|
| Status |
Public on Apr 17, 2014 |
| Title |
S09-AR-CHIP-LNCAP-LM-HES6-VEHICLE_r1 |
| Sample type |
SRA |
| |
|
| Source name |
Hes6_OE
|
| Organism |
Homo sapiens |
| Characteristics |
factor: AR
condition: Vehicle
antibody: ARN20, sc816X, LOT#E0712
|
| Treatment protocol |
Bicalutamide 1µM or Vehicle (Ethanol)
|
| Growth protocol |
RPMI & 10% Foetal Bovine Serum & Puromycin
|
| 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 Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Single-end 36 bp reads generated by the Illumina HiSeq 2000 were aligned against the Human Reference Genome (assemby GRCh37, NCBI Build 37) using BWA version 0.5.9. Reads were filtered by removing those with a BWA alignment quality score less than 15 as well as duplicate reads.
Enriched regions of the genome were identified by comparing ChIP samples to input samples using MACS Version 1.4.2
Genome_build: GRCh37
Supplementary_files_format_and_content: MACS peaks in .bed file format
|
| |
|
| Submission date |
Aug 13, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Chandra Chilamakuri |
| E-mail(s) |
datasubmissions@cruk.cam.ac.uk
|
| Organization name |
Cancer Research UK Cambridge Institute
|
| Street address |
Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE36526 |
Hes6 drives a network with therapeutic potential in castrate-resistant prostate cancer |
| GSE49832 |
Hes6 drives a critical AR transcriptional program to induce castration resistant prostate cancer through activation of an E2F1-mediated cell cycle network |
|
| Relations |
| BioSample |
SAMN02316446 |
| SRA |
SRX334236 |
