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 naïve cells
cell line
KOPT-K1
cell type
T-cell acute lymphoblastic leukemia
treated with
vehicle (naïve)
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

hg38

Number of total reads
27728442
Reads aligned (%)
85.0
Duplicates removed (%)
6.2
Number of peaks
17240 (qval < 1E-05)

hg19

Number of total reads
27728442
Reads aligned (%)
84.4
Duplicates removed (%)
6.9
Number of peaks
17261 (qval < 1E-05)

Base call quality data from DBCLS SRA