Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRD4

Cell type

Cell type Class
Digestive tract
Cell type
SW 480
Primary Tissue
unresolved
Tissue Diagnosis
unresolved

Attributes by original data submitter

Sample

source_name
SW480 Cells
cell line
SW480
cell type
Human Colon Cancer Cell Line
treated with
12.5 ng ml-1 TNF-α for 16 hr
chip antibody
Anti-BRD4: Bethyl laboratories; cat# A301-985A100; lot# A301-985A100-6

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates from sonicated nuclei were prepared and protein-DNA complexes were IP'd overnight with BRD4 antibody. ChIP-seq libraries were prepared according to Illumina's ChIP Truseq protocol. Briefly, ChIP DNA was end-repaired and adaptors were ligated to the ends of the DNA fragments. Adaptor-ligated ChIP DNA fragments with average size of 350 bp were used to construct libraries and single-end sequenced on Illumina HiSeq 4000.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg19

Number of total reads
27301979
Reads aligned (%)
61.1
Duplicates removed (%)
34.8
Number of peaks
12749 (qval < 1E-05)

hg38

Number of total reads
27301979
Reads aligned (%)
63.2
Duplicates removed (%)
33.2
Number of peaks
12752 (qval < 1E-05)

Base call quality data from DBCLS SRA