Bulk TCR sequencing analysis

Alpha and beta TCR repertoire analysis in bulk RNA samples was performed using an adapted rhTCRseq protocol published previously⁴¹. Specifically, 10 ng bulk RNA was used in each RT reaction, and 4 to 8 replicates were done for each sample and excess RT primers were eliminated by exonuclease digestion, and then rhPCR was performed. After the sequencing library was made, it was sequenced using MiSeq 300 cycle Reagent Kit v2 on the Illumina sequencing system according to the manufacturer’s protocol with 248bp read 1, 48bp read 2, 8bp index 1, and 8bp index 2. The sequencing data analysis was done based on the method published previously³⁶ (Source Data Table 8).