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
SW 480
cimp status
CIMP (-)
chip antibody
Brd4
cell line
SW 480

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed with 1% formaldehyde for 15 minutes (Brd4 ChIP) or 5 minutes (H3K27ac ChIP). DNA was sonicated to an average length of 200 - 500 bp. IP and Input DNA was reverse crosslinked and purified for library preparation. Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
33468085
Reads aligned (%)
66.1
Duplicates removed (%)
9.5
Number of peaks
3033 (qval < 1E-05)

hg38

Number of total reads
33468085
Reads aligned (%)
67.7
Duplicates removed (%)
8.1
Number of peaks
3089 (qval < 1E-05)

Base call quality data from DBCLS SRA