Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

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

Attributes by original data submitter

Sample

source_name
VCaP (CaP)
treatment
shARID1A Input

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitation (ChIP) experiments were performed per standard protocols (Millipore, Billerica, MA) with minor modifications. Briefly, 2-5M cells were crosslinked with 1% formaldehyde for 10 min at 37 °C. This reaction was subsequently quenched with 0.125M glycine. All library prep and sequencing were 75bp single end on Illuminia Nextseq 500

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
57795388
Reads aligned (%)
98.1
Duplicates removed (%)
16.6
Number of peaks
1726 (qval < 1E-05)

hg19

Number of total reads
57795388
Reads aligned (%)
97.2
Duplicates removed (%)
17.9
Number of peaks
1192 (qval < 1E-05)

Base call quality data from DBCLS SRA