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Series GSE51239 Query DataSets for GSE51239
Status Public on Jul 23, 2014
Title DNA methylation dynamics of the human pre-implantation embryo
Organisms Homo sapiens; Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary We present genome-scale maps of DNA methylation in early human development and perform comparative analysis to mouse that confirm a conserved global erasure of the paternal genome. We find that while many global features of the early embryo are consistent between the two species, the target sequences in which DNA methylation is maintained are distinct. Repetitive elements show a broader range of class specific behaviors in the human embryo and a larger degree of methylation escape in human sperm. We identify thousands of differentially methylated regions (DMRs) that are likely of maternal origin and found that these gamete contributed DMRs are far more species-specific than expected given the conservation of canonical imprint control regions (ICRs). Finally, we extended our studies to the derivation of new human embryonic stem cell (ESC) lines and found notable divergences in DNA methylation signatures from those found in the human embryo and different mouse ESC derivation conditions.
Overall design Comparison of DNA methylation patterns in human early development, human ESC derivation and mouse ESC derivation
Contributor(s) Smith ZD, Chan MM, Humm KC, Mekhoubad S, Regev A, Eggan K, Meissner A
Citation(s) 25079558
Submission date Sep 27, 2013
Last update date Jul 06, 2022
Contact name Michelle M Chan
Organization name UCSF
Lab Weissman Lab
Street address 1700 4th St.
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
Platforms (2)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (48)
GSM1240860 hSperm-524-90
GSM1240861 hSperm-530-90
GSM1240862 hSperm-533-90
Reanalyzed by GSE171332
BioProject PRJNA221793
SRA SRP030612

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
GSE51239_RAW.tar 478.1 Mb (http)(custom) TAR (of TXT)
GSE51239_hDev100bpMeFinal.txt.gz 70.1 Mb (ftp)(http) TXT
GSE51239_mDer100bpMe.txt.gz 60.5 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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