Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

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

Attributes by original data submitter

Sample

source_name
OT-II, day 3 post immunization
cell type
OT-II CD4+ (Rag1-/-) TCR transgenic cells
condition
Irf4-/-

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
ATAC-seq libraries were constructed using the Nexterra kit (Illumina) and then subjected to 8 rounds of amplification with index-specific primers. The ATAC-seq libraries were quantified by both Bioanalyzer and Qubit measurements and pooled in equimolar ratios. They were sequenced on an Illumina HiSeq 4000 sequencer with paired-end 100bp reads on 6 lanes.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

mm10

Number of total reads
219507508
Reads aligned (%)
66.5
Duplicates removed (%)
58.4
Number of peaks
29447 (qval < 1E-05)

mm9

Number of total reads
219507508
Reads aligned (%)
66.4
Duplicates removed (%)
58.4
Number of peaks
29403 (qval < 1E-05)

Base call quality data from DBCLS SRA