Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
AR

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
cell line
Vertebral Cancer of Prostate (VCaP)
origin
bone metastasis of prostate cancer
antibody
rabbit antiserum against AR
treatment
10nM R1881
time
30min

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were derived from sonicated (Bioruptor, Diagenode) nuclei and AR-, CTCF- and H3K9me3-DNA complexes were isolated with 1 microgram of antibody and protein-A magnetic beads. DNA fragments were purified and libraries were prepared for sequencing using standard Illumina protocol. Samples were deep-sequenced with HiSeq2000 at the GeneCore in EMBL (Heidelberg, Germany).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
13734944
Reads aligned (%)
86.2
Duplicates removed (%)
9.3
Number of peaks
38832 (qval < 1E-05)

hg38

Number of total reads
13734944
Reads aligned (%)
87.4
Duplicates removed (%)
8.5
Number of peaks
38830 (qval < 1E-05)

Base call quality data from DBCLS SRA