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
Prosate cancer cells
cell type
vertebral metastatic lesion derived prostate cancer cells
cell line
VCaP
chip antibody
AR (Millipore, 06-680)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed using HighCell ChIP kit following manufacturers protocol (Diagenode). ChIP DNA was isolated (IPure Kit, Diagenode) from samples by incubation with the antibody at 4°C overnight followed by wash and reversal of cross-linking. The ChIP-seq sample preparation for sequencing was performed according to the manufacturer’s instructions (Illumina). ChIP-enriched DNA samples (1-10 ng) were converted to blunt-ended fragments using T4 DNA polymerase, E.coli DNA polymerase I large fragment (Klenow polymerase) and T4 polynuleotide kinase (New England BioLabs, NEB). A single A-base was added to fragment ends by Klenow fragment (3’ to 5’ exo minus; NEB) followed by ligation of Illumina adaptors (Quick ligase, NEB). The adaptor-modified DNA fragments were enriched by PCR using the Illumina Barcode primers and Phusion DNA polymerase (NEB). PCR products were size selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (QIAGEN). Libraries were quantified with the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2000 Sequencer (100 nucleotide read length).

Sequencing Platform

instrument_model
Illumina HiSeq 1000

hg19

Number of total reads
34992474
Reads aligned (%)
127.8
Duplicates removed (%)
31.8
Number of peaks
29141 (qval < 1E-05)

hg38

Number of total reads
34992474
Reads aligned (%)
129.1
Duplicates removed (%)
31.6
Number of peaks
29565 (qval < 1E-05)

Base call quality data from DBCLS SRA