Unknown,Transcriptomics,Genomics,Proteomics

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DNA methylation data from human iPS cells and fibroblasts

ABSTRACT: DNA methylation is often inversely correlated with gene expression. We used custom Nimblegen microarrays to determine the relationship between DNA methylation and gene expression in 6 iPS cell lines and the fibroblasts from which they were derived. We isolated genomic DNA from iPS cells and fibroblasts and hybridized to custom-designed Nimblegen microarrays (CHARM arrays).

ORGANISM(S): Homo sapiens

SUBMITTER: Akiko Doi 

PROVIDER: E-GEOD-18227 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts.

Doi Akiko A   Park In-Hyun IH   Wen Bo B   Murakami Peter P   Aryee Martin J MJ   Irizarry Rafael R   Herb Brian B   Ladd-Acosta Christine C   Rho Junsung J   Loewer Sabine S   Miller Justine J   Schlaeger Thorsten T   Daley George Q GQ   Feinberg Andrew P AP  

Nature genetics 20091101 12

Induced pluripotent stem (iPS) cells are derived by epigenetic reprogramming, but their DNA methylation patterns have not yet been analyzed on a genome-wide scale. Here, we find substantial hypermethylation and hypomethylation of cytosine-phosphate-guanine (CpG) island shores in nine human iPS cell lines as compared to their parental fibroblasts. The differentially methylated regions (DMRs) in the reprogrammed cells (denoted R-DMRs) were significantly enriched in tissue-specific (T-DMRs; 2.6-fol  ...[more]

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