|
| Status |
Public on Jun 24, 2019 |
| Title |
ChIPseq_FOXA1_DMSO_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
prostate cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: prostate cancer cell line
cell line: LNCaP
treatment: DMSO
chip-antibody: FOXA1 (Abcam, ab23738)
|
| Treatment protocol |
LNCaP cells were treated with vehicle control or 10 uM of UPF-1069 for 16 hours.
|
| Growth protocol |
LNCaP cells were maintaned in RPMI 1640 medium supplemented with 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Protein-DNA complexes were isolated from sonicated LNCaP cell lysates with indicated antibodies, and the ChIP DNA was extracted using phenol chloroform extraction method. Purified ChIP DNA was dissolved in TE buffer and re-sheared using Covaris sonicator to enable enrichment of fragments with an average size of 300 bp. The re-sheared DNA samples were purified for library preparation using the minElute PCR purification kit (Qiagen).
The ChIP-seq libraries were prepared using the ThruPLEX DNA-seq Kit (Rubicon Genomics; R400427) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
bcl2fastq v2.18 used for base calling with default parameters
ChIP-seq data was mapped to human genome (hg19) using Bowtie2 (v2.3.0) with default settings.
Reads that did not map uniquely were removed.
Genomic coverage of each factor was generated with the deepTools2 program (v2.4.0) with the following configurations --binSize 10 --normalizeTo1x 2451960000 --ignoreForNormalization chrX --ignoreDuplicates
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files that contain the genomic coverage of each factor
|
| |
|
| Submission date |
May 10, 2018 |
| Last update date |
Jun 24, 2019 |
| Contact name |
Li Jia |
| E-mail(s) |
ljia@bwh.harvard.edu
|
| Organization name |
Brigham and Women's Hospital
|
| Department |
Surgery
|
| Lab |
Thorn 1529
|
| Street address |
20 Shattuck Street
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE114274 |
Genome-wide occupation of AR, FOXA1, and H3K27AC in LNCaP cells treated with selective PARP2 inhibitor UPF-1069 |
| GSE114275 |
Selective Targeting of PARP2 Inhibits Androgen Receptor Signaling and Prostate Cancer Growth Through Disruption of FOXA1 Function |
|
| Relations |
| BioSample |
SAMN09104554 |
| SRA |
SRX4062884 |
