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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
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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.
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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).
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Contributor(s) |
Scannell DR, Tjian R |
Citation(s) |
21884934 |
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Submission date |
Aug 08, 2011 |
Last update date |
May 15, 2019 |
Contact name |
Devin Scannell |
E-mail(s) |
devin.scannell@gmail.com
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Phone |
001-510-666-3640
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Organization name |
UC Berkeley
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Department |
QB3
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Lab |
Eisen
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Street address |
378 Stanley Hall #3220
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City |
Berkeley |
State/province |
CA |
ZIP/Postal code |
94720 |
Country |
USA |
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Platforms (1) |
GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
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Samples (16)
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GSM774955 |
ES Timepoint, TAF3 KO, replicate 1 |
GSM774956 |
ES Timepoint, TAF3 Control, replicate 1 |
GSM774957 |
ES Timepoint, TAF3 KO, replicate 2 |
GSM774958 |
ES Timepoint, TAF3 Control, replicate 2 |
GSM774959 |
EB Day3 Timepoint, TAF3 KO, replicate 1 |
GSM774960 |
EB Day3 Timepoint, TAF3 Control, replicate 1 |
GSM774961 |
EB Day3 Timepoint, TAF3 KO, replicate 2 |
GSM774962 |
EB Day3 Timepoint, TAF3 Control, replicate 2 |
GSM774963 |
EB Day6 Timepoint, TAF3 KO, replicate 1 |
GSM774964 |
EB Day6 Timepoint, TAF3 Control, replicate 1 |
GSM774965 |
EB Day6 Timepoint, TAF3 KO, replicate 2 |
GSM774966 |
EB Day6 Timepoint, TAF3 Control, replicate 2 |
GSM774967 |
ES Timepoint, TAF3 KO, PE, replicate 1 |
GSM774968 |
ES Timepoint, TAF3 Control, PE, replicate 1 |
GSM774969 |
ES Timepoint, TAF3 KO, PE, replicate 2 |
GSM774970 |
ES Timepoint, TAF3 Control, PE, replicate 2 |
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This SubSeries is part of SuperSeries: |
GSE30959 |
Control of Embryonic Stem Cell Lineage Commitment by Core Promoter Factor, TAF3 |
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Relations |
SRA |
SRP007832 |
BioProject |
PRJNA154139 |
Supplementary file |
Size |
Download |
File type/resource |
GSE31271_RAW.tar |
832.1 Mb |
(http)(custom) |
TAR (of BIGWIG) |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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