Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRD4

Cell type

Cell type Class
Digestive tract
Cell type
NCI-N87
Primary Tissue
Stomach
Site of Extraction
Liver
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
Gastric Cancer
cell line
N87
chip antibody
Brd4
antibody manufacturer
Bethyl
antibody catalog number
A301-985A100
young_id
20160513_4706
tissue
Stomach
drug
Lapatinib / THZ1
concentration
100nM / 25 nM
cell number
50 million
treatment duration
48h

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified. Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
27644726
Reads aligned (%)
82.7
Duplicates removed (%)
13.4
Number of peaks
19527 (qval < 1E-05)

hg38

Number of total reads
27644726
Reads aligned (%)
83.9
Duplicates removed (%)
12.6
Number of peaks
19602 (qval < 1E-05)

Base call quality data from DBCLS SRA