Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
AR

Cell type

Cell type Class
Prostate
Cell type
Prostate cancer-derived fibroblasts
NA
NA

Attributes by original data submitter

Sample

source_name
PCDF2_veh_AR
cell type
prostate cancer-derived fibroblasts
group
PCDF2
treatment
veh
chip antibody
AR (Santa Cruz; sc-816,lot: I0215)

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 (Stelloo et al, 2018, Singh et al 2019). Samples were crosslinked with 2 mM DSG (CovaChem) for 25 min at room temperature followed by 1% formaldehyde for 10 minutes at room temperature 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). 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
20970100
Reads aligned (%)
83.8
Duplicates removed (%)
10.6
Number of peaks
733 (qval < 1E-05)

hg38

Number of total reads
20970100
Reads aligned (%)
85.8
Duplicates removed (%)
9.4
Number of peaks
679 (qval < 1E-05)

Base call quality data from DBCLS SRA