ATAC-sequencing of Th1, Tfh, and memory-like splenic CD4+ T cells on day 14 post LCMV Cl13 infection

CD4+ T cell-derived interleukin 21 (IL-21) sustains CD8+ T cell responses during chronic viral infection, but the helper subset that confers this protection remains unclear. Here, we applied scRNA and ATAC-seq approaches to determine the heterogeneity of CD4+ T cells during LCMV clone 13 infection. ATAC-seq was performed according to a published protocol (Buenrostro, Giresi et al. 2013). 50,000 cells of CXCR6+, CXCR5+ and CXCR6-CXCR5- PD-1hi CD4 T cell subsets (per mouse, with n=3 separate mice) were used for library construction. 37 cycles paired-end sequencing was performed on a Nextseq 550 sequencer and about fifty million reads were generated for each sample.