Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRD4

Cell type

Cell type Class
Blood
Cell type
BCBL1
NA
NA

Attributes by original data submitter

Sample

source_name
TREx-(F3H3)-K-Rta BCBL-1 cells
cell line
TREx-(F3H3)-K-Rta BCBL-1 cells
cell type
human primary effusion lymphoma cells
cell type
KSHV-positive human B cell lymphoma cells
passages
5~10
chip antibody
anti-BRD4 antibody (Bethyl Laboratories)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Following treatment with doxycycline, cells (1 x 10^8) were fixed with 1% formaldehyde, lysed, and chromatin DNA was sonicated to an average size of ~300 bp using a Diagenode Bioruptor. Chromatin immunoprecipitation (ChIP) of BRD4-associated chromatin was performed with anti-BRD4 monoclonal antibody (10 ug). Subsequently, DNA was isolated with the QIAquick PCR Purification Kit (Qiagen) from the BRD4 immunoprecipitates (ChIP DNA) and from input DNA controls. ChIP-enriched and input DNA samples (1 ng) were used to generate indexed, Illumina-compatible libraries with the KAPA LTP Library Preparation Kit (Kapa Biosystems, KK8230) according to manufacturer’s recommendations for end repair and A-tailing, adapter ligation, size selection, and library amplification.

Sequencing Platform

instrument_model
Illumina HiSeq 3000

hg19

Number of total reads
18181591
Reads aligned (%)
55.8
Duplicates removed (%)
36.3
Number of peaks
905 (qval < 1E-05)

hg38

Number of total reads
18181591
Reads aligned (%)
58.2
Duplicates removed (%)
34.4
Number of peaks
585 (qval < 1E-05)

Base call quality data from DBCLS SRA