Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Blood
Cell type
CD8+ T cells
NA
NA

Attributes by original data submitter

Sample

source_name
CD44low naïve CD8+ T cells
tissue
lymph nodes
cell type
CD44low naive CD8+ T cells
age
10 weeks
genotype
CD11cCre x Itgavwt/wt

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Approximately 30,000 CD44low naïve CD8+ T cells per replicate from LNs were sorted by FACS into PBS containing 10% FBS in DNA loBind Eppendorf tubes. Pelleted cells were lysed in 50 μl of reaction mix (25 μl of 2 x TD, 2.5 μl of Tn5 enzyme, 0.25 μl of 2% digitonin, 22.25 μl of nuclease-free water). The mix was incubated at 37°C for 30 minutes with agitation at 300 rpm. DNA was purified using a QIAgen MinElute Reaction Cleanup kit and Nextera sequencing primers ligated using PCR amplification. Agencourt AMPure XP bead cleanup (Beckman Coulter/Agencourt) was used post-PCR and library quality was verified using a Tapestation machine.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
82637164
Reads aligned (%)
95.5
Duplicates removed (%)
50.9
Number of peaks
47217 (qval < 1E-05)

mm9

Number of total reads
82637164
Reads aligned (%)
95.4
Duplicates removed (%)
51.0
Number of peaks
47187 (qval < 1E-05)

Base call quality data from DBCLS SRA