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Sample GSM835556 Query DataSets for GSM835556
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
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.
SRA SRX105945
BioSample SAMN00759051

Supplementary file Size Download File type/resource
GSM835556_R1_1_map.bed.gz 184.0 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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