Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
GATA2

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 type
Human castrate-resistant prostate cancer cell line
cell line
VCaP
chip antibody
GATA2 antibody (Sigma, HPA005633)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells with fixed with 1% formaldehyde and lysed to extract chromatin. Chromatin was sheared using sonication. DNA-protien complexes were immunoprecipitatied using an anti-GATA2 antibody (Sigma, HPA005633) Indexed libraries were prepared from 5 ng of ChIP DNA with TruSeq ChIP Sample Prep Kit (Illumina) according to the manufacturer's instructions. Libraries were quantified using the Tape Station 2200 (Agilent Technologies) and Qubit Fluorometer 1.0 (Invitrogen Co., Carlsbad, CA). Libraries were pooled such that each index-tagged sample was present in equimolar amounts, with final concentration of the pooled samples of 2nM. The pooled samples were subject to cluster generation and sequencing using an Illumina NextSeq 500 System (Illumina) in a 1x75 single-end format

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
51745412
Reads aligned (%)
87.9
Duplicates removed (%)
7.8
Number of peaks
26017 (qval < 1E-05)

hg38

Number of total reads
51745412
Reads aligned (%)
90.0
Duplicates removed (%)
6.7
Number of peaks
26553 (qval < 1E-05)

Base call quality data from DBCLS SRA