Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRD4

Cell type

Cell type Class
Breast
Cell type
HCC1937
Primary Tissue
Breast
Site of Extraction
Soft Tissue
Tissue Diagnosis
Adenocarcinoma Ductal

Attributes by original data submitter

Sample

source_name
breast cancer
cell line
HCC1937
chip antibody
BRD4, A301-985A50

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
HCC1806 and HCC1937 cells were cross-linked with 1 % formaldehyde (for H3K27Ac), or cross-linked with disuccinimidyl glutarate, followed by double cross-linked with 1 % formaldehyde (for BRD4). The libraries were constructed following NEB's Chip-Seq Sample prep kit. Briefly, Chip DNA was end-blunted and added with an 'A' base so the adaptors from Illumina with a 'T' can ligate on the ends. Then 200–400 bp fragments are gel-isolated and purified. The library was amplified by 18 cycles of PCR.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
35347865
Reads aligned (%)
85.9
Duplicates removed (%)
11.8
Number of peaks
10220 (qval < 1E-05)

hg38

Number of total reads
35347865
Reads aligned (%)
88.1
Duplicates removed (%)
10.3
Number of peaks
10256 (qval < 1E-05)

Base call quality data from DBCLS SRA