to 250ng according to the standard Affymetrix protocol.

Cervical cancer, squamous cell carcinoma, microdissected, age 33, stage IIB, HPV 16

Cervical cancer, squamous cell carcinoma, microdissected, age 70, stage IIB, HPV negative

Cervical cancer, squamous cell carcinoma, microdissected, age 63, stage IB, HPV 16, HPV 18

Cervical cancer, squamous cell carcinoma, microdissected, age 36, stage IIB, HPV 16

cell line HCT-116, Ki-RAS-mutation, DNMT1 and 3B double knockout, U0126-treated;common reference sample

MCF7;Breast adenocarcinoma, estrogen receptor-positive;MTDH isoform KD

Notch3 knockout mouse cerebellar microvascular fragments, biological rep1

Notch3 knockout mouse cerebellar microvascular fragments, biological rep2

control mouse cerebellar microvascular fragments, biological rep1

Gene expression data from control mouse cerebellar microvascular fragments

control mouse cerebellar microvascular fragments, biological rep2

Notch3 knockout mouse cerebral microvascular fragments, biological rep2

Gene expression data from mouse Notch3 knockout cerebral microvascular fragments

C57BL/6;cerebral microvascular fragments;Notch3 knockout;2 months

Notch3 knockout mouse cerebral microvascular fragments, biological rep3

control mouse cerebellar microvascular fragments, biological rep3

Notch3 knockout mouse cerebral microvascular fragments, biological rep1

Sample name: TN-769-11R

Sample name: TN-879-11R

Sample name: TN-1109-11R

Agilent Feature Extraction file: Liver_Nrf1 Control_rep2.txt
Gene expression in the liver of  Nrf1 Control mice_rep2.

129/SVE;wild type;tibialis anterior;7-9 wk;129/SVE;50 eccentric contractions 12 hours

RNA isolated from spinal cord of human fetus aborted due to causes not related to Lethal Congenital Contracture Syndrome

HeLa cells at 50% confluence were infected with retroviral supernatants; at 24 hrs split and puromycin selected (1 ug/mL); at 72 hrs harvested at 50-80% confluence

The data were analyzed with GeneChip Operayting Software (GCOS) 1.4 using Affymetrix default analysis settings and global scaling to an arbitrary mean value of 800 as normalization method.

Following cRNA preparation and fragmentation according to Affymetrix protocol, cRNA was hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.

Gene expression data from HeLa cells 72 hours following transfection with anti-GFP retroviral siRNA expression vector, sample 2

Gene expression data from HeLa cells 72 hours following transfection with anti-GFP retroviral siRNA expression vector, sample 1

Gene expression data from HeLa cells 72 hours following transfection with anti-Drosha retroviral siRNA expression vector sidroshaC

Gene expression data from HeLa cells 72 hours following transfection with anti-Drosha retroviral siRNA expression vector sidroshaB

Animal # 3137

Animal #3137
Baseline uninfected sample

Animal # 3133
Three weeks post infection with SIV MAC251

7 Weeks post infection with SIV MAC 251

C57BL/6J female number 3, DNFB-treated allergic ear (#6_Wt-Tr-7)

C57BL/6J female number 3, 2 months old, whole ear tissue, DNFB-treated allergic ear

C57BL/6J female number 2, DNFB-treated allergic ear (#5_Wt-Tr-4)

C57BL/6J female number 2, 2 months old, whole ear tissue, DNFB-treated allergic ear

Quadriceps muscle;P.q.5;Pompe;rhGAA;00 Weeks;M;6.9m;Walking;Decreased;Positive Clinical Outcome

Quadriceps muscle;P.q.4;Pompe;rhGAA;52 Weeks;M;5.9m;No gains;Increased;Poor Clinical Outcome

Quadriceps muscle;P.q.4;Pompe;rhGAA;12 Weeks;M;5.9m;No gains;Increased;Poor Clinical Outcome

Quadriceps muscle;P.q.4;Pompe;rhGAA;00 Weeks;M;5.9m;No gains;Increased;Poor Clinical Outcome

Quadriceps muscle;P.q.3;Pompe;rhGAA;52 Weeks;F;5.7m;No gains;Decreased;Poor Clinical Outcome

Quadriceps muscle;P.q.3;Pompe;rhGAA;12 Weeks;F;5.7m;No gains;Decreased;Poor Clinical Outcome

Quadriceps muscle;P.q.3;Pompe;rhGAA;00 Weeks;F;5.7m;No gains;Decreased;Poor Clinical Outcome

Quadriceps muscle;P.q.2;Pompe;rhGAA;52 Weeks;M;7m;Walking;Stable;Positive Clinical Outcome

Quadriceps muscle;P.q.2;Pompe;rhGAA;12 Weeks;M;7m;Walking;Stable;Positive Clinical Outcome

Quadriceps muscle;P.q.2;Pompe;rhGAA;00 Weeks;M;7m;Walking;Stable;Positive Clinical Outcome

Gene expression data under ER stress from lymphoblastoid cells of twin 1712:1 treated with DMSO.

lymphoblastoid cell line;1712;GM14439;Twin number 1;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1712:1 treated with 500nM thapsigargin.

lymphoblastoid cell line;1712;GM14439;Twin number 1;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1712:2 treated with DMSO.

lymphoblastoid cell line;1712;GM14440;Twin number 2;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1712:2 treated with 500nM thapsigargin.

lymphoblastoid cell line;1712;GM14440;Twin number 2;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1717:1 treated with DMSO.

lymphoblastoid cell line;1717;GM14454;Twin number 1;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1717:1 treated with 500nM thapsigargin.

lymphoblastoid cell line;1717;GM14454;Twin number 1;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1717:2 treated with DMSO.

lymphoblastoid cell line;1717;GM14455;Twin number 2;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1717:2 treated with 500nM thapsigargin.

lymphoblastoid cell line;1717;GM14455;Twin number 2;thapsigargin;500nM;4 hours

heart of mouse subjected 4 week to chronic constant hypoxia (4A)

heart of female mouse subjected 4 week to chronic constant hypoxia.

heart of mouse subjected 1 week to chronic intermittent hypoxia (1B)

heart of female mouse subjected 1 week to chronic intermittent hypoxia.

heart of mouse subjected 4 week to chronic intermittent hypoxia (4A)

heart of female mouse subjected 4 week to chronic intermittent hypoxia.

heart of mouse subjected 4 week to chronic intermittent hypoxia (4B)

This experiment was an out file converted from rana. The original files were not provided to load this experiment in Oracle. Category and Subcategories were made by curators.
Lot batch = 0374-5k

Lot batch = 0376-5k

Gene expression data from mouse undifferentiated female ES cells PGK12.1 after 48h treatment of 100pmol of negative control siRNAs (Invitrogen Stealth control). Kdm6a single-RNAi experiment 4 in PGK12.1.

Derived from blastcysts from a 129 female crossed to a (129 X PGK)F1 male.;PGK12.1;ES cell;14-18

Mouse female ES cells PGK12.1 after single RNAi treatment of negative control siRNAs. Kdm6a RNAi experiment-4 in PGK12.1.

Gene expression data from mouse undifferentiated female ES cells PGK12.1 after 48h treatment of 100pmol of Kdm6a siRNAs. Kdm6a single-RNAi experiment 4 in PGK12.1.

Mouse female ES cells PGK12.1 after single RNAi treatment of Kdm6a siRNAs. Kdm6a RNAi experiment-4 in PGK12.1.

Gene expression data from mouse undifferentiated female ES cells PGK12.1 after double RNAi treatment of negative control siRNAs (Invitrogen Stealth control), in which after 48h of RNAi treatment 8 x105 cells were re-incubated with 400pmol of siRNAs in 100mm plates followed by a 24h culture before harvest. Kdm6a double-RNAi experiment-1 in PGK12.1.

Mouse female ES cells PGK12.1 after double RNAi treatment of negative control siRNAs. Kdm6a RNAi experiment-1 in PGK12.1.

Gene expression data from mouse undifferentiated female ES cells PGK12.1 after double RNAi treatment of Kdm6a siRNAs, in which after 48h of RNAi treatment 8 x105 cells were re-incubated with 400pmol of siRNAs in 100mm plates followed by a 24h culture before harvest. Kdm6a double-RNAi experiment-1 in PGK12.1.

Mouse female ES cells PGK12.1 after double RNAi treatment of Kdm6a siRNAs. Kdm6a RNAi experiment-1 in PGK12.1.

Gene expression data from mouse undifferentiated female ES cells PGK12.1 after double RNAi treatment of negative control siRNAs (Invitrogen Stealth control), in which after 48h of RNAi treatment 8 x105 cells were re-incubated with 400pmol of siRNAs in 100mm plates followed by a 24h culture before harvest. Kdm6a double-RNAi experiment-2 in PGK12.1.

Mouse female ES cells PGK12.1 after double RNAi treatment of negative control siRNAs. Kdm6a RNAi experiment-2 in PGK12.1.

Gene expression data from mouse undifferentiated female ES cells PGK12.1 after double RNAi treatment of Kdm6a siRNAs, in which after 48h of RNAi treatment 8 x105 cells were re-incubated with 400pmol of siRNAs in 100mm plates followed by a 24h culture before harvest. Kdm6a double-RNAi experiment-2 in PGK12.1.

Mouse female ES cells PGK12.1 after double RNAi treatment of Kdm6a siRNAs. Kdm6a RNAi experiment-2 in PGK12.1.

Gene expression data from mouse undifferentiated female ES cells PGK12.1 after 48h treatment of 100pmol of negative control siRNAs (Invitrogen Stealth control). Kdm6a single-RNAi experiment 3 in PGK12.1.

Mouse female ES cells PGK12.1 after single RNAi treatment of negative control siRNAs. Kdm6a RNAi experiment-3 in PGK12.1.

Gene expression data from mouse undifferentiated female ES cells PGK12.1 after 48h treatment of 100pmol of Kdm6a siRNAs. Kdm6a single-RNAi experiment 3 in PGK12.1.

Mouse female ES cells PGK12.1 after single RNAi treatment of Kdm6a siRNAs. Kdm6a RNAi experiment-3 in PGK12.1.

15B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

16B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; not assessable

13B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

14B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

one of four samples (two control, two WTAP knockdown). The experiment studied the effect of knockdown WTAP in HUVEC.

17B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

Agilent Feature Extraction file: Liver_Nrf1 Control_rep1.txt
Gene expression in the liver of  Nrf1 Control mice_rep1.

Agilent Feature Extraction file: Liver_Nrf1 CKO_rep1.txt
Gene expression in the liver of  Nrf1 CKO mice_rep1.

Agilent Feature Extraction file: Liver_Nrf1 Control_rep3.txt
Gene expression in the liver of  Nrf1 Control mice_rep3.

Agilent Feature Extraction file: Liver_Nrf1 CKO_rep3.txt
Gene expression in the liver of  Nrf1 CKO mice_rep3.

Agilent Feature Extraction file: Liver_Nrf1 CKO_rep2.txt
Gene expression in the liver of  Nrf1 CKO mice_rep2.

Embryonic cerebral cortex, Trnp1 knockdown, biological replicate 3

Embryonic cerebral cortex, Trnp1 knockdown, biological replicate 2

The study was performed with aortas isolated from three groups of mice (32-34 weeks of age), i.e. untreated APOE-deficient mice (APOE), APOE-deficient mice treated with vitamin E (2000 IU/kg diet) for 7 months (VitE), and B6 control mice (Cont).

The study was initiated with 4-6 week-old APOE-deficient mice on a B6 (C57BL/6J) background, and non-transgenic B6 controls. Mice had free access to food and water, and were fed a standard rodent chow containing 7 % fat and 0.15 % cholesterol (Ain 93-based diet). For atherosclerosis treatment, a group of APOE-deficient mice received treatment with the antioxidant vitamin E (2000 IU/kg diet) for 7 months. At an age of 32-34 weeks, aortas were isolated from three study groups (APOE-deficient, vitamin E-treated APOE-deficient, and nontransgenic B6 control mice), dissected free of fat, and immediately frozen in liquid nitrogen.

For hybridization, 15 µg of fragmented cRNA were incubated with the chip (Mouse Genome MG430 2.0 Array) in 200 µl of the hybrization solution in a Hybridization Oven 640 (Affymetrix) for 16 h at 45 °C. GeneChips were then washed and stained using the Affymetrix Fluidics Station 450 according to the GeneChip Expression Analysis Technical Manual.

Biotinylated cRNA was prepared according to the protocol of the manufacturer (Affymetrix; GeneChip Expression Analysis Technical Manual).

Gene expression data of aortas isolated from vitamin E-treated APOE-deficient mice

aorta;C57BL/6J;APOE-deficient;vitamin E;aortas from vitamin E-treated APOE-deficient mice

01-04-05 TP4_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2: These samples were previously hybridized on HG-U133A version 1 chips.  This experiment repeats these samples on HG-133A version 2 chips.  HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

01-04-05 TP5_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2: These samples were previously hybridized on HG-U133A version 1 chips.  This experiment repeats these samples on HG-133A version 2 chips.  HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16208.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16218.gif

01-04-05 TP12_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2: These samples were previously hybridized on HG-U133A version 1 chips.  This experiment repeats these samples on HG-133A version 2 chips.  HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16222.gif

Transgenic for alpha tropomyosin slow, snap frozen, diaphragm muscle,10 month age animal

Wild type, snap frozen, extensor digitorum longus muscle, 7month age animal

Wild type, snap frozen, extensor digitorum longus muscle, 10 month age animal

Transgenic for alpha tropomyosin slow, snap frozen, diaphragm muscle, 7month age animal

Transgenic for alpha tropomyosin slow, snap frozen, extensor digitorum longus muscle, 7month age animal

Transgenic, snap frozen, extensor digitorum longus muscle, 7 month age animal

in vitro Treatment: siHSF1_#2 (Sense 5’-rArCrArGrCUUrCrCrArCrGUrGUUrCrGrGTT-3’ Antisense 5’-UrCrGrArArCrArCrGUrGrGrArArGrCUrGUTT-3’), Treatment Repeat: 1, Units of Treatment Repeat: dose, Treatment Duration: 50, Units of Duration: hours, Treatment Time: -48, Units of Treatment Time: hrs, Vehicle for Chemical: Lipofectamine 2000, Amount of Vehicle: 0.44, Route of Exposure: transfection, Units of Amount of Vehicle: ul, Dose or Concentration: 3.3, Units of Dose or Concentration: nM

01-04-05 TP8_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2: These samples were previously hybridized on HG-U133A version 1 chips.  This experiment repeats these samples on HG-133A version 2 chips.  HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

01-04-05 TP9_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2: These samples were previously hybridized on HG-U133A version 1 chips.  This experiment repeats these samples on HG-133A version 2 chips.  HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16228.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16174.gif

Cervical cancer, squamous cell carcinoma, microdissected, stage IIB1, HPV 18, HPV 45

Brain (Dorsal Motor Nucleus of the Vagus)_Parkinson's disease_case1

Gene expression data from the dorsal motor nucleus of the vagus in a parkinson's disease subject.

#11;PD case #1;T-243;77;Female;Dorsal motor nucleus of the vagus

Brain (Dorsal Motor Nucleus of the Vagus)_Parkinson's disease subject_#1

#7;Control case #3;T-638;78;Male;Dorsal motor nucleus of the vagus

#9;Control case #4;T-779;76;Female;Dorsal motor nucleus of the vagus

#1;Control case #1;T-199;82;Female;Dorsal motor nucleus of the vagus

#3;Control case #2;T-346;84;Male;Dorsal motor nucleus of the vagus

The raw data was extracted using Illumina BeadStudio software without normalization. For normalization in GeneSpring, the threshold raw signal was set to 1.0 and the global normalization algorithm (percentile shift) was used with a percentile target of 75. This normalized data was used for statistical analysis, in which our IRF1-expressing cell lines were compared to control. There were 3 biological replicates for each condition. We used student's unpaired t-test to identify genes that had were significantly (p<0.05) changed in expression levels. We then selected a cutoff of 3.0 fold (upregulated) and presented the absolute fold change for this subset of genes in our publication.

Extraction of total cellular RNA was carried out with Qiagen Rneasy Kit according to manufactuer's recommendations.

Peripheral blood mononuclear cells;systemic JIA;GTE6;140min;White;Female;311

NCI-H460;human lung large cell carcinoma cells;radiation;2 hours

NCI-H460;human lung large cell carcinoma cells;cigarette smoke extract;2 hours

The α-tocopherol-supplemented group received a diet supplemented with 1000mg/kg of α-tocopherol since the middle age (15 months).

aT: 30-month-old a-tocopherol supplemented mouse

prefrontal cortex from adult APLP2 knock-out mouse with mixed genetic background

prefrontal cortex from adult APLP2 knock-out mouse with mixed genetic background;back-crossed to C57BL/6 for 1 generation;male

Cells transfected with Stealth HSF1 siRNA (5'CGGAUUCAGGGAAGCAGCUGGUGCA) and subsequently treated for 6 hours with vehicle 0.5% DMSO in DMEM Media containing 10% FBS

RKO cells transfected with HSF1 Stealth siRNA treated 6 h with DMSO 0.5%

Animal #3226

Animal #3220
Seven weeks post-Infection with SIV MAC251

control;male;52;n/a;Vila-Real;Hypertension, hypercholesterolemia;ever drinker

control;male;50;n/a;Lisboa;Hypercholesterolemia;ever smoker, ever drinker

IS patient;female;70;69;Vila-Real;Hypertension, hypercholesterolemia

IS patient;female;53;45;Porto;Hypertension, hypercholesterolemia;ever smoker, ever drinker

IS patient;female;65;65;Porto;Hypertension, hypercholesterolemia

Data were generated using mice of C57Bl/6 background. The ARR2PB-Cre transgenic mice were from Dr. Fen Wang at the Institute of Bioscience and Technology, Texas A&M Health Science Center (Jin et al., 2003, PMID:12949940). The Gt(ROSA)26Sortm1(Notch1)Dam/J (ICNf/f), and B6(Cg)-Gt(ROSA)26Sortm4(Ikbkb)Rsky/J mice were purchased from the Jackson Laboratory (Bar Harbor, ME).

Slide were scanned in an Agilent Microarray Scanner and the data were analyzed using Agilent Feature Extraction Software (v.9.1).

LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent and Bioconductor software was used.

Trizol extraction of total RNA was performed according to the manufacturer's instructions.  Microarray analysis was performed using 2.5 micrograms of total RNA.

The sample and reference probes were mixed with GEx hybridization buffer and blocking solution (Agilent, Santa Clara, CA) and denatured by a 2-minute incubation at 95 degC. Probes were hybridized to Agilent 4x44K Whole Mouse Genome arrays and rotating over night at 65 degC.

Complementary DNA (cDNA) reverse transcription and fluorescent labeling reactions were carried out using SuperScript Plus Direct cDNA Labeling system (Invitrogen, Carlsbad, CA).

C57Bl/6;: control ROSA(N1IC) mice (NICD wild-type);Stratagene, Universal Mouse Reference RNA Catalog #740100

gene expression data from  PPAR(alpha)-null mouse liver treated with DEHP

gene expression data from adipocytes overexpressing spliced XBP1

To induce type 1 diabetes, 65 mg/kg of streptozotocin (STZ) was injected i.p. into 10- to 16-week-old mice on 5 consecutive days while respective controls were mock-injected with citrate buffer. Animals were sacrificed 9-11 weeks after this treatment.

WT Expression Kit (Ambion) and the WT Terminal Labeling Kit (Affymetrix).

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_6-tu2

CD8 T cells isolated from tumor; transduced with shRNA targeting: Alk; Sample name: 6-tu2

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_6-tu3

CD8 T cells isolated from tumor; transduced with shRNA targeting: Alk; Sample name: 6-tu3

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_5-tu3

CD8 T cells isolated from tumor; transduced with shRNA targeting: Arhgap5; Sample name: 5-tu3

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_6-tu1

CD8 T cells isolated from tumor; transduced with shRNA targeting: Alk; Sample name: 6-tu1

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_5-tu2

CD8 T cells isolated from tumor; transduced with shRNA targeting: Arhgap5; Sample name: 5-tu2

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_4-tu2

CD8 T cells isolated from tumor; transduced with shRNA targeting: Ptpn2; Sample name: 4-tu2

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_4-tu3

CD8 T cells isolated from tumor; transduced with shRNA targeting: Ptpn2; Sample name: 4-tu3

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_3-tu3

CD8 T cells isolated from tumor; transduced with shRNA targeting: Egr2; Sample name: 3-tu3

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_4-tu1

CD8 T cells isolated from tumor; transduced with shRNA targeting: Ptpn2; Sample name: 4-tu1

Neonatal rat ventricular myocytes plated in uncoated dishes, incubated for 24 h with 10% serum and for next 48 h in serum-free medium

Affymetrix One Cycle Target and Labeling Protocol Hybridization and Staining, as described in Expression Analysis Technical Manual with following exception(s):  Hybridization volume increased to 250.0µL.  Fluidics Script: EukGE ws2v6

HL-60 cell line infected with scrambled control shRNA, biological rep2
Sample name: HL60_CTRL-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A02_596668.CEL

48 hour control, replicate 1

24 hour RA treated, replicate 4

48 hour RA treated, replicate 3

48 hour control, replicate 2

48 hour RA treated, replicate 1

48 hour control, replicate 4

48 hour RA treated, replicate 2

HL-60 cell line infected with GSK3B Construct 1 shRNA, biological rep1
Sample name: HL60_GSK3B_1-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A03_596652.CEL

HL-60 cell line infected with scrambled control shRNA, biological rep3
Sample name: HL60_CTRL-3
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_A07_596570.CEL

Osteoblasts were infected with adenovirus expressing Cre-recombinase or Green fluorescent protein 48 hours prior to inducing osteoblast differentiation.

Cultured for 7 days in the presence of 50ug/ml Ascorbic Acid and 10mM Beta-glycerol phosphate to induce osteoblast differentiation.

The hybridized Beadchips were scanned by Illumina BeadScan confocal scanner. cRNA synthesis, hybridization and scanning was performed by the Genome Sciences Laboratory in the Center for Public Health Genomics at the University of Virginia.

The expression values were log2 transformed and quantile normalized using the LumiR (v.2.14.2) R package. Matrix non-normalized.txt contains Illumina GenomeStudio (framework 2011.1) generated raw intensity values.

cRNA was quantified and normalized to 77 ng/μl, and then 850 ng was hybridized to Beadchips.

Biotin-labeled cRNA was synthesized by the total prep RNA amplification kit from Ambion (Austin, TX).

C57Bl/6;Lrp5-/-;primary calvarial osteoblasts;day 7 of differentiation

C57Bl/6;Lrp5+/+;primary calvarial osteoblasts;day 7 of differentiation

lymphoblastoid cell line from T21.01, one out of seven of insensitive group, 50*10e6 cells;Pooled RNA from a number of lymphoblastoid cell lines (with and without bleo treatment) and head and neck cancer cell lines.

Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56589.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56598.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56614.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56606.gif

lymphoblastoid cell line from T9.01, one out of seven of insensitive group, 50*10e6 cells;Pooled RNA from a number of lymphoblastoid cell lines (with and without bleo treatment) and head and neck cancer cell lines.

lymphoblastoid cell line from T5.02, one out of seven of sensitive group, 50*10e6 cells;Pooled RNA from a number of lymphoblastoid cell lines (with and without bleo treatment) and head and neck cancer cell lines.

Caco-2 cells of passage 37 were seeded (1 : 10 split ratio) in triplicate on polycarbonate membrane transwell® inserts (Corning Life Sciences, Cambridge, U.K.), with a membrane diameter of 75 mm (growth area 44 cm2, 0.4 µm pore size) at a density of approx. 40,000 cells/cm2. After 2 days, cell cultures reached confluency, and this time point was considered experimental day 0 and the initial exposure to quercetin. Cells were exposed for a total number of 9 days.

Probe sets with an “absent call” (P ≥ 0.065 for HG-U133A 2.0 GeneChip® arrays) across all 8 arrays (n = 7,285) were considered not to be affected by quercetin treatment and/or incubation time and were therefore excluded from further analyses.

Aberrant transcriptional regulation contributes to the pathogenesis of both congenital and adult forms of heart disease. While the transcriptional regulator FOG2 is known to be essential for heart morphogenesis and coronary development, its tissue specific function has not been previously investigated. Additionally, little is known about the role of FOG2 in the adult heart. Here we use spatiotemporally regulated inactivation of Fog2 to delineate its function both in embryo and adult heart. Early cardiomyocyte-restricted loss of Fog2 recapitulated the cardiac and coronary defects of the Fog2 germline knockouts. Later cardiomyocyte-restricted loss of Fog2 (Fog2MC) did not result in defects in cardiac structure or coronary vessel formation. However, Fog2MC adult mice had severely depressed ventricular function and died at 8-14 weeks. Fog2MC adult hearts displayed a paucity of coronary vessels. This was associated with myocardial hypoxia, increased cardiomyocyte apoptosis, and cardiac fibrosis. Induced inactivation of Fog2 in adult heart resulted in similar phenotype, as did ablation of FOG2 interaction with the transcription factor GATA4. Loss of FOG2 or FOG2-GATA4 interaction altered expression of a panel of angiogenesis-related genes. Collectively, our data indicated that FOG2 regulates adult heart function and coronary angiogenesis.

daily tamoxifen injectionx21 days then sacrificed 6 days after last dose

daily tamoxifen injectionx21 days then sacrificed 2 days after last dose

daily tamoxifen injectionx21 days then sacrificed 4 days after last dose

Gene expression data from Huh7 cells treated with mock media for 24 hours

Gene expression data from Huh7 cells treated with mock media for 48 hours

Gene expression data from Huh7 cells treated with mock media for 18 hours

Gene expression data from TLR4-/- sham kidney at 4hr reperfusion(No.1)

Gene expression data from TLR4-/- sham kidney at 4hr reperfusion(No.2)

Gene expression data from TLR4-/- sham kidney at 4hr reperfusion(No.3)

SMhu125

SMhu126

SMhu123

SMhu124

SMhu127

SMhu128

SMhu131

SMhu132

cell line HCT-116, Ki-RAS-mutation, DNMT3B knockout, non-treated;common reference sample

cell line HCT-116, Ki-RAS-mutation, DNMT3B knockout, DMSO-treated;common reference sample

cell line HCT-116, Ki-RAS-mutation, DNMT3B knockout, U0126-treated;common reference sample

cell line HCT-116, Ki-RAS-mutation, DNMT1 and 3B double knockout, non-treated;common reference sample

cell line HCT-116, Ki-RAS-mutation, DNMT1 and 3B double knockout, DMSO-treated;common reference sample

corresponds to sample UC9 in table 1

corresponds to sample UC8 in table 1

corresponds to sample UC7 in table 1

corresponds to sample UC6 in table 1

corresponds to sample UC5 in table 1

corresponds to sample UC4 in table 1

corresponds to sample UC3 in table 1

SMhu079

SMhu080

SMhu081

SMhu082

SMhu069

SMhu070

SMhu071

SMhu072

SMhu083

SMhu084

mixed 129Sv/C57BL6;Col1a1tetO-Nanog/+;Rosa26rtTA/+;male;8 months;liver

After 24 hours, cells were transfected for 72 hours with nonspecific (Scrambled) or siRNA for human VAMP7 (Dharmacon, Lafayette, CO, USA) according to the manufacturer’s procedure

NTERA2/D1 (ATCC CRL-1973) cells were grown in a modified Dulbecco's medium without phenol red supplemented with 10% fetal bovine serum and L-glutamine in an atmosphere of 5% CO2. Cells were plated at 70% confluency in 6-well plates (1 x 105 cells/well) for RNA

Microarray results were normalized using Robust Multichip Average (RMA). Statistical analysis approach of SAM (Significance Analysis of Microarray) was applied using Multiple Experiment Viewer (MeV). We determined a list of about 600 genes that are significantly altered at a 20% False Discovery Rate (FDR) when VAMP7 was knocked down in NT2 cells.

Total RNA was purified using the RNeasy Kit including an optional DNase I treatment according to the manufacturer's instructions (Qiagen, Valencia, CA, USA). USA).

Gene expression data from NTERA2/D1 cells treated with Scrambled siRNA, biological replicate 1

Rat230_2;15;ul;2.222;1.139;1.9;1:5;8.4;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;64;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;3.908;1.959;1.96;1:5;8.2;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;356;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Gene expression data from NTERA2/D1 cells treated with Scrambled siRNA, biological replicate 3

Gene expression data from NTERA2/D1 cells treated with Scrambled siRNA, biological replicate 2

in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 19, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 2, Units of Dose or Concentration: ppm

nasal epithelium, formaldehyde inhalation exposure, 2 ppm, 6 hours per day, 5 days per week, 19 day time point

Rat230_2;15;ul;1.929;1.018;1.86;1:5;8.7;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;233;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.515;0.791;1.89;1:5;8.6;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;232;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;3.469;1.802;1.91;1:5;8.2;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;355;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.675;0.838;1.96;1:5;8.6;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;234;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;2.592;1.273;2.03;1:5;8.2;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;341;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.975;1.082;1.86;1:5;7.8;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;338;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.232;0.618;1.95;1:5;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;230;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;2.408;1.228;1.95;1:5;8.1;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;342;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

BALB/c SCID, gender:male, age:8wks, tissue: whole lung, condition: uninfected control

BALB/c WT, gender:male, age:8wks, tissue: whole lung, condition: uninfected control

Oker_1(tube5)

Oker_1(tube4)

CML CD34+ cells treated with or without 4 µM fenretinide were maintained in culture for 48 hours prior to hybridization.

Fresh bone marrow (BM) cells or leukapheresis products (LP) were obtained from four CML patients with informed consent and approval of Institutional Review Board at the School of Medicine in Shanghai Jiao Tong University. Mononuclear cells were isolated by Ficoll density gradient centrifugation. CD34+ cells were enriched using EasySep® Human CD34 Positive Selection kit (Stem Cell Technologies, Vancouver, BC) according to the manufacturer's instructions. The purity of CD34+ cells ranged between 92 and 98% in all samples determined by flow cytometry. The CD34+ cells were cultured in a STEMPRO-34® SFM Complete Medium (Invitrogen, Carlsbad, CA) supplemented with growth factors (PeproTech, London, UK). The growth factors consisted of GM-CSF (200 pg/mL), G-CSF (1 ng/mL); SCF (200 pg/mL); LIF (50 pg/mL), MIP-1α (200 pg/mL) and IL-6 (1 ng/mL).

An affymetrix Gene Chip Scanner 3000 was used to scan the arrays.

Raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization. The normalized expression data was subsequently imported into Linear Models for Microarray Data (LIMMA) bioconductor library for the detection of differentially expressed probesets using paired t-tests for the fenretinide versus control comparison across 4 CML patients.

The fragmented, biotinylated cRNA were used for hybridization at 45C for 17 hours with Affymetrix HG-U133 Plus 2.0 GeneChip microarrays (Affymetrix, Santa Clara, CA).

Untreated CD34+ cells isolated from the patient CML32, harvested after 48h in culture

CML chronic phase (CP);leukapheresis products (LP);CD34+ mononuclear cells

Fenretinide-treated CD34+ cells isolated from the patient CML32, harvested after 48h in culture

Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 0 hours, replica 2

Gene expression data from Oct4-Gip ES cells 72h after Panct1-esiRNA treatment.

Tsc1-deficient CD4 naïve cells with CD3-CD28 stimulation for 4h KAI280

Control (Ovol2flox/+ or Ovol2flox/+;K14-Cre, 2 mice/array) and conditional knockout (Ovol2flox/-;K14-Cre, 3 mice/array)

Terminal end bud (mammary gland);female;4.5 week old;Ovol2flox/+;C57/BL6

Terminal end bud (mammary gland);female;4.5 week old;Ovol2flox/-;K14-Cre;C57/BL6

G42 cells from Cerebellum, wild type control, biological replicate 3

C57BL6/J;No;10/15/07;60;male;CB (cerebellum);Y/X;G42/-;G42 GFP labeled Purkinje neurons from the cerebellum

G42 cells from Cerebellum, wild type control, biological replicate 2

C57BL6/J;No;10/09/07;87;male;CB (cerebellum);Y/X;G42/-;G42 GFP labeled Purkinje neurons from the cerebellum

Gene expression data from G42 GFP labeled Purkinje neurons from the cerebellum (CB), Mecp2 null

C57BL6/J;No;10/09/07;65;male;CB (cerebellum);Y/Mecp2-;G42/-;G42 GFP labeled Purkinje neurons from the cerebellum

C57BL6/J;No;10/09/07;58;male;CB (cerebellum);Y/Mecp2-;G42/-;G42 GFP labeled Purkinje neurons from the cerebellum

C57BL6/J;No;10/15/07;84;male;CB (cerebellum);Y/Mecp2-;G42/-;G42 GFP labeled Purkinje neurons from the cerebellum

mPIN (mouse prostatic intraepithelial neoplasia);20 weeks;ventral prostate;FVB

bone marrow;CD34+ hematopoietic stem cells (HSC);myelodysplastic syndromes (MDS);refractory anemia (RA);del5q plus monosomy7/del7q plus other

Healthy control;42;Male;N/A;N/A;6.6;27;Right;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 0

Healthy control;29;Female;N/A;N/A;6.2;42;Left;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 0

Healthy control;68;Female;N/A;N/A;6.3;13;Left;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 0

Healthy control;41;Male;N/A;N/A;6.0;11;Right;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 1

6816115008_F

skeletal muscle;insulin sensitive;untreated;0.9;195;28;1310;64.5;27;44.9;1741.5

Clinical information: Sample.ID=856;Tumor.type=D;Size=1.6;Grade=2;Nodes=0/16;ER=Pos;PR=Pos;HER2=ND;Age=73;DFS=88;Status=non-recur

Clinical information: Sample.ID=878;Tumor.type=D/L;Size=1.6;Grade=2;Nodes=0/9;ER=Pos;PR=Neg;HER2=Neg;Age=76;DFS=138;Status=non-recur

Clinical information: Sample.ID=871;Tumor.type=D;Size=4;Grade=3;Nodes=0/16;ER=Pos;PR=Pos;HER2=Neg;Age=61;DFS=6;Status=recur

Clinical information: Sample.ID=1045;Tumor.type=D;Size=2.5;Grade=3;Nodes=1/12;ER=Pos;PR=Neg;HER2=Pos;Age=73;DFS=121;Status=non-recur

Clinical information: Sample.ID=1037;Tumor.type=D/L;Size=1.5;Grade=2;Nodes=0/4;ER=Pos;PR=Pos;HER2=Neg ;Age=85;DFS=83;Status=non-recur

Pool of total RNA from 3 Ts1Cje cerebella (segmental trisomy of chromosome 16) at P0 postnatal stage

Ts1Cje (segmental trisomy of chromosome 16);cerebellum;P0 postnatal stage

D1RMKOS516

C57BL/6;Ager null, Myd88 null;male;10-12 weeks;liver;85%;2 hours

Ager/Rage null/Myd88 null C57BL/6 mice, liver, 10-12 weeks old, sacrificed 2 hours after 85% liver resection

Treated with 10uM Motexafin gadolinium and 50uM Zinc for 4 hrs -- replicate #2

Trasnsformed Lymphocytes Unaffected (Unaffected pateint of MZ twin pair 2)

Trasnsformed Lymphocytes Unaffected (Unaffected pateint of MZ twin pair 3)

human peripheral blood memory B cells (MBCs);LZRS-IRES-YFP;negative control

OCI-Ly7;diffuse large B-cell lymphoma (DLBCL);sigenome non-targeting siRNA;negative control

OCI-Ly1;diffuse large B-cell lymphoma (DLBCL);siRNA targeting FOXP1;siRNA-mediated FOXP1 knockdown

OCI-Ly1;diffuse large B-cell lymphoma (DLBCL);sigenome non-targeting siRNA;negative control

OCI-Ly10;diffuse large B-cell lymphoma (DLBCL);siRNA targeting FOXP1;siRNA-mediated FOXP1 knockdown

LRRK2 mutant knockin H9 hESC derived NSC treated with inhibitor 2

LRRK2 mutant knockin H9 hESC derived NSC treated with inhibitor 1

LRRK2 mutant knockin H9 hESC derived NSC treated with inhibitor 3

Sciatic nerves from post natal day 90 GNMT (wt and KO)  mice of either sex were dissected and pooled together.

After background correction with GenomeStudio and log2 transformation, probes with a detection p-value greater than 0.01 for all samples were discarded, using the detectionCall function in the lumi R package. The data were normalised using quantile normalisation with lumi in R.

TargetAmp™ Nano-g™ Biotin-aRNA Labeling Kit for the Illumina® System (Cat.Num. TAN07924)

Sciatic nerves from GNMT-KO mice_Replicate 1_Gene Expression Array

Sciatic nerves from GNMT-WT mice_Replicate 2_Gene Expression Array

Sciatic nerves from GNMT-WT mice_Replicate 1_Gene Expression Array

Lot batch = EEG0076

Injured Rat Rat retinas from male Sprague-Dawley. Injuries were induced by a single scrape or Retina.  Retinas from two animas were pooled.
Lot batch = EEG0081

Injured Rat Rat retinas from male Sprague-Dawley. Injuries were induced by a single scrape of Retina.  Retinas from two animas were pooled.
Lot batch = EEG0082

Normal Rat Rat retina from male Sprague-Dawley.  Retinas from two animas were pooled.
Lot batch = EEG094

Lot batch = EEG0078

Lot batch = EEG036

Lot batch = EEG0079

Lot batch = EEG0080

T/C-28 cells (fetal human sternal chondrocytes, immortalized, M.Goldring)

Immortalized MEFs WA, v-src expression retroviral vector infected, rep3

v-src retroviral vector-infected immortalized mouse embryonic fibroblasts

Immortalized MEFs WB, v-src expression retroviral vector infected, rep2

Immortalized MEFs WA, v-src expression retroviral vector infected, rep1

Immortalized MEFs WA, v-src expression retroviral vector infected, rep2

Immortalized MEFs WC, v-src expression retroviral vector infected, rep2

Immortalized MEFs WC, v-src expression retroviral vector infected, rep3

Immortalized MEFs WB, v-src expression retroviral vector infected, rep3

Immortalized MEFs WC, v-src expression retroviral vector infected, rep1

HepG2 cell cultures were incubated with serum free medioum for 2 hours after overnight serum starvation.

HepG2 cell cultures were incubated with quercetin (3μM) for 2 hours after overnight serum starvation.

KO Vdr -/- mice; Bone marrow derived macrophages (BMDMs); Briefly, femora and tibia of the hind legs were flushed with cold DMEM (Invitrogen) containing 10 % heat-inactivated fetal calf serum (Biowest), 200 mM L-glutamine, and penicillin/streptomycin (Invitrogen). This complete medium was supplemented with M-CSF (50 ng/ml) and bone marrow cells were cultured at 37°C in a humidified 5% CO2 atmosphere for 7 days. Thioglycolate-elicited macrophages were obtained 4 days after the intraperitoneal injection of sterile 4 % thioglycolate medium. Cells were harvested by peritoneal lavage with cold PBS, 1% FCS and were cultured in RPMI 1640 (Invitrogen) including 10 % heat-inactivated fetal calf serum, L-glutamine, and penicillin/streptomycin (P/S). Macrophages were plated at 8 x 104/well in 96-well plates and cultured in P/S-free medium in the presence or absence of IFN-gamma, 1alpha,25(OH)2D3, or both for 24-48 hours.

wild type mice; Bone marrow derived macrophages (BMDMs); Briefly, femora and tibia of the hind legs were flushed with cold DMEM (Invitrogen) containing 10 % heat-inactivated fetal calf serum (Biowest), 200 mM L-glutamine, and penicillin/streptomycin (Invitrogen). This complete medium was supplemented with M-CSF (50 ng/ml) and bone marrow cells were cultured at 37°C in a humidified 5% CO2 atmosphere for 7 days. Thioglycolate-elicited macrophages were obtained 4 days after the intraperitoneal injection of sterile 4 % thioglycolate medium. Cells were harvested by peritoneal lavage with cold PBS, 1% FCS and were cultured in RPMI 1640 (Invitrogen) including 10 % heat-inactivated fetal calf serum, L-glutamine, and penicillin/streptomycin (P/S). Macrophages were plated at 8 x 104/well in 96-well plates and cultured in P/S-free medium in the presence or absence of IFN-gamma, 1alpha,25(OH)2D3, or both for 24-48 hours.

wild type mice; Bone marrow derived macrophages (BMDMs); Briefly, femora and tibia of the hind legs were flushed with cold DMEM (Invitrogen) containing 10 % heat-inactivated fetal calf serum (Biowest), 200 mM L-glutamine, and penicillin/streptomycin (Invitrogen). This complete medium was supplemented with M-CSF (50 ng/ml) and bone marrow cells were cultured at 37°C in a humidified 5% CO2 atmosphere for 7 days. Thioglycolate-elicited macrophages were obtained 4 days after the intraperitoneal injection of sterile 4 % thioglycolate medium. Cells were harvested by peritoneal lavage with cold PBS, 1% FCS and were cultured in RPMI 1640 (Invitrogen) including 10 % heat-inactivated fetal calf serum, L-glutamine, and penicillin/streptomycin (P/S).
Macrophages were plated at 8 x 10^4/well in 96-well plates and cultured in P/S-free medium in the presence or absence of IFN-gamma, 1alpha,25(OH)2D3, or both for 24-48 hours

Vdr tm1 Rge knockout mice; Bone marrow derived macrophages (BMDMs); Briefly, femora and tibia of the hind legs were flushed with cold DMEM (Invitrogen) containing 10 % heat-inactivated fetal calf serum (Biowest), 200 mM L-glutamine, and penicillin/streptomycin (Invitrogen). This complete medium was supplemented with M-CSF (50 ng/ml) and bone marrow cells were cultured at 37°C in a humidified 5% CO2 atmosphere for 7 days. Thioglycolate-elicited macrophages were obtained 4 days after the intraperitoneal injection of sterile 4 % thioglycolate medium. Cells were harvested by peritoneal lavage with cold PBS, 1% FCS and were cultured in RPMI 1640 (Invitrogen) including 10 % heat-inactivated fetal calf serum, L-glutamine, and penicillin/streptomycin (P/S).

Primary CLL cells (treated with 0.1uM CDKI-73 and 10 μM fludarabine for 4h)

plaque type psoriasis;epidermis;40;male;> 20 y;phototherapy;pre-UV

plaque type psoriasis;epidermis;73;female;Unknown;phototherapy;pre-UV

#3;healthy individual, non-inflamed;primary mucosal tissue,  colon;31.5

#2;diseased individual, inflamed;primary mucosal tissue,  colon;31.5

#2;healthy individual, non-inflamed;primary mucosal tissue,  colon;31.5

Nontransgenic littermate mouse;C57 BL/6;male;~30wk;heart LV;vehicle

Nontransgenic littermate mouse;C57 BL/6;Male;~30wk;heart LV;vehicle

Nontransgenic littermate mouse;C57 BL/6;male;~30wk;heart LV;tamoxifen

C3-2

C3-1

A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factors can be identified. This entry corresponds to the RNA isolated from tet-induced INS-1 cell line #3b containing MODY5 mutant A263insGG of hepatocyte nuclear factor-1b (HNF1b).

A YOKE_B095

A HID U_B054

A YOKE_B093

A YOKE_B094

A HID U_B084

A HID I_B087

miosge_KO_Tal2_20110505_(MoGene-1_0-st-v1).rma-gene-default.chp
miosge_KO_Tal2_20110505_(MoGene-1_0-st-v1).CEL

Mice were bred and held under conventional housing conditions in filtertop cages

Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 262

The dataset was preprocessed using the following procedures: (1) background correction; (2) normalization using the quantile method (Bolstad et al. 2003); (3) summarization of probe set values using the RMA (Robust Multi-array Analysis) method, which fits a specified robust linear model to the probe level data. The abovementioned procedures were performed using the Bioconductor package “affyPLM”.

Hybridized washed and stained with streptavidin-PE per the manufacturer's protocol (Affymetrix).

B cells from wild type mice treated with IFN-b
Array 23 - 23.N.B._565.CEL

129SV/EV;Female;8-12weeks;Lymph node B cell;17h treatment IFN-beta (2000U/ml)

Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 263

Array 25 - 25.N.B._569.CEL

Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 264

Array 26 - 26.N.B._581_1.CEL

Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 265

Array 34 - 34.N.B._638.CEL

Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 258

B cells from flu-infected mice (IFNR knockout)
Array 22 - 22.N.B._561.CEL

129SV/EV;Female;8-12weeks;Mediastinal lymph node B cell;Influenza A/Mem71 48h

Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 259

Array 24 - 24.N.B._566.CEL

129SV/EV IFNAR1-/-;Female;8-12weeks;Mediastinal lymph node B cell;Influenza A/Mem71 48h

Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 260

Array 27 - 27.N.B._620.CEL

Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 261

Array 32 - 32.N.B._630.CEL

All protocols from Affymetrix GeneChip Expression Analysis technical manual

Fluoxetine dissolved in drinking water to provide a dose of 18 mg/kg/day for 21 days

miosge_WT_Tal6_20110623_(MoGene-1_0-st-v1).rma-gene-default.chp
miosge_WT_Tal6_20110623_(MoGene-1_0-st-v1).CEL

Gene expression data from liver after 14 day feeding of 1.0% quercetin diet

Gene expression data from liver after 14 day feeding of 0.5% quercetin diet

Gene expression data from HEK cells non-expressing WT TRPM7 channel
WT no3

WT no1

WT tet2

Testicular germ cell tumor (embryonal carcinoma) cell line 2102Ep (clone 2A6). Embryonal carcinoma cell lines are generally pluripotent and share features with embryonic stem cells. However, the 2102Ep cell line is relatively nullipotent. Time point 0 days of culturing with retinoic acid (untreated). Maintained at high cell density (>5 000 000 cells per 75 cm2 tissue culture flask) in Dulbecco Modified Eagles Medium (DMEM high glucose formulation; GIBCO LifeTechnologies, UK) supplemented with 10% fetal calf serum.
Keywords = nullipotency
Keywords = nullipotent

Testicular germ cell tumor; histological subtype teratoma
Keywords = teratoma

TGCT cell line 2102Ep/clone 2A6, treated 3 days with retinoic acid, undifferentiated

Testicular germ cell tumor (embryonal carcinoma) cell line 2102Ep (clone 2A6). Embryonal carcinoma cell lines are generally pluripotent and share features with embryonic stem cells. However, the 2102Ep cell line is relatively nullipotent. Time point 3 days of culturing with retinoic acid (still undifferentiated). Maintained at high cell density (>5 000 000 cells per 75 cm2 tissue culture flask) in Dulbecco Modified Eagles Medium (DMEM high glucose formulation; GIBCO LifeTechnologies, UK) supplemented with 10% fetal calf serum.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12044 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12043 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12005 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12004 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12004 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12003 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12043 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12006 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12006 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12005 treated with DMSO 8 hours.

RNA characterization of tissue from the injury site, 35 days post-injury. From the Christopher Reeve Paralysis Foundation Research Consortium microarray study (www.crpf.org/microarray)

RNA characterization of tissue from the injury location (~T8) in an uninjured animal. From the Christopher Reeve Paralysis Foundation Research Consortium microarray study (www.crpf.org/microarray)

The presence of transcripts was generated according to a detection p-value described in the Statistical Algorithms Reference Guide (Affymetrix, Santa Clara).  The one-sided Wilcoxon’s Signed Rank was the statistical method employed to generate detection p-values.  Transcripts with a p-value lower than 0.05 were considered present in RNA samples.  Global scaling was used to remove differences and facilitate comparison analysis.

Raji_Mi_3p_24h_3_56779_4

Raji_Mi_3p_24h_1_56779_3

Raji_Mi_CTRL_24h_3_56779_4

Raji;human Burkitt's lymphoma;male;expression of control mimic;24 hrs

Raji_Mi_CTRL_24h_1_56779_3

Raji_Mi_CTRL_24h_4_56779_2

Raji_Mi_CTRL_24h_2_56779_1

Mice were infected intranasally with 2.5 x 106 of C. pneumoniae in 30 µl of PBS

lung rna from wt mice, 3 days after Chlamydia pneumoniae infection, replicate B

lung rna from wt mice, 3 days after Chlamydia pneumoniae infection, replicate C

lung rna from myd88 knockout mice, 3 days after mock infection, replicate B

Phenytoin brainstem 1

Phenytoin brainstem 2

Mammary epithelial organoids harvested from age-matched female mice were plated in growth factor-reduced Matrigel ± 5 µM DOX, cultured for 14 d

The mammary glands of  ErbB3 DOX-KO mice were harvested under sterile conditions, minced, and digested in 1 mg/ml collagenase/0.3 mg/ml hyaluronidase (Stem Cell Technologies, Vancouver, Canada). Organoids were processed according to protocol provided by Stem Cell Technologies, resuspended in growth factor-reduced Matrigel (BD Life Sciences) and plated in 8-well chamber slides.

Data were processed using RMA normalization in R using the affy package and the justRMA function

Phenytoin brainstem 5

Phenytoin brainstem 6

Crohn's Disease subject (32 year old caucasian male, SAK_1287459252)

Subject Age : 32

Phenytoin brainstem 4

Cells were treated with 100 µM Diclofenac or equal amounts of DMSO for 48 hours

Cells were cultured in RPMI-1640 supplemented with 10% fetal bovine serum

CEL files were analyed using dChip after smooth spline normalization

Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45°C on HG-U133A Gene Expression Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 µg total RNA

Phenytoin frontal cortex 3

Phenytoin frontal cortex 2

Phenytoin frontal cortex 1

Levitiracetam frontal cortex 7

Phenytoin frontal cortex 7

Phenytoin frontal cortex 6

Phenytoin frontal cortex 5

Phenytoin frontal cortex 4

Control frontal cortex 2

Control frontal cortex 1

breast cancer histologically normal breast epithlieum patient 304B

breast cancer histologically normal breast epithlieum patient 351

breast cancer histologically normal breast epithlieum patient 248

breast cancer histologically normal breast epithlieum patient 226

breast cancer histologically normal breast epithlieum patient 258

breast cancer histologically normal breast epithlieum patient 274

breast cancer histologically normal breast epithlieum patient 232

breast cancer histologically normal breast epithlieum patient 237

Comparisons: postnatal day effect/P1, Genotype effect on postnatal gene expression comparitor/P1

mRNA extracted from lung fibroblasts derived from open lung biopsies of a patient (IPF3) with idiopathic pulmonary fibrosis (usual interstitial pneumonia pattern on biopsy). Lung fibroblasts were grown to confluence in DMEM with 10% fetal calf serum. At confluence, lung fibroblasts were serum-deprived overnight, and exposed to 4 ng/ml of activated TGF-ß1 (R&D Systems) in serum-free culture-medium with the addition of 0.1% BSA for 4 hours. At the end of treatment period total RNA was harvested, quantified, and integrity was verified by denaturing gel electrophoresis.

lung fibroblasts from a patient (IPF3) with idiopathic pulmonary fibrosis

mRNA extracted from lung fibroblasts derived from open lung biopsies of a patient (IPF3) with idiopathic pulmonary fibrosis (usual interstitial pneumonia pattern on biopsy). Lung fibroblasts were grown to confluence in DMEM with 10% fetal calf serum. At confluence, lung fibroblasts were serum-deprived overnight, and exposed to serum-free culture-medium with the addition of 0.1% BSA for 4 hours. At the end of treatment period total RNA was harvested, quantified, and integrity was verified by denaturing gel electrophoresis.

For serum starvation, cells were maintained without serum during 72 h.

Wt, CK and p27KO MEFs were cultured in DMEM supplemented with 10% fetal bovin serum (FBS). All cultures were maintained at 37ºC and 5% CO2.

The normalization of the arrays was done using the rma method as implemented in the Affy package of R Bioconductor. Quality control measurements were done using ArrayQualityMetrics package of R Bioconductor.

Total RNA was extracted using the RNeasy Kit (QIagen). RNAs from quiescent MEFs from wt or delta51 mice were analyzed using a Bioanalyzer (Agilent). Only samples with RIN number greater than 9 and a ratio A260/280 over than 2 were further used in microarray analysis. Retrotranscription was made followed by labeling with biotin.

Following fragmentation, cRNA were hybridized for 16 hr at 45ºC on Affymetrix 1.0 ST murine array. Chips were washed and stained in the Affymetrix Fluidics Station.

Sample was pooled on basis of total-RNA extracted from CD3+ T cells derived from bone marrow of two healthy volunteers

Pool of two samples (n=2);;CD3+ T cells, bone marrow;;one male, one female; age: 58 and 42 years old

Sample was pooled on basis of total-RNA extracted from CD3+ T cells derived from bonemarrow of all SAA patients..

Pool of four samples (n=4);;three female/one male;;19/57/40/70 years old;;CD3+ T cells, bone marrow;;(severe) aplastic anemia (SAA)

Sample was pooled on basis of total-RNA extracted from CD3+ T cells derived from peripheral blood of three healthy volunteers

Pool of three samples (n=3);;CD3+ T cells, peripheral blood;;two females, one male; age: 25 and 37 years old

Gene expression data from late passage LP50 cells treated with vehicle and control shRNA

Gene expression data from late passage LP50 cells treated with R1881 and control shRNA

K562 (Iscoves + 10% FCS) and TF-1 (RPMI + 10%FCS + rhGM-CSF.  Cells were cultured at 37oC, 5% CO2 and split every 3 to 4 days.  The CREB specific shRNA sequences were selected and validated based on accepted parameters established by Tuschl et al.

K562 (Iscoves + 10% FCS) and TF-1 (RPMI + 10%FCS + rhGM-CSF.  Cells were cultured at 37oC, 5% CO2 and split every 3 to 4 days.  . The CREB specific shRNA sequences were selected and validated based on accepted parameters established by Tuschl et al.

0.5 mg/kg/ml Isoproterenol treatment, 72 hour time point,  biological rep 5

CHIPEXP_NAME: 230_2_050531tpj_62h

0.5 mg/kg/ml Isoproterenol treatment, 72 hour time point,  biological rep 2

CHIPEXP_NAME: 230_2_050531tpj_59h

0.5 mg/kg/ml Isoproterenol treatment, 72 hour time point,  biological rep 3

CHIPEXP_NAME: 230_2_050531tpj_60h

PC3 cells were transfeted  either a non-specific siRNA or with a TRPM2-AS siRNA in replicates for 48 hours.

Data were normalized using the Rank Invariant normalization algorithm implemented on the Illumina BeadStudio software, using all probes on the array for the extraction of the rank invariant set of transcripts. After normalization, the expression dataset was further corrected by setting the bottom threshold signal to 140. This value was estimated from background noise obtained using Illumina negative controls, representing an estimation of both  the image background and the signals derived from non-specific binding or cross-hybridization. Differential expression of transcripts was assesed using the limma package (http://www.bioconductor.org/packages/release/bioc/html/limma.html).

Wild-type, dgcr8 knockout, and dicer1 knockout ES cells were plated on 60-mm plates in triplicate.

Gladstone Genomic Core facility standard protocols were used (http://www.gladstone.ucsf.edu/gladstone/site/genomicscore/section/1914).

Sample_ID:n16 // Patient:J-277 // Histology:Normal // Metastasis:NA // p53_mut:NA // E-cadherin_mut:NA // beta-Catenin_mut:NA

MCF7 pre-treated for 1h with cycloheximide, treated with vehicule for 24h

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D1;11

Chips were scanned using an Affymetrix GeneChip Scanner 3000. Chip target intensity was arbitrarily scaled to 100 before rendering CHP file

Cells (LIN-FLT3+CD127+LY6D- bone marrow) were directly sorted into buffer RLT and RNA prepared using RNeasy Micro (Qiagen) according to manufacturer's instructions.

Biotinylated cRNA was prepared according to the standard AffymetrixTM; Small Sample Labelling Protocol v.2, with the exception that the second round of in vitro transcription (IVT) was performed using AffymetrixTM GeneChipTM Expression 3íamplification kit.

Gene expression data from FACS sorted LY6D- CLP cells (LIN-FLT3+CD127+)

bone marrow;E2A-KO;C57bl/6;10-13 weeks old;FACS sorted LY6D- CLP cells (LIN-FLT3+CD127+)

bone marrow;HEB-KO;C57bl/6;10-13 weeks old;FACS sorted LY6D- CLP cells (LIN-FLT3+CD127+)

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D72 (30 days post-EBRT);11

bone marrow;Wild type;C57bl/6;10-13 weeks old;FACS sorted LY6D- CLP cells (LIN-FLT3+CD127+)

male;non-metastatic prostate cancer;peripheral blood;white blood cells;baseline;13

blast count: 8

blast count: 20

P13_wildtype_rep1

Gene expression data from cochleas of nicotinic cholinergic receptor alpha9 subunit knockout mice at P7.
P7_a9knockout_rep3

Gene expression data from cochleas of wild type mice at P7.
P7_wildtype_rep3

P7_wildtype_rep2

P7_a9knockout_rep2

P7_a9knockout_rep1

Gene expression data from cochleas of nicotinic cholinergic receptor alpha9 subunit knockout mice at P3.
P3_a9knockout_rep2

P3_a9knockout_rep1

P7_wildtype_rep1

P3_a9knockout_rep3

Some mice were treated with imatinib 600 mg/L in the drinking water.

GIST mice were maintained under standard specific pathogen free conditions.

TAMs sorted from imatinib treated tumors, biological replicate#1

Feature intensity was extracted by Affymetrix GeneChip Command Console as CEL files. The data were analyzed with MAS 5.0 algorithm using Affymetrix Gene Expression Console.

10 ug of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

200 ng total RNA converted to cRNA using Affymetrix GeneChip®3' IVT Kit and in vitro transcription resulting into biotin-labeled cRNA, fragmented prior to hybridization (Affymetrix Expression Analysis Technical Manual, as described).

gastrointestinal stromal tumor (GIST);freshly sorted tumor associated macrophages (TAMs)

Male C57Bl/6 mice injected i.p. 2x/week for 4 weeks with 50mg/kg miR-122 ASO, sacrificed 2 days after last dose.

mir-122 antisense used is a 2'-O-methoxyethyl phosphorothioate modified antisense RNA oligonucleotide with sequence 5'-ACAAACACCAUUGUCACACUCCA-3'

Human GFAP-negative lamina cribrosa cells were treated for 24 hours with 10ng/ml TGFB1.  RNA extraced using Qiagen RNeasy mini collumns. *.Cel file normalised using Robust multichip average (RMA). Cell cultures from human donor A. Experiment conducted in duplicate (separate passages).

Human GFAP-negative lamina cribrosa cells were generated from optic nerve head tissue. They were treated for 24 hours with 4mM HCL/ 1% BSA (vehicle).  RNA extraced using Qiagen RNeasy mini collumns. *.Cel file normalised using Robust multichip average (RMA). Cell cultures from human donor A. Experiment conducted in duplicate (separate passages).

Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_5-tu1

CD8 T cells isolated from tumor; transduced with shRNA targeting: Arhgap5; Sample name: 5-tu1

This is a study of the change in gene expression in mouse kidney after feeding control or low phosphate diet to normal or Hyp mice for 5 days.  RNA from 3 mice were pooled for each microarray.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12248 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12239 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12239 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12236 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12264 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12249 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12249 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12248 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12716 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12264 treated with DMSO 8 hours.

Replicate 3 unstimulated.

Replicate 3 after stimulation for 100 minutes with 10 ng/ml IL-6.

Replicate 3 after stimulation for 400 minutes with 10 ng/ml IL-6.

Fetal liver cells from SOCS3-/-embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages.
Replicate 2 after stimulation for 400 minutes with 10 ng/ml IL-6.

Human melanoma cell line;M229_R5;V600E BRAF mutant;1 uM PLX4032 for 6h

Gene expression data from HSCs isolated from male mice treated with E2
ME1 HSC

MO2 HSC

FO2 HSC

ME2 HSC

ME3 HSC

Du145-PCAT1 cells transfected with cMyc siRNA #3, RNA was harvested after 48 hours, replicate #2

Du145-PCAT1 cells transfected with cMyc siRNA #3, RNA was harvested after 48 hours, replicate #1

Du145-PCAT1 cells transfected with cMyc siRNA #4, RNA was harvested after 48 hours, replicate #2

Du145-PCAT1 cells transfected with cMyc siRNA #4, RNA was harvested after 48 hours, replicate #1

RWPE-PCAT1 cells transfected with cMyc siRNA #4, RNA was harvested after 48 hours, replicate #1

RWPE-PCAT1 cells transfected with cMyc siRNA #3, RNA was harvested after 48 hours, replicate #1

RWPE-PCAT1 cells transfected with cMyc siRNA #4, RNA was harvested after 48 hours, replicate #2

RWPE-PCAT1 cells transfected with cMyc siRNA #3, RNA was harvested after 48 hours, replicate #2

Du145-PCAT1 cells transfected with non-targeting siRNA, RNA was harvested after 48 hours, replicate #2

RWPE-PCAT1 cells transfected with non-targeting siRNA, RNA was harvested after 48 hours, replicate #2

breast cancer derived cell line treated with 0.9 uM of Doxorubicin for 24 hours

Sprague-Dawley;Dorsal root ganglia;2 months;Spare nerve injury;Adult Ipsilateral

L4/L5 dorsal root ganglia from young rats (10 days old) 7 days after sham surgery

Sprague-Dawley;Dorsal root ganglia;17 days;Spare nerve injury;Young Contralateral

Cnr1-/-/Cnr2-/- female number 2, DNFB-treated allergic ear (#11_Ko-Tr-5)

Cnr1-/-/Cnr2-/- female number 2, 2 months old, whole ear tissue, DNFB-treated allergic ear

HaCat cells infected with a BCL-3-expressing  lentiviral construct. Replicat 3

TP_D1
Gene expression from the pineal gland of a NeuroD1 cKO mouse at ZT6.

C57BL/6J; NeuroD1flox::Crx-Cre+/-;NeuroD1 cKO;2 months;pineal gland;ZT6

Gene expression data from spleen of Npc1-/- mouse1 of age 54 days

mcad -/-;Male;BL6/SV129 mixed;50-60 days of age;12 hrs fasted;LPS;liver

Human skin biposy (uninvolved) from male patient, 34 years old, 15 years of psoriasis, clear erythema, clear induration, clear scaling.

B;male;34 years;15 years;6 percent;clear;clear (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe);clear (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)

Human skin biposy (lesional) from male patient, 34 years old, 15 years of psoriasis, severe erythema, moderate induration, mild scaling.

B;male;34 years;15 years;6 percent;severe;moderate (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe);mild (classified by the investigators according to the following six grades: clear  -  minimal  -  mild  -  moderate  -  severe  -  very severe)

lymphoblastoid cell line from T6.01, one out of seven of insensitive group, 50*10e6 cells;Pooled RNA from a number of lymphoblastoid cell lines (with and without bleo treatment) and head and neck cancer cell lines.

218;Sulphasalazine Asprin Metoprolol Atorvastatin;9/27/24;F;CAUCASIAN;1/1/58;1/1/58;FALSE;FALSE;FALSE;NO;FALSE;FALSE;12/3/04;0;0;0;0;0;0;0;0;TRUE;0;BOTH;unknown;unknown;unknown;unknown;12/3/04;BOTH;unknown;unknown;unknown;unknown;3/4/05;DISEASE IN REMISSION;never;unknown;Breast cancer;UC;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

216;NONE;5/10/36;M;CAUCASIAN;2/19/66;8/20/66;FALSE;FALSE;FALSE;NO;FALSE;FALSE;11/18/04;0;0;0;0;0;0;0;0;FALSE;0;11;11;11;11;11;11;11;11;12;BOTH;BOTH;BOTH;unknown;unknown;11/18/04;unknown;unknown;unknown;unknown;unknown;12/9/04;DISEASE IN REMISSION;never;unknown;NONE;UC;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

232;Pentaza 2g BD;1/9/63;F;CAUCASIAN;1/1/95;1/1/95;FALSE;FALSE;FALSE;unknown;FALSE;FALSE;1/31/05;1;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;BOTH;BOTH;BOTH;1/31/05;BOTH;BOTH;BOTH;BOTH;BOTH;3/7/05;FAILURE OF THERAPY;never;unknown;None;UC;8-9-01;ascending colon;Inflamed;total RNA from 10 human cell lines

231;prednisolone 40mg heparin clarithromycin;10/29/77;F;CAUCASIAN;10/1/00;11/19/02;FALSE;FALSE;FALSE;unknown;FALSE;FALSE;1/28/05;7;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;BOTH;unknown;unknown;9/14/05;BOTH;BOTH;BOTH;unknown;unknown;9/14/05;FAILURE OF THERAPY;never;unknown;None;UC;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

227;Asacol Prednisolone 5 Omeprazole Warfarin Cal VitD;4/17/28;M;CAUCASIAN;1/1/90;1/1/90;FALSE;FALSE;FALSE;NO;FALSE;FALSE;1/14/05;3;0;0;0;0;0;0;0;TRUE;0;BOTH;BOTH;BOTH;BOTH;BOTH;1/14/05;BOTH;BOTH;BOTH;BOTH;BOTH;3/7/05;FAILURE OF THERAPY;ex;1/1/72;5-14;Prostate cancer 1985, Previous DVT's on warfarin;UC;8-9-01;ascending colon;Inflamed;total RNA from 10 human cell lines

226;Azathioprine 150mg Asacol 1.6g Ca Vit D B12;6/15/74;F;CAUCASIAN;1/1/89;1/1/89;FALSE;FALSE;FALSE;YES;FALSE;TRUE;1/11/05;8;0;0;0;0;0;0;0;FALSE;0;BOTH;unknown;unknown;unknown;unknown;1/11/05;BOTH;unknown;unknown;unknown;unknown;3/7/05;FAILURE OF THERAPY;current;15-24;None;UC;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

215;Prednisolone 5ng Balsalazide Lansoperazole;5/6/60;M;CAUCASIAN;5/1/02;8/16/02;FALSE;FALSE;FALSE;NO;FALSE;FALSE;11/16/04;3;0;0;0;0;0;0;0;TRUE;0;BOTH;BOTH;BOTH;BOTH;unknown;11/16/04;unknown;unknown;unknown;unknown;unknown;5/31/05;DISEASE IN REMISSION;ex;1/1/03;1/1/04;5-14;None;UC;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

214;NONE;1/10/37;M;CAUCASIAN;1/1/59;1/10/61;FALSE;FALSE;TRUE;NO;FALSE;FALSE;11/12/04;0;0;0;0;0;0;0;0;TRUE;1;BOTH;BOTH;BOTH;BOTH;BOTH;11/12/04;BOTH;BOTH;BOTH;BOTH;BOTH;12/9/04;FAILURE OF THERAPY;never;unknown;CENTRAL RETINAL VEIN OCCLUSION 01/04;UC;8-9-01;ascending colon;Inflamed;total RNA from 10 human cell lines

Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56588.gif

female;juvenile, 8 weeks (P59);Sv129 / C57BL/6N mixed background;Cldn16 +/-;renal tissue

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D14;13

Embryoid body formation (10 days) of Bmi1 transduced embryonic stem cells (CCE ES cells).

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D7;13

male;non-metastatic prostate cancer;peripheral blood;white blood cells;baseline;P1

TP_D3

bone marrow macrophages from 1 female and 1 male IRAK4 kinase dead Balb/c mouse

IRAK4 kinase dead mouse bone marrow macrophages, LPS stimulated, 4 hours

whole right lung, when moribund after a bleomycin dose of 125mg/kg, given by osmotic minipump.

whole right lung, when moribund after a bleomycin dose of 100mg/kg, given by osmotic minipump.

Primary hepatocytes isolated from Donor 1 treated with DMSO for 24h

Primary hepatocytes isolated from Donor 2 treated with Wy14643 for 6h

Primary hepatocytes isolated from Donor 1 treated with DMSO for 6h

Primary hepatocytes isolated from Donor 1 treated with Wy14643 for 24h

Primary hepatocytes isolated from Donor 2 treated with DMSO for 24h

Primary hepatocytes isolated from Donor 3 treated with Wy14643 for 6h

Primary hepatocytes isolated from Donor 2 treated with DMSO for 6h

Primary hepatocytes isolated from Donor 2 treated with Wy14643 for 24h

Primary hepatocytes isolated from Donor 3 treated with DMSO for 6h

Primary hepatocytes isolated from Donor 3 treated with Wy14643 for 24h

C57BL/6, ADNP+/- Gender: mixed Age:E9 Tissue: whole embryonic body;Activity-dependent neuroprotective protein: a novel gene essential for brain formation.;83-90. PMID: 12888219 [PubMed - indexed for MEDLINE]

MCI-021 was from a postmenopausal low BMD woman.

MCI-011 was from a postmenopausal low BMD woman.

SBC-5 cells, siEGFP (control), 24 hr after siRNA, duplicate sample 2

SBC-5 cells, at 0 hr (= 24 hr after passaged), no treatment, duplicate sample 2

SBC-5 cells, at 0 hr (= 24 hr after passaged), no treatment, duplicate sample 1

KCL-22 leukemia cells were cultured in absence of STI571 (Imatinib).
Q246_A_HG_U133_Plus_2_01_1__UCL22_.CEL

KCL-22 leukemia cells were incubated with 10 µM STI571 (Imatinib) for 16 hours.
Q247_A_HG_U133_Plus_2_01_1__UCL22_STI_.CEL

KU-812 leukemia cells were cultured in absence of STI571 (Imatinib).
Q248_A_HG_U133_Plus_2_01_1__UU812_.CEL

SBC-5 cells, siEGFP (control), 48 hr after siRNA, duplicate sample 1

SBC-5 cells, siEGR4 (target), 24 hr after siRNA, duplicate sample 2

Clinical information: Sample.ID=829;Tumor.type=D;Size=1.2;Grade=2;Nodes=0/9;ER=Pos;PR=Pos;HER2=Neg ;Age=69;DFS=136;Status=non-recur

Clinical information: Sample.ID=823;Tumor.type=D;Size=2;Grade=2;Nodes=0/6;ER=Pos;PR=Pos;HER2=Neg;Age=51;DFS=69;Status=recur

Clinical information: Sample.ID=849;Tumor.type=D;Size=2;Grade=1;Nodes=0/26;ER=Pos;PR=Pos;HER2=Neg;Age=75;DFS=23;Status=recur

Clinical information: Sample.ID=843;Tumor.type=D;Size=3.4;Grade=2;Nodes=11/20;ER=Pos;PR=Neg;HER2=Neg;Age=76;DFS=122;Status=recur

A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factors can be identified. This entry corresponds to the RNA isolated from uninduced INS-1 cell line #2b containing hepatocyte nuclear factor-1b (HNF1b).

Rat liver, treated with ANIT, 125 mg/kg in corn oil per orally, extrated 48 hours after treatment, biological rep3

Rat liver, treated with ANIT, 125 mg/kg in corn oil per orally, extrated 48 hours after treatment, biological rep2

Rat liver, treated with ANIT, 125 mg/kg in corn oil per orally, extrated 48 hours after treatment, biological rep5

Rat liver, treated with ANIT, 125 mg/kg in corn oil per orally, extrated 48 hours after treatment, biological rep4

Rat liver, treated with Caerulein, 50 µg/kg in saline i.p., extrated 48 hours after treatment, biological rep2

Rat liver, treated with Caerulein, 50 µg/kg in saline i.p., extrated 48 hours after treatment, biological rep1

Rat liver, treated with Caerulein, 50 µg/kg in saline i.p., extrated 48 hours after treatment, biological rep4

Rat liver, treated with Caerulein, 50 µg/kg in saline i.p., extrated 48 hours after treatment, biological rep3

Rat liver, treated with DMN, 15 mg/kg in water per orally, extrated 48 hours after treatment, biological rep1

Rat liver, treated with Caerulein, 50 µg/kg in saline i.p., extrated 48 hours after treatment, biological rep5

JLI_74

Gene expression data from NSC SA-01 treated with DMSO (0.1 % final)

Conditional beta cell specific KO mouse model using RIP2-Cre and Vhlh(fl/fl);Herrera PL (2000), Haase VH et al. (2001);male;26 weeks;control

MAT1A_8_3

MAT1A_8_4

MAT1A_3_5

MAT1A_wt_3_1
Gene expression data from the wild type used for MAT1A knockout at 3 month.

MAT1A_wt_3_2

MAT1A_wt_3_3

MAT1A_wt_3_4

MAT1A_wt_3_5

MAT1A_8_1

MAT1A_8_2

Human CD34+ cells isolated from umbilical cord blood;ZMYM2/FGFR1;3

*Data analysis. *The array image scan is processed with Affymetrix Microarray Suite, version 5.0 (MAS 5.0) software. The GeneChip expression arrays contain control probe sets for both spiked and endogenous RNA transcripts (e.g., BioB, BioC, BioD, CreX and species-specific actin and GAPDH). Following image processing and absolute analysis of the array pattern with MAS, six values are examined to assess overall assay performance: background, noise, average Signal, % Present, ratio of Signal values for probe sets representing the 5’ and 3’ ends of actin and GAPDH transcripts, and total Signal for probe sets for BioC, BioD and CreX. Assays demonstrating poor or marginal performance are flagged.

MO-B10-Tg 5

MO-B10-Tg 4

MO-B10-Tg 7

MO-B10-Tg 6

MO-B10-Tg 1

Gene expression data from CF cell line cultivated on Air-liquid Interface

Image analysis was performed by Affymetrix GCOS Software, and data was normalized by RMA.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

Total RNA was reverse-transcribed, and the double stranded cDNAs were used to generate biotin-labeled cRNA.

MI operated rat 7 day post-operation

A pool of two pure subsets of peripheral blood CD4+ T cells (CD19- CD3+ CD4+ CD8- CD16- CD56-), stringently sorted by flow cytometry, from two age and gender matched healthy donors.;Pooled RNA from the total peripheral lymphocyte fraction from 20 healthy donors, used as a common reference.

Gene expression data from mouse organ of Corti base, Dicer1 conditional knockout

Dicer1tm1Bdh (MGI:3589208) X Tg(Atoh1-cre)1Bfri (MGI:3775845);Dicer1 conditional knockout, Atoh1-Cre;Dicer1(flox/flox);organ of Corti from cochlea, basal half;postnatal day 16

Mouse organ of Corti from cochlea, basal half, Dicer1 conditional knockout

U2OS osteosarcoma cell line transfected with shBAP1 #2 construct

Three male 8-week-old Wistar rats were used. The peroneal nerve of the animals was transected and sutured to the biceps femoris muscle. Four weeks later, the proximal stump was sutured to the distal stump. The animals survived for 8 weeks.

All experiments were performed under Ketanest (ketamine hydrochloride, Essex Pharma GmbH, Munich, Germany; 100 mg/kg) and Rompun (xylazine hydrochloride, Bayer, Leverkusen, Germany; 10 mg/kg) anesthesia. Both substances were injected intraperitoneally. RNA was extracted from the ipsilateral and contralateral tibialis anterior muscles of each animal. The gene array analysis compared the ipsilateral muscle with the contralateral muscle of each animal.

10(-) 4d

primary unilateral non-metastatic postmenopausal ERα-positive breast tumor;woman;57 years

15(-) 4d

15(+) 4d

10(-) 12d

10(+) 12d

10(-) 4d (II)

10(+) 4d (II)

205;Pentaza 3g/d;6/8/79;M;CAUCASIAN;10/1/03;8/30/04;FALSE;TRUE;FALSE;NO;FALSE;FALSE;10/8/04;4;0;15;19;110;5;3;43;FALSE;0;BOTH;BOTH;BOTH;unknown;unknown;10/8/04;BOTH;BOTH;BOTH;unknown;unknown;12/9/04;NEW;ex;1/1/85;3/1/03;15-24;None;UC;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

primary unilateral non-metastatic postmenopausal ERα-positive breast tumor;woman;67 years

251;Bumetanide Asprin Lisinopril Colifoam;5/22/21;F;CAUCASIAN;1/1/05;6/6/05;FALSE;TRUE;FALSE;NO;FALSE;FALSE;6/6/05;9;0;0;0;0;0;0;0;TRUE;0;BOTH;BOTH;unknown;unknown;unknown;6/6/05;BOTH;BOTH;unknown;unknown;unknown;7/7/05;NEW;never;unknown;Vaginal Prolapse-Angina;UC;11-15-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

Scd1+/+ on very low fat diet (TD03045 from Harlan Teklad) replicate 4

Mus musculus (backcrossed to C57BL/6J mice for 5+ generations);Scd1 wild type mouse, Harlan Teklad TD03045 diet, liver

Scd1+/+ on very low fat diet (TD03045 from Harlan Teklad) replicate 3

Scd1+/+ on very low fat diet (TD03045 from Harlan Teklad) replicate 5

Scd1+/+ on very low fat diet (TD03045 from Harlan Teklad) replicate 2

Scd1+/+ on very low fat diet (TD03045 from Harlan Teklad) replicate 1

Gene expression data from CD4+ splenocytes from a septic mouse 6h after the induction of septic peritonitis.

normal;IA, IB, II, IIIA, IIIB, or IV=IB;61;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=moderately differentiated;intestinal type, diffuse type, mixed type, or not determined=intestinal type

normal;IA, IB, II, IIIA, IIIB, or IV=IB;66;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=moderately differentiated;intestinal type, diffuse type, mixed type, or not determined=intestinal type

normal;IA, IB, II, IIIA, IIIB, or IV=II;58;female, male:female;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

normal;IA, IB, II, IIIA, IIIB, or IV=II;69;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

normal;IA, IB, II, IIIA, IIIB, or IV=II;67;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=intestinal type

normal;IA, IB, II, IIIA, IIIB, or IV=II;61;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

normal;IA, IB, II, IIIA, IIIB, or IV=II;62;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

AZ521;inducible dnSox2;gastric cancer cell line;doxycycline induced;8h

Human HeLa cells were propagated in DMEM medium (GIBCO-BRL) containing 10% fetal bovine serum. 2 X 106 HeLa cells were transiently transfected with in vitro-synthesized Stau1 siRNA.

Human HeLa cells were transiently transfected with in vitro-synthesized Stau1 siRNA.

Gene expression data from 3 uM EPZ004777 treated, DAY 6, biological rep.3, MOLM-13 cells

MOLM-13;acute myeloid leukemia (MLL-AF9 rearrangement);RPMI with 10% FBS;EPZ004777;day 6;3

Gene expression data from Vehicle treated, DAY 6, biological rep.1, MOLM-13 cells

MOLM-13;acute myeloid leukemia (MLL-AF9 rearrangement);RPMI with 10% FBS;Vehicle;day 6;1

tibial muscular dystrophy (TMD);extensor digitorum longus;53;male

Gene expression data from Vehicle treated, DAY 6, biological rep.2, MV4-11 cells

MV4-11;biphenotypic B myelomonocytic leukemia (MLL-AF4 rearragenment);IMDM with 10% FBS;Vehicle;day 6;2

Gene expression data from Vehicle treated, DAY 6, biological rep.3, MV4-11 cells

MV4-11;biphenotypic B myelomonocytic leukemia (MLL-AF4 rearragenment);IMDM with 10% FBS;Vehicle;day 6;3

Gene expression data from 3 uM EPZ004777 treated, DAY 6, biological rep.1, MOLM-13 cells

MOLM-13;acute myeloid leukemia (MLL-AF9 rearrangement);RPMI with 10% FBS;EPZ004777;day 6;1

Gene expression data from 3 uM EPZ004777 treated, DAY 6, biological rep.2, MOLM-13 cells

MOLM-13;acute myeloid leukemia (MLL-AF9 rearrangement);RPMI with 10% FBS;EPZ004777;day 6;2

Gene expression data from 3 uM EPZ004777 treated, DAY 6, biological rep.1, MV4-11 cells

MV4-11;biphenotypic B myelomonocytic leukemia (MLL-AF4 rearragenment);IMDM with 10% FBS;EPZ004777;day 6;1

Gene expression data from 3 uM EPZ004777 treated, DAY 6, biological rep.2, MV4-11 cells

MV4-11;biphenotypic B myelomonocytic leukemia (MLL-AF4 rearragenment);IMDM with 10% FBS;EPZ004777;day 6;2

Gene expression data from 3 uM EPZ004777 treated, DAY 6, biological rep.3, MV4-11 cells

MV4-11;biphenotypic B myelomonocytic leukemia (MLL-AF4 rearragenment);IMDM with 10% FBS;EPZ004777;day 6;3

Gene expression data from Vehicle treated, DAY 6, biological rep.1, MV4-11 cells

MV4-11;biphenotypic B myelomonocytic leukemia (MLL-AF4 rearragenment);IMDM with 10% FBS;Vehicle;day 6;1

bone marrow;CD34+ hematopoietic stem cells (HSC);myelodysplastic syndromes (MDS);refractory anemia with ringed sideroblasts (RARS);monosomy7/del(7q)

rat, hepatocellular carcinoma (DEN 50mg), treated with erlotinib 2mg (week 18)

Comparison of GATA6 null mouse tissue and wild type controls to determine the role GATA6 plays in lung development and regeneration.

Mouse Lung AIN Diet 8hr Saline Injection, biological replicate F
AN080206_Sample 52 Lung.CEL

Mouse Lung AIN Diet 5wk 100ppb As Drinking Water Expousre, biological replicate C
AN080306_Sample 53.CEL

Mouse Lung AIN Diet 5wk 10ppb As Drinking Water Exposure, biological replicate A
AN080406_Sample 54.CEL

Mouse Lung AIN Diet 5wk 100ppb As Drinking Water Expousre, biological replicate B
AN080906_Sample 56.CEL

Mouse Lung AIN Diet 5wk Control, biological replicate C
AN080206_Sample 57 Lung.CEL

Mouse Lung AIN Diet 5wk 10ppb As Food Exposure, biological replicate F
AN080806_Sample 58.CEL

Mouse Lung LRD Diet 5wk 10ppb As Drinking Water Exposure, biological replicate D
AN080906_Sample 59.CEL

Mouse Lung AIN Diet 8hr Saline Injection, biological replicate E
AN080906_Sample 60.CEL

Mouse Lung AIN Diet 8hr 1mg/kg Dex and 1mg/kg As Injection, biological replicate D
AN080906_Sample 61.CEL

Mouse Lung AIN Diet 5wk 10ppb As Drinking Water Exposure, biological replicate D
AN080206_Sample 62 Lung.CEL

um-uc-3 (atcc# crl-1749) bladder cancer cells were stably transfected with gfp, sorted for expression of gfp by fluorescence activated cell sorting as described (moissoglu et al. cancer res 2009. pmid: 19276387).  RNA was isolated for microarray hybridization from cells in log phase growth.

As a control for other samples transfected with GFP-RhoGDI2 fusion transgene, UM-UC-3 cells were cotransfected with GFP (empty vector) and pBABE PURO (for selection) and sorted by FACS as described before (Moissoglu et al. Cancer Res 2009. PMID:19276387).

um-uc-3 (atcc# crl-1749);bladder cancer cells;transfected with gfp

UM-UC-3 bladder cancer cells, stably transfected with GFP (control), biological replicate A

um-uc-3 (atcc# crl-1749) bladder cancer cells were stably transfected with gfp, sorted for expression of gfp by fluorescence activated cell sorting as described (moissoglu et al. cancer res 2009. pmid: 19276387). RNA was isolated for microarray hybridization from cells in log phase growth.

As a control for other samples transfected with GFP-RhoGDI2 fusion transgene, UM-UC-3 cells were cotransfected with GFP (empty vector) and pBABE PURO (for selection) and sorted by FACS as described before (Moissoglu et al. Cancer Res 2009. PMID:19276387). Two biological replicates were prepared, A and B, which are paired (prepared at the same times) as biological replicates A and B, respectively, of the GFP-RhoGDI2 experimental samples.

UM-UC-3 bladder cancer cells, stably transfected with GFP (control), biological replicate B

Clinical information: Sample.ID=868;Tumor.type=D;Size=3;Grade=3;Nodes=0/13;ER=Pos;PR=Pos;HER2=Neg;Age=65;DFS=130;Status=non-recur

NB192

NB190

NB191

Total cellular RNA from untreated and IFN-treated (2500 units/ml for 5 h) MEFs was extracted with TRIzol reagent (Invitrogen) according to the manufacturer's instructions.

Gene expression data from generated FTO1_C1 clone, 48h after induced espression of integrated copy of the FTO gene

Gene expression data from generated FTO1_C1 clone, 24h after induced espression of integrated copy of the FTO gene

STAT3-deficient naïve T cells stimulated for 3 hours with medium alone 1

Gene expression data from STAT3KO naïve CD4+ T cells stimulated for 3 hours with medium alone

CD4+ T;C57BL/6J;Cd4-Cre_C57BL6-STAT3<tm1Dlv> (STAT3KO);stimulated for 3 hours with medium alone

3rd Gen.FVB/N from 129Sv/Ev and Black Swiss mix;8 Weeks;Mammary Gland;Epithelial Cells;MMTV-cre; PtenF341V/loxP

Epithelials cells isolated from mouse mammary glands with PtenF341V expression

4th Gen. FVB/N from 129Sv/Ev and Black Swiss mix;8 Weeks;Mammary Gland;Epithelial Cells;MMTV-cre; Pten+/+

Epithelials cells isolated from mouse mammary glands with Wild-type Pten expression

NB169

Medulloblastoma cell line D425;doxycyline inducible shRNA against OTX2;16 hrs;3

3rd Gen.FVB/N from 129Sv/Ev and Black Swiss mix;8 Weeks;Mammary Gland;Epithelial Cells;MMTV-cre; Pten+/loxP

Epithelials cells isolated from mouse mammary glands with mono-allelic Pten expression

3rd Gen.FVB/N from 129Sv/Ev and Black Swiss mix;8 Weeks;Mammary Gland;Epithelial Cells;MMTV-cre; Pten+/+

NB170

Medulloblastoma cell line D425;doxycyline inducible shRNA against OTX2;24 hrs;3

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Tibolone treated. Patient 32.

Male;25;17h;6.9;control;superior temporal cortex (Brodmann Area 22, BA22)

Agilent TIFF High File = US22502532_251486820888_S01_H.tif
Agilent TIFF Low File = US22502532_251486820888_S01_L.tif

C57BL/6;RORasg/sg;male;5 Month old;Liver;35% Fat Diet (High Fat Diet; HFD)

Agilent TIFF High File = US22502532_251486820887_S01_H.tif
Agilent TIFF Low File = US22502532_251486820887_S01_L.tif

RWPE-1;Immortalized normal prostate epithelial cells.;100 nM 1,25(OH)2D;6 hours

RWPE-1;Immortalized normal prostate epithelial cells.;Vehicle (0.1% ethanol);6 hours

240;Asacol 800mg BD;1/10/59;M;ASIAN;8/2/04;12/14/04;FALSE;FALSE;FALSE;NO;FALSE;FALSE;3/3/05;1;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;BOTH;BOTH;BOTH;3/3/05;BOTH;BOTH;BOTH;BOTH;BOTH;5/31/05;DISEASE IN REMISSION;current;5-14;None;UC;8-9-01;descending colon;Inflamed;total RNA from 10 human cell lines

240;Asacol 800mg BD;1/10/59;M;ASIAN;8/2/04;12/14/04;FALSE;FALSE;FALSE;NO;FALSE;FALSE;3/3/05;1;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;BOTH;BOTH;BOTH;3/3/05;BOTH;BOTH;BOTH;BOTH;BOTH;5/31/05;DISEASE IN REMISSION;current;5-14;None;UC;8-9-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

237;Omep 20mg Losartan 50mg Bisoprolol 5mg Prav 40mg;11/12/28;M;CAUCASIAN;10/1/95;11/13/95;FALSE;FALSE;FALSE;NO;FALSE;FALSE;2/18/05;0;0;0;0;0;0;0;0;FALSE;0;12;12;12;12;12;11;11;11;11;BOTH;unknown;unknown;unknown;unknown;6/5/03;BOTH;BOTH;BOTH;unknown;unknown;5/30/05;DISEASE IN REMISSION;ex;1/1/50;1/1/52;0-4;Hypercholesteremia Prev CABG;UC;8-9-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

239;Asacol Fybogel Amitriptiline;4/10/41;F;CAUCASIAN;12/1/63;12/12/64;FALSE;FALSE;TRUE;NO;FALSE;FALSE;3/3/05;6;0;0;0;0;0;0;0;FALSE;1;BOTH;BOTH;unknown;unknown;unknown;3/3/05;BOTH;BOTH;BOTH;BOTH;BOTH;6/1/05;DISEASE IN REMISSION;never;unknown;None;UC;8-9-01;descending colon;Inflamed;total RNA from 10 human cell lines

234;Aza 150mg Atenolol Atorvastatin BFZ Clopidogril;9/29/46;M;CAUCASIAN;2/1/88;9/29/95;FALSE;FALSE;FALSE;YES;TRUE;FALSE;2/3/05;4;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;BOTH;unknown;unknown;2/3/05;BOTH;BOTH;BOTH;BOTH;BOTH;5/31/05;FAILURE OF THERAPY;never;unknown;IHD Angina;UC;8-9-01;sigmoid colon;Inflamed;total RNA from 10 human cell lines

236;None;11/20/53;M;CAUCASIAN;5/1/05;FALSE;FALSE;FALSE;unknown;FALSE;FALSE;2/18/05;15;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;BOTH;BOTH;BOTH;2/18/05;BOTH;BOTH;BOTH;BOTH;BOTH;8/15/05;DISEASE IN REMISSION;current;1/1/71;15-24;None;UC;8-9-01;terminal ileum;Uninflamed;total RNA from 10 human cell lines

234;Aza 150mg Atenolol Atorvastatin BFZ Clopidogril;9/29/46;M;CAUCASIAN;2/1/88;9/29/95;FALSE;FALSE;FALSE;YES;TRUE;FALSE;2/3/05;4;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;BOTH;unknown;unknown;2/3/05;BOTH;BOTH;BOTH;BOTH;BOTH;5/31/05;FAILURE OF THERAPY;never;unknown;IHD Angina;UC;8-9-01;ascending colon;Inflamed;total RNA from 10 human cell lines

234;Aza 150mg Atenolol Atorvastatin BFZ Clopidogril;9/29/46;M;CAUCASIAN;2/1/88;9/29/95;FALSE;FALSE;FALSE;YES;TRUE;FALSE;2/3/05;4;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;BOTH;unknown;unknown;2/3/05;BOTH;BOTH;BOTH;BOTH;BOTH;5/31/05;FAILURE OF THERAPY;never;unknown;IHD Angina;UC;8-9-01;descending colon;Inflamed;total RNA from 10 human cell lines

225;Asacol;5/30/76;F;CAUCASIAN;1/1/03;6/2/03;FALSE;FALSE;FALSE;NO;FALSE;FALSE;1/6/05;3;0;0;0;0;0;0;0;TRUE;0;BOTH;unknown;unknown;unknown;unknown;1/6/05;BOTH;unknown;unknown;unknown;unknown;3/7/05;DISEASE IN REMISSION;ex;1/1/99;5-14;None;UC;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

233;Asacol 1.2g Asprin 75mg Amilodipine 10mg;2/2/29;M;CAUCASIAN;1/1/92;1/1/92;FALSE;FALSE;FALSE;NO;FALSE;FALSE;2/1/05;3;0;0;0;0;0;0;0;FALSE;0;BOTH;BOTH;unknown;unknown;unknown;2/1/05;BOTH;BOTH;unknown;unknown;unknown;3/7/05;DISEASE IN REMISSION;ex;1/1/86;15-24;MI 1986, Prostate cancer 1994;UC;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

Gene expression data from microdissected epithelial cells of normal main pancreatic duct

microdissected epithelial cells from normal main pancreatic duct 7

microdissected epithelial cells from normal main pancreatic duct 5

microdissected epithelial cells from normal main pancreatic duct 6

microdissected epithelial cells from normal main pancreatic duct 3

microdissected epithelial cells from normal main pancreatic duct 4

Gene expression data from HeLa cells trnasfected with control siRNA

Cell strain 7 of cyclin D1KO 3T3 cells obtained by serial passaging MEFs from E14 embryos, stably infected with MSCV murine stem cell virus expressing cyclin D1b.

Sample from retroviral MSCV-D1b infected cyclin D1 knockout 3T3 cells (Line 7).

Gene expression data from cyclin D1 knockout 3T3s (cell line 7) infected with cyclin D1 splice variant (variant D1b) using Murine Stem Cell Virus (MSCV) system.

Cell strain 12 of cyclin D1KO 3T3 cells obtained by serial passaging MEFs from E14 embryos, stably infected with MSCV-D1a murine stem cell virus.

Sample from retroviral MSCV-D1a infected cyclin D1 knockout 3T3 cells (line 12).

Gene expression data from cyclin D1 knockout 3T3s (cell line 12) infected with full length cyclin D1 (variant D1a) using Murine Stem Cell Virus (MSCV) system.

whole lungs overexpressing an nmyc-gfp fusion protein via the lung surfactant c promoter

lungs were over expressing nmyc-gfp fusion protein using the lung surfactant  c promoter.

Lot batch = 5176

Lot batch = 5217

Cry1 and Cry2 double knockout mice. male mice. 8- to 10-weeks-old.
Keywords = circatian rhythm

Cry deficient mice. male mice. 8- to 10-week-old.

Clock mutant mice. male mice. 8- to 10-week-old.

Clock mutant mice. male mice. 8- to 10-week-old

C57BL/6 background mice. male mice. 8- to 10-week-old.

C57BL/6 background mice. male. 8- to 10-week-old.

LC-MI10

JLI_83

JLI_76

JLI_77

JLI_78

JLI_79

JLI_80

JLI_81

JLI_82

RNA interference (RNAi) against HNF4a1 was performed in HepG2 cells using siRNAs corresponding to nucleotides +179 to +197 of human HNF4A (NM_178849, sense siRNA: 5’-UGUGCAGGUGUUGACGAUGdTdT-3’, antisense siRNA 5’-CAUCGUCAACACCUGCACAdTdT-3’) purchased from Dharmacon Research, Inc. (An NCBI Blast search indicated that this sequence is unique to HNF4A). Approximately 24 hr prior to transfection, cells were plated at a density of ~1.5 x105 or  ~2.5 x105 cells/well in a 12- or 6-well plate, respectively (~50-70% confluency) without antibiotics. The siRNAs (100 or 200 pmol, respectively) were introduced into the cells using TransIT-TKO transfection reagent purchased from Mirus Bio Corporation (Madison, WI). Each experiment included a control containing just the transfection reagent as well as a nonspecific siRNA control against firefly luciferase (PGL3: sense siRNA 5’-CUUACGCUGAGUACUUCGAdTdT-3’; antisense siRNA 5’-dTdTGAAUGCGACUCAUGAAGCU). To verify HNF4a protein levels, cells were lysed in RIPA buffer purchased from Santa Cruz Biotechnology and analyzed by SDS-PAGE followed by immunoblotting

DMEM containing 10% Fetal Bovine Serum (FBS), 1% non-essential amino acids, and 1% sodium pyruvate. All cell lines were  supplemented with 1%

Total RNA was extracted using Trizol Reagent (Invitrogen, Carlsbad, CA) and reverse transcribed using the Reverse Transcription System kit (Promega, Madison, WI). PCR amplification was performed in the linear range using a PTC-100 TM programmable thermal controller (MJ Research, Inc., Hercules, CA). One-fifth of each reaction was electrophoresed on a 2% agarose gel, stained with ethidium bromide and visualized by UV light (see Supplementary Table S3B for a list of PCR primers used).

vHigh_24h_2

vHigh_24h_3

Gene expression was measured in adrenal glands of the Spontaneously Hypertensive Rat (SHR) using Affymetrix RG-U34A GeneChips. Replicate 1 of 3.

vHigh_8h_2

Gene expression was measured in adrenal glands of the Spontaneously Hypertensive Rat (SHR) using Affymetrix RG-U34A GeneChips. Replicate 3 of 3.

Gene expression was measured in adrenal glands of the Spontaneously Hypertensive Rat (SHR) using Affymetrix RG-U34A GeneChips. Replicate 2 of 3.

Gene expression was measured in adrenal glands of the Wistar-Kyoto rat (WKY) using Affymetrix RG-U34A GeneChips. Replicate 2 of 3.

Gene expression was measured in adrenal glands of the Wistar-Kyoto rat (WKY) using Affymetrix RG-U34A GeneChips. Replicate 1 of 3.

Gene expression was measured in adrenal glands of the Wistar-Kyoto rat (WKY) using Affymetrix RG-U34A GeneChips. Replicate 3 of 3.

vHigh_8h_4

vHigh_24h_1

Low_48h_2

Low_48h_3

vHigh_8h_1

MCF-7;human breast adenocarcinoma cells;1 nM final conc. vehicle (ethanol) + 1 uM vehicle (ethanol) for 24hr;1

MCF-7;human breast adenocarcinoma cells;1 nM final conc. vehicle (ethanol) + 1 uM vehicle (ethanol) for 24hr;2

MCF-7;human breast adenocarcinoma cells;1 nM final conc. vehicle (ethanol) + 1 uM vehicle (ethanol) for 24hr;3

MCF-7;human breast adenocarcinoma cells;1 nM final conc. vehicle (ethanol) + 1 uM 27-Hydroxycholesterol (27HC) for 24hr;3

MCF-7;human breast adenocarcinoma cells;1 nM final conc. E2 + 1 uM vehicle (ethanol) for 24hr;1

MCF-7;human breast adenocarcinoma cells;1 nM final conc. E2 + 1 uM vehicle (ethanol) for 24hr;2

MCF-7;human breast adenocarcinoma cells;1 nM final conc. E2 + 1 uM vehicle (ethanol) for 24hr;3

SMhu129

SMhu130

Gene expression data from the Caudate-Putamen of naive AChE-S mice

NCI-H460;human lung large cell carcinoma cells;cisplatin;24 hours

NCI-H460;human lung large cell carcinoma cells;cisplatin and cigarette smoke extract;24 hours

Gene expression data from the Caudate-Putamen of MPTP-exposed AChE-S mice

Eed mutant generated by gene targeting (Schoeftner et al., 2006);ES

These samples were derived from liver grafts of normal subjects with normal body mass index. The ages of these normal controls were matched with our NASH patients. No liver diseases were diagnosed with these normal controls. Although the biochemistry data provided by Admet were limited, the healthy status of these livers was ascertained by the lower transcription levels of marker genes for inflammation and fibrosis.

normal;IA, IB, II, IIIA, IIIB, or IV=IB;69;female, male:female;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=moderately differentiated;intestinal type, diffuse type, mixed type, or not determined=intestinal type

C57BL/6;C-DGCR8 KO (D4-cre/DGCR8 KO/Ai9 tdTomato);retina;cone photoreceptors;postnatal day 50

C57BL/6;C-DGCR8 KO (D4-cre/DGCR8 KO/Ai9 tdTomato);retina;cone photoreceptors;postnatal day 60

C57BL/6;C-DGCR8 KO (D4-cre/DGCR8 KO/Ai9 tdTomato);retina;cone photoreceptors;postnatal day 90

Bone marrow-derived macrophages (BMMs) from Pias1 null mice were treated with IFN-gamma (10 ng/ml)  for 4 h. Total RNA was prepared with RNA-STAT60 (TEL-TEST) and purified with the RNeasy kit (Qiagen). Double stranded complementary DNA was synthesized from 20 ug of total RNA according to Affymetrix methodology, and purified with Phase Lock Gels (Eppendorf). Biotin-labeled RNA was synthesized with the BioArray High Yield RNA Transcript Labeling Kit (Enzo). Samples were cleaned, fragmentated and hybridized to murine genome (MGU74Av2) Genechips (Affymetrix) as instructed. GeneChips were stained with phycoerythrin-streptavidin (Molecular Probes) and scanned with a GeneChip scanner (Affymetrix). Data were analyzed with the GeneSpring software.

Bone marrow-derived macrophages (BMMs) from Pias1 null mice were treated with IFN-gamma (10 ng/ml)  for 2 h. Total RNA was prepared with RNA-STAT60 (TEL-TEST) and purified with the RNeasy kit (Qiagen). Double stranded complementary DNA was synthesized from 20 ug of total RNA according to Affymetrix methodology, and purified with Phase Lock Gels (Eppendorf). Biotin-labeled RNA was synthesized with the BioArray High Yield RNA Transcript Labeling Kit (Enzo). Samples were cleaned, fragmentated and hybridized to murine genome (MGU74Av2) Genechips (Affymetrix) as instructed. GeneChips were stained with phycoerythrin-streptavidin (Molecular Probes) and scanned with a GeneChip scanner (Affymetrix). Data were analyzed with the GeneSpring software.

Bone marrow-derived macrophages (BMMs) from Pias1 null mice were treated with IFN-beta (500 U/ml)  for 4 h. Total RNA was prepared with RNA-STAT60 (TEL-TEST) and purified with the RNeasy kit (Qiagen). Double stranded complementary DNA was synthesized from 20 ug of total RNA according to Affymetrix methodology, and purified with Phase Lock Gels (Eppendorf). Biotin-labeled RNA was synthesized with the BioArray High Yield RNA Transcript Labeling Kit (Enzo). Samples were cleaned, fragmentated and hybridized to murine genome (MGU74Av2) Genechips (Affymetrix) as instructed. GeneChips were stained with phycoerythrin-streptavidin (Molecular Probes) and scanned with a GeneChip scanner (Affymetrix). Data were analyzed with the GeneSpring software.

Bone marrow-derived macrophages (BMMs) from Pias1 null mice were treated with IFN-beta (500 U/ml)  for 2h. Total RNA was prepared with RNA-STAT60 (TEL-TEST) and purified with the RNeasy kit (Qiagen). Double stranded complementary DNA was synthesized from 20 ug of total RNA according to Affymetrix methodology, and purified with Phase Lock Gels (Eppendorf). Biotin-labeled RNA was synthesized with the BioArray High Yield RNA Transcript Labeling Kit (Enzo). Samples were cleaned, fragmentated and hybridized to murine genome (MGU74Av2) Genechips (Affymetrix) as instructed. GeneChips were stained with phycoerythrin-streptavidin (Molecular Probes) and scanned with a GeneChip scanner (Affymetrix). Data were analyzed with the GeneSpring software.

C57BL6  X 129sv mixed;liver;sphingosine-1-phosphate (S1P) lyase knock-out

The Identification of gene expression changes in human embryonic fibroblast cells depleted of SUZ12. Sample C

The Identification of gene expression changes in human embryonic fibroblast cells depleted of SUZ12. Sample B

Gene expression data from mouse ESC after 48h RNAi against Rad21

Gene expression data from NTERA2/D1 cells treated with Vamp7 siRNA, biological replicate 1

brain microvessels from SHR treated with vehicle for 4 weeks subcutaneously by osmotic minipump.

12-week-old 12-week-old spontaneously hypertensive rats (SHR), male, brain microvessels, treated with vehicle for 4 weeks subcutaneously by osmotic minipump

brain microvessels from SHR treated with candesartan (0.3 mg/kg/day) for 4 weeks subcutaneously by osmotic minipump.

12-week-old 12-week-old spontaneously hypertensive rats (SHR), male, brain microvessels, treated with AT1 antagonsit (candesartan, 0.3 mg/kg/day) for 4 weeks subcutaneously by osmotic minipump.

12-week-old spontaneously hypertensive rats (SHR), male, brain microvessels, treated with vehicle for 4 weeks subcutaneously by osmotic minipump.

12-week-old 12-week-old spontaneously hypertensive rats (SHR), male, brain microvessels, treated with vehicle for 4 weeks subcutaneously by osmotic minipump.

primary whole splenic B-lymphocytes from wild type CBA adult mice

microarray analysis of gene expression after transverse aortic constriction in mice - 48 hours sham group No.1

microarray analysis of gene expression after transverse aortic constriction in mice - 48 hours sham group No.2

microarray analysis of gene expression after transverse aortic constriction in mice - 10 days TAC group No.2

microarray analysis of gene expression after transverse aortic constriction in mice - 10 days TAC group No.3

microarray analysis of gene expression after transverse aortic constriction in mice - 10 days TAC group No.4

microarray analysis of gene expression after transverse aortic constriction in mice - 10 days sham group No.2

microarray analysis of gene expression after transverse aortic constriction in mice - 10 days sham group No.3

microarray analysis of gene expression after transverse aortic constriction in mice - 10 days sham group No.4

microarray analysis of gene expression after transverse aortic constriction in mice - 10 days TAC group No.1

The R package aroma.affymetrix (v2.9.0) from Bioconductor was used to generate RMA expression and perform QC.

Biotinylated cRNA were prepared according to the standard Affymetrix protocol (2-cycle amplification)

kidney epithelial proximal tubule cells;NRK-52E;Osborne-Mendel;DMSO 72 hr

kidney;Male, Wistar-derived-Liverpool John Moores University rats;7-9 weeks of age;monuron 72 hr

gemcitabine resistant Calu3 were treated over 10 consecutive 10-day treatment cycles with 50 nM gemcitabine and 1 micromolar bexarotene for the first 3 days of the cycle followed by 7 days of 1 micromolar bexarotene alone

gemcitabine resistant Calu3 cells, treated for 10 cycles of 10 days each with gemcitabine plus bexarotene (still largely gemcitabine resistant since cells resensitized during culturing were eliminated from the culture by gemcitabine before harvest)

Primary cultures of fetal human telencephalon cells were transformed with a retroviral vector pLSNmyc carrying the v-myc oncogene and the neomycin resistance gene. Following selection with G418, a single continuously dividing clone with a capacity to self-renew and differentiate into neurons and glial cells both in vitro and in vivo was isolated and designated HB1.F3. It carried normal human karyotype of 46 XX. After transducing a retroviral vector pBabePNgn1 carrying the open-reading frame (ORF) of the human Ngn1 gene and the puromycin resistance gene into HB1.F3 cells, a single puromycin-resistant clone was selected, expanded, and designated HB1.F3-Ngn1. In the present study, the wild-type HB1.F3 cells and the HB1.F3-Ngn1 cells are abbreviated as F3-WT and F3-Ngn1.

The cells were incubated in the feeding medium composed of Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/ml streptomycin. The medium was renewed every three days.

The arrays were scanned by the GeneChip Scanner 3000 7G (Affymetrix).

The data expressed as CEL files were normalized by the robust multiarray average (RMA) method with the Expression Console software version 1.1 (Affymetrix).

Total RNA was isolated from subconfluent cells by using the TRIZOL Plus RNA Purification kit (Invitrogen). The quality of total RNA was evaluated on Agilent 2100 Bioanalyzer (Agilent Technologies). Total RNA of F3-WT and F3-Ngn1 was processed for two times (names as 1st and 2nd) different hybridization experiments.

Hybridization was performed at 45℃ for 17 hours. The arrays were washed and stained in the GeneChip Fluidic Station 450 (Affymetrix) by using Hybridization, Wash and Stain kit (Affymetrix).

One hundred ng of total RNA was processed for cRNA synthesis, fragmentation, and terminal labeling with the GeneChip Whole Transcript Sense Target Labeling and Control Reagents (Affymetrix).

Neural stem cells (NSC) with self-renewal and multipotent properties serve as an ideal cell source for transplantation to treat spinal cord injury, stroke, and neurodegenerative diseases. To efficiently induce neuronal lineage cells from NSC for neuron replacement therapy, we should clarify the intrinsic genetic programs involved in a time and place-specific regulation of human NSC differentiation. Recently, we established an immortalized human NSC clone HB1.F3 to provide an unlimited NSC source applicable to genetic manipulation for cell-based therapy. To investigate a role of neurogenin 1 (Ngn1), a proneural basic helix-loop-helix (bHLH) transcription factor, in human NSC differentiation, we established a clone derived from F3 stably overexpressing Ngn1. Genome-wide gene expression profiling identified 250 upregulated genes and 338 downregulated genes in Ngn1-overexpressing F3 cells (F3-Ngn1) versus wild-type F3 cells (F3-WT). Notably, leucine-rich repeat-containing G protein-coupled receptor 5 (LGR5), a novel stem cell marker, showed a robust increase in F3-Ngn1.

Murine fibroblast-like synoviocytes (FLS) were isolated from the hind paws of hTNFtg and hTNFtg;Rsk2-/y (background: C57BL/6) 6 - 9 week-old mice via collagenase digestion. Cells were cultured in DMEM medium supplemented with 10% heat inactivated fetal calf serum, penicillin (100 U/ml), streptomycin (100 µg/ml) and gentamycin (0.5 µg/ml). All cell cultures were carried out at 37 °C in 5% CO2. The cells of two mice were pooled and cultivated for at least 3 passages before usage. For characterization, the cells were tested for the surface expression of CD90.2 and VCAM1 by flow cytometric analysis (> 95%), whereas CD11b as a monocytic marker had to be absent (< 5%).

Gene expression of murine fibroblast-like synoviocytes Grp1_C57BL6_2_FLS_TNFtg_plus_RSK2-KO

Arrays were scanned with an Affymetrix GeneChip Scanner 3000, using the GCOS software version 1.4 from Affymetrix.

Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Grün) with the Bioretis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the Bioretis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All 3 chips of group 1 were compared to the 3 chips of group 2 and chips within one group were compared to each other in both directions. The following parameters of absolute and comparative analysis were included in the Bioretis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p-value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal I, MI; Decrease, D; Marginal D, MD; No Change, NC), and the p value for that call. Additionally – not calculated with GCOS – t-tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using strict Bonferroni corrected Welch t-tests between 9 SLR values of Experiment group vs. Baseline group and 12 SLR values within both groups (the latter 12 giving a mean SLR value of zero; p-value had to be <= 5.279E-08) or more than 50% of non-parametrically calculated Change calls (Mann-Whitney U test, GCOS) i.e. 5 or more of all 9 Change calls of Experiment group vs. Baseline group have to be in the same direction. Significantly differentially expressed genes, were filtered using both default parameter sets of filter criteria. These are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips and validated with the Affymetrix Latin Square dataset as shown in Menssen et al., 2009. You can find these validation experiments in BioRetis without registering, using the public content and public login. Click on view single results, select any existing Analysis beginning with first 3 letters "SGU" and click on "Next". Click on "Chose an existing parameterset" and select "JRG_Increase" for increased or "JRG_Decrease" for decreased probesets and click on "Fill". At the bottom of the site check the box named "* use Bonferroni correction" and click on "Search only" to get the list of significantly changed increased or decreased probesets, respectively. The Affymetrix Latin Square dataset, consisting of 42 chips in 14 experiments with three replicates each were analyzed in BioRetis with all possible 3 vs. 3 chip comparisons (in one direction only).

Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including the recommended DNase digest. The purity and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and amount was checked with a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).

Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Expression Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG_U430_2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C, rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 450.

Gene-expression profiling of primary murine hTNFtg FLS, Rsk2-/y; chip 2. Samples were analyzed using murine MG_U430_2 arrays (Affymetrix)

C57BL/6;male;primary murine fibroblast-like synoviocytes (FLS);human TNF transgenic and knockout in Rsk2 gene (Rsk2-/y FLS);CD90.2pos/VCAM1pos/CD11bneg

Gene expression of murine fibroblast-like synoviocytes Grp1_C57BL6_1_FLS_TNFtg_plus_RSK2-KO

Gene-expression profiling of primary murine hTNFtg FLS, Rsk2-/y; chip 1. Samples were analyzed using murine MG_U430_2 arrays (Affymetrix)

IRAK4 kinase dead mouse bone marrow macrophages, LPS stimulated, 1 hour

IRAK4 kinase dead mouse bone marrow macrophages, unstimulated, 4 hours

EFLmDREAM;stimulated with LPS and mouse recombinant IL-4 (day 2);B cells

Region of the left ventricle [lv2] below the LAD artery of a sham operated mouse

Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450.  Arrays were then scanned with an Affymetrix Scanner 3000 and data was obtained using the Genechip Operating Software (Version 1.2.0.037).

The resulting files (.dat, .cel and .chp) were imported into the Rosetta Resolver system (Version 7.1).  This system performs data pre-processing and error modeling as described in Weng (2006).  Resolver generated fold-changes and p values, based on ratios built in the system, were exported for further analysis.

Qiagen Rneasy protocol using mini columns; elute RNA with 70 degree water

Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix Amplification One-Cycle Target labeling kit according to manufacturer's protocol.

Embryonic day 14.5;wild type (WT);fetal liver;b6, 129 mixed background strain

Embryonic day 14.5;Zfp36l2 knockout (KO);fetal liver;b6, 129 mixed background strain

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Untreated control. nr 38.

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Untreated control. nr 17.

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Untreated control. nr 21.

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Untreated control. nr 12.

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Untreated control. nr 37.

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Untreated control. nr 22.

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Untreated control. nr 33.

Gene expression data from  C57BL/6GT(ROSA)26tm9(creEsr1)Arte (TamoxCre)  control CTL treated with 4OHT
TamoxCreKG168

Gene expression data from C57BL/6GT(ROSA)26tm9(creEsr1)Arte (TamoxCre) control CTL treated with 4OHT
TamoxCreKG167

Gene expression data from PDK1 null CTL ( C57BL/6GT(ROSA)26tm9(creEsr1)Arte PDK1fl/fl treated with 4OHT)
TamoxCrePDK1KC248

CTL made from PDK1fl/fl TamoxCre splenocytes and treated with 4OHT

TamoxCreKG169

TamoxCrePDK1KC283

TamoxCrePDK1KC252

unfractionated thymocytes from a 3-week old IkL/L mouse (C57Bl6 background)

unfractionated thymocytes from a 3-week old WT mouse (C57Bl6 background)

Hela tet off cells expressing IkBa mutant cultured in absence of Dox, TNF stimulated 0h

anaplastic thyroid carcinoma (ATC);subtype spindle/giant cell;unmatched

This sample is from Rotavirus infection convalescence phase of patient RI34

This sample is from Rotavirus acute phase infection of patient #10 (see Table 1 in paper)

This sample is from Rotavirus acute phase infection of patient #9 (see Table 1 in paper)

This sample is from Rotavirus acute phase infection of patient #8(see Table 1 in paper)

This sample is from Rotavirus acute phase infection of patient #7(see Table 1 in paper)

This sample is from Rotavirus acute phase infection of patient #6(see Table 1 in paper)

This sample is from Rotavirus acute phase infection of patient #5(see Table 1 in paper)

This sample is from Rotavirus acute phase infection of patient #4(see Table 1 in paper)

This sample is from Rotavirus infection convalescence phase of patient RI39

-0.025641026;exon 11;GIST Tumor;Universal Human Reference RNA (Stratagene)

-0.075949367;exon 11;GIST Tumor;Universal Human Reference RNA (Stratagene)

-0.153846154;wildtype;GIST Tumor;Universal Human Reference RNA (Stratagene)

0.276315789;wildtype;GIST Tumor;Universal Human Reference RNA (Stratagene)

BioBreeding  DRlyp/lyp rat, day 65, mast cells derived from pancreatic lymph node

HDAC2 conditionally mutated mice were provided by Dr EN Olson (University of Texas Southwestern Medical Center, Dallas, TX) (Montgomery et al., 2007). Floxed HDAC2 mice were crossed with villin-Cre transgenic mice to insure specific intestinal epithelial cell gene deletion (Madison et al., 2002). Genomic DNA was recovered with the Spin Doctor genomic DNA kit (Gerard Biotech, Oxford, OH). Mouse genotypes were determined with already published RT-PCR protocols (Montgomery et al., 2007). Mice were fed a normal diet in a transgenic mouse facility.

arrays are scanned using a GeneArray Scanner at an excitation wavelength of 488nm. Light emissions at 570nm are proportional to the bound target at each oligonucleotides position on the GeneChip® array.

Data analysis, normalization average difference and expression measurements were subsequently completed with Flexarray software version 1.6.1.  Background correction and normalization were assessed with a multi-array average (RMA) algorithm. Significant statistical differences were calculated with the Student’s t test, with the cut-off for statistical significance set to a p value of 0.05 or below.

Total RNAs from the colon of three control and three HDAC2 IEC-specific knockout mice were isolated with the Rneasy kit (Qiagen, Mississauga, ON, Canada). cDNA preparation and microarray assay were performed at the Microarray platform of the McGill University and Génome Quebec Innovation Centre

Hybridized target cRNA is stained with streptavidin phycoerythrin

Target RNA is reverse transcribed into cDNA and in-vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization

gene expression data in colon epitelial cells from HDAC1/2 KO mice

Female;97;3.5h;6.2;schizophrenic;superior temporal cortex (Brodmann Area 22, BA22)

MAT1A_wt15_3

MAT1A_wt15_2

MAT1A_wt15_1

Rats were sacrificed eighteen hours after the injection with methylprednisolone

STAT1-deficient naïve T cells stimulated for 3 hours with IL-27 3

Gene expression data from STAT1KO naïve CD4+ T cells stimulated for 3 hours with IL-27

CD4+ T;C57BL/6J;C57BL6-STAT1<tm1Dlv> (STAT1KO);stimulated for 3 hours with IL-27 (20 ng/ml)

STAT1-deficient naïve T cells stimulated for 3 hours with IL-27 2

STAT1-deficient naïve T cells stimulated for 3 hours with IL-27 1

STAT1-deficient naïve T cells stimulated for 3 hours with IL-6 3

MCF10A cells were cultured at 37°C in 5% CO2 and 95% air to no more than 80% confluence in Dulbecco's modified Eagle's medium/nutrient mixture F-12 medium (Invitrogen, Mulgrave, Vic, Australia) supplemented with 5% (v/v) horse serum (Invitrogen), 20 ng/ml human recombinant EGF (R&D Systems), 0.5 μg/ml hydrocortisone (Sigma), 0.1 ng/ml cholera toxin (Sigma), 10 μg/ml bovine insulin (Sigma), 50 units/ml penicillin G (Invitrogen), and 50 μg/ml streptomycin sulfate (Invitrogen).

Arrays were scanned at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.

Data was RMA normalised using NormalizeAffymetrixST (version 2.0) GenePattern module from the Peter Wills Bioinformatics Centre's GenePattern Server: http://pwbc.garvan.unsw.edu.au/gp

Total RNA was extracted by using the Qiagen RNeasy minikit (Qiagen, Doncaster, Vic, Australia) according to manufacturer’s protocol. Following extraction, RNA concentration and purity were analysed using the NanoDrop® ND-1000 Spectrophotometer (Nano-Drop Technologies, Wilmington, DE, USA). For Affymetrix GeneChip® analysis, the integrity of RNA was analysed using the Agilent Bioanalyser 2100 6000 Nano Assay (Agilent Technologies, Palo Alto, CA, USA) according to the manufacturer’s instructions.

Labeled, fragmented cDNA hybridized to Affymetrix Human Gene 1.0 ST Gene Arrays at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.

Total RNA was converted to cDNA. The cDNA was fragmented, biotin labeled at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.

STAT3-deficient naïve T cells stimulated for 3 hours with medium alone 3

STAT3-deficient naïve T cells stimulated for 3 hours with medium alone 2

T26;Mouse tumorgraft, cohort 8;Male;73;Clear-cell renal cell carcinoma;mutant;wild type;mutant

Gene expression profiling of mouse tumorgraft, cohort 8 of patient T26

T79;Mouse tumorgraft, cohort 0;Male;59;Clear-cell renal cell carcinoma;wild type;mutant;mutant

Gene expression profiling of mouse tumorgraft, cohort 0 of patient T79

T26;Mouse tumorgraft, cohort 0;Male;73;Clear-cell renal cell carcinoma;mutant;wild type;mutant

Gene expression profiling of mouse tumorgraft, cohort 0 of patient T26

T26;Mouse tumorgraft, cohort 4;Male;73;Clear-cell renal cell carcinoma;mutant;wild type;mutant

Gene expression profiling of mouse tumorgraft, cohort 4 of patient T26

T183;Clear-cell renal cell carcinoma (ccRCC) tumor;Male;56;Clear-cell renal cell carcinoma;T1NxM1;IV;2;wild type;mutant;mutant

Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient T183

T166;Normal cortex;Male;56;Clear-cell renal cell carcinoma;wild type;wild type;wild type

T166;Clear-cell renal cell carcinoma (ccRCC) tumor;Male;56;Clear-cell renal cell carcinoma;T3N1M0;III;4;mutant;wild type;mutant

Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient T166

T164;Clear-cell renal cell carcinoma (ccRCC) tumor;Male;75;Clear-cell renal cell carcinoma;T4NxM0;IV;4;wild type;wild type;wild type

Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient T164

T165;Clear-cell renal cell carcinoma (ccRCC) tumor;Male;40;Clear-cell renal cell carcinoma;T3NxM0;n/a;3;wild type;mutant;mutant

Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient T165

Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 0 hours, replica 1

Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 0 hours, replica 3

Polyamide 2 treated LNCaP cells not stimulated with DHT, biological replicate 3

Polyamide 2 treated LNCaP cells not stimulated with DHT, biological replicate 2

Polyamide 2 treated LNCaP cells not stimulated with DHT, biological replicate 1

SK-MEL-2 cells treated with Ad-LacZ at MOI 2 plus doxorubicin (sample 1)

SK-MEL-2 cells treated with Ad-LacZ at an MOI of 2 plus doxorubicin 0.1 uM(sample1)

SK-MEL-2 cells treated with Ad-LacZ at MOI 2 plus doxorubicin (sample 2)

SK-MEL-2 cells treated with Ad-LacZ at an MOI of 2 plus doxorubicin 0.1 uM(sample2)

121;Cp-tenedone, Enalapril, Loperamide.;4/8/59;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;2/1/05;Diarrhoea, Blastocytitis on stool cultures.;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;terminal ileum;Uninflamed;total RNA from 10 human cell lines

120;Minicycline;5/6/54;M;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;1/18/05;Altered bowel habit;0;TRUE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

120;Minicycline;5/6/54;M;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;1/18/05;Altered bowel habit;0;TRUE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

119;Salubtamol, Bricanyl;9/30/70;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;1/27/05;FH Colon Ca;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;descending colon;Uninflamed;total RNA from 10 human cell lines

115;Frusemide, Codine Phosphate;9/14/28;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;12/21/04;Diarrhoea, Also has Prostate Ca;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

122;Venlafaxine;7/10/61;M;JEWISH;FALSE;FALSE;FALSE;FALSE;FALSE;2/10/05;FH Colon Ca;0;TRUE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

heart of mouse subjected 4 week to chronic constant hypoxia (4B)

Cerebellum_transgenic nuclear localization signal Htt exon1 142Q S25_3 months_replicate 1

S25 NLS 142Q TG1	F4/23	S25	NLS Htt exon 1 142Q	Mouse	3 months	Cerebellum	Male

Crohn's Disease subject (28 year old caucasian female, SAK_1316711535)

Crohn's Disease subject (46 year old black female, SAK_1307657998)

Crohn's Disease subject (27 year old caucasian male, SAK_1313693880)

Crohn's Disease subject (54 year old caucasian male, SAK_1316666829)

Crohn's Disease subject (28 year old black male, SAK_1313738586)

Csbm/m Mouse_cerebellum_Standard diet supplemented with resveratrol_Ad Lib_Replicate-5

Sample name: CSB_Resv_5

Csbm/m Mouse_cerebellum_Standard diet supplemented with resveratrol_Ad Lib_Replicate-6

Sample name: CSB_Resv_6

Sample name: CSB_SD_2

Csbm/m Mouse_cerebellum_Standard diet supplemented with resveratrol_Ad Lib_Replicate-2

Sample name: CSB_Resv_2

Sample name: CSB_SD_3

Sample name: CSB_SD_4

wild-type control (littermate) of "P16_exPKO_pancreas"; mixed genetic background; postnatal day 16; total pancreas; replicate mouse #2.

CCL3-injected Ccl3-/-, replicate 1

Hybridized Mouse Genome 430 2.0 Arrays (3'-arrays, Affymetrix, 900495) were scanned following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility

Raw image files were processed using Affymetrix GCOS 1.3 software to calculate individual probe cell intensity data and generate CEL data files. Using GCOS and the MAS 5.0 algorithm, intensity data was normalized per chip to a target intensity TGT value of 500, and expression data and present/absent calls for individual probe sets were calculated. Gene symbols and names for data analyzed with the MAS 5.0 algorithm were from the Affymetrix NetAffx Mouse430_2 annotations file (http://www.affymetrix.com/support/technical/byproduct.affx?product=moe430-20). Quality control was performed by examining raw DAT image files for anomalies, confirming each GeneChip array had a background value less than 100, monitoring that the percencelle present calls was appropriate for the cell type, and inspecting the poly(A) spike in controls, housekeeping genes, and hybridization controls to confirm labeling and hybridization consistency. In addition, the quantity of RNA purified per cell, the labeling efficiency for each cycle of amplification, and the fragmentation efficiency were carefully monitored.; CEL data files were also independently analyzed using the dChip algorithm. Gene expression values were normalized and modeled across arrays using the dChip software package with invariant-set normalization and a PM model (www.dchip.org, Li and Wong, 2001).

Total RNA was isolated from cells with the RNeasy micro kit (Qiagen, Valencia, CA)

Labeled-cRNA was fragmented and hybridized to Mouse Genome 430 2.0 Arrays (3'-arrays, Affymetrix, 900495) following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility

Biotinylated cRNAs for hybridization to Affymetrix 3'-arrays were prepared from 1ug total RNA using the Affymetrix two-cycle target labeling assay with spike in controls (Affymetrix Inc., Santa Clara, CA, 900494).

Cultured oligodendrocytes;Myelin-gene Regulatory Factor control littermate

Cultured oligodendrocytes;Myelin-gene Regulatory Factor conditional knockout

Background correction using variance stabilizing transformation (VST) and quantile normalization were performed using the LUMI package (v.1.14.0) in R v.2.11.1 (2010-05-31).

1μg of RNA from four replicates each from wildtype and claudin-18 knockout whole lung was converted into cRNA and was used for Illumina mouseRef-8 v2 whole genome expression analysis. Expression arrays were carried out at the Southern California Genotyping Consortium (SCGC) at the University of California, Los Angeles.

mixed 129S6/SvEvTac, C57BL/6J, Balb/c;CLDN18_KnockOut;3-4 months;Male;whole lung tissue

mixed 129S6/SvEvTac, C57BL/6J, Balb/c;WildType;3-4 months;Male;whole lung tissue

41B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

42B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

39B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

40B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

44B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

bone marrow derived mast cells;NTAL knock out;C57BL/6;none;none;2 h 100 ng/ml TNP-BSA

Gene expression profile of non-malignant FTE from BRCA1/2-mutation carrier during the follicular phase

female;78 years;thigh;13x10x6;atypical lipoma with partly dedifferentiated areas;high;G2;local recurrence;yes;no

female;74 years;thigh;7x6x4;dedifferentiated liposarcoma;medium;G2;primary tumor;no;no

male;38 years;knee;8.3x4x7;myxoid liposarcoma;high;G3;primary tumor;yes;no

male;76 years;thigh;3.5x3x3;dedifferentiated liposarcoma;high;G3;local recurrence;yes;no

WT-GFP-lamin A Induction: Day 0 Replicate A (CBGE_Hsapiens_WG_progerin1)

BV-173 leukemia cells were incubated with 10 µM STI571 (Imatinib) for 16 hours.

NALM-1 leukemia cells were cultured without STI571 (Imatinib).

FACS-sorted LSK (Lin-Sca1+c-Kit+) cells were isolated from pIpC-treated Srf flx/flx ;Mx1-Cre and Srf+/+;Mx1-Cre pooled animals

Srf flx/flx mice were crossed with the polyinosine-polycytidine (pIpC)-inducible Mx1-Cre recombinase mouse line. Induction was performed on 6 weeks-old mice by three intra-peritoneal (IP) injections of 200 µg/dose pIpC (Invivogen) every 2 days and mice were analyzed 35 days after the last injection.

Total RNAs were collected from invalidated or not 105 LSKs (n=3 per genotype) using the RNeasy micro kit (Qiagen)  according to manufacturer’s protocol

3,75 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Affymetrix MOE430A. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

30 ng of total RNA were amplified and labeled using the NuGen Ovation RNA Amplification System V2 followed by the FL-Ovation cDNA Biotin Module V2 according to manufacturer’s protocol. (NuGEN Technologies Inc.).

BV-173 leukemia cells were cultured without STI571 (Imatinib).

Gene expression data from MRL/MpJ strain mouse heart left ventrical.

Gene expression data from normal C57BL/6 strain mouse left ventrical.

Gene expression from A549 cells after transfection with FAM60A targeting siRNA, replicate 2

Gene expression from A549 cells after transfection with FAM60A targeting siRNA, replicate 3

Gene expression from A549 cells after transfection with FAM60A targeting siRNA, replicate 1

Lot batch = rat 25

blast count: 60

blast count: 96

blast count: 50

blast count: 90

Center code: 6

blast count: 88

blast count: 85

Renal vesicles from Lim1 mutant E12.5 embryos isolated by laser capture microdissection.

E12.5 Lim1 mutant embryo renal vesicles isolated by laser capture microdissection

E12.5 Lim1 mutant renal vesicles isolated by laser capture microdissection.

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D72 (30 days post-EBRT);P2

male;non-metastatic prostate cancer;peripheral blood;white blood cells;baseline;4

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D1;P2

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D72 (30 days post-EBRT);2

male;non-metastatic prostate cancer;peripheral blood;white blood cells;baseline;P2

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D21;P2

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D42;P2

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D7;P2

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D14;P2

pre-iPSC- siRNA to Ehmt1, Ehmt2 and Setdb1- biological replicate2

RE1_H17_1910_U133Plus2.0.CEL

CG
32 mg
1

Air
1
4

Air
1
4

Air
1
4

liver cells from txnrd1 liver-null 8wk male mouse 8 challenged with vehicle (saline)_16

liver cells from txnrd1 liver-null 8wk male mouse 8 challenged with acetaminophen (APAP)_17

liver cells from txnrd1 liver-null 8wk male mouse 8 challenged with acetaminophen (APAP)_3

Affymetrix murine MOE 430 2.0  gene chips were used.GeneChip CEL  files were subjected to RMA  normalization using  the  GeneSpring GX 7.1.
GeneSpring 7.1 (Agilent technologies Inc. Palo Alto, California) was used to normalization, Clustering and filtering. Individual clusters were then analyzed for functional relatedness of genes within the cluster using David 2.0(http://david.abcc.ncifcrf.gov/summary.jsp).

Pancreata were dissected from 12.5, 14.5 and 16.5 day mouse embryos taken from timed matings of Pdx1Cre/+ ; beta-cateninflox/+ mice and immediately submerged in RNAlater [Ambion, Inc., Austin, TX].
Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].

Full Protocol Description: Create a hybridization cocktail for a single probe array that contains 0.067 ug/uL fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer.  Heat hybridization cocktail to 99oC for 5 minutes, to 45oC for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45oC for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45oC for 16 hrs in the Hybridization Oven rotating at 60 rpm.

Wild type [WT] pancreata were dissected from day 14 and 16 mouse embryos. A Pdx1-cre transgenic line was crossed with a floxed allel of beta-catenin to generate beta-catenin knock-out [KO] pancreata at the 14.5 and 16.5 time points.

Gene expression data under ER stress from lymphoblastoid cells of twin HB02070 treated with 500nM thapsigargin.
The Family ID is REQ115 and the individual IDs are HB02069 and HB02070.
HB02069 and HB02070 are a pair of twins, but they were not obtained from Coriell.  They were obtained from HBDI.

lymphoblastoid cell line;REQ115;HB02070;Twin number 2;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin HB02070 treated with DMSO.

lymphoblastoid cell line;REQ115;HB02070;Twin number 2;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1756:2 treated with 500nM thapsigargin.

lymphoblastoid cell line;1756;GM14582;Twin number 2;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1756:2 treated with DMSO.

lymphoblastoid cell line;1756;GM14582;Twin number 2;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin HB02069 treated with 500nM thapsigargin.

lymphoblastoid cell line;REQ115;HB02069;Twin number 1;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin HB02069 treated with DMSO.

lymphoblastoid cell line;REQ115;HB02069;Twin number 1;DMSO;4 hours

Hdh knock-in embryonic stem cells, Q50 line, biological replicate 3

Hdh knock-in embryonic stem cells, Q91 line, biological replicate 1

Hdh knock-in embryonic stem cells, Q50 line, biological replicate 1

Hdh knock-in embryonic stem cells, Q50 line, biological replicate 2

Hdh knock-in embryonic stem cells, Q20 line, biological replicate 2

Hdh knock-in embryonic stem cells, Q20 line, biological replicate 3

Gene expression data from liver after 20 week feeding of western diet

Hdh knock-in embryonic stem cells, Q91 line, biological replicate 2

Hdh knock-in embryonic stem cells, Q91 line, biological replicate 3

RNA extracted from lymphoblastic cell line derived from FCHL (familial combined hyperlipemia) patient.

RNA extracted from cultured lymphoblastic cell line derived from FCHL (familial combined hyperlipemia) patient

RNA extracted from cultured lymphoblastic cell line derived from normal subject

Gene expression data from DN-MAML transduced CUTLL1 cells treated with compound E for 3days and washout compund E for 2 hours

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Estradiol treated. Patient 24.

brain (frontal cortex);healthy control;48 yr;white;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);healthy control;51 yr;white;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);schizophrenia;44 yr;white;295.9;16 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);schizophrenia;31 yr;white;295.3;22 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);healthy control;55 yr;white;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);schizophrenia;40 yr;white;295.9;21 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);schizophrenia;38 yr;Hispanic;295.9;17 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);schizophrenia;47 yr;white;295.3;20 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

After 2 days of differentiation, EBs were then transferred to 6 well ultra low attachment dishes (Corning) and expression of FLAG-Msgn1 was induced using 1ug/ml Dox. Samples were collected at 12h interval up to 48h. Using this protocol, the expression of endogenous markers of the PSM lineage initiate on day 3 of in vitro differentiation. Thus induction of F-Msgn1 expression after 2 days of differentiation results in premature, ectopic Msgn1 expression.

A2loxFMsgn1 ES cells were grown in DMEM, 15%FBS, Pen/Strep and LIF on mitomycin treated mouse embryonic fibroblasts. For EB differentiation, ESC were plated on 10cm Petri dishes at a density of 2.5 million cells per plate in 15ml of DMEM, 10% FBS, 1x NEAA, Pen/Strep, 2-Mercaptoethanol and 50ug/ml ascorbic acid (Sigma).

Data were collected using Affymetrix GCOS software. Statistical and clustering analysis was done using BRB array tools and Genespring GX11 software.

Cells were lysed in RLT buffer (Qiagen) according to manufacturers instructions. Total RNA was purified using RNeasy mini kit (Qiagen). RNA quality was checked on the Agilent Bioanalyzer.  All samples used for microarray analysis had high quality scores (RIN >9).

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Gene expression data of Day2 embryoid bodies cultured for another 24h

129P2 (formerly called 129/Ola);embryoid bodies;Day2 EBs cultured for another 24h

Gene expression data of Day2 embryoid bodies induced with doxycycline and cultured for another 12h

129P2 (formerly called 129/Ola);embryoid bodies;Day2 EBs induced with doxycycline and cultured for another 12h

Gene expression data of Day2 embryoid bodies cultured for another 12h

129P2 (formerly called 129/Ola);embryoid bodies;Day2 EBs cultured for another 12h

Moderate Asthma;Fresh Bronchial Epithelial Cells;female;35.43014

2nd Run - Muscle biopsy (vastus laterlis) from morbidly obese patient (sample name: JGB-2) after gastric bypass surgery (2nd staining)

High_24h_4

Ishikawa;39-year-old parous Japanese female diagnosed with endometrial adenocarcinoma stage 2.;bisphenol A;10 nM;24 hours

High_48h_1

High_24h_2

High_24h_3

High_8h_4

Ishikawa;39-year-old parous Japanese female diagnosed with endometrial adenocarcinoma stage 2.;bisphenol A;10 nM;8 hours

High_24h_1

High_8h_2

High_8h_3

High_48h_2

High_48h_3

Pool of total RNA from 3 euploid cerebella at P15 postnatal stage

Wild type naïve T cells stimulated for 3 hours with medium alone 2

Gene expression data from wild type naïve CD4+ T cells stimulated for 3 hours with medium alone

CD4+ T;C57BL/6J;wild type;stimulated for 3 hours with medium alone

Wild type naïve T cells stimulated for 3 hours with medium alone 1

Wild type naïve T cells stimulated for 3 hours with medium alone 3

Rat230_2;15;ul;1.606;0.744;2.12;1:5;8.2;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;145;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.631;0.833;1.93;1:5;8.1;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;146;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.615;0.851;1.88;1:5;8.3;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;73;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 19, Units of Duration: days, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 0.7, Units of Dose or Concentration: ppm

nasal epithelium, formaldehyde inhalation exposure, 0.7 ppm, 6 hours per day, 5 days per week, 19 day time point

Rat230_2;15;ul;1.221;0.621;1.96;1:5;8.4;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;152;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.139;0.58;1.95;1:5;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;154;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.475;0.755;1.93;1:5;8.1;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;155;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.809;0.918;1.95;1:5;8.8;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;156;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

in vivo Treatment: Formaldehyde, Treatment Repeat: 5, Units of Treatment Repeat: days per week, Treatment Duration: 24, Units of Duration: hrs, Treatment Time: 6, Units of Treatment Time: hrs per day, Route of Exposure: Inhalation (whole-body), Dose or Concentration: 0.7, Units of Dose or Concentration: ppm

nasal epithelium, formaldehyde inhalation exposure, 0.7 ppm, 6 hours per day, 24 h time point

Rat230_2;15;ul;1.789;0.949;1.83;1:5;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;132;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;2.767;1.439;1.87;1:5;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;133;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;2.167;1.069;1.95;1:5;8.3;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;134;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Sample name: GFPMYCneg_8G
Gene expression data from MYC negative GC B cell subpopulation, paired to 7G

Gene expression data from colorectal adenocarcinoma of the experimental group at the end of 20 weeks after intraperitoneal injection of AOM.

Gene expression data from high grade dysplasia of the experimental group at the end of 6 weeks after intraperitoneal injection of AOM.

Gene expression data from high grade dysplasia of the experimental group at the end of 8 weeks after intraperitoneal injection of AOM.

Typically Developing Control, Semitendinosus, Patient Replicate 6

Typically Developing Control, Semitendinosus, Patient Replicate 7

Typically Developing Control, Semitendinosus, Patient Replicate 8

Typically Developing Control, Semitendinosus, Patient Replicate 9

Typically Developing Control, Semitendinosus, Patient Replicate 10

Fenretinide-treated CD34+ cells isolated from the patient CML35, harvested after 48h in culture

Untreated CD34+ cells isolated from the patient CML35, harvested after 48h in culture

Fenretinide-treated CD34+ cells isolated from the patient CML34, harvested after 48h in culture

Untreated CD34+ cells isolated from the patient CML34, harvested after 48h in culture

Fenretinide-treated CD34+ cells isolated from the patient CML33, harvested after 48h in culture

Untreated CD34+ cells isolated from the patient CML33, harvested after 48h in culture

Day: 12; Drug: Methamphetamine; Phase: Drug treatment; Replicate: 2

Total cellular RNA from untreated MEFs was extracted with TRIzol reagent (Invitrogen) according to the manufacturer's instructions.

6_MTDHplus3_4-13-10_s2.CEL

Male;3 months;additional patient information found in Series supplementary file

Male;2.5 months;additional patient information found in Series supplementary file

Male;1.5 months;additional patient information found in Series supplementary file

Male;108 months;additional patient information found in Series supplementary file

Male;60 months;additional patient information found in Series supplementary file

Male;50 months;additional patient information found in Series supplementary file

Male;36 months;additional patient information found in Series supplementary file

Male;33 months;additional patient information found in Series supplementary file

This vehicle is associated with accession No. GSM231519-GSM231525

HepG2 Cells;Male;ATCC;Vehicle Treated 0.1N KOH (equivalent volume to treated) in cell culture media

HepG2 Cells;male;ATCC;Vehicle Treated 0.1N KOH (at equivalent volume as treated) in media

Treated with 100uM Trovafloxacin for 24 hrs
Treatment on a different day than original treatments

OCI-Ly10;diffuse large B-cell lymphoma (DLBCL);LZRS-FOXP1-IRES-YFP;FOXP1 overexpression

OCI-Ly7;diffuse large B-cell lymphoma (DLBCL);siRNA targeting FOXP1;siRNA-mediated FOXP1 knockdown

Trasnsformed Lymphocytes Bipolar Disorder Affected Twin Pair 3 (DCBD3.1)(TP9)

TP9;DCBD3.1;BD1 with psychotic features;18;35;38;Female;sodium valproate (5 years)

Trasnsformed Lymphocytes Bipolar Disorder Affected (Affected pateint of MZ twin pair 3)

Cancers; Prox.Jejunum tumor

GI_canc, Duodenal Tumor

OCI-Ly10;diffuse large B-cell lymphoma (DLBCL);sigenome non-targeting siRNA;negative control

This is Nrl-ko-Gfp P6 replicate 4.

This is wt-Gfp 4 weeks replicate 1.

This is Nrl-ko-Gfp P2 replicate 2.

This is Nrl-ko-Gfp P2 replicate 3.

This is Nrl-ko-Gfp P10 replicate 4.

This is Nrl-ko-Gfp P2 replicate 1.

This is Nrl-ko-Gfp P6 replicate 2.

This is Nrl-ko-Gfp P6 replicate 3.

This is Nrl-ko-Gfp P2 replicate 4.

This is Nrl-ko-Gfp P6 replicate 1.

breast cancer derived cell line treated with 10 uM of etoposide for 12 hours

breast cancer derived cell line treated with 40 uM of etoposide for 36 hours

breast cancer derived cell line treated with 30 uM of etoposide for 12 hours

19_(Mouse430_2).CEL

5;C57Bl/6;STAT6 KO;bone marrow-derived macrophage;IL-4;Control;10 days

20_(Mouse430_2).CEL

5;C57Bl/6;STAT6 KO;bone marrow-derived macrophage;IL-4;Rosiglitazone;10 days

17_(Mouse430_2).CEL

5;C57Bl/6;STAT6 KO;bone marrow-derived macrophage;Control;Control;10 days

18_(Mouse430_2).CEL

5;C57Bl/6;STAT6 KO;bone marrow-derived macrophage;Control;Rosiglitazone;10 days

15_(Mouse430_2).CEL

4;C57Bl/6;STAT6 KO;bone marrow-derived macrophage;IL-4;Control;10 days

16_(Mouse430_2).CEL

4;C57Bl/6;STAT6 KO;bone marrow-derived macrophage;IL-4;Rosiglitazone;10 days

13_(Mouse430_2).CEL

4;C57Bl/6;STAT6 KO;bone marrow-derived macrophage;Control;Control;10 days

14_(Mouse430_2).CEL

4;C57Bl/6;STAT6 KO;bone marrow-derived macrophage;Control;Rosiglitazone;10 days

11_(Mouse430_2).CEL

3;C57Bl/6;Wild-type;bone marrow-derived macrophage;IL-4;Control;10 days

12_(Mouse430_2).CEL

3;C57Bl/6;Wild-type;bone marrow-derived macrophage;IL-4;Rosiglitazone;10 days

Biological replicate 4 of 5. Technical Replicate 1 of 2. Control splenocytes, untreated

Biological replicate 4 of 5. Technical Replicate 2 of 2. Control splenocytes, untreated

Biological replicate 3 of 5. Technical Replicate 1 of 2. Control splenocytes, untreated

Biological replicate 3 of 5. Technical Replicate 2 of 2. Control splenocytes, untreated

Biological replicate 2 of 5. Technical Replicate 1 of 2. Control splenocytes, untreated

Biological replicate 2 of 5. Technical Replicate 2 of 2. Control splenocytes, untreated

Biological replicate 1 of 5. Technical Replicate 1 of 2. Control splenocytes, untreated

Biological replicate 1 of 5. Technical Replicate 2 of 2. Control splenocytes, untreated

Biological replicate 5 of 5. Technical Replicate 1 of 2. Control splenocytes, untreated

Biological replicate 5 of 5. Technical Replicate 2 of 2. Control splenocytes, untreated

LOX-1:213301;LOX1_Untreated_6hr:213301;Classification:Good;Gradient Severity:0.03;Distortion Severity:0.09;Defective Area (%):0;Outlier Area (%):0.02;3'/5' Mean:1.62;Background Mean Dev.:0.52;Absent (%):57.11;Absent (%) Dev.:0.88;Scaling Factor:0.53;Scaling Factor Dev.:0.69;LOX1;6 hours;(Not applicable);213301;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;LOX1_Untreated_6hr;282295653

LOX-1:121203;GFP_oxLDL_2hr:121203;Classification:Good;Gradient Severity:0.03;Distortion Severity:0.02;Defective Area (%):0.01;Outlier Area (%):0.01;3'/5' Mean:1.92;Background Mean Dev.:0.54;Absent (%):59.05;Absent (%) Dev.:0.62;Scaling Factor:0.57;Scaling Factor Dev.:0.38;GFP;2 hours;Oxidized LDL;121203;HAECT;50 ug/ml;Endothelial;Human:Homo sapiens;GFP_oxLDL_2hr;282295523

LOX-1:113402;GFP_Untreated_12hr:113402;Classification:Good;Gradient Severity:0.03;Distortion Severity:0.02;Defective Area (%):0;Outlier Area (%):0.01;3'/5' Mean:1.48;Background Mean Dev.:0.18;Absent (%):59.48;Absent (%) Dev.:0.95;Scaling Factor:0.7;Scaling Factor Dev.:0.72;GFP;12 hours;(Not applicable);113402;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;GFP_Untreated_12hr;282295723

LOX-1:213202;LOX1_Untreated_2hr:213202;Classification:Good;Gradient Severity:0.04;Distortion Severity:0.03;Defective Area (%):0;Outlier Area (%):0.01;3'/5' Mean:1.8;Background Mean Dev.:0.27;Absent (%):57.58;Absent (%) Dev.:0.52;Scaling Factor:0.62;Scaling Factor Dev.:0.05;LOX1;2 hours;(Not applicable);213202;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;LOX1_Untreated_2hr;282295543

LOX-1:113401;GFP_Untreated_12hr:113401;Classification:Good;Gradient Severity:0.03;Distortion Severity:0.02;Defective Area (%):0;Outlier Area (%):0.01;3'/5' Mean:1.56;Background Mean Dev.:0.03;Absent (%):57.6;Absent (%) Dev.:0.5;Scaling Factor:0.61;Scaling Factor Dev.:0;GFP;12 hours;(Not applicable);113401;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;GFP_Untreated_12hr;282295713

LOX-1:113201;GFP_Untreated_2hr:113201;Classification:Medium;Gradient Severity:0.05;Distortion Severity:0.1;Defective Area (%):0;Outlier Area (%):0;3'/5' Mean:1.56;Background Mean Dev.:1.93;Absent (%):59.17;Absent (%) Dev.:0.71;Scaling Factor:0.64;Scaling Factor Dev.:0.22;GFP;2 hours;(Not applicable);113201;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;GFP_Untreated_2hr;282295473

LOX-1:121503;GFP_oxLDL_24hr:121503;Classification:Good;Gradient Severity:0.03;Distortion Severity:0.04;Defective Area (%):0;Outlier Area (%):0;3'/5' Mean:1.8;Background Mean Dev.:0.42;Absent (%):58.99;Absent (%) Dev.:0.57;Scaling Factor:0.73;Scaling Factor Dev.:0.99;GFP;24 hours;Oxidized LDL;121503;HAECT;50 ug/ml;Endothelial;Human:Homo sapiens;GFP_oxLDL_24hr;282295883

LOX-1:221502;LOX1_oxLDL_24hr:221502;Classification:Bad;Gradient Severity:0.06;Distortion Severity:0.03;Defective Area (%):0.07;Outlier Area (%):0.01;3'/5' Mean:1.66;Background Mean Dev.:3.63;Absent (%):58.23;Absent (%) Dev.:0.02;Scaling Factor:0.39;Scaling Factor Dev.:1.93;LOX1;24 hours;Oxidized LDL;221502;HAECT;50 ug/ml;Endothelial;Human:Homo sapiens;LOX1_oxLDL_24hr;282295933

LOX-1:121201;GFP_oxLDL_2hr:121201;Classification:Good;Gradient Severity:0.04;Distortion Severity:0.05;Defective Area (%):0;Outlier Area (%):0;3'/5' Mean:2.11;Background Mean Dev.:1.33;Absent (%):57.64;Absent (%) Dev.:0.48;Scaling Factor:0.43;Scaling Factor Dev.:1.59;GFP;2 hours;Oxidized LDL;121201;HAECT;50 ug/ml;Endothelial;Human:Homo sapiens;GFP_oxLDL_2hr;282295503

LOX-1:213502;LOX1_Untreated_24hr:213502;Classification:Good;Gradient Severity:0.07;Distortion Severity:0.03;Defective Area (%):0;Outlier Area (%):0.01;3'/5' Mean:1.58;Background Mean Dev.:1.06;Absent (%):57.27;Absent (%) Dev.:0.76;Scaling Factor:0.47;Scaling Factor Dev.:1.26;LOX1;24 hours;(Not applicable);213502;HAECT;(Not applicable);Endothelial;Human:Homo sapiens;LOX1_Untreated_24hr;282295903

NB164

Medulloblastoma cell line D425;doxycyline inducible shRNA against OTX2;24 hrs;2

NB163

Medulloblastoma cell line D425;doxycyline inducible shRNA against OTX2;16 hrs;2

NB166

Medulloblastoma cell line D425;doxycyline inducible shRNA against OTX2;96 hrs;2

NB130

Medulloblastoma cell line D425;doxycyline inducible shRNA against OTX2;96 hrs;1

NB129

Medulloblastoma cell line D425;doxycyline inducible shRNA against OTX2;48 hrs;1

NB162

Medulloblastoma cell line D425;doxycyline inducible shRNA against OTX2;8 hrs;2

NB161

Medulloblastoma cell line D425;doxycyline inducible shRNA against OTX2;0 hrs;2

Gene expression data from Trip12 mutant mouse embryonic stem cell

a time series of ConA injections was administered and  20 mg/kg ConA was injected through the mouse caudal vein at one of 4 time points (0 hr, 1 hr, 3 hr, 6 hr),here is  hepatic gene expression at "6hr" (rep3)

a time series of ConA injections was administered and  20 mg/kg ConA was injected through the mouse caudal vein at one of 4 time points (0 hr, 1 hr, 3 hr, 6 hr),here is  hepatic gene expression at "6 hr" (rep1)

a time series of ConA injections was administered and  20 mg/kg ConA was injected through the mouse caudal vein at one of 4 time points (0 hr, 1 hr, 3 hr, 6 hr),here is  hepatic gene expression at "3 hr" (rep3)

a time series of ConA injections was administered and  20 mg/kg ConA was injected through the mouse caudal vein at one of 4 time points (0 hr, 1 hr, 3 hr, 6 hr),here is  hepatic gene expression at "6hr" (rep2)

a time series of ConA injections was administered and  20 mg/kg ConA was injected through the mouse caudal vein at one of 4 time points (0 hr, 1 hr, 3 hr, 6 hr),here is  hepatic gene expression at "3hr" (rep2)

Mammary glands were minced and digested with enzyme mix to generate single cell suspensions. YFP-marked luminal epithelial cells were sorted by FACS.

Mammary tissues were isolated from adult virgin female mice of their corresponding genotypes.

Each cDNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured.

The raw CEL files were imported, normalized and analyzed with GenePattern analysis tools (dCHIP, GSEA) from the Broad Institute.

RNeasy kit (Qiagen, #74134) was used according to manufacturer's protocol.

The biotinylated cDNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C.

Labeling, hybridization and scan performed by team of Dr. E. Fox at the Dana-Farber Cancer Institute Microarray Core Facility. The NuGEN Ovation V2 Amplification System was used to amplify and label the samples, according to manufacturer's protocol.

MD643(L L)
Gene expression data for sorted Runx1-null luminal mammary epithelial cells marked by MMTV-Cre.

mixed B6/129/FVB;MMTV-Cre;Runx1L/L;R26Y;female;adult virgin;mammary gland luminal epithelial cells

MD869(L L)

MD638(+ +)
Gene expression data for sorted wildtype luminal mammary epithelial cells marked by MMTV-Cre.

mixed B6/129/FVB;MMTV-Cre;Runx1+/+;R26Y;female;adult virgin;mammary gland luminal epithelial cells

MD642(+ +)

MD892(+ +)

MD640(L L)

Sample name: C3
GC1963new.CEL

C57BL/6J female number 3, 2 months old, whole ear tissue, untreated control ear

C57BL/6J female number 2, 2 months old, whole ear tissue, untreated control ear

C57BL/6J female number 1, 2 months old , whole ear tissue, untreated control ear

human coronary artery smooth muscle Cells, treated with metoprolol, replicate 3

human coronary artery smooth muscle Cells, treated with metoprolol, replicate 2

human coronary artery smooth muscle Cells, treated with nebivolol, replicate 1

human coronary artery smooth muscle Cells, treated with nebivolol, replicate 3

Only those samples with an RNA Integrity Number (RIN) >7 were used for hybridization. Samples of 500ng/ul were used to perform a Affymetric mouse 430_2 expression array

#3;diseased individual, inflamed;primary mucosal tissue,  colon;31.5

whole blood;Unaffected control;Male;2;n/a;n/a;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

whole blood;Unaffected control;Female;2;n/a;n/a;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

RB1-383 pGIPZ (OpenBiosystems)(shRB1), human osteoblast cell line (hOB)

"female subject, 18-45 yrs, whole blood cells 3 h after intravenous endotoxin challenge"

3 min exposure to halothane, sacrificed by cold saline perfusion.
Keywords = Eckenhoff anesthetics

Sciatic nerves from GNMT-KO mice_Replicate 2_Gene Expression Array

Peripheral blood mononuclear cells;oligoarticular JIA;LT6;145min;White;Female

Peripheral blood mononuclear cells;oligoarticular JIA;LT6;100min;White;Female

Peripheral blood mononuclear cells;oligoarticular JIA;GTE6;80min;White;Female

Peripheral blood mononuclear cells;oligoarticular JIA;GTE6;133min;White;Male

Bipolar disorder;51;Male;23;28;6.67;23;Right;1200;Yes;Yes;No;No;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): 3

Bipolar disorder;41;Male;21;20;6.60;39;Left;4000;No;No;No;No;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): 4

Bipolar disorder;29;Male;22;7;6.39;48;Left;9000;Yes;No;No;Yes;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): 3

Bipolar disorder;45;Male;35;10;6.35;28;Right;10000;Yes;Yes;No;No;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): Unknown

Bipolar disorder;45;Male;16;29;6.03;35;Left;20000;No;No;No;No;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): 5

Bipolar disorder;29;Male;17;12;6.70;60;Left;0;No;No;No;Yes;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): 5

Bipolar disorder;56;Male;28;28;6.07;23;Right;Unknown;No;No;Yes (60 treatments);Yes;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): 4

Bipolar disorder;33;Female;15;18;6.51;24;Left;3000;Yes;No;No;Yes;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): 5

Gastrocnemius-soleus muscles, basal status, integrin alpha7 transgenic mouse

FBN+/+.TGFBRIIko_6
Gene expression data from Tgfbr4 knockout mice

Colonic biopsy was collected during endoscopy from normal control individual. The standard Affymetrix protocols were followed to prepare target from 5ug of total RNA. The expression profiles generated from normal individuals were compared to that from patients with different types of disease.

CP_N3
Gene expression from the pineal gland of a control mouse at ZT20.

C57BL/6J; NeuroD1flox::Crx-Cre-/-;control;2 months;pineal gland;ZT20

CP_N1

CP_N2

CP_D2
Gene expression from the pineal gland of a control mouse at ZT6.

C57BL/6J; NeuroD1flox::Crx-Cre-/-;control;2 months;pineal gland;ZT6

The basal culture medium was Dulbecco’s modified Eagle’s medium (DMEM) containing Glutamax-1 (Gibco BRL, Paisley, Scotland) supplemented with 10% fetal calf serum (FCS; Gibco BRL) and ascorbic acid (100 Ag/ml; Sigma, St. Louis, MO).

Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Murine Genome U74 Av2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

with TCDD added to the medium at 1 µM

The basal culture medium was Dulbecco’s modified Eagle’s medium (DMEM) containing Glutamax-1 (Gibco BRL, Paisley, Scotland) supplemented with 10% fetal calf serum (FCS; Gibco BRL)

with TCDD added to the culture at 1 µM

Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

Control rats 240h after injection with PBS
Treatment, type=time_course, description=Control animals are treated with PBS, measurement=240.0 h

Rats 240h after injection with dose kainate.
Treatment, type=time_course, description=KA animals are treated with kainate., measurement=240.0 h

TP_D2

Additional details provided in accompanying manuscript, BC4 TC_TCR

Additional details provided in accompanying manuscript, BC4 TC_NOC

A549 a pulmonary alveolar epithelial cell line was used in mechanical stretch and parenchymal cell activation experiments. Cells were grown in flexercell plates coated with collagen I, and allowed to grow O/N. Cells were then exposed to cyclic stretch - 20% elongation for 1hr or 4hrs. Two replicates for each time point were performed. This is the second replicate for the 4hr time point. Experiemnt was carried out Jan 31 2003

alveolar epithelial cell line exposed to cyclic stretch 20% elongation for 4hr

AML blasts from bone marrow;training;mutated;M1;internal tandem duplication (ITD)

Sample name: C4
GC1964new.CEL

150N

S-855-N

S-414-N

S-316-N

I-840-N

I-1031-N

H-661-N

H-615-N

H-137-N

in vivo Treatment: MEHP, Treatment Duration: 6, Units of Duration: hours, Treatment Time: 10:00, Units of Treatment Time: am, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.28, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

KJ_1_6_31_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

in vivo Treatment: MEHP, Treatment Duration: 3, Units of Duration: hours, Treatment Time: 1:16, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.225, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

KJ_1_3_51_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

in vivo Treatment: MEHP, Treatment Duration: 1, Units of Duration: hour, Treatment Time: 1:12, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.23, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

KJ_1_1_39_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

in vivo Treatment: MEHP, Treatment Duration: 2, Units of Duration: hours, Treatment Time: 1:02, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.24, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

KJ_1_2_43_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

in vivo Treatment: Corn Oil, Treatment Duration: 2, Units of Duration: hours, Treatment Time: 1:00, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.235, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

KJ_1_2_ 7_Testis_Control_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

in vivo Treatment: MEHP, Treatment Duration: 2, Units of Duration: hours, Treatment Time: 1:14, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.225, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

KJ_1_2_45_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

in vivo Treatment: MEHP, Treatment Duration: 2, Units of Duration: hours, Treatment Time: 1:08, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.21, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

KJ_1_2_44_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

in vivo Treatment: MEHP, Treatment Duration: 3, Units of Duration: hours, Treatment Time: 1:10, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.23, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

KJ_1_3_50_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

in vivo Treatment: MEHP, Treatment Duration: 3, Units of Duration: hours, Treatment Time: 1:04, Units of Treatment Time: pm, Vehicle for Chemical: corn oil, Amount of Vehicle: 0.188, Route of Exposure: oral gavage, Units of Amount of Vehicle: ml, Dose or Concentration: 1, Units of Dose or Concentration: gm/kg bodyweight

KJ_1_3_49_Testis_MEHP_Rat230_2_04005: PND 28 Fischer rats were gavaged with a single dose of 1 gram/kg MEHP in corn oil or corn oil alone.  The animals were sacrified 1, 2, 3, 6, or 12 hours after dosing.  The testis were removed and RNA extracted using the QIAGEN RNeasy Maxi kit

A549 cells control treatment (Mannitol) for 24hrs.  Replicate #3

A549 cells control treatment (Mannitol) for 24hrs.  Replicate #1

A549 cells control treatment (Mannitol) for 24hrs.  Replicate #2

A549 cells control treatment (Mannitol) for 12hrs.  Replicate #3

A549 cells control treatment (Mannitol) for 12hrs.  Replicate #1

A549 cells control treatment (Mannitol) for 12hrs.  Replicate #2

THP-1 cell line infected with scrambled control shRNA, biological rep3
Sample name: THP1_CTRL-3
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B07_596722.CEL

total skin from Hoxc13-overexpressing transgenic mice (GC13) 5 days post natal

Gene expression data from MCF-7 cells treated with vehicle control (DMSO)

Gene expression profiling data of highly purified CD34+ cells from untreated normal donor 3.

Gene expression profiling data of highly purified CD34+ cells from normal donor 3 after in vitro TCDD exposure.

hematopoietic progenitor CD34+ cells;in vitro TCDD exposure;normal donor 3

Gene expression profiling data of highly purified CD34+ cells from untreated normal donor 4.

Gene expression profiling data of highly purified CD34+ cells from normal donor 4 after in vitro TCDD exposure.

hematopoietic progenitor CD34+ cells;in vitro TCDD exposure;normal donor 4

Gene expression profiling data of highly purified CD34+ cells from untreated normal donor 5.

Gene expression profiling data of highly purified CD34+ cells from normal donor 2 after in vitro TCDD exposure.

hematopoietic progenitor CD34+ cells;in vitro TCDD exposure;normal donor 2

Day: 6; Drug: Methamphetamine; Phase: Drug treatment; Replicate: 2

Day: 3; Drug: Methamphetamine; Phase: Drug treatment; Replicate: 2

SAM630138;C57BL/6;spr881;IL17RC Knock out;pooled mouse reference RNA

08-34_ACCX9

adenoid cystic carcinoma grown as xenograft tumor;primary;parotid salivary gland;female

08-34_ACCX6

adenoid cystic carcinoma grown as xenograft tumor;metastasis to lung;parotid salivary gland;male

08-34_ACCX5M1

adenoid cystic carcinoma grown as xenograft tumor;metastasis to lung;oral cavity;male

08-34_ACCX5

adenoid cystic carcinoma grown as xenograft tumor;primary;oral cavity;male

08-34_ACCX4

08-34_ACCX2

adenoid cystic carcinoma grown as xenograft tumor;primary;parotid salivary gland;male

08-34_ACCX16

adenoid cystic carcinoma grown as xenograft tumor;primary;lung bronchus;female

08-34_ACCX12

adenoid cystic carcinoma grown as xenograft tumor;primary;trachea;female

08-34_MAD04-385

adenoid cystic carcinoma grown as xenograft tumor;primary;oral cavity;female

Cyclophosphamide-treated spleen 5 days - Biological Replicate 4 - Technical Replicate 2

Biological replicate 4 of 5. Technical Replicate 2 of 2.Cyclophosphamide-treated splenocytes, day 5

Cyclophosphamide-treated spleen 5 days - Biological Replicate 4 - Technical Replicate 1

Biological replicate 4 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated splenocytes, day 5

Cyclophosphamide-treated spleen 5 days - Biological Replicate 3 - Technical Replicate 2

Biological replicate 3 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated splenocytes, day 5

Cyclophosphamide-treated spleen 5 days - Biological Replicate 3 - Technical Replicate 1

Biological replicate 3 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated splenocytes, day 5

Cyclophosphamide-treated spleen 5 days - Biological Replicate 2 - Technical Replicate 2

Biological replicate 2 of 5. Technical Replicate 2 of 2. Cyclophosphamide-treated splenocytes, day 5

Cyclophosphamide-treated spleen 5 days - Biological Replicate 2 - Technical Replicate 1

Biological replicate 2 of 5. Technical Replicate 1 of 2. Cyclophosphamide-treated splenocytes, day 5

Grown on 6-well collagen type I coated plates
Treatment period: 24 hrs

Primary Human Hepatocytes Incubated In Vitro with quinolones
Growth Media:  In Vitro Technologies Hepatocyte Incubation Media (cat # Z90009

primary human hepatocyte;Female;In Vitro Technologies;Celebral Vascular Accident;Yes

The data were processed and normalised using the BioConductor package VSN (variance stabilisation and normalisation)  in R

RNA was extracted using the RNAqueous®-Micro Kit from Ambion in accordance with manufacturers protocols. RNA quantity and quality was assessed by spectral density.

C57BL/6,;Male,;between 6-8 weeks,;RM3 (E) 801710 Soya-free powdered diet from B.S & S.,;Colon

left ventricle from sedentary animals

Gene expression data from C57BL/6 strain mouse heart left ventrical with 3 day LAD ligation.

Gene expression data from MRL/MpJ strain mouse left ventrical with 3 day LAD ligated heart.

ove26 mice;fvb(cg)-tg(ins2-calm1)26ove tg(cryaa-tag)1ove/pnej;Male;8 weeks;glomerulus;Diabetic

S4_2h_1
Gene expression data from rat tracheal explants exposed to cigarette smoke (treatment) at 2hrs.

S6_2h_28

S5_2h_47

S6_24h_31

S1_2h_16

S2_2h_45

S3_2h_34

SKI-DLCL cells were treated with AraC alone in concentration 20nM for 24h. Total RNA was extracted

SKI-DLCL cells treated with Aplidin (3nM) for 24h. Total RNA was extracted.

SKI-DLCL cells treated with Aplidin 3.0nM for 24h. Total RNA was isolated using RNeasy kit.

SKI-DLCL cells were treated with Aplidin at concentration 3nM for 24h. Total RNA was extracted.

Gene expression data under ER stress from lymphoblastoid cells of twin 1725:1 treated with 500nM thapsigargin.

lymphoblastoid cell line;1725;GM14476;Twin number 1;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1725:1 treated with DMSO.

lymphoblastoid cell line;1725;GM14476;Twin number 1;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1720:1 treated with 500nM thapsigargin.

lymphoblastoid cell line;1720;GM14464;Twin number 1;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1720:1 treated with DMSO.

lymphoblastoid cell line;1720;GM14464;Twin number 1;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1720:2 treated with 500nM thapsigargin.

lymphoblastoid cell line;1720;GM14465;Twin number 2;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1720:2 treated with DMSO.

lymphoblastoid cell line;1720;GM14465;Twin number 2;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1724:1 treated with 500nM thapsigargin.

lymphoblastoid cell line;1724;GM14474;Twin number 1;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1724:1 treated with DMSO.

lymphoblastoid cell line;1724;GM14474;Twin number 1;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1724:2 treated with 500nM thapsigargin.

lymphoblastoid cell line;1724;GM14475;Twin number 2;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1724:2 treated with DMSO.

lymphoblastoid cell line;1724;GM14475;Twin number 2;DMSO;4 hours

Lot batch = 0183-5k

Lot batch = 0182-5k

Lot batch = 0387-5k

Lot batch = 0386-5k

Total RNA was extracted from lymphoblastoid cells of AU0943303 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;AU0943303 is a control male without autism.

Total RNA was extracted from lymphoblastoid cells of AU0995302 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;AU0995302 is a control male without autism.

Total RNA was extracted from lymphoblastoid cells of AU016804 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;AU016804 is a control male without autism.

Total RNA was extracted from lymphoblastoid cells of AU016703 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;AU016703 is a control male without autism.

Total RNA was extracted from lymphoblastoid cells of AU081206 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;AU081206 is a control male without autism.

Total RNA was extracted from lymphoblastoid cells of AU055103 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;AU055103 is a control male without autism.

Total RNA was extracted from lymphoblastoid cells of AU060003 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

Pooled total RNAs from lymphoblastoid cells of 14 individuals;AU060003 is a control male without autism.

Tet2 deficient CD150+ sorted LSKs; replated 5 times-repeat2
Gene expression data from Tet2 deficient CD150+ sorted LSKs; replated 5 times-repeat2

Tet2 deficient CD150+ sorted LSKs; replated 5 times-repeat1
Gene expression data from Tet2 deficient CD150+ sorted LSKs; replated 5 times-repeat1

Peripheral blood mononuclear cells;RF- polyarticular JIA;GTE6;210min;White;Female

Peripheral blood mononuclear cells;RF- polyarticular JIA;GTE6;93min;White;Female

B6.BKS Ighmbp2nmd-2J mouse;6 weeks of age;male;Intratechally transplanted with Spinal cord derived Neural Stem Cells

Peripheral blood mononuclear cells;RF- polyarticular JIA;GTE6;86min;White;Female

Peripheral blood mononuclear cells;RF- polyarticular JIA;GTE6;85min;White;Female

Peripheral blood mononuclear cells;RF- polyarticular JIA;GTE6;132min;White;Female

vastus lateralis biopsy, 72 year-old healthy sedentary male (#23)

vastus lateralis biopsy, 56 year-old healthy sedentary male (#3)

vastus lateralis biopsy, 66 year-old healthy sedentary male (#68)

Keywords = microarray, exercise, fitness, elderly, training effect"

vastus lateralis biopsy, 67 year-old healthy sedentary male (#74B)

vastus lateralis biopsy, 76 year-old healthy sedentary male (#47)

vastus lateralis biopsy, 68 year-old healthy sedentary male (#58)

Gene expression data from mouse CD4+ Wt T-cells with anti-CD3 stimulation

Gene expression data from mouse CD4+ Itk knockout T-cells without stimulation

The Identification of gene expression changes in human embryonic fibroblast cells, background. Sample C

TIG3  diploid lung embryonic fibroblasts were non-transfected. After 44 hours expression analysis was performed.

total RNA extracted from one ApoE-/- mouse infected wtih an adenovirus expressing dominant negative cJun

ApoE-/- mouse infected wtih an adenovirus expressing dominant negative cJun

Brain (Dorsal Motor Nucleus of the Vagus)_Parkinson's disease_case4

Gene expression data from the dorsal motor nucleus of the vagus in a Parkinson's disease subject.

Brain (Dorsal Motor Nucleus of the Vagus)_Parkinson's disease subject_#4

Gene expression data from the inferior olivary nucleus in a parkinson's disease subject.

Brain (Dorsal Motor Nucleus of the Vagus)_Parkinson's disease_case5

Brain (Dorsal Motor Nucleus of the Vagus)_Parkinson's disease subject_#5

Gene expression data from the inferior olivary nucleus in a Parkinson's disease subject.

Brain (Dorsal Motor Nucleus of the Vagus)_Parkinson's disease_case2

Brain (Dorsal Motor Nucleus of the Vagus)_Parkinson's disease subject_#2

Brain (Dorsal Motor Nucleus of the Vagus)_Parkinson's disease_case3

#17;PD case #3;T-3321;77;Female;Dorsal motor nucleus of the vagus

Brain (Dorsal Motor Nucleus of the Vagus)_Parkinson's disease subject_#3

Brain (Dorsal Motor Nucleus of the Vagus)_Parkinson's disease_case6

#23;PD case #6;T-227;76;Female;Dorsal motor nucleus of the vagus

Brain (Dorsal Motor Nucleus of the Vagus)_Parkinson's disease subject_#6

airway epithelium, smal airways, obtained by bronchoscopy and brushing

Bone marrow-derived cells (BMDCs) from the femur and tibia of euthanized mice were flushed with ice-cold Hanks' Balanced Salt Solution (GIBCO) and depleted of red blood cells (RBCs) using RBC lysing buffer (BD Biosciences). Anti-CD11b and anti-Gr-1 labeled myeloid cells were sorted in three HDC-EGFP and three HDCEGFP/HDCKO mice (3-4 months).

Histidine decarboxylase null myeloid-derived suppressor cell from bone marrow, rep1

HDC+ MDSC-HDCKO-BM

Differentially expressed genes of CD11b+Gr-1+ IMCs in the bone marrow of HDC-EGFP/HDC-KO mice.

C57BL/6J;HDC-EGFP/HDC-KO;3-4 months;bone marrow;bone marrow CD11b+Gr-1+ myeloid cells

HDC-expressing CD11b+Gr-1+ myeloid cells sorted from the bone marrow of HDC-EGFP/HDC-KO transgenic mice

Histidine decarboxylase null myeloid-derived suppressor cell from bone marrow, rep2

HDC+ MDSC-HDCKO-BM-R

Wild-type myeloid-derived suppressor cell from bone marrow, rep1

HDC+ MDSC-WT-BM

Differentially expressed genes of CD11b+Gr-1+ IMCs in the bone marrow of HDC-EGFP mice.

C57BL/6J;HDC-EGFP;3-4 months;bone marrow;bone marrow CD11b+Gr-1+ myeloid cells

HDC-expressing CD11b+Gr-1+ myeloid cells sorted from the bone marrow of HDC-EGFP transgenic mice

A HID I_B056

Wild-type myeloid-derived suppressor cell from bone marrow, rep2

HDC+ MDSC-WT-BM-R

Y YOKE_B058

HeLa cells were treated with siRNA directed against RENT1/hUPF1 (as described in Mendell et al., Science, 2002; PubMed ID:12228722).  RNA was isolated using Trizol and Qiagen RNeasy kit.

Mononucleated cells were separated from fresh blood samples by density gradient centrifugation. Subsequently, CD3+ T cells were purified by magnetic beads (Miltenyi Biotec, Bergisch-Gladbach, Germany) using the manufacturer’s protocol (purity >95% with comparable CD4+/CD8+ ratios) followed by total RNA isolation from the TRIzol cell extracts (GIBCO, Karlsruhe, Germany). RNA from 3 donors were pooled.
Keywords = Hodgkin’s Lymphoma
Keywords = T cell
Keywords = immune regulation

CD3+ T cells from patients with classical Hodgkin´s lymphoma (cHl)

Y YOKE_B059

lung;Insig1 ∆/∆ /Insig2 -/- (AT2 cells obtained from 2 months old SpC-rTTA / Otet-CRE / Insig1 flox/flox / Insig2-/- mice treated with doxycycline from E6.5 to E12.5. Control animals lacked either SpC-rtTA or Otet-CRE);Alveolar Type II

A YOKE_B062

NCI-H460;human lung large cell carcinoma cells;control (none);2 hours

Sample 6
Dye swap of 5. 293T cells transfected with si-control, induced with Wnt3A vs control medium for 9 hours.

Gene expression data from MCF-7cells treated with vehicle and RARalpha siRNA
MD41

MCF-7 breast cancer cell line;RARalpha siRNA;control (vehicle);n/a

MD42

251486838929_1_4

Gene expression in non-treated CCRPKO mouse liver
251486838171_1_3

251486838172_1_3

251486838173_1_3

Gene expression data from liver of Npc1-/- mouse1 of age 20 days

Gene expression data from liver of Npc1+/- mouse1 of age 25 days

Gene expression data from liver of Npc1+/- mouse1 of age 20 days

Gene expression data from brain of Npc1-/- mouse1 of age 84 days

Gene expression data from brain of Npc1-/- mouse1 of age 82 days

Gene expression data from brain of Npc1+/- mouse1 of age 82 days

Gene expression data from brain of Npc1-/- mouse1 of age 67 days

Mesodermal Precursor Cells derived from hES cells line VUB03_DM1, biological replicate 1

Mesodermal Precursor Cells derived from hES cells line SA01, biological replicate 3

Gene expression data from liver of Npc1+/- mouse1 of age 54 days

Gene expression data from liver of Npc1-/- mouse1 of age 25 days

JLI_70

MV mice received 2microliter/gm PBS in the oropharynx with a pipette, 30 minutes later they were anesthetized, intubated and ventilated at a tidal volume of 10 microliter/gm body wt, PEEP = 0 and FiO2 = 0.21.  They were sacrificed 4 hrs later, whole lung removed, homogenized and total RNA isolated.  Labeled cRNA was prepared and hybridized to an Affymetrix GeneChip 430A microarray using Affymetrix protocol.  Microarray was scanned with the GeneChip Scanner and image analysis was performed with Affymetrix MAS 5.0 software.  Background adjustment and quantile normalization of microarray data was performed using RMAExpress.

Autoimmune pancreatic islets, no cyclophosphamide treatment, rep 1

Lot batch = jos0995

BSMCs were grown in 25 cm2 flasks in SmGM and starved for 24 hours (SmBM supplemented with 0.1% FBS) before stimulation. Supernatant was removed and cells were incubated for 24 hours in fresh growth factor-free medium with vehicle (ethanol at 0.05%).

Cells were growth in Smooth muscle Growth Medium (SmGM-2 Bulletkit, Cambrex) which included Smooth muscle Basal Medium (SmBM) supplemented with 5 % Fetal Bovine Serum (FBS), hEGF (0.5 ng/ml), hFGF (2 ng/ml), insulin (5 µg/ml) and GA-1000 (100 ng/ml of Gentamicin and 0.1 ng/ml of Amphotericin-B), according to manufacturer's instructions.

Arrays were scanned with the Affymetrix GeneChip® Scanner 3000 7G and the data was extracted using Microarray Analysis Suite 5.0 (Affymetrix).

Expression values were extracted using the Robust Multichip Average method (Irizarry RA, Hobbs B, Collin F, et al. 2003. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-64)

Cells were lysed by adding 2 ml of trizol reagent (Invitrogen) and homogenized by passing through a syringe with a needle (26G). RNA was picked up in the aqueous phase following phase separation by chloroform. The RNA was then precipitate with isopropanol, washed with ethanol (75%), dissolved in DEPC-treated RNAse/DNAse free water and quantified by spectrophotometry (Ultrospec 2100 pro).

Hybridization was performed according to the standard Affymetrix protocol (see complete protocol descriptions: http://www.affymetrix.com/support/technical/manual/expression_manual.affx)

Biotinylated cRNA was prepared according to the standard Affymetrix protocol (see complete protocol descriptions: http://www.affymetrix.com/support/technical/manual/expression_manual.affx)

Human primary bronchial smooth muscle cells were grown to near confluence, starved for 24 hours (medium containing 0.1% FBS) and then treated with vehicle (0.05% ethanol) for an additional 24 hours before RNA extraction.

A549 human lung cancer cells (1X10^5 per T-25 flask in 7 mL complete RPMI 1640 medium) were seeded eights days prior to treatment of non-cycling plateau phase cultures with drug. At four hours prior to RNA isolation, 2.5uM sapphyrin PCI-2050 (final concentration) was added to the culture. After incubation for four hours, the culture was washed twice with HBSS supplemented with 0.5% BSA and total RNA was isolated.

2.5uM sapphyrin PCI-2050 treated A549 human lung cancer cell cultures replicate C

2.5uM sapphyrin PCI-2050 treated A549 human lung cancer cell cultures replicate B

2.5uM sapphyrin PCI-2050 treated A549 human lung cancer cell cultures replicate A

gastrointestinal stromal tumor;Male;HIGH;PDGFRA mutation detected

gastrointestinal stromal tumor;Female;LOW;PDGFRA mutation detected

WT no2

neuronal, age:46, gender:male, diagnostic group: control, PMI:31h

neuronal, age:48, gender:male, diagnostic group: bipolar disorder, PMI:23h

neuronal, age:41, gender:female, diagnostic group: bipolar disorder, PMI:28h

neuronal, age:44, gender:female, diagnostic group: schizophrenia, PMI:26h

neuronal, age:42, gender:male, diagnostic group: bipolar disorder, PMI:32h

neuronal, age:32, gender:male, diagnostic group: control, PMI:13h

neuronal, age:51, gender:male, diagnostic group: bipolar disorder, PMI:23h

neuronal, age:35, gender:male, diagnostic group: bipolar disorder, PMI:35h

neuronal, age:47, gender:female, diagnostic group: schizophrenia, PMI:35h

neuronal, age:52, gender:male, diagnostic group: schizophrenia, PMI:16h

Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16686.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16657.gif

Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16890.gif

mixed reference (CRG + FR);nGSF58, proliferating cells, 24h ETOH

113;OCP;8/17/81;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;12/14/04;Recurrant abcess, ?IBD;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;5-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

114;None;6/27/36;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;12/14/04;Altered bowel habit, Alcohol excess;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;5-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

106;None;5/29/87;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;11/18/04;Abdominal pain, upper GI symptoms.;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;1-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

108;Asacol 400mg BD;8/30/33;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;11/25/04;Altered bowel habbit, ? UC 1974, never on Bx.;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;1-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

104;None;1/2/72;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;11/15/04;IBS type symptoms;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;1-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

107;None;07/28/1060;M;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;11/25/04;FH Colon Cancer;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;1-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

109;None;10/10/57;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;12/2/04;FH of Colon Cancer;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;5-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

110;None;3/13/54;M;JEWISH;FALSE;FALSE;FALSE;FALSE;FALSE;12/2/04;Diarrhoea;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;5-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

111;Paracetamol;9/5/82;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;12/3/04;FH of CD, Path Increased lymphiod in TI Bx.;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;5-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

112;None;7/5/81;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;12/7/04;Altered bowel habit;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;5-25-01;sigmoid colon;Uninflamed;total RNA from 10 human cell lines

Epididymal adipose;wild-type;high fat diet HFD;mixed 129/Sv and C57BL/6;mouse 547

Liver;wild-type;high fat diet HFD;mixed 129/Sv and C57BL/6;mouse 547

Epididymal adipose;wild-type;high fat diet HFD;mixed 129/Sv and C57BL/6;mouse 560

Liver;wild-type;high fat diet HFD;mixed 129/Sv and C57BL/6;mouse 560

Liver;wild-type;normal diet ND;mixed 129/Sv and C57BL/6;mouse 686

Epididymal adipose;wild-type;normal diet ND;mixed 129/Sv and C57BL/6;mouse 687

Liver;wild-type;normal diet ND;mixed 129/Sv and C57BL/6;mouse 687

Epididymal adipose;wild-type;normal diet ND;mixed 129/Sv and C57BL/6;mouse 690

Liver;wild-type;normal diet ND;mixed 129/Sv and C57BL/6;mouse 690

Epididymal adipose;GPR120 KO;normal diet ND;mixed 129/Sv and C57BL/6;mouse 718

3240_H1299_3uM-Dac_1.CHP
H1299 3D
3240_H1299_3uM-Dac_1.CEL

3241_H1299_3uM-Dac_2.CHP
H1299 3D
3241_H1299_3uM-Dac_2.CEL

WI-38 cells, at 24 h after exposure to 1 uM BPDE, biological rep4

WI-38 cells, at 24 h after exposure to 1 uM BPDE, biological rep3

WI-38 cells, at 24 h after exposure to DMSO vehicle control, biological rep3

WI-38 cells, at 24 h after exposure to 1 uM BPDE, biological rep2

WI-38 cells, at 24 h after exposure to 1 uM BPDE, biological rep1

WI-38 cells, at 24 h after exposure to DMSO vehicle control, biological rep2

Gene expression data from Huh7 cells treated with mock media for 12 hours

Gene expression data from Huh7 cells treated with mock media for 6 hours

Gene expression data from Huh7 cells Infected with JFH-1 for 48 hours

Creator: GenePix Pro 3.0.6.89
Scanner: GenePix 4000A [47890]
PMTVolts: 780;; 680
LaserPower: 1.18;; 2.6
Temperature: 35.69

Sample Extraction Protocol
Other: Total RNA was prepared using RNAeasy kit (Qiagen, Valencia, CA).

Other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42°C for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Denature target at 100°C for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42°C just before adding to samples. Add 40 ul of 2X F-hyb buffer and 20ul water to samples. Load 80 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42°C in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), and spin for 3 minutes at 650 rpm to dry.

Invitrogen cDNA Labeling Kit - cy5
Other: Labeled sample with Cy5 using a NHS-ester coupling reaction following the manufacturer's cDNA Labeling Kit protocol (Invitrogen).

Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.;blood;monocytes;smodering ATL

PMTVolts: 750;; 700
LaserPower: 1.24;; 2.27
Temperature: 36.04

PMTVolts: 710;; 650
LaserPower: 1.11;; 2.46
Temperature: 33.62

Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.;blood;monocytes;Normal

PMTVolts: 760;; 650
LaserPower: 1.11;; 2.48
Temperature: 33.18

PMTVolts: 790;; 670
LaserPower: 1.19;; 2.51
Temperature: 36.38

PMTVolts: 660;; 650
LaserPower: 1.17008;; 2.47444
Temperature: 33.9784

TNFa-OMe-P siRNA-C;09/06/19;09/06/30;6.2;159;2.56;0.391;colon;5% DSS

TNFa-OMe-P siRNA-C;09/06/19;09/06/30;6.4;180;2.81;0.031;colon;5% DSS

YES;CD4+/CD25- T effector cell;IPEX disease carrier;FOXP3 wild type;female;anti-CD3, anti-CD28 for 72 h

TNFa-OMe siRNA-B;09/06/19;09/06/30;5.5;164;2.982;0.301;colon;5% DSS

TNFa-OMe siRNA-B;09/06/22;09/06/29;6.2;177;2.855;0.217;colon;5% DSS

TNFa-OMe siRNA-B;09/06/19;09/06/29;6.2;170;2.742;0.643;colon;5% DSS

TNFa-OMe siRNA-B;09/06/19;09/06/30;6;172;2.87;0.384;colon;5% DSS

TNFa-OMe-P siRNA-C;09/06/16;09/06/30;6.6;160;2.42;0.423;colon;5% DSS

TNFa-OMe-P siRNA-C;09/06/19;09/06/29;6.1;170;2.62;0.463;colon;5% DSS

TNFa-OMe siRNA-B;09/06/22;09/06/30;5.7;172;3.02;0.932;colon;5% DSS

Rat230_2;15;ul;1.732;0.907;1.89;1:5;7.9;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;138;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.469;0.766;1.89;1:5;8.4;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;139;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.946;0.992;1.92;1:5;8.3;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;129;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.435;0.745;1.9;1:5;7.8;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;287;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

The data were normalised using Rank Invariant normalisation with Bead Studio

RNA was extracted with  with QIAGEN RNeasy  kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

Morphologically normal testicular parenchyma from area adjacent to a testicular germ cell tumor

Normal testicular parenchyma from a 22 years old organ donor with no known history of cancer

SMhu036

SMhu035

SMhu034

SMhu033

SMhu032

SMhu031

SMhu030

SMhu029

SMhu028

SMhu027

whole blood;Cutaneous psoriasis without arthritis;Male;1;39.807665982204;25;10 human cell lines: Adenocarcinoma, mammary gland; Hepatoblastoma, liver; Adenocarcinoma, cervix; Embryonal carcinoma, testis; Glioblastoma, brain; Melanoma; Liposarcoma; Histiocytic lymphoma, macrophage, histocyte; Lymphoblastic leukemia, T lymphoblast; Plasmacytoma, myeloma, B lymphocyte

A673 treated with Doxorubicin for 3 days with concentration of 119.76 nM (2 x EC50), biological rep2

Gene expression data from A673 cell line that has been treated with Doxorubicin for 3 days with concentration of 119.76 nM (2 x EC50).

A673 cell line that has been treated with Doxorubicin for 3 days with concentration of 119.76 nM (2 x EC50).

A673 treated with Doxorubicin for 3 days with concentration of 119.76 nM (2 x EC50), biological rep3

A673 treated with Doxorubicin for 3 days with concentration of 59.88 nM (EC50), biological rep3

A673 treated with Doxorubicin for 5 days with concentration of 59.88 nM (EC50), biological rep1

Gene expression data from A673 cell line that has been treated with Doxorubicin for 5 days with concentration of 59.88 nM (EC50).

A673 cell line that has been treated with Doxorubicin for 5 days with concentration of 59.88 nM (EC50).

A673 treated with Doxorubicin for 5 days with concentration of 59.88 nM (EC50), biological rep2

A673 treated with Doxorubicin for 5 days with concentration of 59.88 nM (EC50), biological rep3

A673 treated with Doxorubicin for 24 hours with concentration of 119.76 nM (2 x EC50), biological rep1

Gene expression data from A673 cell line that has been treated with Doxorubicin for 24 hours with concentration of 119.76 nM (2 x EC50).

A673 cell line that has been treated with Doxorubicin for 24 hours with concentration of 119.76 nM (2 x EC50).

A673 treated with Doxorubicin for 24 hours with concentration of 119.76 nM (2 x EC50), biological rep2

A673 treated with Doxorubicin for 24 hours with concentration of 119.76 nM (2 x EC50), biological rep3

A673 treated with Doxorubicin for 3 days with concentration of 119.76 nM (2 x EC50), biological rep1

TTF=120min;Race=Black or African American;Sex=Female;Group=A;Prototype_Y

Peripheral blood mononuclear cells;RF- polyarticular JIA;GTE6;150min;Caucasian/White;Female;Con;N

Gene expression data from small intestine not treated with irinotecan

U937 cell line infected with GSK3A Construct 6 shRNA, biological rep1
Sample name: U937_GSK3A_6-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D06_596676.CEL

U937 cell line infected with GSK3A Construct 6 shRNA, biological rep2
Sample name: U937_GSK3A_6-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D11_596666.CEL

U937 cell line infected with GSK3B Construct 2 shRNA, biological rep1
Sample name: U937_GSK3B_2-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D04_596654.CEL

U937 cell line infected with GSK3B Construct 2 shRNA, biological rep2
Sample name: U937_GSK3B_2-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D09_596680.CEL

U937 cell line infected with GSK3A Construct 5 shRNA, biological rep1
Sample name: U937_GSK3A_5-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D05_596632.CEL

U937 cell line infected with GSK3A Construct 5 shRNA, biological rep2
Sample name: U937_GSK3A_5-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_D10_596608.CEL

bone marrow;CD34+ hematopoietic stem cells (HSC);myelodysplastic syndromes (MDS);refractory anemia with ringed sideroblasts (RARS);del5q plus monosomy7/del7q plus other

bone marrow;CD34+ hematopoietic stem cells (HSC);myelodysplastic syndromes (MDS);refractory anemia with excess blasts 2 (RAEB2);monosomy7/del(7q)

To induce transgene activity, cells were treated with induction medium (TS medium + 1 µg/mL tamoxifen (Sigma)).  For microarray analysis, ES cells were seeded at densities of 2 x 105 cells per gelatinized 35-mm well in ES medium, switched to induction medium the following day, and fed daily for the indicated time period.

To create stably transformed lines, 1-3 x 107 ES cells were electroporated with 20-30 µg plasmid (pCAG-mCdx2ER-ires-puror (Niwa et al., 2005), pCAG-hCdx2ERT2-ires-puror, or pCAG-hGata3ERT2-ires-puror), and seeded on two 10 cm gelatinized plates.  Cells were fed with plasmid selection medium (ES medium + 1.2 µg/mL puromycin) until colonies were visible by eye.  Colonies were picked and individually expanded on gelatin.

Healthy control;47;Male;N/A;N/A;6.81;21;Left;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 0

Healthy control;53;Male;N/A;N/A;6.40;9;Left;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 1

Healthy control;35;Male;N/A;N/A;6.70;52;Right;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 0

Healthy control;49;Male;N/A;N/A;6.50;46;Right;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 0

Healthy control;32;Male;N/A;N/A;7.03;24;Left;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 2

Healthy control;34;Male;N/A;N/A;6.48;22;Right;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 0

Healthy control;45;Male;N/A;N/A;6.94;29;Right;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 1

Healthy control;59;Male;N/A;N/A;6.80;47;Right;N/A;N/A;N/A;N/A;No;0 (no use) to 5 (heavy use)): 0;0 (no use) to 6 (heavy use)): 0

Bipolar disorder;50;Female;25;25;6.51;62;Left;15000;No;No;No;Yes;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): 1

Bipolar disorder;29;Female;18;11;6.74;62;Left;0;No;No;No;No;0 (no use) to 5 (heavy use)): Unknown;0 (no use) to 6 (heavy use)): 3

Equal amounts (7 micro-gram) of RNA were pooled from five animals. This is an independent replicate of sample 1.

skeletal muscle;insulin sensitive;untreated;1;379;1510;63.2;25.7;41.6;1624.24

skeletal muscle;insulin sensitive;untreated;56;125;1860;74;26;52;1924

Pool of total RNA from 3 Ts1Cje cerebella (segmental trisomy of chromosome 16) at P30 postnatal stage

Ts1Cje (segmental trisomy of chromosome 16);cerebellum;P30 postnatal stage

Pool of total RNA from 3 Ts1Cje cerebella (segmental trisomy of chromosome 16) at P15 postnatal stage

Ts1Cje (segmental trisomy of chromosome 16);cerebellum;P15 postnatal stage

C57BL/6;Female;6 weeks old;CD4 positive T cell;TCR-stimulated;Trim28CKO

Trim28 conditional KO mice naïve CD4 positive cell, TCR-stimulated, replicate 2

Station	1
Module	3

Station	1
Module	1

Station	1
Module	2

HUVECs were harvested after 24 hours of treatment with atorvastatin (10 microM).

EA.hy926 cells were harvested after 24 hours of treatment with atorvastatin (10 microM).

HUVECs were harvested after 24 hours of treatment with mevalonate (500 microM).

Total RNA was prepared using TRIzol reagent from the pancreas one 58 day old male mouse.  The genotype was gastrin+/-, CFTR-/- on 95% black6, 5% 129Sv background.  Mice were fed Peptamen from age 10 days to prevent intestinal obstruction.

Total RNA was prepared using TRIzol reagent from the pancreas one 56 day old male mouse.  The genotype was gastrin+/-, CFTR-/- on 95% black6, 5% 129Sv background.  Mice were fed Peptamen from age 10 days to prevent intestinal obstruction.

Total RNA was prepared using TRIzol reagent from the pancreas one 57 day old male mouse.  The genotype was gastrin+/-, CFTR-/- on 95% black6, 5% 129Sv background.  Mice were fed Peptamen from age 10 days to prevent intestinal obstruction.

Immortalized MEFs WC, human c-myc expression retroviral vector infected, rep3

human c-myc retroviral vector-infected immortalized mouse embryonic fibroblasts

Immortalized MEFs WC, human c-myc expression retroviral vector infected, rep2

Immortalized MEFs WA, human c-myc expression retroviral vector infected, rep3

Immortalized MEFs WA, human c-myc expression retroviral vector infected, rep2

Immortalized MEFs WA, human c-myc expression retroviral vector infected, rep1

Immortalized MEFs WC, human c-myc expression retroviral vector infected, rep1

Immortalized MEFs WB, human c-myc expression retroviral vector infected, rep3

Immortalized MEFs WB, human c-myc expression retroviral vector infected, rep2

Immortalized MEFs WB, human c-myc expression retroviral vector infected, rep1

Soleus muscles from male BERKO ( estrogen receptor beta knockout).

plaque type psoriasis;epidermis;46;female;> 10 y;phototherapy;post-UV

plaque type psoriasis;epidermis;43;male;> 10 y;phototherapy;post-UV

plaque type psoriasis;epidermis;47;female;> 10 y;phototherapy;post-UV

plaque type psoriasis;epidermis;17;male;> 10 y;phototherapy;post-UV

plaque type psoriasis;epidermis;67;male;< 1 y;phototherapy;post-UV

plaque type psoriasis;epidermis;59;male;> 20 y;phototherapy;post-UV

plaque type psoriasis;epidermis;73;female;Unknown;phototherapy;post-UV

plaque type psoriasis;epidermis;40;male;> 20 y;phototherapy;post-UV

plaque type psoriasis;epidermis;28;female;> 10y;phototherapy;mid-UV

plaque type psoriasis;epidermis;33;female;> 10 y;phototherapy;mid-UV

SAM630137;C57BL/6;spr881;IL17RC Knock out;pooled mouse reference RNA

A HID B_B086

A HID B_B088

A HID B_B021

A HID B_B046

A SIT_B100

brain (frontal cortex);schizophrenia;45 yr;white;295.9;15 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

Sample is skeletal muscle from a morbidly obese patient undergoing elective abdominal surgery

Sample is skeletal muscle from  a morbidly obese patient undergoing elective abdominal surgery

brain (frontal cortex);schizophrenia;44 yr;white;295.9;19 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);schizophrenia;46 yr;white;295.9;22 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);schizophrenia;43 yr;white;295.9;25 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

KO - knock-out Untreated - 0 hrs - repeat 3 - Cy3 - mAdbID:51962

KO - knock-out Untreated - 0 hrs - repeat 3 - Cy5 - mAdbID:51300

27_DBP

30_DBP

HCT116 cells with enforced miR-34a expression, technical replicate 2

Embryonic stem cell medium was composed of KO-DMEM supplemented with 15% FBS, glutamate, nonessential amino acids, 2-mercaptoethanol (all from Gibco/Life Science Technologies), 103 U/mL LIF (Millipore/GE Healthcare) and 10 mM MgCl2. Cells were grown on the layer of irradiated mouse embryonic fibroblasts. In cultured ES cells, the media was changed daily and cells were split 1:5 every other day. For feeder-free conditions, mESC were depleted of feeder cells by pre-plating on gelatin-coated plates and cultured on 0.1% gelatin-coated plates for 3 passages with 2x103 U/mL LIF.

The data were normalised using quantile normalisation with Illumina GenomeStudio software

Total RNA was extracted from cells using Qiagen RNAeasy Plus mini Kit

Biotinylation using Illumina¨ TotalPrep RNA Amplification Kit (Ambion)

mouse embryonic stem cells 3x passaged without feeder cells;TRPM7-/-;C57BL/6

mouse embryonic stem cells 3x passaged without feeder cells;WT;C57BL/6

lung rna from myd88 knockout mice, 3 days after mock infection, replicate C

lung rna from myd88 knockout mice, 3 days after infection with Chlamydia pneumoniae

lung rna from myd88 knockout mice, 3 days after infection with Chlamydia pneumoniae, replicate B

lung rna from myd88 knockout mice, 3 days after infection with Chlamydia pneumoniae, replicate C

lung rna from myd88 knockout mice, 3 days after mock infection, replicate A

male;CABG patient, atrial tissue;propofol anesthesia, after CABG surgery

Lot batch = Joslin core 677

Lot batch = Joslin core 668

Lot batch = Joslin core 950

GNMT_3WT2

Gene expression data from the colon of NHE3-deficient mice

Study of rat femur fracture healing in young rats (6 weeks old at fracture) at 2 weeks after fracture.  RNA from 2 rats were pooled for each array

Study of rat femur fracture healing in young rats (6 weeks old at fracture) at 1 wk after fracture.  RNA from 2 rats were pooled for each array

C3H-HeJ mice were exposed to filtered air. Lungs were removed-frozen in liquid nitrogen-RNA extraction.
Lot batch =

Study of rat femur fracture healing in young rats (6 weeks old at fracture).  RNA from 2 rats were pooled for each microarray

Study of rat femur fracture healing in adult rats (26 weeks old at fracture) at 3 days after fracture.  RNA from two rats were pooled for each array.

Study of rat femur fracture healing in adult rats (26 weeks old at fracture) for intact femora.  RNA from 2 rats were pooled for each array.

C3H-HeOuJ mice exposed to ozone  for 72hrs- lungs were removed-frozen in liquid nitrogen-RNA extraction.
Lot batch =

Monolayers of HUVECs in 9 cm Petri dishes infected with Neisseria meningitidis MC58 delta frpC/frpA were washed and collected into Trizol by cell-scraper

Confluent monolayers of HUVECs in 9 cm Petri dishes were infected with Neisseria meningitidis MC58 delta frpC/frpA (MOI=10) and cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 4 hours

Gene expression data from HUVEC infected with Neisseria meningitidis MC58 delta frpC/frpA, 4 hours infection

Confluent monolayers of HUVECs in 9 cm Petri dishes were infected with Neisseria meningitidis MC58 delta pilD (MOI=10) and cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 6 hours

Gene expression data from HUVEC infected with Neisseria meningitidis MC58 delta pilD, 6 hours infection

breast cancer histologically normal breast epithlieum patient 297B

RNA was extracted from a pool of three spleens taken from three month old nonobese diabetic (NOD) mice kept in sterile, specific pathogen free conditions. Target cRNA was prepared and hybridized to Eos custom GeneChip arrays (GPL24) as described for standard, commercially available Affymetrix GeneChips (Mahadevappa and Warrington 1999) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix).  Data for each GeneChip was normalized using a proprietary method developed at Eos (Ghandour and Glynne 2000).  Briefly, for each probe array in the series background subtracted average cell intensities were fitted to a gamma distribution.  These normalized cell intensities were then used to calculate an average intensity (AI) for each probe set.  The AI was calculated as the trimean (T) of the probes making up a given probe set (Tukey 1977).  These AI values were subjected to a second round of normalization by setting the 70th and 90th percentiles equal to the same value for each array in the series.

reduction mammoplasty histologically normal breast epithlieum patient 328

reduction mammoplasty histologically normal breast epithlieum patient 361

breast cancer histologically normal breast epithlieum patient 318

breast cancer histologically normal breast epithlieum patient 251

breast cancer histologically normal breast epithlieum patient 359

breast cancer histologically normal breast epithlieum patient 320

Comparisons: postnatal day effect/P2, Genotype effect on postnatal gene expression comparitor/P2, Hyperoxia effects on wild type comparitor/1 day treatment, Genotype effect on hyperoxia exposure comparitor/1 day treatment

Comparisons: postnatal day effect/P3, Genotype effect on postnatal gene expression comparitor/P3, Hyperoxia effects on wild type comparitor/2 day treatment, Genotype effect on hyperoxia exposure comparitor/2 day treatment

Comparisons: postnatal day effect comparitor/P4, Genotype effect on postnatal gene expression comparitor/P4, Hyperoxia effects on wild type comparitor/3 day treatment, Genotype effect on hyperoxia exposure comparitor/3 day treatment

A673 treated with Puromycin for 3 days with concentration of 0.18 uM (2 x EC50), biological rep2

Gene expression data from A673 cell line that has been treated with Puromycin for 3 days with concentration of 0.18 uM (2 x EC50).

A673 cell line that has been treated with Puromycin for 3 days with concentration of 0.18 uM (2 x EC50).

A673 treated with Puromycin for 3 days with concentration of 0.18 uM (2 x EC50), biological rep1

A673 treated with Puromycin for 5 days with concentration of 0.18 uM (2 x EC50), biological rep3

Gene expression data from A673 cell line that has been treated with Puromycin for 5 days with concentration of 0.18 uM (2 x EC50).

A673 cell line that has been treated with Puromycin for 5 days with concentration of 0.18 uM (2 x EC50).

A673 treated with Puromycin for 3 days with concentration of 0.18 uM (2 x EC50), biological rep3

A673 treated with Puromycin for 24 hours with concentration of 0.18 uM (2 x EC50), biological rep1

Gene expression data from A673 cell line that has been treated with Puromycin for 24 hours with concentration of 0.18 uM (2 x EC50).

A673 cell line that has been treated with Puromycin for 24 hours with concentration of 0.18 uM (2 x EC50).

A673 treated with Puromycin for 5 days with concentration of 0.09 uM (EC50), biological rep3

A673 treated with Puromycin for 24 hours with concentration of 0.18 uM (2 x EC50), biological rep3

A673 treated with Puromycin for 24 hours with concentration of 0.18 uM (2 x EC50), biological rep2

Data was processed in Affymetrix GeneChip Operating Software (GCOS) 1.2. Values shown are not normalized to the median of each array.

PC-3 prostate cancer cells were either untreated (0hr) or incubated with 5 µg/mL arachidonic acid (AA) in RPMI media containing 0.25 mg/mL albumin for 2 hours. Albumin alone was added to untreated cells which remained inactivated.

H9 hESCs (WiCell Research) and iPSCs were maintained on a layer of mitotically inactivated MEFs in DMEM/F12 (Invitrogen) supplemented with 0.1 mM non-essential amino acids (Invitrogen), 1 mM glutamax (Invitrogen), 20% Knockout Serum Replacement (Invitrogen), 55 μM b-mercaptoethanol (Invitrogen) and 10 ng/ml bFGF (Joint Protein Central). hESCs and iPSCs were also cultured in Matrigel (BD Biosciences) with mTeSR medium (Stem Cell Technologies).

iPSCs Generation. For the generation of human iPSCs, human fibroblasts were seeded in a 6-well plate and spin-infected with a mix of high-quality retroviruses encoding OCT4, SOX2, KLF4, c-MYC, and GFP in the presence of 4 g/ml polybrene. Three infections on consecutive days were performed. 6 days after the first spin-infection, fibroblasts were gently individualized with TrypLE (invitrogen) and seeded onto fresh MEFs in the fibroblast culture medium. After 24 h, the medium was switched to hESC medium. The media was changed every 1–2 days depending on cell density. To establish the iPSC lines, colonies were manually picked and transferred onto MEF feeder cells for several passages before further transfer to Matrigel/mTesR conditions.

hgps-ipsc_1: Human HGPS fibroblasts AG01972, AG11498, AG06297, and normal fibroblasts GM00038 (9 year), AG05247 (87 year), AG09602 (92 year) were purchased from Coriell Cell Repository and reprogrammed using the protocol below

hgps-ipsc_2: Human HGPS fibroblasts AG01972, AG11498, AG06297, and normal fibroblasts GM00038 (9 year), AG05247 (87 year), AG09602 (92 year) were purchased from Coriell Cell Repository and reprogrammed using the protocol below.

bj-ipsc_1: BJ normal human fibroblasts (CRL-2522) were from ATCC and reprogrammed to iPSC with the protocol defined below

bj-ipsc_2: BJ normal human fibroblasts (CRL-2522) were from ATCC and reprogrammed to iPSC with the protocol defined below

WT tet1

Sample was pooled on basis of total-RNA extracted from CD3+ T cells derived from peripheral blood of all SAA patients..

Pool of four samples (n=4);;three female/one male;;19/57/40/70 years old;;CD3+ T cells, peripheral blood;;(severe) aplastic anemia (SAA)

SKGT4 oesophageal cells stimulated with low pH 6.5 for 30 minutes

SKGT4 oesophageal cells stimulated with Low pH 6.5 for 30 minutes

Cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM-high glucose; Gibco, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS, Gibco)

Total RNA were extracted by RNeasy mini kit (Cat. 74106; Qiagen, Hilden, Germany), and 100 ng to 1 ug of total RNA were subjected into reverse transcription using the SuperScriptTM III Reverse transcriptase kit (Invitrogen) as directed by the manufacturer.

SW480 cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM-high glucose; Gibco, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS, Gibco)
atmosphere: air, 95%; carbon dioxide (CO2), 5%
temperature: 37.0°

Cells were cultured in tumor sphere medium consisting of DMEM-F12 (Gibco) with N2 Plus Supplement (R＆D,  Minneapolis, MN, USA ), 10 ng/ml recombinant bFGF (PeproTech Asia, Rehovot, Israel), 10 ng/ml EGF (PeproTech Asia, Rehovot, Israel) and 1% penicillin-streptomycine (Gibco).

The medium for this cell line is DMEM. To make the complete growth medium, add the following components to the base medium: fetal bovine serum to a final concentration of 10%.
temperature: 37.0°C

the medium for this cell line is dmem. to make the complete growth medium, add the following components to the base medium: fetal bovine serum to a final concentration of 10%.

human neuroblastoma cells;SH-SY5Y;M;stably transfected with scramble control

Neuroblastoma SH-SY5Y cells_cloneB_stably transfected with RNAi against DJ-1_replicate2

Neuroblastoma SH-SY5Y cells_cloneG_stably transfected with RNAi against DJ-1_replicate1

TIG3 diploid fibroblasts were were grown in DMEM media supplemented with 10% (v/v) fetal calf serum.

The Identification of gene expression changes in human embryonic fibroblast cells depleted of BMI-1. Sample A

Genechip array scan

TIG3  diploid lung embryonic fibroblasts were transfected with siRNA oligos specific for the Polycomb protein BMI-1. After 44 hours expression analysis was performed.

Human lung adenocarcinoma A549 cells treated without TNFα, in presence of Claudin 1 siRNA

Human lung adenocarcinoma A549 cells treated with TNFα, in presence of Claudin 1 siRNA

Cell strain 1 of cyclin D1KO 3T3 cells obtained by serial passaging MEFs from E14 embryos, stably infected with MSCV-GFP control murine stem cell virus.

Sample from retroviral MSCV-GFP control infected cyclin D1 knockout 3T3 cells (line 1).

Gene expression data from cyclin D1 knockout 3T3s (cell line 1) infected with control retrovirus using Murine Stem Cell Virus (MSCV) system.

Pooled normal myocardium sold commercially;myocardium sold commercially

human embryonic stem (hES) cells line SA01, biological replicate  3

human embryonic stem (hES) cells line SA01, biological replicate  2

human embryonic stem (hES) cells line VUB01, biological replicate  2

Panc6.CEL (unavailable due to loss from servers)
Pancreatic Tumor

Panc5.CEL (unavailable due to loss from servers)

human embryonic stem (hES) cells line VUB01, biological replicate  1

Panc4.CEL (unavailable due to loss from servers)

Panc3.CEL (unavailable due to loss from servers)

Pan21.CEL (unavailable due to loss from servers)

Panc1.CEL (unavailable due to loss from servers)

Female; Uterus - virgin-diestrus

Female; Uterus-virgin estrus

Hair; Awn Hair (back) anagen

Hair; Awn Hair (back) catagen

Peripheral blood mononuclear cells;healthy control;LT6;82min;White;Male

Sample name: TM-908-12R

Sample name: TM-556-10R

Sample name: TM-509-11R

Sample name: TM-164-13R

Sample name: TM-158-13R

Sample name: LN-163-11R

Sample name: TM-993-11R

Sample name: TM-919-12R

P01
JLP_P01_U133_2.CEL

patient1;Systemic lupus erythematosous (SLE);blood;Sorted B cell

P02
JLP_P02_U133_2.CEL

patient2;Systemic lupus erythematosous (SLE);blood;Sorted B cell

P03
JLP_P03_U133_2.CEL

patient3;Systemic lupus erythematosous (SLE);blood;Sorted B cell

P04
JLP_P04_U133_2.CEL

patient4;Systemic lupus erythematosous (SLE);blood;Sorted B cell

Gene expression data under ER stress from lymphoblastoid cells of individual GM12872 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12873 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12812 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12813 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12813 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12814 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12814 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12815 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12815 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM12872 treated with 4 ug/ml tunicamycin 8 hours.

HCC-PBMC-01

normalization parameters were selected for data processing. Logarithmically transformed expression values were used to implement Gene Set Enrichment Analysis (GSEA). DESCRIPTION

Cnr1-/-/Cnr2-/- female number 1, untreated control ear (#7_Ko-C-4)

Cnr1-/-/Cnr2-/- female number 1, 2 months old, whole ear tissue, untreated control ear

Cells were infected with retroviruses (H-RasV12), selected during two days with 2,5 µg/ml puromycin, then treated with water (vehicle) or 5mM metformin during 6 days before RNA extraction.

Cells were cultured in Dulbecco’s modified Eagle medium (DMEM; Wisent, Montréal, QC) supplemented with 10% fetal bovine serum (FBS; Wisent) and 1% penicillin G/streptomycin sulfate (Wisent).

GeneChips were scanned using the GeneChip® Scanner 3000 7G/4 Color Early Access.

The data were analyzed with FlexArray 1.6.1.1 using Affymetrix default analysis settings and RMA as normalization method. Transcripts with a fold change higher or equal to 2 (log2) and a p-value˂ 0.05 according to the two-sample student's t-test were selected for final determination.

Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C with rotation (60 rpm) on Human Gene 1.0 ST Chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

Biotinylated cRNA were prepared according to the protocol from the Ambion® WT Expression kit for Affymettrix® GeneChip®Whole Transcrpit (WT) Expression Arrays.

IMR90 (Normal human diploid lung fibroblast);Female;H-RasV12;Vehicle

IMR90 (Normal human diploid lung fibroblast);Female;H-RasV12;Metformin

GB 9 65A NO LPA.CEL

gastric adenocarcinoma AGS cells;65 shRNA;A;NET1 knockdown;no LPA (control)

GB 8 63B NO LPA.CEL

gastric adenocarcinoma AGS cells;63 shRNA;B;NET1 knockdown;no LPA (control)

GC sensitive clone C7H2-S15 treated for 6 hours with 100nM dexamethasone (a glucocorticoid).

GC sensitive clone C7H2-S2 treated for 6 hours with 100nM dexamethasone (a glucocorticoid).

GC sensitive clone C7H2-S10 treated for 6 hours with 100nM dexamethasone (a glucocorticoid).

GC sensitive clone C7H2-S27 treated for 6 hours with 100nM dexamethasone (a glucocorticoid).

GC sensitive clone C7H2-S12 treated for 6 hours with 100nM dexamethasone (a glucocorticoid).

GB 10 65B NO LPA.CEL

gastric adenocarcinoma AGS cells;65 shRNA;B;NET1 knockdown;no LPA (control)

neurectoderm derived from embryonic stem cells;control, shRNAmir #11;derivative of ES-E14TG2a (ATCC);129P2 (formerly 129/Ola)

neurectoderm derived from embryonic stem cells;control, shRNAmir #9;derivative of ES-E14TG2a (ATCC);129P2 (formerly 129/Ola)

neurectoderm derived from embryonic stem cells;Geminin knockdown, shRNAmir #9;derivative of ES-E14TG2a (ATCC);129P2 (formerly 129/Ola)

gene expression data of hNHEPS human hepatocytes exposed to 10 μM VX 6 h after exposure

Normal human primary hepatocytes isolated from non-transplantable donor tissue;6 h;10 μM;VX (O-ethyl S-[2-(diisopropylamino)ethyl] methylphosphonothiolate)

STARVED MYOTUBES - C2C12 mouse myoblasts (American Type Culture Collection, Manassas, VA) were maintained in growth medium (DMEM supplemented with 10% Fetal Bovine serum, Invitrogen Corporation, Carlsbad, CA) in 5% CO2.  Cells were plated at a density of 40-50% in 100mm dishes.  When cells reached ~90% confluency 24 hours later, they were switched to differentiation media (DMEM containing 2% horse serum; GIBCO, Invitrogen Corporation, Carlsbad, CA) which was subsequently changed every 48 hours. All cells were allowed to differentiate for 4 days with feeding every two days (day 0, 2, and 4).  Beginning at day 4, control cells were re-fed every 48 hours whereas experimental cells were not re-fed.  After an additional 4 days (8 days post differentiation), cells were harvested and total RNA was isolated from control and "starved" (non re-fed cells)

CONTROL MYOTUBES - C2C12 mouse myoblasts (American Type Culture Collection, Manassas, VA) were maintained in growth medium (DMEM supplemented with 10% Fetal Bovine serum, Invitrogen Corporation, Carlsbad, CA) in 5% CO2.  Cells were plated at a density of 40-50% in 100mm dishes.  When cells reached ~90% confluency 24 hours later, they were switched to differentiation media (DMEM containing 2% horse serum; GIBCO, Invitrogen Corporation, Carlsbad, CA) which was subsequently changed every 48 hours. All cells were allowed to differentiate for 4 days with feeding every two days (day 0, 2, and 4).  Beginning at day 4, control cells were re-fed every 48 hours whereas experimental cells were not re-fed.  After an additional 4 days (8 days post differentiation), cells were harvested and total RNA was isolated from control and "starved" (non re-fed cells)

gene expression data of hNHEPS human hepatocytes exposed to 0.1 μM VX 6 h after exposure

Normal human primary hepatocytes isolated from non-transplantable donor tissue;6 h;0.1 μM;VX (O-ethyl S-[2-(diisopropylamino)ethyl] methylphosphonothiolate)

hNHEPS human hepatocytes exposed to 0.1 μM VX 6 h after exposure

Cells were grown in DMEM high glucose media (Gibco) containing 10% FBS (Atlanta Biological).  Cells were washed twice in 1X PBS before RNA extraction was performed.

Arrays were scanned and intensity data extracted using an Affymetrix 7G scanner and the Command Console software suite.

CHP files were generated using Affymetrix Expression Console software using the RMA processing algorithim. Normalized CHP files were entered into Affymetrix Transcriptome Analysis Console and the paired one-way between-subject ANOVA test, p<0.05, was used to calculate fold changes and significance.

RNA was isolated from two 85% confluent 10 cm dishes of both WT and Tfam+/- MEFs at passage 4 using QIAGEN Rneasy Plus mini kits according to the manufacturer's instructions.

Labeled cDNA was hybridized to whole transcriptome Mouse Gene 1.0 ST GeneChip microarrays at 45 degrees C for 16-18 hours. Hybridized microarrays were washed and stained on an Affymetrix GeneChip 450 fluidics station using the appropriate chip dependent fluidics script.

Samples were processed according to the Ambion WT Expression Kit protocol and the Affymetrix GeneChip WT Terminal Labeling and Hybridization kit protocol. Using the Ambion kit, 50ng-500ng of good quality, intact Total RNA was reverse transcribed using a proprietary mix of oligo-dT and random primers designed to prime both poly-A and non-poly-A transcripts, while reducing ribosomal representation. Single stranded cDNA was converted to ds-cDNA, and then amplified in a 16hr IVT reaction. Amplified RNA was then converted back to ss-cDNA. Using the Affymetrix terminal labeling kit, ss-cDNA was fragmented and terminal labeled.

A549 cells were grown on Flexercell plates - coated with Collagen I. They serve as a static control for mechanical stretch experiments. Cells were seeded ever night and stretched for either 1 or 4 hrs the next day. This sample represents static control for the 1 hr sample its the second of 2 replicates.
Keywords = Alveolar epithelial cells RNA static
Lot batch = Affymetrix Human Genome Focus Array

Alveolar Epithelial Cells line A549, were used for mechanical stretch experiments. Cells were grown in Flexercel plates coated with collagen type 1. This sample is the first replicate for the 1 hr static control.
Keywords = A549 RNA static control 1hr

A549 an alveolar epithelial cell line was used in mechanical stretch experiments. Cells were grown in flexercell plates coated with collagen I. This sample represent the static control for the 4 hr sample. This is the second replicate.

Cryptosporidium parvum-infected HCT-8 cells, time course 1, mock

Monolayers of the HCT-8 cells (ATCC CCL-244, American Type Culture Collection) were cultured in RPMI 1640 medium containing 10% fetal bovine serum and additional nutritional supplements. Cells in log phase were plated at 2×106 cells per 150 mm tissue culture dish and infected with sterilised Cryptosporidium parvum oocysts (Iowa strain). Purified oocysts were suspended in phosphate buffered saline, sterilised in 33% bleach for 7 min on ice, washed in Hank's buffered saline solution, and added to HCT-8 cultures at a ratio of one oocyst per cell. Following a 2 h excystation period at 37 °C, cells were washed with warm Hank's buffered saline solution, and cells were incubated in fresh supplemented media. Mock-infected cultures were treated identically, with the exception that oocysts were not added to the cultures.

Three independent mock- and C. parvum-infected cultures were prepared for analysis.

• The origin of mRNA samples

At 6, 12, 24, 48, and 72h post-inoculation, cell culture media were removed and cultures were immediately lysed by the addition of 3.5 ml of Trizol® reagent (GIBCO BRL Life Technologies) directly to the culture plate. Total RNA was prepared as described by the manufacturer, and poly(A) mRNA was isolated using oligo-dT cellulose columns (Amersham Pharmacia Biotech). The qualities of total RNA and poly(A) mRNA preparations were assessed by Northern blot.

• Protocols for conducting microarray hybridization

Poly(A) mRNA was converted into ‘target’ suitable for hybridisation to Affymetrix microarray chips according to protocols provided by Affymetrix Inc. (Santa Clara, CA). Briefly, 2.0 g of poly(A) mRNA was reverse-transcribed to prepare double-stranded cDNA using T7-(dT)24 primer (GENSET Corp., La Jolla, CA) and Superscript II reverse transcriptase (GIBCO). Approximately 1 g of cDNA was used for in vitro transcription in the presence of biotinylated UTP and CTP using the Enzo BioArray High Yield RNA Transcript Labelling Kit (Enzo Diagnostics, Inc). This labelled cRNA was fragmented in 40 mM Tris–acetate (pH 8.1), 100 mM potassium acetate, and 30 mM magnesium acetate at 94 °C for 35 min. The integrity of cRNA and the efficiency of fragmentation were monitored by Northern blot analysis (not shown).
Fragmented biotinylated cRNA targets were hybridised to HG-U95Av2 chips (Affymetrix) that contain probe sets for 12,600 human gene/transcripts. Fifteen micrograms of fragmented cRNA and appropriate controls were hybridised to the chips at 45 °C for 16 h with constant rotation at 60 rev./min. The chips were subsequently washed and stained with streptavidin–phycoerythrin conjugate using the GeneChip Fluidics station protocol EukGE_WS2 (Affymetrix). Following washing and staining, microarray chips were scanned twice at 3 m resolution using a Hewlett-Packard confocal scanner and hybridisation intensities for each of the genes/transcripts were collected from scanned images.

• Analysis of microarray data

Gene expression data were initially analysed with the GeneChip® expression analysis software (Affymetrix Microarray Suite, version 5.0). The fluorescence intensity of the genes/transcripts was measured for each probe array and, to minimise discrepancies due to non-biological variations, normalised by global scaling to 1000.

Further data analyses were performed using GeneSpring software (version 6.0; Silicon Genetics, Redwood City, CA). Per gene normalisation was applied in which the expression signal of each gene in C. parvum-infected cells (raw data) was normalised to the median of its measurements in the mock-infected samples (control); and the ratio of expression levels between mock and infected samples was calculated as the mean value of normalised signal vs. control signal among three replicates. To identify genes with significantly altered expression, a series of statistical analyses (filtering) were performed: cut-off values for ratio of expression levels 1.80 and 0.55 were used to filter genes with expression level fold changes greater than ±1.8 in all three independent samples. Genes with fold change variations >1.5 across the three samples were excluded. Furthermore, a ‘statistical group comparison’ using Student's t-test/ANOVA was conducted to compare mean expression levels between mock-infected and infected samples, and the genes with significant differential expression (P<0.05) were selected. Identified differentially expressed genes were then annotated using GeneSpring's ‘Build Simplified Ontology’ constructor which hierarchically groups genes into meaningful biological categories (gene lists) based on the Gene Ontology Consortium Classifications. Various lists of regulated genes were created by cross-referencing annotated gene lists and applying assorted statistical methods.

Cryptosporidium parvum-infected HCT-8 cells, time course 1, mock (24h post-infection)

Transgenic for alpha tropomyosin slow, snap frozen, tibialis anterior muscle, 10 month age animal

Transgenic, snap frozen, tibialis anterior muscle, 10 month age animal

Air
1
48

lineage depleted cord blood cells;liquid culture day 11;control;control

flow-cytometry: B220+, CD5–, CD19+, CD25–, CD69–, B7-1–, B7-2–, IgD+, sIgM+; clinical-signs: conjunctivitis

Monocytes were plated in 6-well tissue culture plates (Nunclon, Denmark) at 1-2 x10^6 cells per well and incubated in complete IMDM medium containing 10% (v/v) human serum and 1% (v/v) penicillin/streptomycin, in a humidified incubator at 37 °C and 5% CO2.

testis with regular spermatogenesis from orchiectomy cases due to prostate carcinoma, patient age: 67y; W03 002

testis with regular spermatogenesis from orchiectomy cases due to prostate carcinoma, patient age: 67y

testis with regular spermatogenesis from orchiectomy cases due to prostate carcinoma, patient age: 58y; W03 003

testis with regular spermatogenesis from orchiectomy cases due to prostate carcinoma, patient age: 58y

testis with regular spermatogenesis with status after vasectomy, patient age: 34y; W03 020

testis with regular spermatogenesis with status after vasectomy, patient age: 34y

liver from a 42 day old male mouse, mutant 569 was dissected out. Total RNA was extracted using an Ambion RNaqueous RNA extraction kit. Targets were produced using modified Affymetrix procedure from 5ug of total RNA. 3 biological replicates were analysed per each group of animals.Sample also known as A1.

Ctrl_48h_4

Ishikawa;39-year-old parous Japanese female diagnosed with endometrial adenocarcinoma stage 2.;vehicle control;48 hours

High_8h_1

Ctrl_24h_4

Ishikawa;39-year-old parous Japanese female diagnosed with endometrial adenocarcinoma stage 2.;vehicle control;24 hours

Ctrl_48h_1

Ctrl_48h_2

Ctrl_48h_3

Ctrl_8h_4

Ctrl_24h_1

Ctrl_24h_2

Ctrl_24h_3

HIV seropositive, CD4 cells increase over time, sampled at time point1

baseline;M;59;synovial knee biopsy;rheumatoid arthritis;EULAR Moderate-responder;synovium

12 weeks of RTX therapy;M;59;synovial knee biopsy;rheumatoid arthritis;EULAR Moderate-responder;synovium

baseline;F;77;synovial knee biopsy;rheumatoid arthritis;EULAR Moderate-responder;synovium

12 weeks of RTX therapy;F;77;synovial knee biopsy;rheumatoid arthritis;EULAR Moderate-responder;synovium

DRG collected from ipsilateral limb 14d days after sciatic nerve transection surgery

DRG collected from ipsilateral limb 21 days after chronic constriction injury

Lot batch = Replicate 1

DRG collected from ipsilateral limb 21d days after sciatic nerve transection surgery

DRG collected from ipsilateral limb 50d days after sciatic nerve transection surgery

65B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

63B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

64B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

5B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

60B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

Autoimmune pancreatic islets, day 2 cyclophosphamide treatment, Rep 1

Lot batch = jos1074

Chip was normalized using all probe sets scaling option and target signal at 500 (GCOS1.2).

Chip was normalized using all probe sets scaling option and target signal at 500 (GCOS1.2)

Autoimmune pancreatic islets, day 3 cyclophosphamide treatment, rep 2

Lot batch = jos0995x

Autoimmune pancreatic islets, day 3 cyclophosphamide treatment, rep 3

Lot batch = jos1218

HD patient; Gender: female; Age: 43; Tissue: lymphocytes (blood); IT15 CAG repeats: 26/47

HD patient; Gender: female; Age: 43; Tissue: lymphocytes (blood); IT15 CAG repeats: 15/50

HD patient; Gender: female; Age: 36; Tissue: lymphocytes (blood); IT15 CAG repeats: 18/51

HD patient; Gender: female; Age: 41; Tissue: lymphocytes (blood); IT15 CAG repeats: 24/49

control; Gender: male; Age: 50; Tissue: lymphocytes (blood); IT15 CAG repeats: N/A

control; Gender: male; Age: 60; Tissue: lymphocytes (blood); IT15 CAG repeats: N/A

control; Gender: male; Age: 42; Tissue: lymphocytes (blood); IT15 CAG repeats: N/A

control; Gender: male; Age: 46; Tissue: lymphocytes (blood); IT15 CAG repeats: N/A

control; Gender: female; Age: 68; Tissue: lymphocytes (blood); IT15 CAG repeats: N/A

control; Gender: male; Age: 38; Tissue: lymphocytes (blood); IT15 CAG repeats: N/A

GeneChips were scanned using the Affymetrix GeneChip Scanner 3001

GeneChips were scanned using the Affymetrix GeneChip Scanner 3002

GeneChips were scanned using the Affymetrix GeneChip Scanner 3003

Rat liver, untreated (control), extrated 48 hours after treatment (no treatment in this case), biological rep8

Rat liver, untreated (control), extrated 48 hours after treatment (no treatment in this case), biological rep9

Rat liver, untreated (control), extrated 48 hours after treatment (no treatment in this case), biological rep6

Rat liver, untreated (control), extrated 48 hours after treatment (no treatment in this case), biological rep7

Rat liver, untreated (control), extrated 48 hours after treatment (no treatment in this case), biological rep4

Rat liver, untreated (control), extrated 48 hours after treatment (no treatment in this case), biological rep5

Rat liver, untreated (control), extrated 48 hours after treatment (no treatment in this case), biological rep2

Rat liver, untreated (control), extrated 48 hours after treatment (no treatment in this case), biological rep3

by the Center for Array Technologies (University of Washington, Seattle, WA)

The array used was GeneChip Mouse Genome 430 2.0 Array. There are 2 groups, memory P14 and memory HD-/-P14 T cells. Each group has 2 biological replicates. The biological replicates are numbered #1 to #2.
MAS5.0.

RNA was isolated with Trizol (Invitrogen) from FACS-sorted memory P14 T cells after enrichment of CD8 T cells using negative selection. RNA was prepared using RNeasy Mini Kit (Qiagen) before amplification.

FACS sorted CD8 P14 memory cells.
This sample is called memory HD-/- P14 T cells #1.

This sample is called memory HD-/- P14 T cells #2.

This sample is called memory P14 T cells #1.

This sample is called memory P14 T cells #2.

THP-1 cell line infected with scrambled control shRNA, biological rep2
Sample name: THP1_CTRL-2
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_B02_596660.CEL

Primary human erythroid progenitor cells expressing a luciferase control shRNA biological replicate 1

WT Lineage negative, c-Kit and Sca1 (LSK) positive expressing bone marrow progenitors-repeat1
Gene expression data from WT Lineage negative, c-Kit and Sca1 (LSK) positive expressing bone marrow progenitors-repeat1

Lineage(-), Sca-1(+), c-Kit(+) cells derived from Evi-1(flox/flox) mice were transduced with GFP  (control) or Cre-GFP expressing retroviruses. Total RNA was prepared from sorted GFP(+) cells.

After 72 hrs of starvation, the cells were maintained in complete medium without CdCl2 for 4 hrs.

After 72 hrs of starvation, the cells were maintained in complete medium without CdCl2 for 8 hrs.

After 72 hrs of starvation, the cells were briefly exposed to complete medium without CdCl2.

Crohn's Disease subject (61 year old caucasian male, SAK_1316018592)

Subject Age : 61

Crohn's Disease subject (47 year old caucasian female, SAK_1315705650)

Crohn's Disease subject (49 year old caucasian female, SAK_1304617942)

Crohn's Disease subject (46 year old caucasian female, SAK_1313783292)

Crohn's Disease subject (56 year old caucasian female, SAK_1315817415)

NCI-H1299;lung cancer cells;control hairpins targeting luciferase

breast cancer histologically normal breast epithlieum patient 316

Gene expression data from mock RNAi (pSuper.puro transfected cells selected by puromycin for 3 days).

Sample name: WT_1

Sample name: WT_2

Sample name: WT_3

Sample name: WT_4

Sample name: WT_5

Sample name: Het_1

Sample name: Het_2

Sample name: Het_3

Confluent monolayer of HUVEC was treated with a vehicle-control for 24 hours

Ewing family tumor cell-line A673 (wild-type). Experiment 1.
Lot batch =

Ewing family tumor cell-line A673 (wild-type). Experiment 2.
Lot batch =

C57BL/6;male;ESC-like cells;Prdm14 Knockout;Serum+MEK inhibitor (day2)

C57BL/6;male;ESCs;No genetic modification;Serum+MEK inhibitor (day2)

microarray analysis of gene expression after transverse aortic constriction in mice - 3 weeks TAC group No.2

microarray analysis of gene expression after transverse aortic constriction in mice - 48 hours TAC group No.4

microarray analysis of gene expression after transverse aortic constriction in mice - 48 hours TAC group No.3

SMhu162

SMhu161

SMhu158

SMhu160

SMhu159

SMhu154

SMhu153

SMhu156

microarray analysis of gene expression after transverse aortic constriction in mice - 48 hours TAC group No.1

spinal cord, ventral spinal cord: EP131/L - hSOD1(Chan)/e14-wildtype hSOD1

wildtype SOD1 - biological replicate 1/pool of 5 positive embryos

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D7;11

male;non-metastatic prostate cancer;external beam radiation therapy (EBRT);peripheral blood;white blood cells;D14;11

0.5 mg/kg/ml Isoproterenol treatment, 72 hour time point,  biological rep 4

CHIPEXP_NAME: 230_2_050531tpj_61h

Total RNA was prepared from the entire small intestine of one 40 day old CFTR null female mouse, CFTR(-/-), congenic on the black6 background, using TRIzol reagent. Mice were fed Peptamen from age 10 days to prevent intestinal obstruction.

Total RNA was prepared from the entire small intestine of one 40 day old CFTR control female mouse, CFTR(+/+), congenic on the black6 background, using TRIzol reagent. Mice were fed Peptamen from age 10 days to prevent intestinal obstruction.

TH cells from LC, Mecp2 null, young time point, biological replicate 2

TH_LCY_KO_2

C57BL6/J;No;Aug-11;83;male;LC (locus coeruleus);P22;Y/Mecp2-;TH/-;brain;tyrosine hydroxylase (TH)-positive locus coeruleus (LC) neurons

TH cells from LC, Mecp2 null, young time point, biological replicate 1

TH_LCY_KO_1

C57BL6/J;No;Aug-11;80;male;LC (locus coeruleus);P24;Y/Mecp2-;TH/-;brain;tyrosine hydroxylase (TH)-positive locus coeruleus (LC) neurons

15(+) 12d

BALB/c scid, gender:male, age:8wks, tissue: whole lung, condition: 12DPI

BALB/c WT, gender:male, age:8wks, tissue: whole lung, condition: 12DPI

BALB/c scid, gender:male, age:8wks, tissue: whole lung, condition: 8DPI

Top2b+/+ in 129SvEv (minor 129SvJ) background;;E14.5 embryo;;male;;whole brain

normal;IA, IB, II, IIIA, IIIB, or IV=IV;73;female, male:female;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

normal;IA, IB, II, IIIA, IIIB, or IV=IV;63;female, male:female;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

normal;IA, IB, II, IIIA, IIIB, or IV=IV;39;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=mixed type

normal;IA, IB, II, IIIA, IIIB, or IV=IV;52;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

normal;IA, IB, II, IIIA, IIIB, or IV=IV;63;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

normal;IA, IB, II, IIIA, IIIB, or IV=IV;67;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

normal;IA, IB, II, IIIA, IIIB, or IV=IV;65;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type

normal;IA, IB, II, IIIA, IIIB, or IV=IV;NA;female, male:NA;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=not determined

Gene expression data of Day2 embryoid bodies induced with doxycycline and cultured for another 48h

129P2 (formerly called 129/Ola);embryoid bodies;Day2 EBs induced with doxycycline and cultured for another 48h

Gene expression data of Day2 embryoid bodies cultured for another 48h

129P2 (formerly called 129/Ola);embryoid bodies;Day2 EBs cultured for another 48h

Gene expression data of Day2 embryoid bodies induced with doxycycline and cultured for another 24h

129P2 (formerly called 129/Ola);embryoid bodies;Day2 EBs induced with doxycycline and cultured for another 24h

Gene expression data from  3 uM EPZ004777 treated, DAY 4, biological rep.1, MV4-11 cells

MV4-11;biphenotypic B myelomonocytic leukemia (MLL-AF4 rearragenment);IMDM with 10% FBS;EPZ004777;day 4;1

Gene expression data from Vehicle treated, DAY 4, biological rep.1, MV4-11 cells

MV4-11;biphenotypic B myelomonocytic leukemia (MLL-AF4 rearragenment);IMDM with 10% FBS;Vehicle;day 4;1

Gene expression data from  3 uM EPZ004777 treated, DAY 4, biological rep.3, MV4-11 cells

MV4-11;biphenotypic B myelomonocytic leukemia (MLL-AF4 rearragenment);IMDM with 10% FBS;EPZ004777;day 4;3

Gene expression data from Vehicle treated, DAY 2, biological rep.1, MV4-11 cells

MV4-11;biphenotypic B myelomonocytic leukemia (MLL-AF4 rearragenment);IMDM with 10% FBS;Vehicle;day 2;1

Gene expression data from  3 uM EPZ004777 treated, DAY 2, biological rep.3, MV4-11 cells

MV4-11;biphenotypic B myelomonocytic leukemia (MLL-AF4 rearragenment);IMDM with 10% FBS;EPZ004777;day 2;3

Gene expression data from Vehicle treated, DAY 2, biological rep.3, MV4-11 cells

MV4-11;biphenotypic B myelomonocytic leukemia (MLL-AF4 rearragenment);IMDM with 10% FBS;Vehicle;day 2;3

Gene expression data from Vehicle treated, DAY 2, biological rep.2, MV4-11 cells

MV4-11;biphenotypic B myelomonocytic leukemia (MLL-AF4 rearragenment);IMDM with 10% FBS;Vehicle;day 2;2

Gene expression data from Vehicle treated, DAY 4, biological rep.3, MV4-11 cells

MV4-11;biphenotypic B myelomonocytic leukemia (MLL-AF4 rearragenment);IMDM with 10% FBS;Vehicle;day 4;3

Mouse Lung LRD Diet 5wk 10ppb As Drinking Water Exposure, biological replicate E
AN080306_Sample 51.CEL

Mouse Lung AIN Diet 5wk 10ppb As Food Exposure, biological replicate D
AN080906_Sample 50.CEL

Human CD34+ cells isolated from umbilical cord blood;ZMYM2/FGFR1;1

Mouse Lung AIN Diet 8hr 1mg/kg Dex and 1mg/kg As Injection, biological replicate E
AN080406_Sample 43.CEL

Mouse Lung AIN Diet 8hr 1mg/kg As Injection, biological replicate A
AN080306_Sample 42.CEL

Mouse Lung AIN Diet 8hr 1mg/kg As Injection, biological replicate C
AN080906_Sample 45.CEL

Mouse Lung AIN Diet 8hr 1mg/kg Dex Injection, biological replicate F
AN080806_Sample 44.CEL

Mouse Lung AIN Diet 8hr 1mg/kg Dex and 1mg/kg As Injection, biological replicate F
AN080306_Sample 47.CEL

Mouse Lung LRD Diet 5wk 100ppb As Drinking Water Expousre, biological replicate F
AN080406_Sample 46.CEL

Mouse Lung LRD Diet 5wk 100ppb As Drinking Water Expousre, biological replicate D
AN080806_Sample 49.CEL

Mouse Lung LRD Diet 5wk Control, biological replicate F
AN080206_Sample 48 Lung.CEL

MDA-MB-231 Breast Cancer Cells Stably Expressing mutant ERa LQ 2 Hr Treatment of 10 nM E2 Sample B

MDA-MB-231 Breast Cancer Cells Stably Expressing Mutant ERa LQ 2Hr Treatment of 10 nM E2 Sample B

MDA-MB-231 Breast Cancer Cells Stably Expressing mutant ERa LQ 2 Hr Treatment of 10 nM E2 Sample A

MDA-MB-231 Breast Cancer Cells Stably Expressing Mutant ERa LQ 2Hr Treatment of 10 nM E2 Sample A

CCE embryonic stem cells were cultured on gelatin coated dish in DMEM medium with 15% FSC and leukemia inhibitory factor (LIF).

CCE embryonic stem cells were cultured on gelatin coated dish in DMEM medium with 15% FSC and leukemia inhibitory factor (LIF). Lentivirus containing mouse BMI1 cDNA was used to infect CCE ES cells in the presence of 8 microgram polybrene. Empty vector served as control. After two passages eGFP positive CCE ES cells were sorted by flow cytometry and cells were further grown in culture medium as above.

Empty vector transduced CCE embryonic stem cells were cultured on gelatin coated dish in DMEM medium with 15% FSC and leukemia inhibitory factor (LIF).

Empty vector transduced CCE embryonic stem cells were cultured on gelatin coated dish in DMEM medium with 15% FSC and leukemia inhibitory factor (LIF). Lentivirus containing mouse BMI1 cDNA was used to infect CCE ES cells in the presence of 8 microgram polybrene. Empty vector served as control. After two passages eGFP positive CCE ES cells were sorted by flow cytometry and cells were further grown in culture medium as above.

Empty vector transduced CCE embryonic stem cells (empty vector CCE ES cells)

Gene expression data under ER stress from lymphoblastoid cells of twin 1704:1 treated with DMSO.

lymphoblastoid cell line;1704;GM14405;Twin number 1;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1704:1 treated with 500nM thapsigargin.

lymphoblastoid cell line;1704;GM14405;Twin number 1;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1705:1 treated with DMSO.

lymphoblastoid cell line;1705;GM14408;Twin number 1;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1705:1 treated with 500nM thapsigargin.

lymphoblastoid cell line;1705;GM14408;Twin number 1;thapsigargin;500nM;4 hours

Sprague Dawley;male;isocaloric control diet without EtOH for 6wks;Control;Alveolar type 2 cells

Treated with 10uM Motexafin gadolinium and 50uM Zinc for 4 hrs -- replicate #3

Treated with 10uM Motexafin gadolinium and 25uM Zinc for 4 hrs -- replicate #3

Treated with 10uM Motexafin gadolinium and 25uM Zinc for 4 hrs -- replicate #2

Gene expression data from PBMC sample of gastric cancer patient.

Gene expression data from  primary HCL cell of  patient E treated with Vemurafenib 1000 nM for 48h
ET42

peripheral blood;primary leukemic cells;patient E;Vemurafenib 1000 nM for 48h

Gene expression data from  primary HCL cell of  patient E treated with DMSO for 48h
ET41

Gene expression data from  primary HCL cell of  patient D treated with Vemurafenib 1000 nM for 72h
ET32

peripheral blood;primary leukemic cells;patient D;Vemurafenib 1000 nM for 72h

Gene expression data from  primary HCL cell of  patient D treated with DMSO for 72h
ET31

Gene expression data from  primary HCL cell of  patient D treated with Vemurafenib 1000 nM for 48h
ET30

peripheral blood;primary leukemic cells;patient D;Vemurafenib 1000 nM for 48h

Gene expression data from  primary HCL cell of  patient C treated with Vemurafenib 1000 nM for 72h
ET28

peripheral blood;primary leukemic cells;patient C;Vemurafenib 1000 nM for 72h

Gene expression data from  primary HCL cell of  patient C treated with DMSO for 72h
ET27

Gene expression data from  primary HCL cell of  patient C treated with Vemurafenib 1000 nM for 48h
ET26

peripheral blood;primary leukemic cells;patient C;Vemurafenib 1000 nM for 48h

Gene expression data from  primary HCL cell of  patient C treated with DMSO for 48h
ET25

endothelial, age:44, gender:female, diagnostic group: control, PMI:10h

endothelial, age:45, gender:male, diagnostic group: schizophrenia, PMI:18h

rat hippocampus (combined dorsal and ventral aspects), aged PIO, subject 5

rat hippocampus (combined dorsal and ventral aspects), aged PIO, subject 8

rat hippocampus (combined dorsal and ventral aspects), aged PIO, subject 10

Cervical cancer, squamous cell carcinoma, microdissected, age 48, HPV 16, HPV 31, HPV 45

Cervical cancer, squamous cell carcinoma, microdissected, age 47, HPV 16

Cervical cancer, squamous cell carcinoma, microdissected, age 35, HPV 16, HPV 18, HPV 31, HPV 45

Cervical cancer, squamous cell carcinoma, microdissected, age 32, HPV 16, HPV 31, HPV 45

Cervical cancer, squamous cell carcinoma, microdissected, stage IIIA, HPV 16

Cervical cancer, squamous cell carcinoma, microdissected, age 82, HPV 16

Cervical cancer, squamous cell carcinoma, microdissected, age 53, HPV 16

This is wt-Gfp P10 replicate 3.

Pooled skins from rats on vitamin A supplement at 1 week post 9 Gy electron irradiation.

control skin, no treatment, 28 days of age,male rats, resting stage of hair growth

Pooled skins of Vitamin A fed rats at 24 hour after 9 Gy electron irradiation.

121;Cp-tenedone, Enalapril, Loperamide.;4/8/59;F;CAUCASIAN;FALSE;FALSE;FALSE;FALSE;FALSE;2/1/05;Diarrhoea, Blastocytitis on stool cultures.;0;FALSE;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;unknown;0;Normal;8-9-01;ascending colon;Uninflamed;total RNA from 10 human cell lines

MCF7;Breast adenocarcinoma, estrogen receptor-positive;MTDH WT KD

A VIS _B031

Y HID_B038

A HID U_B049

A VIS _B032

A YOKE_B027

Y YOKE_B024

Y VIS _B029

Y VIS _B028

Y YOKE_B060

A HID U_B053

vastus lateralis biopsy, 65 year-old trained COPD patient (male #76).

microdissected epithelial cells from normal main pancreatic duct 2

microdissected epithelial cells from normal main pancreatic duct 1

Large Intestine; Cecum

LC-MI2

LC-MI3

LC-MI1

LC-MI6

LC-MI7

LC-MI4

LC-MI5

LC-MI8

LC-MI9

JLI_11

JLI_8

JLI_7

JLI_4

JLI_21

JLI_14

JLI_13

JLI_12

JLI_23

JLI_22

Gene expression data under ER stress from lymphoblastoid cells of individual GM11830 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM11831 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM07056 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM07345 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM07345 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM07357 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM07357 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM11829 treated with 4 ug/ml tunicamycin 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM11829 treated with DMSO 8 hours.

Gene expression data under ER stress from lymphoblastoid cells of individual GM11830 treated with 4 ug/ml tunicamycin 8 hours.

D2RMKOS617

D3RMKOS1118

C5MKOS2020

D4RMKOS1219

SMhu173

Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 255

B cells from flu-infected mice (wild type)
Array 20 - 20.N.B._494.CEL

Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 254

Array 19 - 19.N.B._493.CEL

Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 253

B cells from control mice (uninfected wild type)
Array 18 - 18.N.B._482.CEL

Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 252

Array 17 - 17.N.B._478.CEL

Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 251

Array 16 - 16.N.B._473.CEL

Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 250

Array 15 - 15.N.B._467.CEL

Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 257

Array 33 - 33.N.B._633.CEL

Affymetrix GeneChip Scanner 3000 and GCOS software using target value = 256

Array 21 - 21.N.B._528.CEL

total RNA from Runx1 knockout mouse embryo, stage E12

total RNA from wild-type mouse embryo, stage E12

Crohn's Disease subject (27 year old caucasian female, SAK_1275500386)

Crohn's Disease subject (20 year old caucasian female, SAK_1287906498)

Crohn's Disease subject (58 year old caucasian female, SAK_1275433327)

Crohn's Disease subject (47 year old caucasian female, SAK_1263249533)

Crohn's Disease subject (33 year old caucasian male, SAK_1280753352)

Crohn's Disease subject (39 year old caucasian female, SAK_1261237763)

Phenytoin brainstem 3

Crohn's Disease subject (52 year old caucasian male, SAK_1280775705)

Phenytoin brainstem 7

Phenytoin hippocampus 1

Crohn's Disease subject (65 year old caucasian female, SAK_1280798058)

Crohn's Disease subject (33 year old caucasian male, SAK_1260857762)

SMhu182

Treatment: 0 mM HOCl in medium

Treatment Duration: 6 hours
Cell Confluency upon Treatment : ~80-90%

RAW 264.7 macrophages (RAW cells) were cultured in DMEM supplemented with 10% FBS, 10 mM HEPES, 100 U penicillin/ml, and 100 µg streptomycin/ml.

STAT3-deficient naïve T cells stimulated for 3 hours with IL-27 3

TAMs sorted from imatinib treated tumors, biological replicate#2

sample 1:
non-steroidal anti-inflammatory drugs (NSAID)
sample 2:
sample 3:

CD1;WT;male;14 weeks;ventricular myocardium;20 mg/kg LPS isolated from E. coli

the third run of normal bladder cell treated with APF. Membrane A is used.

the third run of normal bladder cell treated with mock APF. Membrane B is used.

Peripheral blood mononuclear cells;TTF=95min;Race=White;Sex=Male

Peripheral blood mononuclear cells;TTF=120min;Race=White;Sex=Male

SBC-5 cells, siEGR4 (target), 24 hr after siRNA, duplicate sample 1

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Estradiol treated. Patient 36.

SBC-5 cells, siEGFP (control), 24 hr after siRNA, duplicate sample 1

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Estradiol treated. Patient 28.

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Estradiol treated. Patient 23.

Gene expression data. Endometrium from postmenopausal female (Klaassens et al., 2006, Hanifi-Moghaddam et al., 2007). Estradiol treated. Patient 3.

liver sample of Wistar rat fed for 12 weeks with standard chow diet, after overnight fasts

Gene expression data from wild-type CTL from mouse 2 treated with AktI
4_155IL2Akti

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20581.gif
name: 20581_Infection

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20565.gif
name: 20565_Infection

Common Reference 2 round amplification 2 ug;Mening UNSTIM WB NP 24b

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20544.gif
name: 20544_Infection

Common Reference 2 round amplification 2 ug;Mening UNSTIM WB SW 1a

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20543.gif
name: 20543_Infection

Common Reference 2 round amplification 2 ug;Mening UNSTIM WB SW 6b

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20561.gif
name: 20561_Infection

Common Reference 2 round amplification 2 ug;Mening UNSTIM WB NP 12b

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20528.gif
name: 20528_Infection

Common Reference 2 round amplification 2 ug;Mening Unstim WB SW 24a

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20563.gif
name: 20563_Infection

Common Reference 2 round amplification 2 ug;Mening SWB WB NP 24a

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20546.gif
name: 20546_Infection

Common Reference 2 round amplification 2 ug;Mening UNSTIM WB SW 0a

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20548.gif
name: 20548_Infection

Common Reference 2 round amplification 2 ug;Mening SWB WB NP 24b

Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20580.gif
name: 20580_Infection

Common Reference 2 round amplification 2 ug;Mening UNSTIM WB SW 3b

Signal amplification was done using biotinylated antistreptavidin.  The stained array was scanned on the Affymetrix GeneChip® Scanner 3000.  The images were analyzed and quality control metrics recorded using Affymetrix Command Console v3.

We used the following software packages for data QC, statistical analysis and presentation of the results: Affymetrix Expression Console (www.affymetrix.com), Partek (www.partek.com), BRB Array Tools (linus.nci.nih.gov/BRB-ArrayTools.html), and dChip (biosun1.harvard.edu/complab/dchip). Expressions were estimated using the RMA (Multi-Array Analysis) method [38] with Partek software.
Differentially expressed genes were found using the RVM (Random Variance Model) t-test, which is designed for small sample size experiments [39]. We used BRB Array Tools software, developed by Dr. Richard Simon and the BRB-ArrayTools Development Team. All genes were included in the comparison. For the genes represented by more than one probeset, we used the most highly expressed probeset. The cutoffs for differentially expressed genes were False Discovery Rate (FDR) = 0.05.

Frozen hearts isolated from WT and SRC-2 KO animals were homogenized in buffer RLT and subsequent RNA was isolated using the RNEasy kit according to the manufacturer’s protocol (Qiagen).

A hybridization cocktail containing Affymetrix spike-in controls and 15 μg fragmented, labeled cRNA was loaded onto a GeneChip® Mouse 430 2.0 array.  The array was hybridized for 16 hours at 45°C with rotation at 60 rpm  then washed and stained with a strepavidin, R-phycoerythrin conjugate stain using the FS 450_0001 Fluidics protocol setting.

250ng of RNA isolated from total heart (RNeasy kit, Qiagen) for each sample was labeled using the new standard Affymetrix linear amplification protocol using the 3' IVT Express Kit. This was reverse-transcribed and cRNA was produced and biotinylated via in vitro transcription.

CEL files exported from GCOS were uploaded into ArrayTrack software (National Center for Toxicological Research, U.S. FDA, Jefferson, AR, USA (NCTR/FDA)) and normalized using Total Intensity Normalization after subtracting backgrounds for data management and analysis. ArrayTrack software includes some tools common to other bioinformatics software (e.g., ANOVA, T-test and SAM).To compare the normalized data from dysplasia, normal lung tissue from transgenic mouse, tumor cells and non-transgenic of different mice, we used the Significance Analysis of Microarrays (SAM) algorithm (ArrayTrack), which contains a sliding scale for false discovery rate (FDR) of significantly up- and down-regulated genes. All data were permuted 100 cycles by using the two classes, unpaired data mode of the algorithm. As cut-off for significance an estimated FDR of 0.001 was chosen. Moreover, a cut-off for fold-change of differential expression of 2 was used.

Lung samples were derived from SP-C/c-raf mice in the C57BL/6 background for at least five generations (aged 5 – 14 months); tumor cells were isolated from 11 – 14 month old mice, unaltered lung tissue were isolated from the dysplasia-bearing transgenic mouse (aged 5 – 7 months). Endogenous normal lung tissue was studied of non-transgenic mice (aged 7 – 10 months). The non-transgenic littermates (wild-type) served as control for transgenic effects.

AZ521;inducible dnSox2;gastric cancer cell line;doxycycline induced;18h

AZ521;inducible dnSox2;gastric cancer cell line;doxycycline induced;12h

Gene expression analysis of the kidney of mouse treated with 7 repeat daily doses of vancomycin at 200 mg/kg administered via the intraperitoneal route (ip)

Kidney from mice treated with 7 daily ip injections of vancomycin at 200 mg/kg

mixed (C57Bl/6:129Sv) background;female;Liver;102;JAK2 KO;8 weeks

gavage (n = 8).

Bioanalyzer. We used 10 íg of total RNA from each individual
animal for microarray analysis

gene expression data from pools of 2 hippocampi of WT littermate males

lung;Sporadic IIP;Usual Interstitial Pneumonia;Stratagene;;740000

Gene expression data from PBMC sample of pancreatic cancer patient.

S100a10 cells, p11 KO, cortex, TRAP RNA, FLX treated, biological rep1

Gene expression data from the Caudate-Putamen of MPTP-exposed FVB/N mice

Gene expression data from the Pre-Frontal contex of MPTP-exposed AChE-S mice

Gene expression data from the Caudate-Putamen of naive FVB/N mice

Pathohistological and clinical examination of Patient CD10 (18 year-old female) yielded to diagnosis of Crohn's disease.

Pathohistological and clinical examination of Patient CD09 (50 year-old male) yielded to diagnosis of Crohn's disease.

Pathohistological and clinical examination of Patient UC02 (38 year-old male) yielded to diagnosis of ulcerative colitis

Pathohistological and clinical examination of Patient UC01 (29 year-old male) yielded to diagnosis of ulcerative colitis

Pathohistological and clinical examination of Patient CD06 (66 year-old male) yielded to diagnosis of Crohn's disease.

Pathohistological and clinical examination of Patient CD05 (24 year-old female) yielded to diagnosis of Crohn's disease.

Pathohistological and clinical examination of Patient CD08 (44 year-old male) yielded to diagnosis of Crohn's disease.

Pathohistological and clinical examination of Patient CD07 (25 year-old male) yielded to diagnosis of Crohn's disease.

SMhu180

Pathohistological and clinical examination of Patient UC04 (31 year-old male) yielded to diagnosis of ulcerative colitis

Pathohistological and clinical examination of Patient UC03 (27 year-old male)yielded to diagnosis of ulcerative colitis

SMhu179

ACI rats were obtained from Harlan (Indianapolis, IN). Empty silastic tubing implants were surgically inserted into control animals’ interscapular regions, as sham treatment, at 9 weeks of age. Each animal received an intraperitoneal injection of BrdU (50mg/kg) 4 hours prior to sacrifice. Animals were sacrificed at 21 weeks of age by decapitation and pituitary glands were immediately harvested, weighed and flash-frozen in liquid nitrogen. Tissues were homogenized through a 22-gauge needle and total RNA was extracted using the Absolutely RNA Kit (Stratagene). A total of 3 control males were used, resulting in two independent biological replicates.

ACI rats were obtained from Harlan (Indianapolis, IN). At 9 weeks of age, a silastic tubing implant containing 5mg of the synthetic estrogen diethylstilbestrol (DES) was surgically implanted subcutaneously in the interscapular region of male rats. Each animal received an intraperitoneal injection of BrdU (50mg/kg) 4 hours prior to sacrifice. Animals were sacrificed at 21 weeks of age by decapitation and pituitary glands were immediately harvested, weighed and flash-frozen in liquid nitrogen. Tissues were homogenized through a 22-gauge needle and total RNA was extracted using the Absolutely RNA Kit (Stratagene). A total of 4 DES-treated males were used, resulting in three independent biological replicates.

ACI strain, male, age 21 weeks, treated with the synthetic estrogen diethylstilbestrol (DES) for 12 weeks

COP rats were obtained from Charles River Laboratories (Wilmington, MA). Empty silastic tubing implants were surgically inserted into control animals’ interscapular regions, as sham treatment, at 9 weeks of age. Each animal received an intraperitoneal injection of BrdU (50mg/kg) 4 hours prior to sacrifice. Animals were sacrificed at 21 weeks of age by decapitation and pituitary glands were immediately harvested, weighed and flash-frozen in liquid nitrogen. Tissues were homogenized through a 22-gauge needle and total RNA was extracted using the Absolutely RNA Kit (Stratagene). A total of 3 control males were used, resulting in two independent biological replicates.

Gene expression of murine fibroblast-like synoviocytes Grp2_C57BL6_1_FLS_TNFtg

Gene-expression profiling of primary murine hTNFtg FLS, Rsk2+/y; chip 1. Samples were analyzed using murine MG_U430_2 arrays (Affymetrix)

C57BL/6;male;primary murine fibroblast-like synoviocytes (FLS);human TNF transgenic without knockout (Rsk2+/y FLS);CD90.2pos/VCAM1pos/CD11bneg

Gene expression of murine fibroblast-like synoviocytes Grp1_C57BL6_3_FLS_TNFtg_plus_RSK2-KO

Gene-expression profiling of primary murine hTNFtg FLS, Rsk2-/y; chip 3. Samples were analyzed using murine MG_U430_2 arrays (Affymetrix)

Gene expression of murine fibroblast-like synoviocytes Grp2_C57BL6_3_FLS_TNFtg

Gene-expression profiling of primary murine hTNFtg FLS, Rsk2+/y; chip 3. Samples were analyzed using murine MG_U430_2 arrays (Affymetrix)

Gene expression of murine fibroblast-like synoviocytes Grp2_C57BL6_2_FLS_TNFtg

Gene-expression profiling of primary murine hTNFtg FLS, Rsk2+/y; chip 2. Samples were analyzed using murine MG_U430_2 arrays (Affymetrix)

SMhu181

Patient CCo, stable renal transplant recipients, male, 38 years old, T1 (3 months after the switching of the therapy)

Patient CCo, stable renal transplant recipients, male, 38 years old, T0 (time of enrollment)

Patient CCa, stable renal transplant recipients, female, 70 years old, T1 (3 months after the switching of the therapy)

Patient CCa, stable renal transplant recipients, female, 70 years old, T0 (time of enrollment)

C57Bl/6;: ARR2PB-Cre;ROSA(N1IC) model (a.k.a. PB-NICD) that expresses the Notch1 intracellular domain (NICD or N1IC) in the prostate and develops prostatic intraepithelial neoplasia (PIN lesions).;Stratagene, Universal Mouse Reference RNA Catalog #740100

TRIzol extraction of total RNA was performed according to the manufacturer's instructions.

Cerebellum_transgenic nuclear localization signal Htt exon1 142Q S25_3 months_replicate 2

S25 NLS 142Q TG2	F4/26	S25	NLS Htt exon 1 142Q	Mouse	3 months	Cerebellum	Male

Cerebellum_transgenic nuclear localization signal Htt exon1 142Q S25_3 months_replicate 3

S25 NLS 142Q TG3	F4/34	S25	NLS Htt exon 1 142Q	Mouse	3 months	Cerebellum	Male

Cerebellum_transgenic nuclear localization signal Htt exon1 142Q S46_10 months_replicate 3

S46 NLS 142Q TG7	F4/3	S46	NLS Htt exon 1 142Q	Mouse	10 months	Cerebellum	Female

Cerebellum_transgenic nuclear localization signal Htt exon1 142Q S46_10 months_replicate 1

S46 NLS 142Q TG5	F4/1	S46	NLS Htt exon 1 142Q	Mouse	10 months	Cerebellum	Female

Cerebellum_transgenic nuclear localization signal Htt exon1 142Q S46_10 months_replicate 2

S46 NLS 142Q TG6	F4/2	S46	NLS Htt exon 1 142Q	Mouse	10 months	Cerebellum	Female

S25 WT3	F41/391	S25	wild type	Mouse	2.5 months	Cerebellum	Female

S25 WT2	F41/390	S25	wild type	Mouse	2.5 months	Cerebellum	Female

spinal cord, ventral spinal cord: EP141/L - G93R(Roth)/e14-mutant hSOD1

spinal cord, ventral spinal cord: EP143/L - G93R(Roth)/e14-mutant hSOD1_le2

spinal cord, ventral spinal cord: EP142/L - G93R(Roth)/e14-mutant hSOD1_le2

Gene expression data from A549 cells transfected with siRNA targeting Nrf2 mRNA

T163;Normal cortex;Male;52;Clear-cell renal cell carcinoma;wild type;wild type;wild type

T158;Clear-cell renal cell carcinoma (ccRCC) tumor;Female;82;Clear-cell renal cell carcinoma;T3NxM1;IV;3;wild type;mutant;mutant

Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient T158

T158;Normal cortex;Female;82;Clear-cell renal cell carcinoma;wild type;wild type;wild type

T144;Clear-cell renal cell carcinoma (ccRCC) tumor;Male;74;Clear-cell renal cell carcinoma;T2N1M0;III;4;wild type;wild type;mutant

Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient T144

T144;Normal cortex;Male;74;Clear-cell renal cell carcinoma;wild type;wild type;wild type

T143;Clear-cell renal cell carcinoma (ccRCC) tumor;Female;74;Clear-cell renal cell carcinoma;T4NxM0;IV;4;wild type;wild type;wild type

Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient T143

T142;Clear-cell renal cell carcinoma (ccRCC) tumor;Female;56;Clear-cell renal cell carcinoma;T3NxM0;n/a;3;wild type;mutant;mutant

Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient T142

T142;Normal cortex;Female;56;Clear-cell renal cell carcinoma;wild type;wild type;wild type

T164;Normal cortex;Male;75;Clear-cell renal cell carcinoma;wild type;wild type;wild type

T163;Clear-cell renal cell carcinoma (ccRCC) tumor;Male;52;Clear-cell renal cell carcinoma;T1N0M0;I;4;mutant;wild type;mutant

Gene expression profiling of clear-cell renal cell carcinoma (ccRCC) tumor of patient T163

TGCT cell line NTera2/clone D1, treated 3 days with retinoic acid, differentiated

Testicular germ cell tumor (embryonal carcinoma) cell line NTera2 (clone D1). Embryonal carcinoma cell lines, and especially NTera2, are generally pluripotent and share features with embryonic stem cells. Time point 3 days in a time series of 0, 3, and 7 days of culturing with retinoic acid which stimulates these cells to differentiation. Maintained at high cell density (>5 000 000 cells per 75 cm2 tissue culture flask) in Dulbecco Modified Eagles Medium (DMEM high glucose formulation; GIBCO LifeTechnologies, UK) supplemented with 10% fetal calf serum.

TGCT cell line 2102Ep/clone 2A6, treated 7 days with retinoic acid

TGCT cell line NTera2/clone D1, treated 7 days with retinoic acid, differentiated

Testicular germ cell tumor (embryonal carcinoma) cell line NTera2 (clone D1). Embryonal carcinoma cell lines, and especially NTera2, are generally pluripotent and share features with embryonic stem cells. Time point 7 days in a time series of 0, 3, and 7 days of culturing with retinoic acid which stimulates these cells to differentiation. Maintained at high cell density (>5 000 000 cells per 75 cm2 tissue culture flask) in Dulbecco Modified Eagles Medium (DMEM high glucose formulation; GIBCO LifeTechnologies, UK) supplemented with 10% fetal calf serum.

Total RNA was extracted from U2OS PRC shRNA4 cells using TRIzol reagent (Invitrogen) and purified further using the RNeasy MinElute Cleanup kit (Qiagen).

Total RNA was isolated from U2OS PRC shRNA4 transductants using TRIzol (Invitrogen) and DNase treated with the TURBO DNA-free kit (Ambion). RNA samples were further purified using the RNeasy MinElute Cleanup kit (Qiagen). Integrity of the RNA was evaluated using the Agilent 2100 BioAnalyzer. 500 ng of RNA was used to perform in vitro transcription in the presence of biotin UTP with the Illumina TotalPrep RNA amplification kit (Ambion). The amplified, labeled RNA (1.5 _g) was then hybridized in triplicate to an Illumina Whole-Genome Sentrix Human-6 v2 Expression BeadChip, and detected according to the Illumina user manual.

U2OS, Treatment: infected with PRC shRNA4_pLenti, blasticidin selection

wild-type control (littermate) of "P16_exPKO_pancreas"; mixed genetic background; postnatal day 16; total pancreas; replicate mouse #1.

Cd19-cre mediated deletion of the SRF Gene;spleen: FACS sorted IgM+IgD+ cells

CP_D3

CP_D1

H-c558T

H-c587T

C-c145T

H-c1027T

H-c1095T

H-c340T

c57bl6 mice were sensitized (DNP-HSA) and challenged intravesically (DNP-OVA).  Mice were euthanized 4 hours after OVA and bladders were removed for RNA extraction.
Lot batch = 1/2

c57bl6 mice were sensitized (DNP-HSA) and challenged intravesically (DNP-OVA).  Mice were euthanized 1 hour after OVA.
Lot batch = 1/1

skeletal muscle (gastrocnemius);male;Zucker;fatty (fa/fa);normal chow

skeletal muscle (gastrocnemius);male;Zucker;fatty (fa/fa);AG035029

Subject Age : 36

Subject Age : 35

Subject Race : INDIAN

Primary hepatocytes isolated from BalbC mouse strain treated with Wy14643 for 24h

Primary hepatocytes isolated from BalbC mouse strain treated with DMSO for 6h

Primary hepatocytes isolated from BalbC mouse strain treated with Wy14643 for 6h

Primary hepatocytes isolated from FVB mouse strain treated with DMSO for 24h

Primary hepatocytes isolated from DBA mouse strain treated with Wy14643 for 24h

Primary hepatocytes isolated from DBA mouse strain treated with DMSO for 6h

Primary hepatocytes isolated from DBA mouse strain treated with Wy14643 for 6h

Primary hepatocytes isolated from BalbC mouse strain treated with DMSO for 24h

Primary hepatocytes isolated from Donor 1 treated with Wy14643 for 6h

Primary hepatocytes isolated from DBA mouse strain treated with DMSO for 24h

BMMCs from NTAL WT, NTAL shRNA infected, 2 h activated, biological rep1

bone marrow derived mast cells;NTAL wild type;C57BL/6;lentiviral infection - NTAL knock down;pLKO.1/TRCN0000127243;2 h 100 ng/ml TNP-BSA

BMMCs from NTAL WT, NTAL shRNA infected, 2 h activated, biological rep3

BMMCs from NTAL WT, NTAL shRNA infected, 2 h activated, biological rep2

BMMCs from NTAL WT, pLKO.1 infected, 2 h activated, biological rep2

BMMCs from NTAL WT, pLKO.1 infected, 2 h activated, biological rep3

BSMCs were grown in 25 cm2 flasks in SmGM and starved for 24 hours (SmBM supplemented with 0.1% FBS) before stimulation. Supernatant was removed and cells were incubated for 24 hours in fresh growth factor-free medium with 100 nM of 1alpha,25-Dihydroxyvitamin D3 (Sigma, Saint Louis, Missouri).

Human primary bronchial smooth muscle cells were grown to near confluence, starved for 24 hours (medium containing 0.1% FBS) and then treated with 100 nM of vitamin D (1alpha,25-Dihydroxyvitamin D3) for an additional 24 hours before RNA extraction.

whole brain from nicotinic acetylcholine receptor beta4 subunit null mutant mouse

whole brain from nicotinic acetylcholine receptor beta 4 subunit null mutant mouse

SUP-B15 leukemia cells were cultured without STI571 (Imatinib).

NALM-1 leukemia cells were incubated with 10 µM STI571 (Imatinib) for 16 hours. For more information about the cell line, please check: www.dsmz.de

TOM-1 leukemia cells were cultured without STI571 (Imatinib).

SUP-B15 leukemia cells were incubated with 10 µM STI571 (Imatinib) for 16 hours. For more information about the cell line, please check: www.dsmz.de

U937 cell line, transduced with shSYK_2 and selected with  1 µg/ml puromycin 48 hours post-infection

U937 cell line, transduced with shSYK_1 and selected with  1 µg/ml puromycin 48 hours post-infection

HL-60 cell line, transduced with a control luciferase and selected with  1 µg/ml puromycin 48 hours post-infection

Trim28 conditional KO mice naïve CD4 positive cell, TCR-stimulated, replicate 4

Trim28 conditional KO mice naïve CD4 positive cell, TCR-stimulated, replicate 3

Sprague-Dawley;spinal cord (ipsilateral dorsal horn);Neonate (P10);sham

B6;Xbp1 knockout;8 weeks;female;spleen;regulatory T cells (Tregs);CD4+CD25hi;CD19, CD8a, CD11b, CD11c, NK1.1;MoFlo Sorter

P7 WT3.CEL

P7 WT2.CEL
Gene expression data from wild typel mouse cerebellum.

P7 WT1.CEL

P7 KO5.CEL
Gene expression data from pre-symptomatic Cstb-/- mouse cerebellum.

129SvJ;cystatin B (CSTB)-deficient (Cstb-/-);female;postnatal day 7 (P7);cerebellum

P7 KO3.CEL

129SvJ;cystatin B (CSTB)-deficient (Cstb-/-);male;postnatal day 7 (P7);cerebellum

P7 KO2.CEL

P7 KO1.CEL

P30 KO1.CEL

129SvJ;cystatin B (CSTB)-deficient (Cstb-/-);female;postnatal day 30 (P30);cerebellum

P7 WT4.CEL

01-04-05 TP7_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2: These samples were previously hybridized on HG-U133A version 1 chips.  This experiment repeats these samples on HG-133A version 2 chips.  HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

in vitro Treatment: siHSF1_#2 (Sense 5’-rArCrArGrCUUrCrCrArCrGUrGUUrCrGrGTT-3’ Antisense 5’-UrCrGrArArCrArCrGUrGrGrArArGrCUrGUTT-3’), Treatment Repeat: 1, Units of Treatment Repeat: dose, Treatment Duration: 48, Units of Duration: hours, Treatment Time: -48, Units of Treatment Time: hrs, Vehicle for Chemical: Lipofectamine 2000, Amount of Vehicle: 0.44, Route of Exposure: transfection, Units of Amount of Vehicle: ul, Dose or Concentration: 3.3, Units of Dose or Concentration: nM

01-04-05 TP1_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2: These samples were previously hybridized on HG-U133A version 1 chips.  This experiment repeats these samples on HG-133A version 2 chips.  HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

Female rat pups less than eight hours old were euthanized and rat ovaries were removed according to IACUC-approved animal use protocols.  Newborn rat ovaries were dissected from freshly euthanized rat pups.  Whole ovaries were cultured as previously described (Nilsson, Parrott et al. 2001) on floating filters (0.4 um Millicell-CM, Millipore, Bedford, MD) in 0.5 ml Dulbecco's Modified Eagle's Medium (DMEM)-Ham's F-12 medium (1:1, vol/vol) containing 0.1 % bovine serum albumin (BSA, Sigma, St. Louis, MO), 0.1% Albumax (Gibco BRL, Gaithersburg, MD), 27.5 ug/ml transferrin, 200 ng/ml insulin (human recombinant, Sigma), and 0.05 mg/ml L-ascorbic acid (Sigma) in a 4-well culture plate (Nunc plate, Applied Scientific, South San Francisco, CA).  Ovaries were randomly assigned to treatment groups with 2-3 ovaries per floating filter in each well.   Ovaries were un-treated and used as controls.  Medium was supplemented with penicillin and streptomycin to prevent bacterial contamination.

Auto-scale ON (1-1000).  Scaling = all probe sets.  The microarray image data were converted to numerical data with GeneChip Operating Software using a scaling factor of 125, and then imported into the GeneSpring program (Agilent Technologies, Palo Alto, CA) where raw data were filtered for flags (present/absent calls), expression level, fold change and confidence (t-test p-value) with no multiple testing correction.

Ovaries with the same treatment were pooled to make each RNA sample.  RNA was extracted using the Trizol reagent according to manufacturers instructions (Sigma, St. Louis, MO).  Two pooled independent RNA samples were analysed for each treatment group (control or P4-treated ovaries cultured for two days).

Chip ID=EricBK1P47-C-1-071905.  RNA from zero-day old rat ovaries cultured two days as controls with no treatment.

ovaries dissected from 0-day old Sprague-Dawley rats and cleaned of ovarian bursa.

Chip ID=EricBK1P-C-2-071905.  RNA from zero-day old rat ovaries cultured two days as controls with no treatment.

Female rat pups less than eight hours old were euthanized and rat ovaries were removed according to IACUC-approved animal use protocols.  Newborn rat ovaries were dissected from freshly euthanized rat pups.  Whole ovaries were cultured as previously described (Nilsson, Parrott et al. 2001) on floating filters (0.4 um Millicell-CM, Millipore, Bedford, MD) in 0.5 ml Dulbecco's Modified Eagle's Medium (DMEM)-Ham's F-12 medium (1:1, vol/vol) containing 0.1 % bovine serum albumin (BSA, Sigma, St. Louis, MO), 0.1% Albumax (Gibco BRL, Gaithersburg, MD), 27.5 ug/ml transferrin, 200 ng/ml insulin (human recombinant, Sigma), and 0.05 mg/ml L-ascorbic acid (Sigma) in a 4-well culture plate (Nunc plate, Applied Scientific, South San Francisco, CA).  Ovaries were randomly assigned to treatment groups with 2-3 ovaries per floating filter in each well.   Ovaries were treated with progesterone (P4) (Sigma Chemical Co., St. Louis, MO) at 10-6M.  Medium was supplemented with penicillin and streptomycin to prevent bacterial contamination.

Chip ID=EricBK1P47-P4-1-071905.  RNA from zero-day old rat ovaries cultured two days with progesterone treatment.

Chip ID=EricBK1P35-P4-2-071905.  RNA from zero-day old rat ovaries cultured two days with progesterone treatment.

01-04-05 TP2_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2: These samples were previously hybridized on HG-U133A version 1 chips.  This experiment repeats these samples on HG-133A version 2 chips.  HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

GNMT_3WT3

GNMT_3WT1

01-04-05 TP3_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2: These samples were previously hybridized on HG-U133A version 1 chips.  This experiment repeats these samples on HG-133A version 2 chips.  HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

human cellular RNA_primary airway epithelial cells_tracheobronchial _H511_6h_0.4mM_HG-U133A_2_YCHSUP501

H511_6h_0.4mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;21.169;2.11

human cellular RNA_primary airway epithelial cells_tracheobronchial _H511_6h_4mM_HG-U133A_2_YCHSUP501

H511_6h_4mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;23.741;2.11

human cellular RNA_primary airway epithelial cells_tracheobronchial _H511_6h_1mM_HG-U133A_2_YCHSUP501

H511_6h_1mM_HG-U133A_2_YCHSUP501: Primary epithelial cells from airways of four different healthy individuals were cultivated and grown to full differentiation. Apical sides of the cells were treated with HCLO at different doses (0, 0.4,1, 4mM) for 2 and 6hrs respectively. Total RNA was subjuect to transcriptional analysis.

please return the leftover samples to PI.;HG-U133A_2;12;ug;23.279;2.12

blast count: 70

blast count: 14

gene expression data from undifferentiated hES cells line VUB03_DM1

human ES cells line from AZ-VUB laboratory, Belgium; derived from a blastocyst obtained after an in vitro fertilization carried out during a PGD procedure for DM1;X,X

human embryonic stem (hES) cells line VUB03_DM1, biological replicate  1

human embryonic stem (hES) cells line VUB03_DM1, biological replicate  2

human embryonic stem (hES) cells line VUB03_DM1, biological replicate  3

None
None
0

None
None
0

None
None
0

Nervous System; Spinal Cord

Nervous System; Olfactory Cortex

Nervous System; Nucleus Accumbens

Nervous System; Hypothalamus

Nervous System; Striatum

6_Bsl

6_PC

6_BM

7_BM

7_Bsl

Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. At P14, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.

Pooled inguinal fat from 8 C57BL/6J mice with 'low' weight gain after 4 weeks on a high fat diet (D12331;Research Diets, New Brunswick, NJ).  Microarrays were performed in triplicate, L1, L2 and L3.

Mice were given doxycycline-treated (final concentration 2 mg/mL) water for 7 days. After 7 days, mice were euthanized and the left upper lobes of the lungs were removed for RNA extraction.

The data was analyzed using Matlab R2011b with Bioinformatics Toolbox to read in Affymetrix microarray data and normalize the data using Robust Multi-array Average procedure. Filter to remove probes yielding maximum intensity levels below 100 was applied.

Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Genome Array. GeneChips were washed and stained according to standard Affymetrix protocol.

mouse lung upper left lobe;C57BL/6;wildtype;6-10 weeks old mouse

mouse lung upper left lobe;C57BL/6;CC10-rtTA-IL13 transgenic (TG);6-10 weeks old mouse

lung rna from wt mice, 3 days after Chlamydia pneumoniae infection, replicate A

Gene expression data under ER stress from lymphoblastoid cells of twin 1700:2 treated with DMSO.

lymphoblastoid cell line;1700;GM14382;Twin number 2;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1700:2 treated with 500nM thapsigargin.

lymphoblastoid cell line;1700;GM14382;Twin number 2;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1700:1 treated with DMSO.

lymphoblastoid cell line;1700;GM14381;Twin number 1;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1700:1 treated with 500nM thapsigargin.

lymphoblastoid cell line;1700;GM14381;Twin number 1;thapsigargin;500nM;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1704:2 treated with DMSO.

lymphoblastoid cell line;1704;GM14406;Twin number 2;DMSO;4 hours

Gene expression data under ER stress from lymphoblastoid cells of twin 1704:2 treated with 500nM thapsigargin.

lymphoblastoid cell line;1704;GM14406;Twin number 2;thapsigargin;500nM;4 hours

MOLM-14 cell line infected with scrambled control shRNA, biological rep3
Sample name: MOLM14_CTRL-3
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C07_596588.CEL

MOLM-14 cell line infected with GSK3B Construct 1 shRNA, biological rep1
Sample name: MOLM14_GSK3B_1-1
CREME_p_KimSteg_June10_96HT_HT_HG-U133A_96-HTA_C03_596594.CEL

BioBreeding DR+/+ rat, day 65, mast cells derived from pancreatic lymph node

PtenL/L (isogenic wildtype);embryonic fibroblasts;control;C57BL\6

HeLa-Ctrl-siRNA-3d;HeLa;Ctrl-siRNA;3d interferon alpha;interferon alpha

HeLa-Ctrl-siRNA-4d;HeLa;Ctrl-siRNA;4d interferon alpha;interferon alpha

IA, IB, II, IIIA, IIIB, or IV=II;62;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=II;61;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=II;67;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=intestinal type;normal

IA, IB, II, IIIA, IIIB, or IV=II;69;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=II;58;female, male:female;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=IB;66;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=not determined;normal

IA, IB, II, IIIA, IIIB, or IV=IB;63;female, male:female;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=IB;40;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=poorly differentiated;intestinal type, diffuse type, mixed type, or not determined=diffuse type;normal

IA, IB, II, IIIA, IIIB, or IV=IB;66;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=moderately differentiated;intestinal type, diffuse type, mixed type, or not determined=intestinal type;normal

IA, IB, II, IIIA, IIIB, or IV=IB;female, male:male;early gastric cancer or advanced gastric cancer=advanced gastric cancer;moderately differentiated or poorly differentiated=moderately differentiated;intestinal type, diffuse type, mixed type, or not determined=intestinal type;normal

brain (frontal cortex);healthy control;46 yr;white;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);bipolar disorder;59 yr;white;296.5;48 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);bipolar disorder;29 yr;white;296.89;17 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);bipolar disorder;33 yr;white;296.53;15 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);bipolar disorder;35 yr;white;296.54;21 yr;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

brain (frontal cortex);healthy control;33 yr;white;pool of total RNAs extracted from 15 distinct human cell lines (in-house)

Female;87;5.5h;6.1;schizophrenic;superior temporal cortex (Brodmann Area 22, BA22)

Female;70;4.5h;6.2;schizophrenic;superior temporal cortex (Brodmann Area 22, BA22)

Male;79;4.5h;6.1;schizophrenic;superior temporal cortex (Brodmann Area 22, BA22)

Female;53;11h;6;schizophrenic;superior temporal cortex (Brodmann Area 22, BA22)

Female;28;11h;6.3;schizophrenic;superior temporal cortex (Brodmann Area 22, BA22)

sample 1:
sample 2:

gastrocnemius-30 months of age, resveratrol diet-biological replicate5

gastrocnemius-30 months of age-resveratrol diet-biological replicate4

gastrocnemius-30 months of age-resveratrol diet-biological replicate3

gastrocnemius-30 months of age-resveratrol diet-biological replicate2

gastrocnemius-30 months of age-resveratrol diet-biological replicate1

Human CD34+ cells isolated from umbilical cord blood;MIG control;3

Human CD34+ cells isolated from umbilical cord blood;BCR/FGFR1;3

Gene expression data of male hearts after a 90 day treatment of PBS

Gene expression data of female hearts after a 90 day treatment of PBS

Gene expression data from Deltoid, control, cohort 13, subject 13U

Gene expression data from Biceps, control, cohort 18, subject 18U

Gene expression data from Deltoid, control, cohort 12, subject 12V

Gene expression data from Biceps, control, cohort 13, subject 13U

Gene expression data from Deltoid, control, cohort 18, subject 18U

Crohn's Disease subject (44 year old hispanic female, SAK_1307613224)

Rat230_2;15;ul;1.814;0.932;1.91;1:5;8.1;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;137;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

Rat230_2;15;ul;1.301;0.666;1.88;1:5;7.8;Good;Cells resuspended in RNAlater and stored at 4 degrees Centigrade;F344/NCrl;10116;136;Adult;Deep pentobarbital anesthesia followed by exsanguination;Male;weeks

test;male;ApoE-/-;suprarenal aorta, aneurysm;Ang II;28d;reference

Trizol extracted total RNA from myometrium tissue. Trizol extracted total RNA from myometrium tissue (HLRCC).

Control RNA 02

Control RNA 03

Gene expression data from Prmt6 overexpressed embryonic stem cells
P+6 OE 01

P+6 OE 02

P+6 OE 03

This group received a diet supplemented with 1000mg/kg of α-tocopherol since the age of 15 months.

Ht: heart

Ht: heart

Ht: heart

Ht: heart

Ht: heart