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Series GSE31848 Query DataSets for GSE31848
Status Public on May 14, 2012
Title Recurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and their Differentiated Derivatives [Illumina Infinium 450K DNA Methylation]
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary Human pluripotent stem cells (hPSCs) are potential sources of cells for modeling disease and development, drug discovery, and regenerative medicine. However, it is important to identify factors that may impact the utility of hPSCs for these applications. In an unbiased analysis of 205 hPSC and 130 somatic samples, we identified hPSC-specific epigenetic and transcriptional aberrations in genes subject to X chromosome inactivation (XCI) and genomic imprinting, which were not corrected during directed differentiation. We also found that specific tissue types were distinguished by unique patterns of DNA hypomethylation, which were recapitulated by DNA demethylation during in vitro directed differentiation. Our results suggest that verification of baseline epigenetic status is critical for hPSC-based disease models in which the observed phenotype depends on proper XCI or imprinting, and that tissue-specific DNA methylation patterns can be accurately modeled during directed differentiation of hPSCs, even in the presence of variations in XCI or imprinting.
 
Overall design To obtain a comprehensive view of hPSC-specific epigenomic patterns, we collected 136 hESC and 69 hiPSC samples representing more than 100 cell lines for analysis. In order to establish expected variation in human tissues, we collected 80 high-quality and well-replicated samples representing 17 distinct tissue types from multiple individuals. Finally, we selected 50 additional samples from primary cell lines of diverse origin to control for any aberrations that may arise as a general, non-hPSC-specific, consequence of in vitro manipulation. With these samples, we performed genome-wide DNA methylation and mRNA expression profiling using the Illumina Infinium 27K and 450K DNA Methylation BeadChips as well as the Illumina HT12v3 Gene Expression BeadArray.
 
Contributor(s) Nazor KL, Altun G, Lynch C, Tran H, Harness JV, Slavin I, Garitaonandia I, Müller F, Wang Y, Boscolo FS, Fakunle E, Lee S, Park HS, Martynova M, Ole T, D'Lima DD, Semechkin R, Parast MM, Galat V, Laslett AL, Schmidt U, Keirstead HS, Loring JF, Laurent LC
Citation(s) 22560082
Submission date Sep 02, 2011
Last update date Mar 22, 2019
Contact name Kristopher L. Nazor
E-mail(s) kristopher.nazor@gmail.com
Organization name The Scripps Research Institute
Department Regenerative Medicine
Lab Loring
Street address 10550 North Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (153)
GSM867936 ES__WA09_passage39_Female____87.1429.1.1
GSM867937 ES__WA09_passage39_Female____87.1429.2.1
GSM867938 ES__MEL4_passage35_Female____127.378.3.1
This SubSeries is part of SuperSeries:
GSE30654 Recurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and their Differentiated Derivatives
Relations
BioProject PRJNA155257

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
GSE31848_RAW.tar 183.1 Mb (http)(custom) TAR
GSE31848_raw.txt.gz 644.4 Mb (ftp)(http) TXT
Processed data included within Sample table
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