|
| Status |
Public on Jan 22, 2020 |
| Title |
LNCaP-DHT-DMSO_AR DMSO + 5 nM DHT, 6 hrs |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP-FGC immortalized prostate cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: AR (Santa Cruz, Cat SC-13062)
cell line: LNCaP-FGC prostate adenocarcinoma cancer cell line
agent: DMSO + 5 nM DHT, 6 hrs
|
| Treatment protocol |
Cells were pretreated with indicated inhibitors for 45 minutes followed by 24 hr stimulation with 5 nM DHT
|
| Growth protocol |
LNCaP-FGC or 22RV1 cells were grown for 72 hrs in charcoal stripped (steroid free) serum,
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated, fixed cell pellets and protein-DNA complexes were isolated with antibody.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina Casava1.8.2 software used for basecalling
Reads were aligned to the human genome (hg19) using the BWA algorithm
Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were used for further analysis.
Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files were generated from BedGraph to BigWig. Scores represent peak density.
|
| |
|
| Submission date |
Apr 24, 2019 |
| Last update date |
Jan 25, 2020 |
| Contact name |
Josh Plotnik |
| E-mail(s) |
[email protected]
|
| Organization name |
AbbVie Inc.
|
| Street address |
1 North Waukegan Rd, AP10/210A
|
| City |
North Chicago |
| State/province |
IL |
| ZIP/Postal code |
60064 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE118247 |
Selective Inhibition of the Second Bromodomain of BET Family Maintains Anti-Tumor Efficacy and Improves Tolerability |
|
| Relations |
| BioSample |
SAMN11490917 |
| SRA |
SRX5729948 |
