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| Status |
Public on May 26, 2015 |
| Title |
Chip-seq_CHD8_exp |
| Sample type |
SRA |
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| Source name |
T47D-MTVL
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| Organism |
Homo sapiens |
| Characteristics |
cell line: Cell line derived from T47D that contain one copy of MMTV promoter
chip antibody: anti-CHD8 (A301-224A, Bethyl Laboratories)
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| Treatment protocol |
For R5020 treatments, cells were subjected to serum-free conditions in RPMI medium without phenol red during 48 h. After serum starvation, cells were incubated with 10 nM R5020 or vehicle (ethanol; EtOH) for 5 or 45 min.
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| Growth protocol |
Cells were routinely grown in RPMI 1640 medium supplemented with 10% FBS, 2mM L-glutamine, 100 U/ml penicillin and 100 mg/ml streptomycin
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
After 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
Libraries were prepared according to Illumina's instructions.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Data processing |
ChIP-seq reads were aligned to the hg19 human genome assembly using ELANDv2 allowing up to 2 mismatches in the first 32 bases
ChIP-seq peak calling, genomic annotation of peaks and comparison between ChIP-seq and ENCODE datasets were performed using ChIPseeqer (v.2.1), using default parameters. Minimum peak width 100bp. Mininum distance between peaks 100bp. Significance negative log p-value, t = 10^-10
Genome_build: hg19
Supplementary_files_format_and_content: Format: wig files generated using Chipseeqer (v.2.1). Content: read density track for the UCSC Genome Browser.
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| Submission date |
Oct 16, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jose C. Reyes |
| E-mail(s) |
jose.reyes@cabimer.es
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| Phone |
34-954467842
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| Organization name |
CABIMER
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| Department |
Molecular biology
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| Lab |
2
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| Street address |
Av. Américo Vespucio
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| City |
Sevilla |
| ZIP/Postal code |
41092 |
| Country |
Spain |
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| Platform ID |
GPL9052 |
| Series (1) |
| GSE62428 |
Chip-seq analysis of CHD8 distribution in T47D cells |
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| Relations |
| BioSample |
SAMN03113010 |
| SRA |
SRX734338 |
| Named Annotation |
GSM1526889_CHD8.wig.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1526889_CHD8.wig.gz |
516.5 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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