Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
GABPA

Cell type

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

Attributes by original data submitter

Sample

source_name
VCaP cell line
cell line
VCaP
chip antibody
GABPa
treatment
vehicle
chip antibody manufacturer
Santa Cruz

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Briefly, 54 ul of ChIP DNA or 50 ng of total input control DNA were subjected to end-repair using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase, before purification using the DNA Clean and concentrator-5 kit (Zymo Research). Adenine overhangs were added using Klenow 5¡¦-3¡¦exo-minus, Illumina Solexa sequencing adapters were ligated using T4 DNA ligase and amplified with 18 PCR cycles using Phusion DNA polymerase (Finnzymes) and Illumina Solexa sequencing primers 1.1 and 2.1. Libraries were size selected by electrophoresis, excising the DNA smear between 200-300 bp on a Dark Reader non-UV transilluminator, purified using a Qiagen gelextraction mini-elute kit and quantified using an Agilent Bioanalyser.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
88902663
Reads aligned (%)
73.0
Duplicates removed (%)
23.2
Number of peaks
18754 (qval < 1E-05)

hg38

Number of total reads
88902663
Reads aligned (%)
75.2
Duplicates removed (%)
21.5
Number of peaks
18791 (qval < 1E-05)

Base call quality data from DBCLS SRA