|
| Status |
Public on Dec 06, 2013 |
| Title |
2-HPC-iPSC-16 H3K4me2 ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
HPC-iPSC H3K4me2 ChIPseq
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129-M2rtTA
cell type: HPC-derived induced pluripotent stem cells
passage: 10-12
chip antibody: H3K4me2
chip antibody vendor: Millipore
chip antibody cat #: 07-030
chip antibody lot #: DAM1724042
|
| 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 |
1.5x108 cells were resuspended in lysis buffer and digested with micrococcal nuclease about 5 minutes at 37℃.Then, the lysate was immunoprecipitated with antibody anti-H3K4me2, anti-H3K4me3, anti-H3K27me3; meanwhile, retaining a fraction of input ‘whole-cell extract’ as sequencing control. Immunoprecipitation-enrichment of chromatin fragments were defined and the bound DNA were purified using phenol:chloroform extractions. Chiped DNA was quantified by Qubit 2.0 Fluorometer (life technologies) and Q-PCR was performed to validate the enrichment efficiency. Then the enriched DNA was sonicated to 100-500bp fragments. DNA-end was repaired to overhang a 3’-dA, then adapters was ligated to the end DNA fragments. DNA fragments about 100-300bp, were recovered and amplified to construct the sequencing library. Thirty-nine ChIP library and thirteen input controls were used for sequencing.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 44
|
| Data processing |
The ChIP sequencing reads were mapped to mouse reference genome (mm9/NCBI37) using Bowtie (v0.12.7) software allowing the max mismatch 3nt. And only the unique mapped reads were used. The CCAT (v3.0) software was chosen to identify the modification enriched regions (peaks). The histone ChIPseq datasets were feed to CCAT software and the corresponding input dataset were taken as negative control. The parameters were referred to the original paper (Xu et al. 2010) in that sliding widow 2000nt for the H3K27me3 modification and 500nt for the H3K4me3, H3K4me2 modification. The FDR 0.05 was taken as cutoff.
Genome Build:
H3K4me2_16_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) |
| GSE36292 |
High-throughput sequencing of sequentially reprogrammed iPS cells reveals key epigenetic modifications correlated with reduced pluripotency of iPS cells [ChIP-seq] |
| GSE36294 |
High-throughput sequencing of sequentially reprogrammed iPS cells reveals key epigenetic modifications correlated with reduced pluripotency of iPS cells |
|
| Relations |
| SRA |
SRX127400 |
| BioSample |
SAMN00808838 |
