Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRD4

Cell type

Cell type Class
Blood
Cell type
CAL-1
NA
NA

Attributes by original data submitter

Sample

source_name
Cal-1 DMSO BRD4
cell line
Cal-1
cell type
BPDCN (blastic plasmacytoid dendritic cell neoplasm) cells
disease state
BPDCN (blastic plasmacytoid dendritic cell neoplasm)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
BRD4 Antibody Extraction Other: For “Super-enhancer” ChIP-Seq, 1x10(8) exponentially growing cells were collected by centrifugation, resuspended in room temperature RPMI without FBS ( 2x10(6) cells/ml) and cross-linked with 1% formaldehyde for 5 min at RT. Cross-linking was quenched by addition of 125 mM Glycine for 5 min at RT. Cross-linked cells were first washed with ice-cold PBS and then resuspended in ice-cold RIPA buffer (10mM Tris-HCl pH8, 140 mM NaCl, 1mM EDTA pH 8, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS and 0.1% Sodium Deoxycholate) to a final concentration of 5x10(6) cell/ml. DNA was sheared with a Misonix XL sonicator, by performing 12 x 45'' sonication cycles at power setting of 5. For the immune precipitation reaction, 2.0x10(7) chromatin cell equivalents were incubated overnight with 10 ug of BRD4 antibody (Bethyl, Cat No. A301-985A). The following day, chromatin/antibody complexes were incubated with 50 ul of Protein G magnetic beads (Invitrogen) for 4 h at 4C. Protein G bound complexes were washed 4 times with RIPA Buffer, once with LiCl Buffer (10 mM Tris-HCl pH8, 250 mM LiCl, 0.5% NP40, 0.5% Sodium Deoxycholate, 1 mM EDTA), once with TE pH 8.0 and finally resuspended in 100 ul TE pH8 containing RNAse A (0.2 ug/ul). Reverse cross-link was performed overnight at 65C, followed by treatment with 20 ug Proteinase K (Invitrogen) for 2 h at 50C. Final DNA purification was performed with QIAquick PCR Purification columns (QIAGEN). ChIP DNA was used to generate ChIP-Seq libraries with the NEXTflexTM Illumina ChIP- Seq Library Prep Kit (Bio Scientific), according to manufacturer's instructions.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
42033242
Reads aligned (%)
70.1
Duplicates removed (%)
26.8
Number of peaks
1636 (qval < 1E-05)

hg38

Number of total reads
42033242
Reads aligned (%)
73.0
Duplicates removed (%)
24.5
Number of peaks
2303 (qval < 1E-05)

Base call quality data from DBCLS SRA