Bulk RNA-sequencing of IL-21-tRFP+ CD44+ Th1, Tfh, and memory-like CD4+ T cell subsets 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 IL-21+CD4+ T cells during LCMV clone 13 infection. IL-21-tRFP+ CD44+ CXCR6+ (Th1), CXCR5+ (Tfh), and CXCR6-CXCR5- (memory-like) CD4+ T cells were FACS-sorted from LCMV Cl13-infected IL-21-tRFP 10Bit reporter mice on day 14 p.i. ( 5,000 cells per subset from 3 replicate (independent) donor mice were used to prepare RNA-seq libraries, which were prepared using SMART-seq technology (Picelli et al., 2014) and sequenced on an Illumina NextSeq.