|
| Status |
Public on Dec 23, 2017 |
| Title |
ChIP-seq H2A T0 |
| Sample type |
SRA |
| |
|
| Source name |
Breast cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: T47D-MTVL
treatment: unstimulated cells
chip-antibody: H2A; Kindly obtained from Stephan Dmitrov
|
| Treatment protocol |
For the experiments, cells were plated in RPMI medium without phenol red supplemented with 10% dextran-coated charcoal-treated FBS and 48 hr later medium was replaced by fresh medium without serum. After 1 day in serum-free conditions, cells were incubated with R5020 (10 nM) for different times between 0 and 360 minutes
|
| Growth protocol |
Cells were routinely grown in RPMI 1640 medium supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin, and 100 mg/ml streptomycin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After hormone treatment, the medium was replaced by medium containing 1% formaldehyde and incubated 10 min at 37ºC for cross-linking. The reaction was stop by adding 125 mM glycine and incubated 5 min at room temperature. Cells were washed twice with cold PBS, and collected. Preparation of chromatin and ChIP experiments were performed as previously described (Strutt et al, Methods Mol Biol. 1999; 119:455-567). Immunoprecipitated DNA was purified by phenol:chloroform followed by ethanol precipitation
It was performed using the NEBNext DNA sample prep Reagents set 1
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RPKM.H2A.hg19-proteinCoding-genes.txt
|
| Data processing |
Basecalls performed using Illumina pipeline version 1.4.0
ChIP-Seq Single-end reads were processed by aligning to the reference human genome (GRCh37/hg19) using Bowtie v1.0.0, an ultrafast short-read mapping program (Langmead et al. 2009), keeping only tags that mapped uniquely and with no more than two mismatches.
The integrated software MACS (Zhang et al. 2008) was used to detect peaks that were enriched from background reads with default parameters for BPTF, and a p-value of 1e-3 and no-model parameters set for HP1g and LSD1.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq data files are peak results “TSV” files with genomic coordinates of peaks
Supplementary_files_format_and_content: RPKM.H2A.hg19-proteinCoding-genes.txt: Homer v4.7.2 RPKM calculation for H2A ChIP-seq using hg19 protein-coding genes
|
| |
|
| Submission date |
Dec 23, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Miguel Beato |
| E-mail(s) |
miguel.beato@crg.eu
|
| Organization name |
CRG
|
| Street address |
Aiguader 88
|
| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE64467 |
ADP-ribose derived Nuclear ATP is Required for Chromatin Remodeling and Hormonal Gene Regulation |
|
| Relations |
| BioSample |
SAMN03272701 |
| SRA |
SRX822006 |
