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Series GSE29071 Query DataSets for GSE29071
Status Public on May 05, 2011
Title High-throughput sequencing of ES cell lines, ES-derived cells, and fetal and normal livers
Project ENCODE
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
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
 
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
Web link http://www.ncbi.nlm.nih.gov/geo/info/ENCODE.html
 
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
Organization name Stanford U
Street address 300 Pasteaur Dr
City Stanford
State/province CA
ZIP/Postal code 94305-5317
Country USA
 
Platforms (1)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
Samples (17)
GSM378628 HCT116 rep1 Msp I MethylSeq
GSM378629 HCT116 rep2 Msp I MethylSeq
GSM378630 HCT116 rep3 Msp I MethylSeq
This SubSeries is part of SuperSeries:
GSE14966 Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver

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
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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