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| Status |
Public on Mar 06, 2009 |
| Title |
Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver |
| Organism(s) |
Homo sapiens |
| Experiment type |
Expression profiling by array
Methylation profiling by high throughput sequencing
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| Summary |
Publication title: Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver
To investigate the role of DNA methylation during human development, we developed Methyl-seq, a method that assays DNA methylation at more than 90,000 regions throughout the genome. Performing Methyl-seq on human embryonic stem cells (hESCs), their derivatives and human tissues allowed us to identify several trends during hESC and in vivo liver differentiation. First, differentiation results in DNA methylation changes at a minimal number of assayed regions, both in vitro and in vivo (2-11%). Second, in vitro hESC differentiation is characterized by both de novo methylation and demethylation, whereas in vivo fetal liver development is characterized predominantly by demethylation. Third, hESC differentiation is uniquely characterized by methylation changes specifically at H3K27me3-occupied regions, bivalent domains and low-density CpG promoters (LCPs) suggesting that these regions are more likely to be involved in transcriptional regulation during hESC differentiation. Although both H3K27me3-occupied domains and LCPs are also regions of high variability in DNA methylation state during human liver development, these regions become highly unmethylated, which is a distinct trend from that observed in hESCs. Taken together, our results indicate that hESC differentiation has a unique DNA methylation signature that may not be indicative of in vivo differentiation.
Keywords: Methyl-seq, hESC differentiation
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| Overall design |
lumina gene expression beadchips of human ES cell lines, ES-derived cells, and normal liver (15 samples). High-throughput sequencing of ES cell lines, ES-derived cells, and fetal and normal livers (17 samples). Raw data: SRA008154 http://www.ncbi.nlm.nih.gov/sites/entrez?db=sra&cmd=search&term=SRA008154
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| Contributor(s) |
Brunner AL, Johnson DS, Kim SW, Valouev A, Reddy TE, Neff NF, Anton E, Medina C, Nguyen L, Chiao E, Oyolu CB, Schroth GP, Absher DM, Baker JC, Myers RM |
| Citation(s) |
19273619
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| Submission date |
Feb 24, 2009 |
| Contact name |
Rami Rauch |
| E-mail(s) |
rrauch@stanford.edu
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| Organization name |
Stanford U
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| Street address |
300 Pasteaur Dr
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| City |
Stanford |
| ZIP/Postal code |
94305-5317 |
| Country |
USA |
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| Platforms (2) |
| GPL5060 |
HumanRef-8 v2 Expression BeadChip |
| GPL9052 |
Illumina Genome Analyzer (Homo sapiens) |
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| Samples (32)
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| Supplementary file |
Size |
Download |
File type/resource |
| GSE14966_HudsonAlpha_Methyl-Seq_Alayne_Feb0909.tar |
3.2 Gb |
(ftp)(http) |
TAR (of TXT) |
| GSE14966_RAW.tar |
41.6 Mb |
(ftp)(http) |
TAR (of TXT) |
| GSE14966_readme.txt |
52 b |
(ftp)(http) |
TXT |
| GSE14966_sequence_annotations.txt.gz |
2.4 Mb |
(ftp)(http) |
TXT |
| Raw data provided as supplementary file |
| Processed data included within Sample table |
| Processed data is available on Series record |
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