|
| Status |
Public on Nov 17, 2012 |
| Title |
R1 |
| Sample type |
SRA |
| |
|
| Source name |
R1 ES cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: ES cells
stage or passages: p20-25
strain: 129
cell line: R1
hmedip: 5hmC
|
| Growth protocol |
R1 ES cells and iPS cells were cultured on mitomycin C treated MEFs in ES medium containing DMEM medium (Gibco Invitrogen, Carlsbad, CA) supplemented with 15% (v/v) fetal bovine serum (FBS), 1 mM L-glutamine, 0.1 mM mercaptoethanol, 1% nonessential amino acid stock, and 1000 U/ml LIF. The O/TSKM 2nd induction cells were derived from O/TSKM iPS mice and cultured with Feeder Medium for 3 passages. On passages 4 the culture were changed to ES Medium with doxycycline for 3 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
In brief, the sonicated genomic DNA was treated using NEBNext master Mix to repair the ends of DNA fragments and ligate the paired-end sequencing specific adaptors (Illumina), the DNA product was then immunoprecipitated and purified. Here we used 500ng ligation product for each IP reaction. Fragments were amplified with 14–16 cycles using adaptor specific primers (Illumina). The final product (300-500bp) was gel-purified (Qiagen) before cluster generation and sequencing.
library strategy: hMeDIP-seq
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
genome build: mm9/ncbi37
|
| |
|
| Submission date |
Nov 17, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Tao Cai |
| E-mail(s) |
[email protected]
|
| 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 |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE33781 |
Genome-wide maps of 5hmC state in pluripotent and (T-)iPS induction cells. |
|
| Relations |
| SRA |
SRX105945 |
| BioSample |
SAMN00759051 |
