Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BCOR

Cell type

Cell type Class
Prostate
Cell type
VCaP
Primary Tissue
Prostate
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
VCaP cells
treatment 1
steroid-depleted medium, 72h
treatment 2
ethanol, 1h
chip antibody
rabbit polyclonal anti-BCOR antibody (A310-672A, Bethyl Laboratories)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, VCaP cells were silenced using siRNA transfection for three days when indicate, grown on steroid-depleted medium for two days and treated for 1h with R1881 (10nM) or equal volume of vehicle (ethanol). Samples were fixed for 10 min. in room temperature with 1% (v/v) formaldehyde, fragmented to 200-400bp fragments by sonication (Bioruptor, Diagenode), chromatin immunoprecipitation was done using rabbit polyclonal anti-BCOR antibody (A310-672A, Bethyl Laboratories), rabbit antiserum against AR or anti-H2AK119ub antibody (#8240, Cell Signaling Technology). Two biological replicates of each condition were sequenced using Illumina HiSeq 2000 or NextSeq500 at EMBL GeneCore (Heidelberg, Germany). For RNA-seq, VCaP cells were transfected with siRNA against BCOR (siBCOR, 20mM, Dharmacon, ON-TARGETplus SMARTpool, L-004584-01-0005) or control siRNA (siNON, Dharmacon, non-targeting pool) using Lipofectamine RNAiMAX (Invitrogen). After three days, medium was changed to steroid-depleted medium for 32h, followed by treatment with dihydrotestosterone (DHT, 100nM) or equal volume of vehicle (ethanol) for 16h. RNA was extracted using RNease Plus Mini kit (Qiagen) and mRNA using NEBNext Poly(a) mRNA Magnetic Isolation Module (New England Biolabs). Libraries were prepared using NEBNext Ultra II kit (New England Biolabs) and sequenced with HiSeq 2000 at EMBL GeneCore (Heidelberg, Germany). Library preparation was done using NEBNext Ultra II kit (New England Biolabs) and sequenced using Illumina HiSeq 2000 or NextSeq 500 at EMBL GeneCore (Heidelberg, Germany).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
102814433
Reads aligned (%)
71.2
Duplicates removed (%)
23.3
Number of peaks
50650 (qval < 1E-05)

hg38

Number of total reads
102814433
Reads aligned (%)
73.4
Duplicates removed (%)
21.5
Number of peaks
51147 (qval < 1E-05)

Base call quality data from DBCLS SRA