GSM3897740: ATACseq KO Rep1 Cl13 d8; Mus musculus; ATAC-seq
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
P14 CD8 T cells
tissue
Spleen
cell type
P14 CD8 T cell
genotype
TOX-/-
Sequenced DNA Library
library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
To assess the transcriptional and epigenetic impact of TOX deletion in T cells, 250 WT and 250 TOX-/- naïve CD44LOWCD62LHI P14 cells sorted from peripheral blood of donors, mixed, and co-transferred into WT mice. Recipients were subsequently infected with LCMV Cl-13 and splenocytes were harvested 8 days following infection. Ten spleens were pooled for each of the 3 replicates prior to processing, CD8+ T cell enrichment (using EasySep CD8+ T cell negative selection kit, Stem Cell Technologies), and staining of single cell suspensions. 1x105 WT and TOX-/- P14 cells were sorted to a purity of >98% for each replicate. 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.