design: Cells were sorted for infection based on mCherry expression, and then submitted for analysis using the 10x Genomics Chromium 5 v2 V(D)J kit with a barcode construct-specific primer spiked in prior to droplet encapsulation (see Supplementary Methods for further details). TCR amplicons were prepared and sequenced according to the manufacturers instructions. Following cDNA amplification, mCherry barcodes were enriched via separate PCRs and sequenced on an Illumina MiSeq (150150nt paired end reads).