Extended Data Fig. 3: RNA-seq and ATAC-seq analyses of sorted CD8 T cell subsets on days 5 and >45 after chronic infection.
From: An early precursor CD8+ T cell that adapts to acute or chronic viral infection
a, Gating strategy for sorting of day 5 and >45 PD-1+ stem-like (CD73+ Tim-3−) and effector/terminally differentiated (CD73−Tim-3+) CD8+ T cells for RNA-seq. b, 2,500 P14 cells were transferred into congenically distinct naïve mice prior to intravenous infection with 2 × 106 LCMV clone 13. Gating strategy for sorting of day 5 and >45 LCMV GP33-specific P14 stem-like (CD73+ Tim-3−) and effector/terminally differentiated (CD73−Tim-3+) CD8+ T cells for ATAC-seq. Naïve CD8+ T cells (CD44−PD-1−) from uninfected mice were used as a control in each analysis. c,d, Genome plots showing chromatin accessibility (ATAC-seq, left) and normalized counts (RNA-seq, right) for Slamf6 (c) and Xcl1 (d) in naïve CD8 T cells from uninfected mice and day 5 vs. >day 45 stem-like and effector CD8 T cells from chronic infection. The location of the transcription start site is indicated by an arrow and a bar depicts the location of the gene body. Bar graphs for normalized counts are based on technical replicates with n = 3 per group. e, Density scatter plot comparing the log2 fold-change in ATAC-seq (x-axis) to the corresponding RNA-seq (y-axis) data for the indicated comparison. Each dot represents accessibility of a single peak and the matching gene expression of the nearest gene. Blue lines indicate data density. Linear correlation trend lines are plotted, and Pearson correlation coefficient and significance of trend are indicated. Coloured dots correspond to the data for Pdcd1, Xcl1, Tcf7, and Gzmb as indicated. f, Heatmap of the Pearson correlation coefficient between ATAC-seq and RNA-seq data for each pairwise comparison between the sample groups. RNA- and ATAC-seq results are each from 1 independent experiment.
