|
| Status |
Public on Aug 16, 2018 |
| Title |
22Rv1_MOCK_C19 |
| Sample type |
SRA |
| |
|
| Source name |
22Rv1 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: prostate carcinoma epithelial cell line 22Rv1
chip antibody: anti-AR-FL specific (Santa cruz bio#C-19)
treatment: vehicle (charcoal stripped)
|
| Treatment protocol |
For ChIP-seq experiments, 22Rv1 cells were grown in regular medium to about 50% confluent and then switched to phenol red free RPMI medium containing 10% charcoal-stripped FBS for 3 days and then treated with either vehicle, or 10nM of DHT, or DHT plus 10uM of MDV3100, or DHT plus 500nM of JQ1, for 6hrs before the cells were collected.
|
| Growth protocol |
22Rv1 cells were grown in RPMI plus 10% FBS and 1% antibiotics.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with specific antibodies against AR-FL, AR-V7, BRD4 or ZFX.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for up to 18 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2000 following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Barcode: CTTGTA
|
| Data processing |
All reads were mapped to the human genome (hg19) using the BWA alignment software. Unique reads mapped to a single best-matching location with no more than two mismatches were kept, which were then subject to removal of reads generated by PCR- caused duplicates using the Picard and Samtools.
Profiles of ChIP-Seq read densities were displayed in the Integrative Genomics Viewer (IGV, Broad Institute) and the Integrative Genomics Browser (IGB, Affymetrix).
The MACS2 software was used for peak identification with data from input as controls and default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph
|
| |
|
| Submission date |
Feb 19, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Greg Wang |
| E-mail(s) |
greg_wang@med.unc.edu, greg.wang@duke.edu
|
| Organization name |
Duke University School of Medicine, and Department of Biochemistry and Biophysics, UNC at Chapel Hill (adjunct)
|
| Department |
Duke Department of Pharmacology and Cancer Biology and Duke Cancer Institute
|
| Street address |
3 Genome Court
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE94013 |
Canonical and non-canonical regulatory roles of androgen receptor variant 7 in prostate cancer |
|
| Relations |
| BioSample |
SAMN06347985 |
| SRA |
SRX4824359 |
| SRA |
SRX2576593 |
