|
| Status |
Public on Apr 14, 2015 |
| Title |
E2F1_ChIPSeq_abl |
| Sample type |
SRA |
| |
|
| Source name |
prostate cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP-abl
cell type: androgen-independent prostate cancer cells
passages: 61-64
chip antibodies: Santa Cruz Biotechnology (sc-193) and BD Pharmingen (554213)
|
| Treatment protocol |
For the purpose of ChIP experiments, the cells were kept in androgen-depleted medium for 3 days before the cells were collected.
|
| Growth protocol |
LNCaP-abl (abl) cells were routinely maintained in phenol-red-free RPMI with 10% charcoal-stripped FBS plus 1% antibiotics.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with specific antibodies. Libraries were prepared using ThruPLEX-FD Prep Kit (Rubicon Genomics). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina NextSeq 500 system following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalls performed using CASAVA 1.6.0
ChIP-Seq reads are aligned to hg19 using Bowtie with default configurations, only uniqly mapped reads are kept
Redundant reads (reads mapped to exactly the same location) are removed
Peaks are called using MACS2 2.0.9
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files are generated using MACS2+bedGraphToBigWig
|
| |
|
| Submission date |
Apr 13, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Kexin Xu |
| E-mail(s) |
kxuthscsa@gmail.com
|
| Organization name |
UT Health Science Center at San Antonio
|
| Department |
Molecular Medicine
|
| Street address |
7703 Floyd Curl, MC 8257
|
| City |
San Antonio |
| State/province |
TX |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE67809 |
Genome-wide chromatin binding of transcription factor E2F1 in castration resistant prostate cancer (CRPC) cells |
|
| Relations |
| BioSample |
SAMN03481181 |
| SRA |
SRX992662 |
