Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRD4

Cell type

Cell type Class
Digestive tract
Cell type
Gastrointestinal Stromal Tumors
MeSH Description
All tumors in the GASTROINTESTINAL TRACT arising from mesenchymal cells (MESODERM) except those of smooth muscle cells (LEIOMYOMA) or Schwann cells (SCHWANNOMA).

Attributes by original data submitter

Sample

source_name
KIT-dependent GIST cell line
chip antibody
BRD4, Bethyl Laboratories A301-985A100
treatment
DMSO for 24 hours.

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 with antibody. Libraries for single-end 75 bp sequencing on an Illumina NextSeq 500 were prepared with a ThruPLEX DNA-seq Kit (Rubicon).

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
48195323
Reads aligned (%)
92.5
Duplicates removed (%)
5.4
Number of peaks
940 (qval < 1E-05)

hg38

Number of total reads
48195323
Reads aligned (%)
94.1
Duplicates removed (%)
4.1
Number of peaks
1265 (qval < 1E-05)

Base call quality data from DBCLS SRA