|
| Status |
Public on Feb 19, 2017 |
| Title |
LNCaP_Ctrl AR ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
prostate tumor
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP
genotype: Ctrl
antibody: AR (santa cruz, sc-815X, lot K0713)
|
| Treatment protocol |
LNCaP cells stably expressing doxycycline inducible NOV were treated with water (Ctrl) or doxycycline (NOV) for 2-3days before fixation by 1% formaldehyde.
|
| Growth protocol |
Cell lines were maintained in RPMI supplemented with 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin in nuclear fraction were sheared to 200-500bp using an ultrasonic sonicator (Misonix), Lysates were clarified from sonicated nuclei and protein-DNA complexes were immunoprecipitated using the indicated antisera. DNA was then uncrosslinked from protein, purified and sequenced using Illumina Genome Analyzers followig protocols recommended by the manufacturer.
Libraries were prepared according to Illumina's instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
Chromatin IP against AR
|
| Data processing |
Reads were aligned to the hg19 reference human genome using bwa v0.6.1
Peak-calling by HOMER v4.1
Genome_build: hg19
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph file and peak txt file
|
| |
|
| Submission date |
Mar 17, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jindan Yu |
| E-mail(s) |
jindan.yu@emory.edu
|
| Organization name |
Emory University
|
| Department |
Urology
|
| Lab |
Jindan Yu's lab
|
| Street address |
E330, 1760 Haygood Dr NE
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30322 |
| Country |
USA |
| |
|
| Platform ID |
GPL15456 |
| Series (2) |
| GSE79357 |
Polycomb-mediated deactivation of AR-feedback loop leads to castration-resistant prostate cancer [ChIP-seq] |
| GSE79358 |
Polycomb-mediated deactivation of AR-feedback loop leads to castration-resistant prostate cancer |
|
| Relations |
| BioSample |
SAMN04565989 |
| SRA |
SRX1640090 |
