Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ERG

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 type
VCaP Prostate Cancer cell line
treatment
Treated with DMSO on day 1, day 3, and day 6.
chip antibody
ERG (CM421 Biocare)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Nuclear lysates were incubated with 5uL of indicated antibody and 50uL of Dynabeads for 4 hours in dilution buffer(20mM Tris, 2mM EDTA,150mM NaCl, 1% Triton X-100, 2 mg/mL BSA) followed by 4 washes with wash buffer(20mM Tris, .25% NP-40, .05% SDS, 2mM EDTA, 250mM NaCl). ChIPs were then incubated with RNAse A (5Prime) and Proteinase K (Sigma) followed by DNA extraction with Qiagen PCR purification kit. Total Cellular RNA was extracted using Qiagen RNeasy kit followed DNAse treatment (Turbo) and poly-A selection using oligo dT beadsd (Ambion). Poly-A selected RNA was then reverse transcribed using random hexamer primers and SuperScript III. Double stranded DNA was then produced from cDNA fragments using DNA ligase and DNA polymerase. Isolated DNA was sonicated for 30 minutes (30sec on / 30 sec off) followed by End Repair with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. End repaired DNA was 3' Adenylated with Klenow exo (3' to 5') followed by ligation of Illumina TruSeq adaptors with T4 DNA ligase. Ligated DNA fragments were subject to 15 cycles of PCR with Q5 polymerase followed by size selection with AMPure XP beads. ATAC-Seq libraries were generated using ActiveMotif ATAC-Seq kit. 50,000 cells were spun down, washed with PBS, and lysed with ATAC-Lysis buffer followed by tagmentation. Tagmented DNA was purified and PCR amplified for 10 cycles followed by SPRI bead cleanup.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
40163131
Reads aligned (%)
93.2
Duplicates removed (%)
42.0
Number of peaks
539 (qval < 1E-05)

hg19

Number of total reads
40163131
Reads aligned (%)
92.5
Duplicates removed (%)
42.5
Number of peaks
461 (qval < 1E-05)

Base call quality data from DBCLS SRA