Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRD4

Cell type

Cell type Class
Gonad
Cell type
OVCAR-3
Primary Tissue
Ovary
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
JQ1-treated cells
cell line
OVCAR3
agent
JQ1
chip antibody
rabbit polyclonal anti-BRD4 (Bethyl Laboratories, catalog# A301-985A, lot# A301-985A50-4)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
cells were cross-linked with 1% formaldehyde for 10 min, followed by quenching with 125 mM glycine for 5 min at room temperature. Fixed cells were washed with TBS and the pellets were kept on -70 °C. The pellets were thawed and resuspended in cell lysis buffer (10 mM Tris-HCl, pH7.5, 10 mM NaCl, 0.5% NP-40) and incubated on ice for 10 min. The lysates were washed with MNase digestion buffer (20 mM Tris-HCl, pH7.5, 15 mM NaCl, 60 mM KCl, 1 mM CaCl2) once and incubated for 20 minutes at 37 °C in the presence of 1,000 Gel units of MNase (NEB, M0247S) in 250 ul reaction volume. After adding the same volume of sonication buffer (100 mM Tris-HCl, pH8.1, 20 mM EDTA, 200 mM NaCl, 2% Triton X-100, 0.2% Sodium deoxycholate), the lysates were sonicated for 5 min (30 sec-on / 30 sec-off) in Diagenode bioruptor and centrifuged at 15,000 rpm for 10 min. ChIP performed with rabbit polyclonal anti-BRD4 (Bethyl Laboratories, catalog# A301-985A). Ovation Ultralow DR Multiplex system (NuGEN).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
18017851
Reads aligned (%)
183.5
Duplicates removed (%)
6.3
Number of peaks
252 (qval < 1E-05)

hg38

Number of total reads
18017851
Reads aligned (%)
186.2
Duplicates removed (%)
5.7
Number of peaks
316 (qval < 1E-05)

Base call quality data from DBCLS SRA