|
| Status |
Public on Oct 23, 2017 |
| Title |
1_A375 DMSO_BRD4 [lab: Hammerman-DFCI] |
| Sample type |
SRA |
| |
|
| Source name |
Melanoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A375
chip antibody: Brd4
antibody manufacturer: Bethyl
antibody catalog number: A301-985A100
young_id: 20160603_4845
tissue: Skin
drug: DMSO
concentration: 0.1%
cell number: 50 million
treatment duration: 48h
|
| Treatment protocol |
Cells were treated with DMSO for 48 hours prior to cross linking with formaldehyde.
|
| Growth protocol |
A375 cells were grown in DMEM, 10% FBS, PSG at 37 degrees and 5% CO2. Cells were maintained between 40-90% confluency.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 40
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1
|
| |
|
| Submission date |
Oct 24, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard A Young |
| E-mail(s) |
young_computation@wi.mit.edu
|
| Phone |
617-258-5219
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Lab |
Young Lab
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE89128 |
Suppression of adaptive responses to targeted cancer therapy by transcriptional repression [ChIP-seq] |
| GSE89129 |
Suppression of adaptive responses to targeted cancer therapy by transcriptional repression |
|
| Relations |
| BioSample |
SAMN05938355 |
| SRA |
SRX2267438 |
