Supplementary Figure 3: Comparison of single-cell transcriptomes between progenitor-like CD8+ T cells and memory precursor cells.
From: Single-cell RNA-seq reveals TOX as a key regulator of CD8+ T cell persistence in chronic infection
(a) Enrichment (log2 P-values) of progenitor-like gene signature in each cell (n = 16,042 cells) from the clusters defined in Fig. 2c was determined by one-sided Fisher’s exact test, illustrated in violin plots. The violin represents the probability density at each value; each dot represents one cell. (b) Enrichment (log2 P-values) of memory precursor gene signature in each cell (n = 16,042 cells) was determined by one-sided Fisher’s exact test. Left panel: t-SNE plots with P-values color-coded. Middle panel: Enrichment (log2 P-values) in each cell from the clusters defined in Fig. 2c, illustrated in violin plots. The violin represents the probability density at each value; each dot represents one cell. Right panel: Percentages of cells in each cluster with P-values above (red) or below (turquoise) 0.05. (c) Relationships among gene modules defined in Fig. 3e. The heatmap depicts adjacencies among module eigengenes. At the top of the heatmap is a hierarchical clustering of module eigengenes. Color-codes on the left side and the bottom of the heatmap represent the modules defined in Fig. 3e. Asterisks indicate modules 29 (saddlebrown) and 12 (tan). (d) Enrichment (log2 P-values) of genes in module 29 (saddlebrown) in each cell (n = 16,042 cells) from the clusters defined in Fig. 2c was determined by one-sided Fisher’s exact test, illustrated in violin plots. The violin represents the probability density at each value; each dot represents one cell. (e) Enrichment (log2 P-values) of genes in module 12 (tan) in each cell (n = 16,042 cells) from the clusters defined in Fig. 2c was determined by one-sided Fisher’s exact test, illustrated in violin plots. The violin represents the probability density at each value; each dot represents one cell. (f) Gating strategy used to sort progenitor-like (Tim3loBlimp-1lo) and terminally exhausted (Tim3hiBlimp-1hi) P14 cells on day 7 after LCMV clone 13 infection. (g) Gating strategy used to sort memory precursor (KLRG1lo) and short-lived effector (KLRG1hi) P14 cells on day 7 after LCMV Armstrong infection. (h) RNA-seq analysis of Tox mRNA in D4.5 Arm (n = 3 biological replicates), D4.5 Cl13 (n = 3 biological replicates), D7 Arm memory precursor (n = 3 biological replicates), D7 Arm short-lived effector (n = 3 biological replicates), D7 Cl13 progenitor-like (n = 2 biological replicates), and D7 Cl13 terminally exhausted (n = 2 biological replicates) P14 cells. (i) Left panel: Representative FACS plots of TOX and TCF1 expression in P14 cells from mice seven days after LCMV clone 13 infection. Right panel: FACS analysis of TOX expression in progenitor-like (TCF1hi, red), terminally exhausted (TCF1lo, green), memory precursor (KLRG1lo, orange), and short-lived effector (KLRG1hi, blue) P14 cells on day 7 post-infection. (j) TOX protein levels in D4.5 Arm (n = 5 mice), D4.5 Cl13 (n = 5 mice), D7 Arm memory precursor (n = 4 mice), D7 Arm short-lived effector (n = 4 mice), D7 Cl13 progenitor-like (n = 5 mice), and D7 Cl13 terminally exhausted (n = 5 mice) P14 cells, as determined by TOX mean fluorescent intensity (MFI) divided by isotype control MFI. In h and j, statistical significance was determined by two-sided Student’s t-test; centers and error bars represent the mean and SD. Data in f, g, i are representative of two independent experiments. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001.