S1 File -

S1 Table. Sample metadata for individual mice. S2 Table. CD3+ + T cell recovery and sequence yield from 10X single-cell library. S3 Table. Expression of marker genes across T cell clusters. S4 Table. Results of find all markers reported with average Log Fold Change, percent expression of cells, Gene name and both identified and simplified cluster name. S5 Table. Results of find markers show differential expression of genes in Naïve populations of DN T cells compared to CD4 T cells. S6 Table. Results of find markers show differential expression of genes in IL7r negative DN T cells compared to IL7r- CD4 T cells. S7 Table. Results of find markers show differential expression of genes in a mixed DN and CD4 effector T cell population compared to IL7 positive CD4 Teff and effector Tregs. S8 Table. Results of find markers show differential expression of genes in a mixed DN and CD4 effector T cell population compared to IL7 positive DN effector T cells. S9 Table. Results of find markers show differential expression of genes in IL7r negative DN T cells compared to Il7r+ + DN T cells. S10 Table. Results of find markers show differential expression of genes in Gzma positive CD8 T cells compared to Gzma negative CD8 T cells. S11 Table. Table showing GO enrichment of differentially expressed genes between populations of mixed DN and CD4 effector T cells and CD4 effector Tcells and Tregs. S12 Table. Table showing GO enrichment of differentially expressed genes between populations of Gzma positive CD8 T cells and Gzma negative CD8 T cells. S13 Table. Frequency of T cell clones separated by cluster appearance. Clusters refer to simple classification. Rows listed by specific TCRab clone CDR3 sequence. S14 Table. Differential expression of genes in clones specific to each clustered group. Fold change and Pct 1 refer to the group in the group column and pct 2 represents the proportion of expressing cells in all clones from other groups. S15 Table. Infiltrating (matching) TCR clones counted by sample type. Alpha beta TCR sequence for CDR3 region is reported. S16 Table. Differential expression of genes between islets-matching cells in blood and blood-matching cells in islets. The positive fold change shows enriched blood. S17 Table. Differential expression of genes between islets-matching and non-matching cells in blood. Positive Log fold-change shows enriched in matching. S18 Table. Differential expression of genes between blood-matching and non-matching cells in islets. Positive log fold-change. S19 Table. Exact matches between TCR-seq predicted CDR3 regions and experimentally validated TCR-pMHC interactions in the VDJdb.
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