Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
EWSR1

Cell type

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

Attributes by original data submitter

Sample

source_name
VCaP Prostate cancer cell line
cell line
VCaP
cell type
prostate cancer
antibody
Anti-EWS clone G5 sc-28327

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP DNA was extracted as described in Hollenhorst et al., Genes and Dev. 2011 Sequencing libraries were generated using a modified Illumina Truseq sample preparation protocol. ChIP DNA's were sheared to ~150 nucleotides using a Diagenode BioRuptor and the size was confirmed by DNA gel electrophoresis. DNA end repair of the cDNA was performed using Klenow DNA polymerase (New England BioLabs), T4 DNA polymerase (New England BioLabs), and T4 DNA ligase (New England BioLabs) before the sample was subjected to QIAquick PCR purification (Qiagen). Adapters were ligated to DNA fragments using the T4 DNA ligase (New England BioLabs). The product was run on a 2% agarose gel and size selected between 200 and 300 nucleotides to then be purified by a Gel Extraction kit (Qiagen). Universal and indexing adapters were taken from the TruSeq sample preparation kit (Illumina).

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
34489295
Reads aligned (%)
71.3
Duplicates removed (%)
5.4
Number of peaks
985 (qval < 1E-05)

hg38

Number of total reads
34489295
Reads aligned (%)
73.0
Duplicates removed (%)
3.9
Number of peaks
1178 (qval < 1E-05)

Base call quality data from DBCLS SRA