Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRD4

Cell type

Cell type Class
Blood
Cell type
KOPT-K1
NA
NA

Attributes by original data submitter

Sample

source_name
KOPT-K1 persister cells
cell line
KOPT-K1
cell type
T-cell acute lymphoblastic leukemia
treated with
1uM gamma Secretase inhibitor over 7wks
chip antibody
BRD4
chip antibody vendor
Bethyl

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin from formaldehyde-fixed cells (1 - 5 x 106 per histone mark, 107 for BRD4) was fragmented to a size range of 200 - 700 bases with a Branson 250 Sonifier. Solubilized chromatin was isolated. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Cat #: FC-102-1001). Briefly, DNA was end-repaired using Epicentre’s End-it™ DNA-Repair Kit (Cat #: ER81050). The blunt, phosphorylated ends were treated with Klenow fragment (3 to 5 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of custom adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were isolated using Angencourt® Ampure® XP. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq 2500 following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
24154925
Reads aligned (%)
69.6
Duplicates removed (%)
8.2
Number of peaks
12719 (qval < 1E-05)

hg38

Number of total reads
24154925
Reads aligned (%)
70.7
Duplicates removed (%)
7.4
Number of peaks
12735 (qval < 1E-05)

Base call quality data from DBCLS SRA