Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
AR

Cell type

Cell type Class
Prostate
Cell type
Prostate cancer cells
NA
NA

Attributes by original data submitter

Sample

source_name
primary prostate cancer
chip antibody
AR (Santa Cruz, catalog# sc-816, mix of 4 lot#s B2114, H2914, A0515, J0614)
patient id
P416T
case/control
Control
tissue
primary prostate cancer

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitations were performed as described previously with minor changes (Zwart et al., 2013). Samples were crosslinked in solution A with 2mM DSG (CovaChem) for 25 minutes at room temperature. After 25 minutes, 1% formaldehyde was added for 20 minutes and subsequently quenched with glycine. Samples were lysed as described (Schmidt et al., 2009) and sonicated for at least 10 cycles of 30s on, 30s off using a Diagenode Bioruptor Pico. For each ChIP, 5ug of antibody was conjugated with 50ul Protein A magnetic beads. Antibodies used were AR (sc-816, Santa Cruz), H3K27ac (39133, Active Motif), H3K4me3 (Ab8580, Abcam) and H3K27me3 (39155, Active Motif). Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303, KAPA biosystems kit). Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303, KAPA biosystems kit).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
21707438
Reads aligned (%)
89.3
Duplicates removed (%)
3.7
Number of peaks
6869 (qval < 1E-05)

hg38

Number of total reads
21707438
Reads aligned (%)
90.8
Duplicates removed (%)
2.8
Number of peaks
6836 (qval < 1E-05)

Base call quality data from DBCLS SRA