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Series GSE52457 Query DataSets for GSE52457
Status Public on Feb 18, 2015
Title Global Reorganization of Chromatin Architecture during Embronic Stem Cell Differentiation
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Other
Summary The 3D organization of the genome is important for regulation of diverse nuclear processes ranging from transcription to DNA replication. Knowledge of the higher order chromatin structure is critical for understanding mechanisms of gene regulation by long-range control elements such as enhancers and insulators. We describe high resolution, genome-wide dynamic chromatin interaction maps in human embryonic stem cells (hESC) as they differentiate into four distinct embryonic cell lineages. Extensive reorganization of higher-order chromatin structure occurs during hESC differentiation. In this process, topological domains remain largely intact but inter-domain association patterns change dramatically, coincident with widespread changes in chromatin state and gene expression. Moreover, using proximity ligation sequencing to generate chromosome span haplotypes, widespread allele biased gene activities are detected. The allelic gene expression patterns can be correlated to epigenetic state at distal enhancers, supporting the role of these elements in regulating gene expression over a distance.
 
Overall design Two biological replicates of Hi-C experiment and one replicate of CTCF ChIP-Seq experiment in embryonic stem cells and 4 other differentiated cell-types from H1 cell line. Re-analysis of data from GSE16256 in an allele specific manner is linked as supplementary data.

Hi-C data generated in this study can be visualized at www.3dgenome.org.
 
Contributor(s) Dixon JR, Jung I, Selvaraj S, Ren B
Citation(s) 25693564
Submission date Nov 18, 2013
Last update date May 15, 2019
Contact name Jesse R Dixon
E-mail(s) jedixon@salk.edu
Organization name Salk Institute for Biological Studies
Lab PBL-D
Street address 10010 N. Torrey Pines Rd.
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (27)
GSM1267196 Hi-C, H1 embryonic stem cells, replicate one
GSM1267197 Hi-C, H1 embryonic stem cells, replicate two
GSM1267198 Hi-C, H1 Mesendoderm cells, replicate one
Relations
BioProject PRJNA228983
SRA SRP033089

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

Supplementary file Size Download File type/resource
GSE52457_BED_files.tar.gz 7.3 Gb (ftp)(http) TAR
GSE52457_H1_haps.vcf.gz 22.3 Mb (ftp)(http) VCF
GSE52457_RAW.tar 280.0 Kb (http)(custom) TAR (of BEDGRAPH)
GSE52457_inference_files.tar.gz 22.3 Mb (ftp)(http) TAR
GSE52457_reanalyzed_data_detail.xls.gz 8.4 Kb (ftp)(http) XLS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data is available on Series record
Processed data provided as supplementary file

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