Panel A shows a vertical bar graph with the number of differentially expressed genes on the y-axis and CD4 clusters on the x-axis. Panel B presents a dot plot with gene ratio on the x-axis and -log10(FDR) on the y-axis, highlighting pathway analysis of genes upregulated in CD4-1 (Naive) cells. Panel C is a stacked bar graph showing the cluster distribution of the top 10 expanded islet CD4 T cell clones in WT and KO mice, with different colors representing various CD4 clusters. Panel D features a line graph with percent clonotype overlap on the y-axis and CD4 T cell clones with more than n cells on the x-axis, comparing WT and KO mice. Panel E includes two bar graphs showing the cell distribution in Treg or non-Treg clusters for cells within overlapping clones with more than 3 cells and more than 5 cells, respectively. Panel F displays bar plots of the proportions of islet-infiltrating NOD and NOD.Tnfrsf9 CD8 T cells projected onto the clusters. Panel G shows violin plots of the expression levels of Sat1 in WT and KO CD4 T cell clusters.
Differential gene expression and clonotype analysis of islet-infiltrating T cells, related to Fig. 3 and 4. (A) Number of differentially expressed genes between Cre+-Tnfrsf9+/+ or Cre+-Tnfrsf9fl/fl mice in each islet CD4 T cell cluster. (B) Pathway analysis of genes upregulated in Cre+-Tnfrsf9fl/fl versus Cre+-Tnfrsf9+/+ cluster CD4-1 (naïve) cells. (C) Cluster distribution of the top 10 expanded islet CD4 T cell clones in Cre+-Tnfrsf9+/+ (WT) and Cre+-Tnfrsf9fl/fl (KO) mice. (D) Percentage of clonotype overlap between Foxp3+ Tregs and non-Tregs in Cre+-Tnfrsf9+/+ (WT) and Cre+-Tnfrsf9fl/fl (KO) mice. The analysis was done for all clones or restricted to clones with more than one, three, or five cells. (E) Cell distribution in Treg or non-Treg clusters for cells within overlapping clones with more than three cells (left) or with more than five cells (right). Statistical significance was determined by the chi-square test. (F) Bar plots show the proportions of islet-infiltrating NOD and NOD.Tnfrsf9−/− CD8 T cells projected onto the clusters defined in Fig. 4 A. (G) Expression levels of Sat1 in Cre+-Tnfrsf9+/+ (WT) and Cre+-Tnfrsf9fl/fl (KO) CD4 T cell clusters shown in Fig. 3 A.