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  • Disrupted skin barrier due to altered keratinocyte differentiation is common in pathologic conditions such as atopic dermatitis, ichthyosis and psoriasis. However, the molecular cascades governing keratinocyte terminal differentiation are still poorly understood. We have previously demostrated that a dominante mutation in ZNF750 leads to a clinical phenotype that reminiscent of psoriasis and seborrehic dermatitis. We defined ZNF750 as a nuclear effector that is atrongly activated in and essiential for keratinocyte terminal differentiation. ZNF750 knockdown in HaCaT keratinocytes markedly reduced the expression of epidermal late differentiation markers, including gene subsets of epidermal differentiation complex and skin barrier formation such as FLG, LOR, SPINK5, ALOX12B and DSG1, known to be mutated in various human skin diseases. Furthermore, ZNF750 over-expression in undifferentiated cells induced terminal differentiation genes. Thus, ZNF750 is a regulator of keratinocyte terminal differnetiation, and with its downstream targets can serve in future elucidation of therapeutics for common disease of skin barrier Gene expression analysis: To determine the differentaition signature for HaCaT keratinocytes, with ZNF750 gene silencing, total RNA was isolated in biologic triplicates from cells induced to differentiate for twelve days and hybridized to Affymerix Human Gene 1.0 ST arrays.
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  • Gene expression induced by IL-4 and IL-4 superkines on CD14+ monocytes cultured in the presence of GM-CSF. Super-4 and KFR signal preferentially through the type I and type II IL-4 receptor, respectively. Five biological replicates (n=5 healthy donors), four conditions: GM-CSF alone or in combination with IL-4, Super-4 or KFR. Two colors: Cy3 for GM-CSF alone, Cy5 for any combination. Cells were cultured for 6 hours with 50 ng/ml of GM-CSF and 20 ng/ml of IL-4, Super-4 or KFR.
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  • Parthenogenetic embryos are one attractive alternative as a source of embryonic stem cells, although many aspects related to the biology of parthenogenetic embryos and parthenogenetically derived cell lines still need to be elucidated. The present work was conducted to investigate the gene expression profile of rabbit parthenote embryos cultured under in vivo conditions using microarray analysis. Transcriptional microarray study that compares gene expression of 6 day parthenote rabbit embryos to their in vivo counterparts. Biological replicates used: 4 replicates for control embryos, 4 replicates for parthenote embryos
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  • Background: Endothelial progenitor cells (EPCs) play a fundamental role in post-natal vascular repair, yet EPCs from different anatomic locations possess unique biological properties. The underlying mechanisms are unclear. Method: We performed transcriptome analysis for EPCs isolated from 2 different sources: cord blood (CB) or adult peripheral blood (PB). Both gene expression microarray and small RNA sequencing (smRNA-seq) technologies were applied. Results: EPCs from CB expressed abundant genes involved in cell cycle, hypoxia signalling and blood vessel development, correlating with the phenotypes that CB-EPCs proliferated more rapidly, migrated faster, and formed tubule structure more efficiently. smRNA-seq further deciphered miRNome patterns in EPCs isolated from CB or PB: 54 miRNAs were enriched in CB-EPCs, while another 50 in PB-EPCs. Specifically, CB-EPCs expressed more angiogenic miRNAs such as miR-31, while PB-EPCs possessed more tumor suppressive miRNAs including miR-10a. Knocking down miR-31 levels in CB-EPCs suppressed cell migration and microtubule formation, while overexpressing miR-31 in PB-EPCs helped to recapitulate some of CB-EPC functions. Conclusion: Our results show the foundation for a more detailed understanding of EPCs from different anatomic sources. Stimulating the expression of angiogenic microRNAs or genes in EPCs of low activity (such as those from patients with cardiovascular diseases) might allow the development of novel therapeutic strategies. EPC from cord blood or peripheral blood that outgrown after 2-4 week culture were collected. The RNA are extracted and profiled by Affymetrix GeneChip U133 plus 2.0 expression array. This submission represents gene expression microarray component of study.
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  • Gene expression of HSC (Lin-Sca-Kit+Flt3-) hematopoietic stem cells from Dicer D/+ mice was compared with LT-HSC from DicerD/D mice. BM cells were noncompetitively transplanted into irradiant recipients, and deletion induced by poly(IC) injection. Donor-derived HSCs were isolated by FACS sorting of recipient bone marrow. Biological replicates of each (2 per genotype) were generated and expression profiles were determined by hybridization to Affymetrix Moe430_2 arrays.
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  • An branched-chain amino acids auxotroph eca39∆ mutant fission yeast exhibits an unusual adaptive growth phenotype on solid minimal media containing Ile, Leu and Val when other strains are growing nearby. The transcriptional profiles of an eca39∆ mutant before and after the adaptation were determined using Affymetrix DNA microarrays. Wild-type, the eca39∆ mutant, and the adapted eca39∆ mutant fission yeasts were inoculated in YE+2mM Ile, Leu and Val, and harvested at OD ~ 1. Total RNAs were purified from the 3 samples.
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  • Bcl6 germline deletion causes a prominent inflammatory disease, owing to over-expression of Th2 cytokines, and affects the properties of B cells prior to immunization. Therefore we established the B cell-specific Bcl6 deletion mice and analyze the gene expression of naive B cells under physiological conditions. Total RNAs of splenic follicular and marginal zone B cells from Bcl6(flox/flox), Bcl6(+/flox) or Bcl6(+/+) mice heterozygous for mb1-cre were extracted and analysed on Affymetrix microarrays.
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  • Elf5 (or ESE-2) is an ETS transcription factor that is abundantly expressed in the mammary epithelium, where it plays a critical role in dictating cell fate and lineage choices. These changes are in part mediated by alterations in the expression and activity of critical components of the Jak/Stat pathway. While the biological function of Elf5 in mammary gland development has been well characterized, its role in breast cancer remains to be elucidated. Here we show that loss of Elf5 leads to features associated with epithelial-mesenchymal transition (EMT) in the mouse mammary gland during pregnancy and lactation. These cellular changes in Elf5-null mammary epithelia are also reflected at the molecular level by the global enrichment of EMT-related gene signatures. ELF5 is expressed in higher level in weakly metastatic breast cancer cells that retained epithelial features compared to highly metastatic cells with mesenchymal features. ELF5 knockdown in T47D breast cancer cells resulted in EMT and increased migration. Conversely, ectopic expression of Elf5 revert mesenchymal-like MDA-MB-231 cells and its lung-tropic variant LM2 to an epithelial phenotype, with reduced migration, invasion and lung metastatic abilities. Finally, we showed that Elf5 binds directly to the promoter of the EMT transcriptional factor Snail2 (Slug) and repress its expression. Taken together, these data established a novel function for Elf5 in inhibiting EMT in normal mammary epithelium and in breast cancer through direct targeting of Snail2. This SuperSeries is composed of the following subset Series: GSE32143: LM2 cell: infected with lentivirus to stably express Elf5 vs GFP GSE32144: MDA-MB-231 cell: infected with lentivirus to stably express mut-Elf5 vs WT-Elf5
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  • PRR5 transcription factor acts in the circadian clock system. To elucidate regulated genes by PRR5, Chimeric protein PRR5-VP, which activates direct target genes of PRR5, was over-expressed in Col-0. Microarray analsysis was performed using these plants with Affymetrix ATH1 genechip. PRR5-VP expressing plants and its parental plants (accession Col-0, described as Wild) were grown under 12 hr light / 12 hr dark conditions, and harvested at ZT6(6 hr after light on), ZT12, and ZT18
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  • The delta smelt (Hypomesus transpacificus) is a pelagic fish species endemic to the Sacramento-San Joaquin Estuary in Northern California, listed as endangered under both the USA Federal and Californian State Endangered Species Acts and acts as an indicator of ecosystem health in its habitat range. Interrogative tools are required to successfully monitor effects of contaminants upon the delta smelt, and to research potential causes of population decline in this species. We used microarray technology to investigate genome-wide effects in 47-day old larvae after a 7-day exposure to ambient water samples from the Sacramento River at a monitoring field station (Hood) situated 8 miles downstream of the Sacramento regional Wastewater Treatment Plant. Genomic assessments were carried out on surviving organisms and contrasted to laboratory controls. Microarray assessments were conducted on larvae exposed for 7-days to Sacramento River water collected at Hood and pooled laboratory controls. Assessments were carried out in quadruplicate, using 3 fish per treatment. RNA was extracted from frozen whole, individual organisms, using Trizol Reagent (Invitrogen) as per manufacturer's guidelines. Total RNA from 5 fish was pooled per treatment and cDNA was synthesized from a total of 2ug total RNA, amplified using a SuperScripttm Indirect RNA Amplification System (Invitrogen). Resulting aRNA was labeled with Alexa fluor dyes (Invitrogen) as per manufacturer’s instructions. Two color microarray assessments were carried out on quadruplicate treatments, using 5µg of aRNA for pooled controls vs exposed sample, (total 4 samples). Microarray hybridizations were performed manually, and incubated in a waterbath at 42C for 16 hours. Slides were scanned using a GenePix 4000B scanner (Axon Instruments). Data was analyzed using LIMMA GUI (Linear model for microarray analysis graphical user interface) (Smyth, 2005), written in the R-programming language available through Bioconductor http://www.Bioconductor.org. Data was normalized within using print-tip Lowess and between arrays applying average intensity quantile (Aquantile) normalization methods with background correction (Smyth, 2005). A linear model fit was computed using the duplicates on the arrays and the least-squares method, with Benjamin Hochberg false discovery rate adjustment.
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