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Series GSE33781 Query DataSets for GSE33781
Status Public on Nov 17, 2012
Title Genome-wide maps of 5hmC state in pluripotent and (T-)iPS induction cells.
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary We performed 5hmC DNA Immunoprecipitation followed high-throughput sequencing using R1 ESCs, OT ESCs, TSKM ESCs, Day3 TSKM and OSKM induction cells. We compared the profiling of 5-hydroxymethylcytosine modifications in these different cell lines. We found that: the TSKM and OT iPSCs shared similar 5hmC modification pattern while apart from that of R1 ESCs. However the comparison based on the gene promoter (-1000/+500 of gene’s TSS) showed less differences. The TSKM 2nd induction samples were quite like each other and have shared the basic pattern with traditional OSKM 2nd sample. However comparison based on the gene promoter showed sharp increase. Moreover higher enrichment of 5hmC on the distal enhancer of Oct4 was specifically detected in Day 3 TSKM 2nd cells as well as TSKM and OT iPSCs, which might be helpful for us to study the Tet1-mediated somatic reprogramming.
Overall design Examination of 5-hydroxymethylcytosine modifications in 5 different cell lines.
Contributor(s) Gao Y, Chen J, Cai T, Gao S
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Submission date Nov 17, 2011
Last update date May 15, 2019
Contact name Tao Cai
Organization name National Institute Of Biological Sciences, Beijing (NIBS)
Lab Sequencing Facility
Street address No. 7 Science Park Road, Zhongguancun Life Science Park
City Beijing
ZIP/Postal code 102206
Country China
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (5)
GSM835556 R1
GSM835557 OSKM 2nd 1#-3D
GSM835558 TSKM 2nd 2#-3D
SRA SRP009375
BioProject PRJNA148601

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Supplementary file Size Download File type/resource
GSE33781_RAW.tar 960.2 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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