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Series GSE38596 Query DataSets for GSE38596
Status Public on Sep 22, 2012
Title Genome-wide maps of cytosine methylation, cytosine hydroxylmethylation and small non coding RNAs in mouse ES cells and upon guided differentiation to mesoendoderm cells
Organism Mus musculus
Experiment type Non-coding RNA profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Genome-wide maps of cytosine methylation, cytosine hydroxylmethylation and small non coding RNAs in mouse ES cells and upon guided differentiation to mesoendoderm cells. Mouse embryonic stem cells (E14) were guided differentiated into mesoendoderm lineages by activin-A induction. cells in three time points (day0, day4 and day6) were collected. The genome-wide studies on three cell types were summerized as following: cytosine methylation data were generated using methylated DNA immunoprecipitation followed by sequencing (MeDIP-seq) and DNA digestion by methyl-sensitive restriction enzymes followed by sequencing (MRE-seq); DNA product for 5-hmC_ChIP-seq is generated by a selctive chemical labeling method (Nat. Biotechnol. 2011, 29, 68-72). E14 Day0 data for MRE-seq and MeDIP-seq are released first in previous publication and included in prior series GSE36114
 
Overall design ChIP-seq, 5-hmC-seq, MeDIP-Seq, MRE-Seq, ncRNA-Seq, and RNA-seq on activin-induced differentiating ES cells at 3 time points.

 
Contributor(s) Xiao S, Yu P, Huang W, Xin X, Song C, McDee D, Tanaka T, Wang T, He C, Zhong S
Citation(s) 23033340
Submission date Jun 08, 2012
Last update date May 15, 2019
Contact name Pengfei Yu
E-mail(s) yupf05@gmail.com
Organization name University of California San Diego
Department Bioengineering
Lab Dr. Sheng Zhong
Street address 9500 Gilman Drive MC 0419
City La Jolla
State/province CA
ZIP/Postal code 92093-0419
Country USA
 
Platforms (4)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (36)
GSM881346 E14_Day0_MeDIP-seq
GSM881347 E14_Day0_MRE-seq
GSM881348 E14_Day0_H2AZ_ChIP-seq
Relations
BioProject PRJNA168204
SRA SRP013622

Download family Format
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Supplementary file Size Download File type/resource
GSE38596_RAW.tar 19.9 Gb (http)(custom) TAR (of BAM, BED, GTF, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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