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GEO help: Mouse over screen elements for information. |
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| 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
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| 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
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| 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.
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| 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 |
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| Submission date |
Jun 08, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Pengfei Yu |
| E-mail(s) |
[email protected]
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| Organization name |
University of California San Diego
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| Department |
Bioengineering
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| Lab |
Dr. Sheng Zhong
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| Street address |
9500 Gilman Drive MC 0419
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093-0419 |
| Country |
USA |
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| Platforms (4)
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| GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (36)
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| Relations |
| BioProject |
PRJNA168204 |
| SRA |
SRP013622 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE38596_RAW.tar |
19.9 Gb |
(http)(custom) |
TAR (of BAM, BED, GTF, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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