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Series GSE31271 Query DataSets for GSE31271
Status Public on Sep 02, 2011
Title Control of Embryonic Stem Cell Lineage Commitment by Core Promoter Factor, TAF3 (RNA-Seq data)
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary We report that TAF3, a TBP-associated core promoter factor, is highly enriched in ES cells. In addition to its role in the core promoter recognition complex TFIID, genome-wide binding studies reveal that TAF3 localizes to chromosomal regions bound by CTCF and cohesin. Enrichment for TAF3/CTCF/cohesin bound regions distinguishes TAF3-activated from TAF3-repressed genes. Our findings support a new role of TAF3 in mediating long-range chromatin regulatory interactions to safeguard the finely-balanced transcriptional programs that give rise to pluripotency.
Overall design Comparison of genome-wide expression patterns between TAF3-knockdown and WT embryonic stem cells using mRNA-Seq. Significantly differentially expressed protein-coding genes were identified by comparing control and knock-down samples at each timepoint (ES, embryoid body day 3 (EB3), EB6). Single and paired-end samples were combined at each timepoint, resulting in 3 tests for each gene (based on 8, 4, 4 independent measurements at ES ,EB3, EB6, respectively).
Contributor(s) Scannell DR, Tjian R
Citation(s) 21884934
Submission date Aug 08, 2011
Last update date May 15, 2019
Contact name Devin Scannell
Phone 001-510-666-3640
Organization name UC Berkeley
Department QB3
Lab Eisen
Street address 378 Stanley Hall #3220
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (16)
GSM774955 ES Timepoint, TAF3 KO, replicate 1
GSM774956 ES Timepoint, TAF3 Control, replicate 1
GSM774957 ES Timepoint, TAF3 KO, replicate 2
This SubSeries is part of SuperSeries:
GSE30959 Control of Embryonic Stem Cell Lineage Commitment by Core Promoter Factor, TAF3
SRA SRP007832
BioProject PRJNA154139

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Supplementary file Size Download File type/resource
GSE31271_RAW.tar 832.1 Mb (http)(custom) TAR (of BIGWIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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