library_construction_protocol: To maximize cell viability, cell isolation, staining, enrichment, and FACS sorting was performed over a 12hr period directly before sequencing, and cells were kept cold or on ice whenever possible. Cells were isolated from the spleens of infected mice in two “batches”: the first consisting of 4 C4WT and 5 C4ΔTEC mice, and the second consisting of 5 C4WT and 5 C4ΔTEC mice. For each batch, individual spleens were first enriched for CD4+ T cells using CD4+ T cell negative selection kit (Miltenyi Biotec) following the manufacturers protocol. Individual samples were subsequently stained with C4/I-Ab tetramers as described above. Following tetramer staining, individual samples were incubated with anti-PE and anti-APC microbeads (Miltenyi Biotec) for 15 min on ice (100ul each antibody cocktail / ml), washed, and enriched over an autoMACS magnetic column. Following enrichment, the individual bound fractions were stained with separate surface marker antibody master mixes as described above in minimal staining buffer. Each surface stain master mix contained uniform surface markers common to all mixes, but contained 1 of 10 TotalseqTM-C030X hashing antibodies (Biolegend) used to identify cells derived from each mouse. Following surface staining, all samples within a batch were pooled and C4/I-Ab tetramer+ cells were sorted by FACS using a BD FACSAria Fusion 5-18 cytometer. Ultimately, two sorted samples (one per batch) containing C4/I-Ab tetramer+ cells from pooled and hashtagged mice resulted after isolation. These samples were resuspended in 45ul of sequencing buffer (0.04% BSA in PBS), and 40ul of each sample was loaded into one of two lanes of a sequencing chip and then subjected to Drop-seq (10X Genomics) to coencapsulate individual cells in reverse emulsion droplets in oil together with one uniquely barcoded mRNA-capture bead. Libraries were derived from single cells, then subjected to next-generation sequencing. 5' cDNA libraries were constructed for individual cells using a 10X Genomica Chromium Controller (gene expression, VDJ, and feature barcode). The two samples containing constructed libaries were sequenced across two lanes of a SP-100 flowcell. scRNA-seq, plus feature barcoding (sample hashing) and VDJ sequencing of the TCR