Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRD4

Cell type

Cell type Class
Breast
Cell type
MDA-MB-231
Primary Tissue
Breast
Site of Extraction
Effusion, Pleural
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
MDA-MB-231
cell line
breast cancer cell line MDA-MB-231
er/pr/her2 statue
triple negative – ER-; PR-; HER2-
chip antibody
anti-BRD4-S(a)
bet inhibitor jq1 treatment
active JQ1, i.e. JQ1_pos or JQ1(+)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated by IP with anti-BRD4-L or BRD4-S [i.e., S(a)] antibody or with Abcam EN1 antibody (Cat# ab108598). Sequencing libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) following manufacturer's protocol.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
45320044
Reads aligned (%)
89.2
Duplicates removed (%)
6.0
Number of peaks
1088 (qval < 1E-05)

hg38

Number of total reads
45320044
Reads aligned (%)
92.1
Duplicates removed (%)
3.8
Number of peaks
1479 (qval < 1E-05)

Base call quality data from DBCLS SRA