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Series GSE36570 Query DataSets for GSE36570
Status Public on Nov 16, 2012
Title OSKM factors cooperatively engage chromatin to initiate reprogramming
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Reprogramming cells from one fate to another, using transcription factors, generates cells for research and potential therapy, yet little is known about the initial engagement of reprogramming factors with the genome. We mapped the interactions between Oct4, Sox2, Klf4, and c-Myc (OSKM) and the human genome during the first 48 hours of cellular reprogramming to pluripotency. Unlike that reported in ES/iPS cells, we find extensive overlap in the initial binding of OSKM, demonstrating that the initial regulatory network differs markedly from that in pluripotency. OSK act as pioneer factors for c-Myc, and c-Myc enhances the engagement of OSK, including at many genes that are required for conversion to pluripotency. Distal enhancer sites in closed chromatin dominate the initial OSKM distribution. Hierarchical chromatin binding during reprogramming resembles that employed during development.
Overall design Four chIP-seq data sets (Oct4, Sox2, Klf4, and c-Myc) are included, one lane per factor, no replicates. Also included is an input lane from the same conditions and two mock lentiviral controls (no exogenous OSKM factors) treated with Oct4 IP and c-Myc IP.
Contributor(s) Soufi A, Donahue G, Zaret KS
Citation(s) 23159369
Submission date Mar 16, 2012
Last update date May 15, 2019
Contact name Kenneth S. Zaret
Phone 2155735813
Organization name University of Pennsylvania School of Medicine
Department Cell and Developmental Biology
Lab Zaret lab
Street address 9-132, SCTR, 3400 Civic Center Boulevard
City Philadelphia
State/province PA
ZIP/Postal code 19104-5157
Country USA
Platforms (1)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (7)
GSM896985 Oct4 ChIP-Seq at 48hrs Post-Induction
GSM896986 Sox2 ChIP-Seq at 48hrs Post-Induction
GSM896987 Klf4 ChIP-Seq at 48hrs Post-Induction
SRA SRP011557
BioProject PRJNA153727

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Supplementary file Size Download File type/resource
GSE36570_All_48hrs_MTFBRs.bed.gz 1.9 Mb (ftp)(http) BED
GSE36570_DBRs.bed.gz 2.9 Kb (ftp)(http) BED
GSE36570_RAW.tar 3.4 Gb (http)(custom) TAR (of BED, BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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