Single-cell RNA-sequencing of IL-21-tRFP+ GP66+ splenic CD4+ T cells on days 7 and 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+ GP66-specific CD4+ T cells were FACS-sorted from LCMV Cl13-infected IL-21-tRFP 10Bit reporter mice on days 7 and 14 p.i. (with 2 donor mice per time point) and were loaded on the Chromium Controller (10x Genomics). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3′ v2 Reagent Kit (10x Genomics) according to manufacturer’s protocol