|
| Status |
Public on Nov 03, 2017 |
| Title |
A general transcription co-factor, Smad3, potentiates master transcription factor mediated cell identity conversions [ChIP-seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We have identified that expression of constitutive active Smad3 (Smad3CA) significantly enhanced reprogramming by Oct4, Sox2, Klf4, c-Myc. Smad3 is known to interact with several master transcription factors and boost their activity during development. Therefore, we hypothesized that Smad3CA is recruited to Oct4 binding sites during reprogramming. To test this hypothesis, we investigated genome-wide Smad3 binding sites in the presence and absence of reprogramming factor expression.
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| |
|
| Overall design |
Oct4, Smad3 ChIP-seq on day 3 of reprogramming in the presence of Smad3CA expression, Smad3 ChIP-seq in MEFs with Smad3CA expression for 3 days.
|
| |
|
| Contributor(s) |
Ruetz T, Ashmore J, Keisuke K |
| Citation(s) |
29174331 |
| |
| Submission date |
Aug 03, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Keisuke Kaji |
| E-mail(s) |
kkaji@exseed.ed.ac.uk
|
| Organization name |
University of Edinburgh
|
| Department |
MRC Centre for Reproductive Health
|
| Street address |
47 Little France Crescent
|
| City |
Edinburgh |
| State/province |
Midlothian |
| ZIP/Postal code |
EH16 4TJ |
| Country |
United Kingdom |
| |
|
| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
|
| Samples (13)
|
|
| This SubSeries is part of SuperSeries: |
| GSE85178 |
A general transcription co-factor, Smad3, potentiates master transcription factor mediated cell identity conversions |
|
| Relations |
| BioProject |
PRJNA336441 |
| SRA |
SRP080896 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE85177_D3_3CA_Dox_Oct4.bigwig |
169.5 Mb |
(ftp)(http) |
BIGWIG |
| GSE85177_D3_3CA_Dox_Oct4.narrowPeak.gz |
44.7 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE85177_D3_3CA_Dox_Oct4.tab.gz |
591.3 Kb |
(ftp)(http) |
TAB |
| GSE85177_D3_3CA_Dox_Oct4_Rep1.narrowPeak.gz |
24.9 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE85177_D3_3CA_Dox_Oct4_Rep2.narrowPeak.gz |
23.4 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE85177_D3_3CA_Dox_Oct4_Rep3.narrowPeak.gz |
2.8 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE85177_D3_3CA_Dox_Smad3.bigwig |
175.2 Mb |
(ftp)(http) |
BIGWIG |
| GSE85177_D3_3CA_Dox_Smad3.broadPeak.gz |
307.7 Kb |
(ftp)(http) |
BROADPEAK |
| GSE85177_D3_3CA_Dox_Smad3.gappedPeak.gz |
427.7 Kb |
(ftp)(http) |
GAPPEDPEAK |
| GSE85177_D3_3CA_Dox_Smad3.tab.gz |
583.6 Kb |
(ftp)(http) |
TAB |
| GSE85177_D3_3CA_Dox_Smad3_Rep1.broadPeak.gz |
10.6 Kb |
(ftp)(http) |
BROADPEAK |
| GSE85177_D3_3CA_Dox_Smad3_Rep1.gappedPeak.gz |
13.7 Kb |
(ftp)(http) |
GAPPEDPEAK |
| GSE85177_D3_3CA_Dox_Smad3_Rep2.broadPeak.gz |
580.9 Kb |
(ftp)(http) |
BROADPEAK |
| GSE85177_D3_3CA_Dox_Smad3_Rep2.gappedPeak.gz |
814.0 Kb |
(ftp)(http) |
GAPPEDPEAK |
| GSE85177_D3_3CA_Dox_Smad3_Rep3.broadPeak.gz |
251.6 Kb |
(ftp)(http) |
BROADPEAK |
| GSE85177_D3_3CA_Dox_Smad3_Rep3.gappedPeak.gz |
350.5 Kb |
(ftp)(http) |
GAPPEDPEAK |
| GSE85177_D3_3CA_Dox_Smad3_vs_D3_3CA_Dox_Oct4_DiffBind.tsv.gz |
119.1 Kb |
(ftp)(http) |
TSV |
| GSE85177_D3_3CA_Dox_Smad3_vs_D3_3CA_NoDox_Smad3_DiffBind.tsv.gz |
121.2 Kb |
(ftp)(http) |
TSV |
| GSE85177_D3_3CA_NoDox_Smad3.bigwig |
165.1 Mb |
(ftp)(http) |
BIGWIG |
| GSE85177_D3_3CA_NoDox_Smad3.broadPeak.gz |
281.1 Kb |
(ftp)(http) |
BROADPEAK |
| GSE85177_D3_3CA_NoDox_Smad3.gappedPeak.gz |
388.7 Kb |
(ftp)(http) |
GAPPEDPEAK |
| GSE85177_D3_3CA_NoDox_Smad3.tab.gz |
445.2 Kb |
(ftp)(http) |
TAB |
| GSE85177_D3_3CA_NoDox_Smad3_Rep1.broadPeak.gz |
40.8 Kb |
(ftp)(http) |
BROADPEAK |
| GSE85177_D3_3CA_NoDox_Smad3_Rep1.gappedPeak.gz |
53.9 Kb |
(ftp)(http) |
GAPPEDPEAK |
| GSE85177_D3_3CA_NoDox_Smad3_Rep2.broadPeak.gz |
450.0 Kb |
(ftp)(http) |
BROADPEAK |
| GSE85177_D3_3CA_NoDox_Smad3_Rep2.gappedPeak.gz |
627.2 Kb |
(ftp)(http) |
GAPPEDPEAK |
| GSE85177_D3_3CA_NoDox_Smad3_Rep3.broadPeak.gz |
97.6 Kb |
(ftp)(http) |
BROADPEAK |
| GSE85177_D3_3CA_NoDox_Smad3_Rep3.gappedPeak.gz |
130.1 Kb |
(ftp)(http) |
GAPPEDPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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