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Accession Number: GSE95008 Platform: GPL21493: Illumina HiSeq 3000 (Mus musculus) Organism: Mus musculus Published on 2018-01-02 Summary: Purpose: PKA plays a crucial role in vasopressin signaling of renal collecting duct cells. To understand regulation of mRNA expression mediated by vasopressin/PKA signaling, mRNA expression was profiled by RNA-Seq in double knockout cells (both PKA catalytic genes) generated from mouse cortical collecting duct mpkCCD cell line versus control lines with intact PKA expression. Methods: PKA double knockout (dKO) cell lines were generated from mouse cortical collecting duct mpkCCDc11 cells by CRISPR/Cas-9 genome editing method. For mRNA profiling using RNA-Seq analysis, three biological replicates of control (not mutated in PKA two catalytic subunits) cell lines and PKA double knockout cell lines were used. The reads uniquely mapped on GENCODE mouse gene set were analyzed with HOMER (v4.8) and edgeR (v3.10.5). Results and conclusion: About 40-50 million sequence reads per sample were sucessfully mapped in the mouse genome (GENCODE, GPCm38.p5). Among total transcripts of the mouse genome, 10,190 transcripts (cutoff: Counts Per Million > 4 by edgeR) were considered as genes expressed in the cell lines. In differential expression analysis by standard edgeR analysis, 354 transcripts were differentially expressed between control cell lines and PKA dKO cell lines (FDR 2, FDR < 0.05). These results suggest PKA signaling is important for regulation of expression of a very limited number of genes in vasopressin-responsive renal collecting duct cells. Overall Design: Total mRNA profiling of three control cell lines and three PKA double knockout cell lines generated from mpkCCDc11 cell line were carried out by standard RNA-Seq protocols with deep sequencing on an Illumina HiSeq 3000. Contact: Name: Hyun Jun Jung Organization: NHLBI/NIH Laboratory: Epithelial Systems Biology Lab Deparment: Systems Biology Center Address: 9000 Center Dr. Bldg.10 6N314 Bethesda MD 20892 USA Email: hynjn.jung@gmail.com Organization: GEO Address: USA
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Accession Number: GSE108408 Platform: GPL11154: Illumina HiSeq 2000 (Homo sapiens) Organism: Homo sapiens Published on 2018-01-02 Summary: The role of Gata2 in regulating the expression of HLA in huamn decidual stromal cells Overall Design: Examination of GATA2 binding in pooled primary human endometrial stromal cells from 6 healthy women upon decidualization with a hormone cocktail of cAMP, E2 and medroxyprogesterone acetate. Contact: Name: Francesco J DeMayo Organization: National Institute of Environmental Health Sciences Deparment: Reproductive & Developmental Biology Laboratory Address: 111 TW Alexander Drive Research Triangle Park NC 27709 USA Organization: GEO Address: USA
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Accession Number: GSE96528 Platform: GPL17586: [HTA-2_0] Affymetrix Human Transcriptome Array 2.0 [transcript (gene) version] Organism: Homo sapiens Published on 2018-01-02 Summary: We have analyzed the gene expression-based consensus molecular subtypes of colorectal cancer. These samples represent a subset of the total series analyzed. Overall Design: This subset consists of 174 colorectal cancer tissue samples analyzed on Affymetrix Human Transcriptome 2.0 Arrays. Contact: Name: Anita Sveen Organization: Institute for Cancer Research, Oslo University Hospital Deparment: Department of Molecular Oncology Address: P.O.Box 4953, Nydalen Oslo Norway Email: anita.sveen@rr-research.no Organization: Affymetrix, Inc. Address: Santa Clara CA 95051 USA Email: geo@ncbi.nlm.nih.gov, support@affymetrix.com Phone: 888-362-2447 Web-Link: http://www.affymetrix.com/index.affx
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Accession Number: GSE107678 Platform: GPL15103: Illumina HiSeq 1000 (Mus musculus) Organism: Mus musculus Published on 2018-01-02 Summary: To identify the potential microRNAs (miRNAs) involved in the regulation of cardiomyocyte (CM) proliferation during homeostasis and injury, RNA sequencing (RNA-seq) in mouse cardiac ventricles was performed on postnatal day 1, 7, and 28 (P1, P7, and P28). Significant upregulation of MiR-128 was found in P7 hearts as compared to P1. To further specify the effect of miR-128 in the heart, RNA-Seq was performed in control mice (Ctrl) and miR-128 overexpression mice (miR-128OE) on P7. These data provide novel insights into the mechanisms by which adult CMs exit the cell cycle arrest and is fundamental for therapeutic manipulation to stimulate endogenous CM proliferate in cardiac regeneration. Overall Design: RNA-seq profilig of heart tissues from wild type mice on postanatal day 1, 7, and 28 (P1, P7, and P28), RNA-seq of hearts from control (Ctrl) and miR-128 overexpression transgenic mice (miR-128OE) at P7. Contact: Name: Mario Medvedovic Organization: University of Cincinnati Laboratory: Laboratory for Statistical Genomics and Systems Biology Deparment: Department of Environmental Health Address: 3223 Eden Av. ML 56 Cincinnati OH 45267-0056 USA Organization: GEO Address: USA
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Accession Number: GSE80588 Platform: GPL11002: Illumina Genome Analyzer IIx (Mus musculus) Organism: Mus musculus Published on 2018-01-02 Summary: The cis-regulatory code is the cellular lexicon by which the transcriptional machinery converts sequence information within cis-regulatory modules (CRMs) into gene expression output. Tissue-specific transcription factors such as MyoD orchestrate gene expression programs by binding to short DNA motifs called E-boxes within their target CRMs to modulate chromatin state and to fine-tune gene expression output. Despite extensive research, how the relatively short and ubiquitously distributed E-box motifs contribute to binding specificity, assembly and the functional output of the transcriptional machinery remains poorly understood. Here, we have carried out an integrative analysis of the relationship between MyoD occupancy, nucleosome positioning, CRMs-associated histone marks and motif sequences within the myogenic CRMs in differentiating muscle cells. Our data suggests that variant sequences within MyoD-binding motifs and their multiplicity within the CRMs, as well as the spatial arrangement of the motifs, in combination confer binding affinity of MyoD, nucleosome occupancy and the epigenetic state of the myogenic CRMs. Our comparative genomic analysis of single nucleotide polymorphism (SNPs) across publically available data from 17 strains of laboratory mice suggests that variant sequences within MyoD-bound motifs, but not their genome-wide counterparts, are under selection. Taken together, our data suggests that variant sequences within MyoD-binding motifs are retained and have functional role to confer a dynamic range of affinities, enabling MyoD to establish a broad spectrum of activity across myogenic CRMs. Overall Design: Genome-wide binding of MyoD and the association with gene expression and histones in Myotubes Contact: Name: Carol Perez-Iratxeta Organization: Ontario Genomics Innovation Centre (OGIC) Laboratory: Cellular and Molecular Medicine, Bioinformatics Deparment: Ottawa Hospital Research Institute Address: 501 Smyth Rd. Ottawa ON Canada Email: ogicinfo@ohri.ca Phone: (613) 737-8899 -73255 Organization: GEO Address: USA
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Accession Number: GSE81198 Platform: GPL20301: Illumina HiSeq 4000 (Homo sapiens) Organism: Homo sapiens Published on 2018-01-02 Summary: Background: Prior analyses of mRNA expression in intestinal tissue as related to HIV cohorts has been on whole biopsies. More targeted isolation and enrichment of intestinal epithelial cells is needed to identify pathways specifically altered in the epithelium that may not be picked up at a global tissue scale. Results: Analysis of intestinal epithelial cells isolated from primary human tissues taken from HIV-infected cohorts as well as uninfected controls. Results demonstrate key genes differentially expressed in HIV in the absence or presence of ART-therapy. Overall Design: Cross-sectional sampling and comparison of epithelial isolates from 9 uninfected, 6 viremic untreated, and 19 HIV-infected ART-treated patients. Whole biopsy RNA from 5 uninfected, 6 viremic untreated, and 5 HIV-infected ART-treated patients. Contact: Name: Charlie Kim Organization: University of California, San Francisco Laboratory: Kim Deparment: Medicine Address: 1001 Potrero Ave San Francisco CA 94110 USA Email: cckim47@gmail.com Organization: GEO Address: USA
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Accession Number: GSE107898 Platform: GPL16791: Illumina HiSeq 2500 (Homo sapiens) Organism: Homo sapiens Published on 2018-01-02 Summary: The purpose of this study was to assess transcriptome changes in primary human airway epithelial cells following stimulation with RIG-I ligand. Overall Design: MRNA profiles were generated from primary human airway epithelial cells at rest or following stimulation with RIG-I ligand SLR-14. Contact: Name: Ellen Flescher Foxman Organization: Yale University Laboratory: Foxman Lab Deparment: Laboratory Medicine Address: 330 Cedar St. New Haven CT 06520-8035 USA Email: ellen.foxman@yale.edu Organization: GEO Address: USA
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Accession Number: GSE95009 Platform: GPL13112: Illumina HiSeq 2000 (Mus musculus) GPL21493: Illumina HiSeq 3000 (Mus musculus) Organism: Mus musculus Published on 2018-01-02 Summary: This SuperSeries is composed of the SubSeries listed below. Overall Design: Refer to individual Series Contact: Name: Hyun Jun Jung Organization: NHLBI/NIH Laboratory: Epithelial Systems Biology Lab Deparment: Systems Biology Center Address: 9000 Center Dr. Bldg.10 6N314 Bethesda MD 20892 USA Email: hynjn.jung@gmail.com Organization: GEO Address: USA
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Accession Number: GSE108409 Platform: GPL570: [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array GPL11154: Illumina HiSeq 2000 (Homo sapiens) Organism: Homo sapiens Published on 2018-01-02 Summary: This SuperSeries is composed of the SubSeries listed below. Overall Design: Refer to individual Series Contact: Name: Francesco J DeMayo Organization: National Institute of Environmental Health Sciences Deparment: Reproductive & Developmental Biology Laboratory Address: 111 TW Alexander Drive Research Triangle Park NC 27709 USA Organization: Affymetrix, Inc. Address: Santa Clara CA 95051 USA Email: geo@ncbi.nlm.nih.gov, support@affymetrix.com Phone: 888-362-2447 Web-Link: http://www.affymetrix.com/index.affx
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Accession Number: GSE43809 Platform: GPL1261: [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array Organism: Mus musculus Published on 2018-01-02 Summary: Limited term administration of tamoxifen for 2-8 years results in long-term prevention of estrogen receptor positive (ER+) breast cancer as demonstrated in several clinical trials. How the memory of tamoxifen is initiated and maintained, as well as which cells are involved and what molecular messages are transmitted, is undefined. Understanding these features of this robust chemopreventive agent will lead to significant advancement in our knowledge of how a healthy breast environment is supported. The purpose of this study was to determine the molecular message that reflects a long-term and efficacious memory of tamoxifen. We used microarrays to identify genes with a significant long-term alteration in expression level following a short-term exposure to tamoxifen as a chemopreventive. Overall Design: A total of 20 samples were analyzed, 10 from tamoxifen treated animals and 10 from placebo treated animals. One number 4 mammary gland was isolated and used in preparation of the microarray probe 30 days after the completion of treatment. Animals were monitored for mammary tumor formation up to 2 years of age following collection of the microarray sample gland and tumor outcome was scored. Statistical comparisons of gene expression were made between animals that presented with tumor formation (10 animals) and those that did not form tumors (10 animals) up to 2 years of age. Contact: Name: Amy Greene Organization: Mercer University Deparment: Biomedical Sciences Address: 4700 Waters Avenue Savannah GA 31404 USA Email: greene_al@mercer.edu Organization: Affymetrix, Inc. Address: Santa Clara CA 95051 USA Email: geo@ncbi.nlm.nih.gov, support@affymetrix.com Phone: 888-362-2447 Web-Link: http://www.affymetrix.com/index.affx
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