Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRD4

Cell type

Cell type Class
Uterus
Cell type
HeLa
Primary Tissue
Cervix
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
HeLa cells
treatment
JQ1
cell line
HeLa cells
cell type
Human cervical cancer epithelial cells
passages
P3
chip antibody
BRD4, CST, 13440S

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The ChIP protocol has been adapted from previous studies (Library preparation for Illumina NextSeq was performed using the NEBNext Ultra II DNA library prep kit (NEB) as per manufacturer's protocol. ) with the following modification. Diagenode Bioruptor was used to sonicate with 30 cycles of 30 sec on, 30 sec off. The samples were sonicated in 15ml polystyrene tubes at 4°C while samples were immersed in ice cold water. Antibodies used for ChIP include: ~200 ng of DNA was submitted to SPRI-works Fragment Library System I (Beckman Coulter) for each library prepared. Briefly, the DNA is subjected to size selection (200-400bp) with magnetic beads, end repaired, then a single adenine nucleotide is added to allow for directional ligation of adaptors. For this study, a 1:100 dilution of Single End read adapters (Illumina) was used in the ligation reaction. Each sample was then amplified for 19 cycles, using the Illumina protocol, adding additional bases from the PCR primers that aid sequences to anneal to the Illumina Genome Analyzer flow cell. The samples were then purified on a Qiagen MinElute column, and libraries were quantified by Quant-it DNA Assay (Invitrogen, Q-33120), and examined for proper size and structure by Bioanalyzer (Agilent) and qPCR.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
53834765
Reads aligned (%)
136.8
Duplicates removed (%)
25.7
Number of peaks
52058 (qval < 1E-05)

hg38

Number of total reads
53834765
Reads aligned (%)
137.5
Duplicates removed (%)
25.5
Number of peaks
52406 (qval < 1E-05)

Base call quality data from DBCLS SRA