|
| Status |
Public on Sep 15, 2016 |
| Title |
Reconstructing divergent retinoid-induced cell fate-regulatory programs in stem cells [ChIP-Seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We have integrated dynamic RXRa binding, chromatin accessibility and promoter epigenetic status with the transcriptional activity inferred from RNA polymerase II mapping and transcription profiling. This demonstrated a temporal organization structure, in which early events are preferentially enriched for common GRNs, while cell fate specification is reflected by the activation of late programs in a cell-type specific manner. Furthermore, significant differences in cell lines' promoter status of genes associated with cell-line specific programs were inferred. Finally, a variety of transcription factors (TFs) playing a direct role in the signal transduction cascade downstream of the RXR/RAR initiated wiring were identified, several of them commonly regulated in both model systems, but in addition cell-type specific TF drivers were also identified.
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| |
|
| Overall design |
profiling of time series ChIP-seq datasets in two related embryonic stem cells. 5 different factors assessed in 5 timepoints in 2 different cell lines. In addition two input control samples (one per cell line): Total=52 datasets.
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| |
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| Contributor(s) |
Mendoza-Parra M, Malysheva V, Saleem MA, Gronemeyer H |
| Citation(s) |
27650846, 36446525 |
| Submission date |
May 05, 2015 |
| Last update date |
Dec 15, 2022 |
| Contact name |
Marco Antonio Mendoza-Parra |
| E-mail(s) |
marco@igbmc.fr
|
| Organization name |
IGBMC
|
| Street address |
1, rue Laurent Fries
|
| City |
Illkirch; Strasbourg |
| ZIP/Postal code |
67400 |
| Country |
France |
| |
|
| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
|
| Samples (52)
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| This SubSeries is part of SuperSeries: |
| GSE68291 |
Reconstructing divergent retinoid-induced cell fate-regulatory programs in stem cells |
|
| Relations |
| BioProject |
PRJNA283042 |
| SRA |
SRP058001 |
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