Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RELA

Cell type

Cell type Class
Blood
Cell type
CD4+ T cells
NA
NA

Attributes by original data submitter

Sample

source_name
primary blood
individual
donor 206
cell type
CD4pos_T
lineage
CD4
chip antibody
p65 (ab16502, Abcam, Cambridge, UK)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The cells were harvested, fixed with 1% formaldehyde (Thermo Fisher Scientific, MA, USA) for 10 min, washed twice with cold PBS and frozen at -80C. The chromatin was sonicated to generate fragments of 200-500bp in length, followed by incubation with rabbit polyclonal p50 (#3035, Cell Signaling, Danvers, MA, USA) and p65 (ab16502, Abcam, Cambridge, UK) antibodies overnight. Precipitated chromatin was washed, de-crosslinked and DNA extraction was carried out using phenol-chloroform (Sigma). ChIP DNA was prepared for high throughput sequencing using Accel-NGS 2S Plus DNA library kit (Swift Biosciences) as per manufacturer's protocol. DNA libraries were sequenced on an Illumina Hiseq4000 with a paired-end 75bp run (CAT, UCSF).

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg19

Number of total reads
121643210
Reads aligned (%)
189.7
Duplicates removed (%)
2.6
Number of peaks
949 (qval < 1E-05)

hg38

Number of total reads
121643210
Reads aligned (%)
192.4
Duplicates removed (%)
2.3
Number of peaks
2568 (qval < 1E-05)

Base call quality data from DBCLS SRA