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Series GSE61475 Query DataSets for GSE61475
Status Public on Feb 19, 2015
Title Transcription factor binding dynamics during human ES cell differentiation
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Pluripotent stem cells provide a powerful system to dissect the underlying molecular dynamics that regulate cell fate changes during mammalian development. Here we report the integrative analysis of genome wide binding data for 38 transcription factors with extensive epigenome and transcriptional data across the differentiation of human embryonic stem cells to the three germ layers. We describe core regulatory dynamics and show the lineage specific behavior of selected factors. In addition to the orchestrated remodeling of the chromatin landscape, we find that the binding of several transcription factors is strongly associated with specific loss of DNA methylation in one germ layer and in many cases a reciprocal gain in the other layers. Taken together, our work shows context-dependent rewiring of transcription factor binding, downstream signaling effectors, and the epigenome during human embryonic stem cell differentiation.
 
Overall design 200 ChIP-seq experiments profiling 38 transcription factors (TFs) and several chromatin marks in 5 cell types--male human ES cell line HUES64 and directed differentiation of HUES64 towards mesendoderm (dMS, 12 hours), endoderm (dEN, 120 hours), mesoderm (dME, 120 hours), and ectoderm (dEC, 120 hours). In addition, three ES cell lines were derived with shRNA mediated knockdown of GATA4 and differention toward endoderm (dEN_shGATA4) and mesoderm (dME_shGATA4). These cell lines were used for MNChIP-seq of GATA4, SMAD1, and H3K27Ac and for 4 RRBS experiments in GATA4 knockdown and control cell lines.
 
Contributor(s) Meissner A
Citation(s) 25693565
Submission date Sep 16, 2014
Last update date May 15, 2019
Contact name Alexander Tsankov
E-mail(s) atsankov@alum.mit.edu
Organization name Harvard University
Street address 7 Divinity Drive
City Cambridge
State/province MA
ZIP/Postal code 02138
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (204)
GSM1505615 PRDM1 MNChIP-seq in cell type dMS Blimp1_022813_mesendo
GSM1505616 PRDM1 MNChIP-seq in cell type dEN Blimp1_061112_endo
GSM1505617 PRDM1 MNChIP-seq in cell type HUES64 Blimp1_070213_h64
Relations
BioProject PRJNA261253
SRA SRP047193

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Supplementary file Size Download File type/resource
GSE61475_RAW.tar 46.8 Gb (http)(custom) TAR (of BIGBED, BW, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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