ATAC seq of TIM3- Prdm1-YFP- cells 22 dpi LCMV-c13
Prdm1-YFP reporter mice were infected with LCMV-c13, and PD1+TIM3-Prdm1YFP- CD8+ T cells were sorted on 22 days post-infection for ATAC-sequencing. 10,000 to 50,000 freshly sorted cells from LCMV-c13-infected mice on 22 dpi were washed twice in cold PBS and prepared for tagmentation using the Illumina Tagment DNA TDE1 Enzyme and Buffer Small Kit. Libraries were indexed using a custom-synthesized set of oligonucleotides, amplified, and purified using the Zymo DNA Clean and Concentrator 5 Kit prior to next generation sequencing. Reads were mapped to the mm9 genome using the package Bowtie2, and HOMER 68 was used to find peaks and generate bedGraphs of the data.