Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRD4

Cell type

Cell type Class
Pancreas
Cell type
L3.6
NA
NA

Attributes by original data submitter

Sample

source_name
L3.6_BRD4
cell type
L3.6 pancreatic cancer cells
chip antibody
N-terminal BRD4 antibody, Wu et al., 2006

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The ChIP was performed with 20 min crosslinking in 1 % formaldehyde in PBS. Following chromatin shearing , 1-2µg antibody was used for immunoprecipitation overnight. The immunocomplexes were incubated 2 additional hours with protein A sepharose beads and subjected to washes. After reversing the cross-linking, the DNA was isolated by standart phenol-chloroform-isoamyl extraction procedure. ChIP-Seq libraries were prepared with MicroPlex Library Preparation Kit following the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
14862188
Reads aligned (%)
22.8
Duplicates removed (%)
75.3
Number of peaks
6140 (qval < 1E-05)

hg38

Number of total reads
14862188
Reads aligned (%)
24.3
Duplicates removed (%)
73.9
Number of peaks
6018 (qval < 1E-05)

Base call quality data from DBCLS SRA