Extended Data Fig. 10: Autoimmune NOD pLN IGRP-specific CD8 T cells in T1D are distinct from CD8 T cells generated during acute and chronic infections.

scRNA-seq datasets from pLN NRP-V7+ CD8 T cells (Fig. 4) were compared to scRNA-seq datasets of memory precursor effector cells (MPEC) and central memory CD8 T cells (T_CM) generated during acute LCMV infection (day 7 and day 129 respectively), as well as to progenitor exhausted CD8 T cells (T_PEX) from day 7 during chronic (clone 13) LCMV infection. a, Principal component analysis (PCA) of pseudo-bulk RNA-seq samples representing TCF1^hiCD62L^hi, TCF1^hiCD62L^lo (intermediate), and TCF1^loCD62L^lo NOD pLN NRP-V7+ CD8 T cells from 3 technical replicates from Gearty et al (Fig. 4; T1D), T_CM cells from Schauder et al (PNAS 2021; GSE130130; acute LCMV, day 129) and MPEC as well as T_PEX as defined by Yao et al (Nat. Immunology, 2019; GSE119943; acute and chronic LCMV, day 7). The bar charts to the left and on the bottom of the PCA plot represent the genes that are most strongly (anti)correlated with a given principal component (PC). b, Dendrogram representing the results of hierarchical clustering based on the pseudo-bulk RNA-seq samples. c, Heatmap displaying row-normalized expression values of individual cells for genes identified as marker genes when comparing the single cells of the different populations (TCF1^hiCD62L^hi, intermediate, and TCF1^lo, MPEC, T_PEX, T_CM) to each other. d, Top, GO terms (biological processes) that are enriched based on genes that are specifically overexpressed in the different populations compared to all others. Bottom, the network-like representations display the genes (small circles) that belong to the respective GO terms (large circles), highlighting genes shared among individual GO terms and upregulated in indicated cell populations.