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Series GSE69646 Query DataSets for GSE69646
Status Public on Nov 22, 2015
Title 3D Chromosome Regulatory Landscape of Human Pluripotent Cells [ChIP-Seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The control of cell identity is orchestrated by transcriptional and chromatin regulators in the context of specific chromosome structures. With the recent isolation of human naive embryonic stem cells (ESCs) representative of the ground state of pluripotency, it is possible to deduce this regulatory landscape in one of the earliest stages of human development. Here we generate cohesin ChIA-PET chromatin interaction data in naive and primed human ESCs and use it to reconstruct and compare the 3D regulatory landscapes of these two stages of early human development. The results reveal shared and stage-specific regulatory landscapes of topological domains and their subdomains, which consist of CTCF-CTCF/cohesin loops and enhancer-promoter/cohesin loops. The enhancer-promoter loop data reveal that genes with key roles in pluripotency are nearly always regulated by one or more super-enhancers, and show that these genes tend to occur in insulated neighborhoods. Our results reveal the key features of the 3D regulatory landscape of early human cells that form the foundation for embryonic development.
 
Overall design ChIP-seq data from naive and primed human embroynic stem cells.
 
Contributor(s) Ji X
Citation(s) 26686465
Submission date Jun 08, 2015
Last update date May 15, 2019
Contact name Richard A Young
E-mail(s) young_computation@wi.mit.edu
Phone 617-258-5219
Organization name Whitehead Institute for Biomedical Research
Lab Young Lab
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (18)
GSM1705251 Naive_H3K27ac_R1
GSM1705252 Naive_H3K27ac_R2
GSM1705253 Naive_CTCF_R1
This SubSeries is part of SuperSeries:
GSE69647 3D Chromosome Regulatory Landscape of Human Pluripotent Cells
Relations
BioProject PRJNA286086
SRA SRP059231

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE69646_RAW.tar 1.5 Gb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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