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Series GSE18292 Query DataSets for GSE18292
Status Public on Oct 14, 2009
Title Chromatin States in Human ES Cells Reveal Key Regulatory Sequences and Genes Involved in Pluripotency and Self-renewal
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Human embryonic stem cells (hESCs) are offering a new therapeutic approach because of their unique ability to proliferate indefinitely in vitro and differentiate into multiple cell types. However, our understanding of the molecular mechanisms of pluripotency and self-renewal remain incomplete. To elucidate the key regulatory sequences and genes responsible for these cellular properties, we have determined potential enhancers and insulators in the genome of human ES cells and examined the dynamics of four key chromatin modifications (H3K4me1, H3K4me3, H3K27ac and H3K27me3) at both promoters and enhancers during the differentiation of these cells. We observe that most enhancers gain or lose H3K4me1 and H3K27ac during differentiation in a manner that correlates with expression of their potential target genes. By contrast, chromatin modifications at promoters remain stable and largely invariant during hESC differentiation, with the exception of a small number of promoters where a dynamic switch between acetylation and methylation at H3K27 marks the transition between activation and silencing of gene expression. Our results reveal more than 50,000 potential enhancers for early human development, and identify key genes that are involved in differentiation and maintenance of pluripotency in human ES cells.
 
Overall design ChIP-Seq Analysis of SOX2 and NANOG in hESC H1 cells. 36 cycles of sequencing was done on the Illumina Genome Analyzer II platform.
 
Contributor(s) Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo Q, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR
Citation(s) 19829295, 23526891
Submission date Sep 25, 2009
Last update date Feb 12, 2020
Contact name Bing Ren
E-mail(s) biren@ucsd.edu
Organization name University of California, San Diego
Street address 9500 Gilman Drive
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
 
Platforms (1)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
Samples (3)
GSM456570 hESC-SOX2-1a
GSM456571 hESC-NANOG-1a
GSM456572 hESC-NANOG-1b
Relations
SRA SRP001264
BioProject PRJNA117929

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Supplementary file Size Download File type/resource
GSE18292_RAW.tar 1.5 Gb (http)(custom) TAR (of BED, TXT)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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