Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRD4

Cell type

Cell type Class
Pluripotent stem cell
Cell type
hESC H9
NA
NA

Attributes by original data submitter

Sample

source_name
human H9 cell lines
cell line
H9
chip antibody
BRD4 Bethyl (A301-985A)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
RNeasy kit (Qiagen) for RNA-seq; 1% formaldheyde crosslinked chromatin for ChIP-seq Poly-A+ selection (magnetic oligodT-containing beads) was used for RNA-seq library preparation. cDNA preparation and library construction was performed as described by the manufacturer (Illumina, CA, USA) . RNA libraries were sequenced using Genome Analyzer IIx System 50bp single-read method. Llibraries for ChIP-sequencing were generated as described in (Ntziachristos et al., 2012), including end-repair, A-tailing, adapter (Illumina Truseq system) ligation and PCR amplification of the libraries. We performed cluster amplification and 50-nucleotide single-read sequencing using the Illumina HiSeq 2000, following manufacturer’s protocols. Library construction was performed as described by the manufacturer (Illumina, CA, USA)

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
77716191
Reads aligned (%)
79.9
Duplicates removed (%)
14.2
Number of peaks
2968 (qval < 1E-05)

hg38

Number of total reads
77716191
Reads aligned (%)
81.9
Duplicates removed (%)
12.9
Number of peaks
3910 (qval < 1E-05)

Base call quality data from DBCLS SRA