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
CD8 T cells
tissue
Spleen
cell type
CD8 T cells
transduction
control retrovirus

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
In ectopic and enforced expression experiments, in vitro differentiated CD8+ T cells transduced with TOX+GFP or control GFP only (>2 biological replicates each) were sorted on GFP expression 6 days following initial activation to a purity of >98%. ATAC libraries were generated as described previously with minor changes. Briefly, nuclei from 50,000 cells were isolated using a lysis solution composed of 10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, and 0.1% IGEPAL CA-630. Immediately following cell lysis, nuclei were pelleted in low-bind 1.5ml tubes (Eppendorf) and resuspended in TD Buffer with Tn5 transposase (Illumina). Transposition reaction was performed at 37 degrees Celsius for 45 minutes. DNA fragments were purified from enzyme solution using MinElute Enzyme Reaction Cleanup Kit (Qiagen). Libraries were barcoded (Nextera Index Kit, Illumina) and amplified with NEBNext High Fidelity PCR Mix (New England Biolabs). Library quality was assessed using a TapeStation instrument.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
21400937
Reads aligned (%)
95.6
Duplicates removed (%)
8.1
Number of peaks
27052 (qval < 1E-05)

mm9

Number of total reads
21400937
Reads aligned (%)
95.5
Duplicates removed (%)
8.2
Number of peaks
27158 (qval < 1E-05)

Base call quality data from DBCLS SRA