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| Status |
Public on May 05, 2011 |
| Title |
High-throughput sequencing of ES cell lines, ES-derived cells, and fetal and normal livers |
| Project |
ENCODE
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| Organism |
Homo sapiens |
| Experiment type |
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
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
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| Overall design |
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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| Web link |
http://www.ncbi.nlm.nih.gov/geo/info/ENCODE.html
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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 |
| BioProject |
PRJNA63443 |
| Submission date |
May 04, 2011 |
| Last update date |
Feb 21, 2019 |
| 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 |
| State/province |
CA |
| ZIP/Postal code |
94305-5317 |
| Country |
USA |
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| Platforms (1) |
| GPL9052 |
Illumina Genome Analyzer (Homo sapiens) |
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| Samples (17)
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| GSM378631 |
HCT116 meDIPSeq data |
| GSM378632 |
H9 hESC Hpa II MethylSeq |
| GSM378633 |
H9 endoderm Hpa II MethylSeq |
| GSM378634 |
H9 AFP+ hESC-derived cells Hpa II MethylSeq |
| GSM378635 |
H9 AFP- hESC-derived cell negative Hpa II MethylSeq |
| GSM378636 |
H9 embryoid bodies Hpa II MethylSeq |
| GSM378637 |
H9 conditioned medium Hpa II MethylSeq |
| GSM378638 |
H9 EB-derived cells Hpa II MethylSeq |
| GSM378639 |
BG02 hESC Hpa II MethylSeq |
| GSM378640 |
BG02 EB-derived cells rep1 Hpa II MethylSeq |
| GSM378641 |
BG02 EB-derived cells rep2 Hpa II MethylSeq |
| GSM378642 |
Fetal liver 11 weeks Hpa II MethylSeq |
| GSM378643 |
Fetal liver 24 weeks Hpa II MethylSeq |
| GSM378644 |
Adult liver Hpa II MethylSeq |
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| This SubSeries is part of SuperSeries: |
| GSE14966 |
Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSE29071_HudsonAlpha_Methyl-Seq_Alayne_Feb0909.tar.gz |
1.1 Gb |
(ftp)(http) |
TAR |
| GSE29071_readme.txt |
52 b |
(ftp)(http) |
TXT |
| GSE29071_sequence_annotations.txt.gz |
2.4 Mb |
(ftp)(http) |
TXT |
| Raw data provided as supplementary file |
| Processed data included within Sample table |
| Processed data are available on Series record |
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