|
| Status |
Public on Jan 01, 2015 |
| Title |
LNCaP_CON_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP
cancer: Prostate adenocarcinoma
type: Androgen-sensitive
chip antibody: anti-AR (N20) from Santa Cruz Biotechnology (Santa Cruz, CA)
agent: vehicle, control
|
| 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 |
For AR ChIP-seq, 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-AR antibody. After overnight incubation, 20 ul protein A-agarose was added to pull down the complex. The enriched DNA was purified by QIAquick Purification kit. For MNase-Seq, native chromatin from LNCaP cells were digested with MNase for 10-20 min to generate mainly mononucleosomes. Digestion was stopped by adding EDTA to a final concentration of 50 mM. The chromatin immunoprecipitation was performed using antibodies against different marks. After overnight incubation, 20 ul protein A-agarose was added to pull down the complex. The enriched DNA was purified by QIAquick Purification kit.
The library was generated by using the NEBNext Ultra DNA Library Prep Kit. NEBNext End Prep Enzyme Mix was used for end polishing. Adaptor was ligated with Blunt/TA ligase Master mix at 20°C for 15 minutes. After gel-based size selection, the library was amplified with 16 PCR cycles using NEBNext High Fidelity 2X PCR Master Mix.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
replicate 1
|
| 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: four column bed files contains mapped reads information.
|
| |
|
| Submission date |
Jan 24, 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 |
GPL10999 |
| Series (2) |
| GSE43720 |
Redefinition of Human Androgen Responsive Elements [MNase-Seq, ChIP_seq] |
| GSE43791 |
Redefinition of Human Androgen Responsive Elements |
|
| Relations |
| SRA |
SRX219988 |
| BioSample |
SAMN01906154 |
| Named Annotation |
GSM1069669_LNCaP_CON_rep1.bed.gz |
