Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRD2

Cell type

Cell type Class
Blood
Cell type
Acute myeloid leukemia
NA
NA

Attributes by original data submitter

Sample

source_name
AML cells
cell type
Biphenotypic B Myelomonocytic Leukemia
chip antibody
BRD2 (Bethyl Labs #A302-583A)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
K562 and MV4;11 cells were treated with either DMSO or increasing concentration of I-BET151 for 6 hours at 37C. After treatment, cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and cross-linking was stopped by the addition of 0.125 M glycine. Cells were then lysed using the SimpleChIP® Enzymatic Chromatin IP Kit (CST #9004) and DNA was digested to mostly mononucleosomes as recommended by the manufacturer Library preparation of immunoprecipitated DNA was done using the NEBNext® ChIPSeq Library Prep Master Mix Set for Illumina® (NEB) and samples were sequenced in a 50bp single end run on the Illumina HiSeq-2000 K562 and MV4;11 cells were treated with either DMSO or increasing concentration of I-BET151 for 6 hours at 37C. After treatment, cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and cross-linking was stopped by the addition of 0.125 M glycine. Cells were then lysed using the SimpleChIP® Enzymatic Chromatin IP Kit (CST #9004) and DNA was digested to mostly mononucleosomes as recommended by the manufacturer Library preparation of immunoprecipitated DNA was done using the NEBNext® ChIPSeq Library Prep Master Mix Set for Illumina® (NEB) and samples were sequenced in a 50bp single end run on the Illumina HiSeq-2000

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
41212002
Reads aligned (%)
43.1
Duplicates removed (%)
56.0
Number of peaks
740 (qval < 1E-05)

hg38

Number of total reads
41212002
Reads aligned (%)
46.1
Duplicates removed (%)
53.4
Number of peaks
728 (qval < 1E-05)

Base call quality data from DBCLS SRA