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, DHT 2hr, AR ChIP
cell line
VCaP
cell type
prostate cancer cell line
treatment
DHT for 2hrs
chip antibody
anti-AR (vendor: Santa Cruz; catalog number: sc-815x; lot#: D1709)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIA-PET: ChIP Chromatin was divided into two aliquots and each aliquot was ligated with two different barcoded biotinylated half-linkers (linker A or linker B) that contain a flanking MmeI site using T4 DNA ligase. These chromatins ligated with different linkers were pooled and molecular circularization/ligation was carried out in extremely dilute condition. After ligation, DNA was purified and digested with MmeI. The biotinylated PETs purified on Streptavidin Dynabeads were ligated with a sequencing adapter by T4 DNA ligase (RT for 16h with rotation). The nick on one strand of the DNA at the ligation site was subsequently repaired by incubation with E. coli DNA polymerase I at RT for 2h, followed by 18-20 rounds of PCR. This PCR product was used as the template for Illumina GAIIx 2x36 bp pair end sequencing.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg19

Number of total reads
65501762
Reads aligned (%)
1.6
Duplicates removed (%)
1.5
Number of peaks
0 (qval < 1E-05)

hg38

Number of total reads
65501762
Reads aligned (%)
1.6
Duplicates removed (%)
1.4
Number of peaks
0 (qval < 1E-05)

Base call quality data from DBCLS SRA