|
| Status |
Public on Jan 08, 2014 |
| Title |
CDK2.T30_ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
Breast cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: CDK2
time: 30 min
cell line: T47D-MTVL
treatment: progestin
|
| 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 30 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 Genome Analyzer |
| |
|
| Description |
ChIP-seq
|
| 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
ChIP-seq signals were summed in windows of 10 Kb
Genome_build: hg19
Supplementary_files_format_and_content: TXT file with read counts all over the genome of all ChIP-seq samples
|
| |
|
| Submission date |
Jan 07, 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 |
GPL9052 |
| Series (1) |
| GSE53855 |
CDK2-dependent activation of PARP-1 is required for hormonal gene regulation in breast cancer cells. |
|
| Relations |
| BioSample |
SAMN02570303 |
| SRA |
SRX423003 |
