Supplementary Figure 2: scRNA-seq analysis of virus-specific CD8+ T cells from acute and chronic LCMV infections.
From: Single-cell RNA-seq reveals TOX as a key regulator of CD8+ T cell persistence in chronic infection
Experimental setup has been described in Fig. 2. (a) t-SNE plots of scRNA-seq data merged from two independent batches of D4.5 Arm, D4.5 Cl13, D7 Arm and D7 Cl13 P14 CD8+ T cells. Batch#1: n = 19,497 cells; and batch#2: n = 16,042 cells. (b) Correlation of gene expression (27,998 genes) between scRNA-seq replicates (upper panel) and between scRNA-seq data and bulk RNA-seq data (lower panel) with Pearson’s R indicated. Numbers on the axes are in TPM+1. (c) Violin plots showing the numbers of unique mRNA molecules (left panel) and detected genes (right panel) in cells from each sample (D4.5 Arm: 4,651 cells; D4.5 Cl13: 4,116 cells; D7 Arm: 4,678 cells; D7 Cl13: 2,597 cells). The violin represents the probability density at each value; each dot represents one cell. (d) Enriched pathways of top expressed genes in P14 cells (n = 2,597 cells) from day 7 after LCMV clone 13 infection, determined by Metascape. (e) Enriched pathways of top expressed genes in P14 cells (n = 4,678 cells) from day 7 after LCMV Armstrong infection, determined by Metascape. (f) Violin plots showing the expression of genes in cells (n = 16,042 cells) from cluster 0 through cluster 10, as defined in Fig. 2c. The violin represents the probability density at each value; each dot represents one cell.
