Sample preparation for scRNA-seq, scTCR-seq and CITE-seq

Female NOD mice aged 13–20 weeks were used. Samples were prepared as described above for RNA-seq, except before pooling samples were incubated with hashtags (Biolegend Total-Seq C0301–10, cat. no. 155861) to e,nable multiplexing. Samples were stained with NRP-V7 tetramer, Live/dead Zombie dye and antibodies against CD8α and CD45.1; in addition, Biolegend feature barcoding antibodies against CD44, CD62L, CD127, CD73, PD1, CD38 and CD39 were added for CITE-seq analysis. 2,000–16,000 cells were sorted into PBS + 0.04% BSA, immediately analysed for viability and processed.