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Series GSE87165 Query DataSets for GSE87165
Status Public on Sep 22, 2016
Title Sequencing analysis for 5hmC pull-down DNA
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary The gene body regions of cardiomyocyte-specific genes in cardiomyocytes are hypomethylated. We confirmed that the DNA methylation in gene body regions were demethylated during development. We speculated that the demethylation of gene body regions in cardiomyocyte-specific genes might be associated with active demethylation by Tet oxidation.To explore 5hmC distribution in cells and tissues, we performed 5hmC-specific chemical labeling-mediated pull-down DNA sequencing (hMe-Seal)(Song 2011 Nat genet, PMID:21151123). We found that the 5hmC in gene body regions are associated with demethylation, but not exclusively, and also with transcriptional activity. We concluded that gene body DNA hypomethylation in cardiomyocyte specific genes were mediated by oxidative demethylation.
Overall design Genomic DNA from ESC and heart and liver tissues from different developmental periods was used for the analysis.
Contributor(s) Oda M, Wakabayashi S
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Submission date Sep 21, 2016
Last update date May 15, 2019
Contact name Mayumi Oda
Organization name Keio University
Department School of Medicine
Lab Institute of Integrated Medical Research
Street address 35 Shinanomachi, Shinjuku
City Tokyo
ZIP/Postal code 1608582
Country Japan
Platforms (2)
GPL16417 Illumina MiSeq (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (12)
GSM2323813 5hmC EB5 rep1
GSM2323814 5hmC EB5 rep2
GSM2323815 5hmC C57BL6/j heart (P1) rep1
BioProject PRJNA343772
SRA SRP090225

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
GSE87165_RAW.tar 5.9 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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