|
| Status |
Public on Dec 06, 2013 |
| Title |
2-HPC MeDIP sequencing |
| Sample type |
SRA |
| |
|
| Source name |
HPC_MeDIPseq
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129-M2rtTA
cell type: mouse hematopoietic progenitor cells (HPC)
passage: 0
|
| Growth protocol |
ES cells and iPS cells were maintained in ES cell media containing 15% FBS and 1,000 Uml-1 of LIF.MEF and APCs were cultured in DMEM supplemented with 10% FBS and penicillin/streptomycin. HPCs was freshly isolated from bone marrow
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from cell pellets and 5μg original gDNA were prepared for a library. DNA quality was analyzed by Qubit 2.0 Fluorometer (life technologies). gDNA was sonicated to 100-500bp, and repaired to overhang a 3’-dA; then the adapters were ligated to the end of DNA fragments according to the Paired-End DNA Sample Prep Kit (Illumina). For the immunoprecipitation, DNA was first denatured, followed by immunoprecipitated by 5mC antibody using Magnetic Methylated DNA Immunoprecipitation kit (Diagenod). Q-PCR was used to validate the efficiency of the enriched products. Then the pull-down DNA were amplified about 12-15 cycles, and fragments with proper size, usually 200-300bp, were gel-purified using Gel Extraction Kit (Qiagen) and quantified by 2100 Bioanalyzer (Agilent Technologies)
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 12
|
| Data processing |
The MeDIP/ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt, the max insert length constraints is 1000nt. Only unique mapped reads were extracted for the following analysis.The aligned reads were further feed to MACS (v1.4.1) software to identify the DNA methylation enriched regions.
Genome Build:
medip_HSC_peaks.bed: mm9
|
| |
|
| Submission date |
Mar 06, 2012 |
| 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 |
GPL13112 |
| Series (2) |
| GSE36293 |
High-throughput sequencing of sequentially reprogrammed iPS cells reveals key epigenetic modifications correlated with reduced pluripotency of iPS cells [MeDIP-seq] |
| GSE36294 |
High-throughput sequencing of sequentially reprogrammed iPS cells reveals key epigenetic modifications correlated with reduced pluripotency of iPS cells |
|
| Relations |
| SRA |
SRX127421 |
| BioSample |
SAMN00808860 |
