Primers were designed for human TCR constant genes using Primer341,42, and appended to a tailing sequence to produce the reverse primers N7tail-TRAC-2 and N7tail-TRBC-2 (Supplementary Table 4). Forward primers (DS_N5xx_5TSO) contained a sequence complementary to the Template Switch Oligo and an index sequence (I5). TCR sequences were amplified using KAPA HiFi HotStart Readymix, 0.3 μM of each primer and 1 μl pre-amplified cDNA library (see RNA Sequencing) in 10 μl volume with 16 cycles of 95 °C for 20 s, 62 °C for 20 s and 72 °C for 30 s, followed by purification with 1.5× volume of HighPrep PCR reagent. The TCR libraries were dual indexed using the same forward primer as in the previous step, and one of Nextera N7xx primers. PCR was done using KAPA HiFi HotStart Readymix, 0.3 μM of each primer and 3 μl template in 10 μl volume with 10 cycles of 95 °C for 20 s, 62 °C for 20 seconds and 72 °C for 30 s. The libraries were pooled according to concentration and purified first with 1× and then with 1.5× volume of HighPrep PCR reagent. The quality of the libraries was assessed with a LabChip GXII Touch HT electrophoresis instrument and quantitative PCR. Libraries were sequenced with a MiSeq Reagent Kit v3 (600-cycle) using the 300 + 300 bp paired-end protocol, a custom read 1 primer (DS-CustomRead1_5TSO) and 10% PhiX on an Illumina Miseq instrument at Department of Virology, University of Helsinki, Finland.

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