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Sample GSM1207887 Query DataSets for GSM1207887
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

Supplementary file Size Download File type/resource
GSM1207887_S09-AR-CHIP-LNCAP-LM-HES6-VEHICLE.bwa_Processed_peaks.bed.gz 425.1 Kb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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