TCR sequences for CD8 T cells
cDNA from single cells was obtained using a modified version of the SmartSeq2 protocol. Briefly, single cells were sorted into plates containing lysis buffer and cDNA was generated by template switch reverse transcription using SMARTScribe Reverve Transcriptase (Clontech, catalog: 639538), a template-switch oligo and primers kit designed for the constant regions of Trac and Trbc genes. TCR amplification was achieved by performing two rounds of nested PCR using Phusion High-Fidelity PCR Master Mix (New England Biolabs, catalog: M0531S). During the first PCR priming, indexes were included to identify each cell. A final PCR was performed to add the Illumina adaptors. TCR libraries were sequenced on Illumina MiSeq using MiSeq Reagent Kit V2 300-cycle (Illumina).