GSM9862451: NDLN tdTomato+ CD8+ T cells ATAC-seq (replicate 2); Mus musculus; ATAC-seq
Tumors, draining lymph nodes (DLNs), and non-draining lymph nodes (NDLNs) were harvested from tumor-bearing mice. Tumor-infiltrating lymphocytes were isolated by enzymatic digestion with collagenase IV (1 mg/mL), dispase (1 mg/mL), and DNase (5 mg/mL) at 37°C for 30 min, followed by mechanical dissociation and red blood cell lysis. Lymph node samples were processed into single-cell suspensions. CD8^+^ T cell subsets (LAG3^-^tdT^-^, LAG3^+^tdT^+^, LAG3^-^tdT^+^, and CD44^+^tdT^+^ where applicable) were flow sorted prior to 10x Genomics single-cell RNA-seq/CITE-seq/TCR-seq or ATAC-seq library preparation. Nuclei were isolated from fluorescence-activated cell sorted CD8+ T cell subsets. Chromatin accessibility libraries were generated using the Omni-ATAC protocol as previously described. Briefly, nuclei were incubated with Tn5 transposase to simultaneously fragment genomic DNA and insert sequencing adapters. Following transposition, libraries were PCR amplified, purified, quality assessed, and sequenced on an Illumina NovaSeq 6000 platform.