|
| Status |
Public on Feb 12, 2016 |
| Title |
AR_C42_NS_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
prostate cancer cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: C4-2 cell
chip antibodies: Santa Cruz AR (N-20) sc-816
|
| Treatment protocol |
The cells were cultures with charcoal-stripped (steroid depleted) serum medium for 48 hours and then were transfected with siRNAs. For PSA eRNA knocking down, the cells were transfected with control siRNA or PSA si-eRNA for 48 hours and two roundly.
|
| Growth protocol |
Prostate cancer cells were cultures (typically 2–3 × 106 cells into a T75 flask) in RPMI 1640 medium (Gibco, Unite State) with charcoal-stripped serum (CSS).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
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 15 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 2500 |
| |
|
| Data processing |
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (hg19) using BWA (v0.5.9) with defautl parameters
Peak calling was performed using MASC2 (v2.0.10)
Pol2 differential binding was analyzed by edgeR(v3.6.8)
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: bigWig file
|
| |
|
| Submission date |
Aug 04, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
LIGUO WANG |
| E-mail(s) |
wang.liguo@mayo.edu
|
| Organization name |
Mayo Clinic
|
| Department |
Division of Computational Biology
|
| Street address |
200 1st St SW
|
| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55905 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE55032 |
Activation of the P-TEFb Complex by Lethal Prostate Cancer-Associated Enhancer RNAs |
| GSE71704 |
Activation of P-TEFb by androgen receptor-regulated enhancer RNAs in androgen deprivation conditions [ChIP-Seq] |
|
| Relations |
| BioSample |
SAMN03956193 |
| SRA |
SRX1132445 |
