Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
AR

Cell type

Cell type Class
Prostate
Cell type
Prostate cancer
NA
NA

Attributes by original data submitter

Sample

source_name
Human prostate tumor
tissue
primary prostate tumor
antibody
anti-AR (sc-618, Santa Cruz)
tumor id
Primary_4
gleason score
9

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
FAIRE experiments were performed as described (Giresi PG et al. Methods 2009;48(3):233-9): fresh frozen tissues were crosslinked with 1% formaldehyde for 20 min. Cells were washed, nuclei isolated. Chromatin was sonicated and cleared by centrifugation. The soluble chromatin was subjected to three consecutive phenol-chloroform-isoamyl alcohol (25:24:1) extractions. The samples were reverse crosslinked overnight at 65°C and purified by ethanol precipitation. Purified samples were treated with RNase A and proteinase K and repurified by PCR purification kit. Chromatin Immunoprecipitation was performed as described (Zwart W et al. BMC Genomics 2013;14:232): 10mg (ChIP-seq) or 5mg (ChIP-QPCR) of antibody was used, with 100ml (ChIP-seq) of Protein A magnetic beads. Antibody used was AR-N20 (sc-618; Santa Cruz). DNA was amplified as described (Ross-Innes CS et al. Nature 2012;481(7381):389-93). Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
12243485
Reads aligned (%)
89.8
Duplicates removed (%)
2.8
Number of peaks
3012 (qval < 1E-05)

hg38

Number of total reads
12243485
Reads aligned (%)
91.7
Duplicates removed (%)
1.6
Number of peaks
2971 (qval < 1E-05)

Base call quality data from DBCLS SRA