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Series GSE21141 Query DataSets for GSE21141
Status Public on May 28, 2010
Title Derivation of pre-X inactivation human embryonic stem cells under physiological oxygen concentrations
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The presence of two active X chromosomes (XaXa) is a hallmark of the ground state of pluripotency specific to murine embryonic stem cells (ESCs). Human ESCs invariably exhibit signs of X chromosome inactivation (XCI) and are considered developmentally more advanced than their murine counterparts. We describe the establishment of the first XaXa hESCs derived under physiological oxygen concentrations. Using these cell lines we demonstrate that (1) differentiation of hESCs induces random XCI in a manner similar to murine ESCs, (2) chronic exposure to atmospheric oxygen is sufficient to induce irreversible XCI with minor changes of the transcriptome, (3) the Xa exhibits heavy methylation of the XIST promoter region, and (4) XCI is associated with demethylation and transcriptional activation of XIST along with H3K27-me3 deposition across the Xi. These findings indicate that the human blastocyst contains pre-X-inactivation cells and that this state is preserved in vitro through culture under physiological oxygen.
 
Overall design Examination of 2 different histone modifications (H3K4me3 and H3K27me3) in 3 ES cell lines in 5% and 20% oxygen.
 
Contributor(s) Lengner CJ, Erwin JA, Gimelbrant AA, Cheng AW, Guenther MG, Welstead GG, Alagappan R, Frampton GM, Xu P, Muffat J, Powers D, Barrett CB, Young RA, Lee JT, Jaenisch R, Mitalipova M
Citation(s) 20471072
Submission date Mar 30, 2010
Last update date May 15, 2019
Contact name Garrett M Frampton
E-mail(s) frampton@mit.edu
Organization name Whitehead Instute - MIT
Department Biology
Lab Richard Young
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platforms (1)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
Samples (12)
GSM529408 H3K4me3 WIBR1 5% O2
GSM529409 H3K4me3 WIBR2 5% O2
GSM529410 H3K4me3 WIBR3 5% O2
Relations
SRA SRP002240
BioProject PRJNA126661

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
GSE21141_RAW.tar 452.7 Mb (http)(custom) TAR (of TXT, WIG)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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