Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
EN1

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 3F:BRD4-S(a)
cell line
breast cancer cell line MDA-MB-231 ectopic 3f:BRD4-S(a) expression
er/pr/her2 statue
triple negative – ER-; PR-; HER2-
chip antibody
anti-EN1
bet inhibitor jq1 treatment
inactive enantiomer JQ1, i.e. JQ1_neg 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
64715047
Reads aligned (%)
87.3
Duplicates removed (%)
8.7
Number of peaks
1199 (qval < 1E-05)

hg38

Number of total reads
64715047
Reads aligned (%)
89.6
Duplicates removed (%)
7.2
Number of peaks
1273 (qval < 1E-05)

Base call quality data from DBCLS SRA