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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 |
| 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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