Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRD3

Cell type

Cell type Class
Blood
Cell type
Chronic myeloid leukemia
NA
NA

Attributes by original data submitter

Sample

source_name
CML cells
cell type
Chronic Myelogenous Leukemia
chip antibody
BRD3 (Bethyl Labs #A302-368A)

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
46164167
Reads aligned (%)
52.2
Duplicates removed (%)
45.9
Number of peaks
659 (qval < 1E-05)

hg38

Number of total reads
46164167
Reads aligned (%)
54.9
Duplicates removed (%)
43.7
Number of peaks
687 (qval < 1E-05)

Base call quality data from DBCLS SRA