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Series GSE68540 Query DataSets for GSE68540
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.
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.
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
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)
GSM1674792 F9_FAIRE-seq_48h_EtOH
GSM1674793 F9_FAIRE-seq_2h_ATRA
GSM1674794 F9_FAIRE-seq_6h_ATRA
This SubSeries is part of SuperSeries:
GSE68291 Reconstructing divergent retinoid-induced cell fate-regulatory programs in stem cells
BioProject PRJNA283042
SRA SRP058001

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Supplementary file Size Download File type/resource
GSE68540_RAW.tar 31.2 Gb (http)(custom) TAR (of BED, PDF, TXT)
GSE68540_readme_peaksMed_files_and_PDF-QC_reports.txt.gz 781 b (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file

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