Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRD4

Cell type

Cell type Class
Blood
Cell type
Acute myeloid leukemia
NA
NA

Attributes by original data submitter

Sample

source_name
AML cultured cell line
cell type
leukemia blast cells
chip antibody
BRD4 rabbit monoclonal [ clone BL-149-2H5] (Bethyl Labs) catalog #A700-004
genotype/variation
Control

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
AML cells (10 million) were treated with 1% formaldehyde for 10 minutes with rotation. The crosslinking reaction was quenched with 2.5 M Glycine for 5 minutes. Chromatin lysates were clarified from ultra-sonicated nuclei and histone-DNA complexes or BRD4-containing complexes were isolated with H3K27Ac or BRD4 antibody, respectively. Following ChIP washes, the immunoprecipitated DNA fragments were treated with mutant Tn5 transposase for 10 minutes at 37°C to attach sequencing adapters to the DNA. Tagmented DNA was eluted and formaldehyde-induced crosslinks were reversed. Tagmented, eluted DNA was purified over a column and utilized for library preparation. For ATAC-Seq analysis, isolated nuclei were treated with Tn5 transposase in tagmentation buffer at 37°C for 30 minutes. Tagmented, eluted DNA was purified over a column and utilized for library preparation. Libraries were prepared according to Illumina's instructions accompanying the Nextera DNA Library Prep Kit (Cat. No. FC-121-1030). After adapter ligation, DNA was PCR amplified with Illumina universal primer for 15 cycles (12 cycles for ATAC-Seq) and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were isolated utilizing AMP-XP beads. For ATAC-Seq, fragments larger than 200 bp were isolated utilizing AMP-XP beads. The purified DNA was captured on an Illumina NExt-Seq 500 flow cell for cluster generation. Libraries were sequenced following the manufacturer's protocols.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
29464649
Reads aligned (%)
0.0
Duplicates removed (%)
40.8
Number of peaks
0 (qval < 1E-05)

hg19

Number of total reads
29464649
Reads aligned (%)
0.0
Duplicates removed (%)
40.3
Number of peaks
0 (qval < 1E-05)

Base call quality data from DBCLS SRA