Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRD2

Cell type

Cell type Class
Lung
Cell type
NCI-H1299
Primary Tissue
Lung
Tissue Diagnosis
Carcinoma Non-Small Cell

Attributes by original data submitter

Sample

source_name
H23_rabbit polyclonal
cell line
H23
cell type
Non-small lung cancer cell
antibody
BRD2
antibody type
rabbit polyclonal

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cross-linked with 1% formaldehyde for 10 min at RT. The crosslink reaction was stopped by addition of Glycin at the final concentration of 0.2M. H23 Chromatin extract was prepared as follows: the cell pellets were dissolved and incubated in the ice-cold 0.1% SDS lysis buffer (50 mM Hepes KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Sodium Deoxycholate, 0.1% SDS, protease inhibitors) for 10 min on a rotation at 4°C. Following centrifugation, the cells were incubated in the ice-cold second lysis buffer (10 mM Tris-CL pH 8.0, 200 mM NaCl, 1 mM EDTA pH. 8.0, 0.5 mM EGTA pH 8.0, protease inhibitors) as described above. The cells were then dissolved in 0.5% SDS sonication buffer (3.106 cells per 135mg sonication buffer), directed to chromatin fragmentation by Covaris for 10 min ChIP-seq library for sequencing was prepared as the manufacture's protocol: Mondrian™ SP+ Library Preparation (NuGen)

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
32565786
Reads aligned (%)
92.3
Duplicates removed (%)
7.4
Number of peaks
1555 (qval < 1E-05)

hg38

Number of total reads
32565786
Reads aligned (%)
93.0
Duplicates removed (%)
6.8
Number of peaks
1558 (qval < 1E-05)

Base call quality data from DBCLS SRA