|
| Status |
Public on Jan 01, 2015 |
| Title |
LNCaP DHT treated FoxA1 |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP cells
|
| Organism |
Homo sapiens |
| Characteristics |
agent: 10 nm DHT
cell line: LNCaP
cancer: Prostate adenocarcinoma
type: Androgen-sensitive
chip antibody: anti-FoxA1 from Santa Cruz Biotechnology (Santa Cruz, CA)
|
| Treatment protocol |
For hormone responsive experiments, LNCaP cells were maintained in phenol red-free RPMI medium with 5% charcoal-stripped FBS for 3 days, and then treated with 10 nM DHT.
|
| Growth protocol |
The androgen-dependent prostate cancer cell line LNCaP was obtained from the American Type Culture Collection, and cultured in the RPMI complete medium.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After treatment with 10 nm DHT or vehicle for 4 h, LNCaP cells were crosslinked with 1% formaldehyde for 10 min. Sonicated chromatin was enriched by immunoprecipatation with an anti-FoxA1 antibody.
T4 DNA polymerase, T4 PNK, and Klenow DNA Polymerase were used together for end polishing. The ligation step was performed with less reducing agent. Protein A Dynal magnetic beads were washed using modified RIPA buffer (50mM Tris-HCL pH 7.8, 1mM EDTA, 0.25% Na Deoxycholate, 1% NP-40, 0.5M LiCl). The library was amplified with only 10 or 12 PCR cycles, and prepared without gel-based size selection.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
ChIP-exo
|
| Data processing |
Alignment: Sequence reads were obtained and mapped to the human (hg19) genomes using the Bowtie. All reads mapping with two or fewer mismatches were retained. Only reads with unique mapping location is used for downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: bed files contains mapped reads information.
|
| |
|
| Submission date |
Jan 23, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Xun Lan |
| E-mail(s) |
xlan@stanford.edu
|
| Phone |
7738345917
|
| Organization name |
Stanford University
|
| Department |
Genetics
|
| Lab |
Pritchard's Lab
|
| Street address |
318 Campus Dr. Room S240
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE43678 |
Redefinition of Human Androgen Responsive Elements [FOX_ChIP_exo] |
| GSE43791 |
Redefinition of Human Androgen Responsive Elements |
|
| Relations |
| SRA |
SRX219285 |
| BioSample |
SAMN01894454 |
| Named Annotation |
GSM1068137_120404_ChipEXO6_NoIndex_L006_R1.fastq.tagAlign.bed.gz |
| Named Annotation |
GSM1068137_120404_ChipEXO6_NoIndex_L006_R2.fastq.tagAlign.bed.gz |
