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| Status |
Public on Feb 20, 2013 |
| Title |
ChIP-Seq of Sox2 and Brn2 in ESCs, NPCs, and differentiating ESCs |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
We analyzed the genome-wide binding of Sox2 and POU factor partner factors, Oct4 in ESCs (using published datasets PMID:18692474 and GSM307137, GSM307154, GSM307155) and Brn2 in NPCs. We found that Sox2 and Oct4 co-occupied a large subset of promoters and enhancers in ESCs, but that Sox2 and Brn2 co-occupy predominantly enhancers. Further, we overexpressed Brn2 in differentiating ESCs and showed that ectopic Brn2 recruited Sox2 to NPC-specific targets, resulting in skewed differentiation towards the neural lineage.
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| Overall design |
Examination of transcription factor binding in ESCs, NPCs, and differentiating ESCs by ChIP-Seq.
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| Contributor(s) |
Lodato MA, Jaenisch R, Boyer LA |
| Citation(s) |
23437007 |
| Submission date |
Feb 02, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Lodato |
| E-mail(s) |
lodato@wi.mit.edu
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| Organization name |
Whitehead Institute
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| Street address |
9 Cambridge Center
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platforms (2) |
| GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (30)
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| GSM1050289 |
Sox2 NPC ChIP-Seq, rep2 |
| GSM1050290 |
NPC WCE Seq |
| GSM1050291 |
Sox2 ESC ChIP-Seq |
| GSM1050292 |
ESC WCE Seq, rep1 |
| GSM1050293 |
ESC WCE Seq, rep2 |
| GSM1050294 |
Brn2 ChIP-Seq Day2 TetoBrn2, rep1 |
| GSM1050295 |
Sox2 ChIP-Seq Day2 TetoBrn2, rep1 |
| GSM1050296 |
Day2 TetoBrn2 WCE Seq, rep1 |
| GSM1050297 |
Brn2 ChIP-Seq Day2 rtta, rep1 |
| GSM1050298 |
Sox2 ChIP-Seq Day2 rtta, rep1 |
| GSM1050299 |
Day2 rtta WCE Seq, rep1 |
| GSM1050300 |
Brn2 ChIP-Seq Day2 TetoBrn2, rep2 |
| GSM1050301 |
Sox2 ChIP-Seq Day2 TetoBrn2, rep2 |
| GSM1050302 |
Day2 TetoBrn2 WCE Seq, rep2 |
| GSM1050303 |
Brn2 ChIP-Seq Day2 rtta, rep2 |
| GSM1050304 |
Sox2 ChIP-Seq Day2 rtta, rep2 |
| GSM1050305 |
Day2 rtta WCE Seq, rep2 |
| GSM1050306 |
H3K4me1 ChIP-Seq Day2 TetoBrn2 |
| GSM1050307 |
H3K27Ac ChIP-Seq Day2 TetoBrn2, rep1 |
| GSM1050308 |
H3 ChIP-Seq Day2 TetoBrn2, rep1 |
| GSM1050309 |
H3K27Ac ChIP-Seq Day2 TetoBrn2, rep2 |
| GSM1050310 |
H3 ChIP-Seq Day2 TetoBrn2, rep2 |
| GSM1050311 |
H3K4me1 ChIP-Seq Day2 rtta |
| GSM1050312 |
H3K27Ac ChIP-Seq Day2 rtta, rep1 |
| GSM1050313 |
H3 ChIP-Seq Day2 rtta, rep1 |
| GSM1050314 |
H3K27Ac ChIP-Seq Day2 rtta, rep2 |
| GSM1050315 |
H3 ChIP-Seq Day2 rtta, rep2 |
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| Relations |
| Reanalysis of |
GSM307154 |
| Reanalysis of |
GSM307155 |
| Reanalysis of |
GSM307137 |
| SRA |
SRP010714 |
| BioProject |
PRJNA152295 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE35496_Brn2_NPC_Wig_min0.1.WIG.gz |
21.0 Mb |
(ftp)(http) |
WIG |
| GSE35496_Brn2_TetOBrn2_Day2_Wig_min0.1.WIG.gz |
25.6 Mb |
(ftp)(http) |
WIG |
| GSE35496_Brn2_rtta_Day2_Wig_min0.1.WIG.gz |
23.9 Mb |
(ftp)(http) |
WIG |
| GSE35496_H3K27Ac_TetOBrn2_Day2_Wig_min0.1.WIG.gz |
19.1 Mb |
(ftp)(http) |
WIG |
| GSE35496_H3K27Ac_rtta_Day2_Wig_min0.1.WIG.gz |
17.5 Mb |
(ftp)(http) |
WIG |
| GSE35496_H3K4me1_TetOBrn2_Day2_Wig_min0.1.WIG.gz |
19.8 Mb |
(ftp)(http) |
WIG |
| GSE35496_H3K4me1_rtta_Day2_Wig_min0.1.WIG.gz |
20.2 Mb |
(ftp)(http) |
WIG |
| GSE35496_Sox2_ESC_Wig_min0.1.WIG.gz |
17.1 Mb |
(ftp)(http) |
WIG |
| GSE35496_Sox2_NPC_Wig_min0.1.WIG.gz |
21.3 Mb |
(ftp)(http) |
WIG |
| GSE35496_Sox2_TetOBrn2_Day2_Wig_min0.1.WIG.gz |
25.4 Mb |
(ftp)(http) |
WIG |
| GSE35496_Sox2_rtta_Day2_Wig_min0.1.WIG.gz |
24.4 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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