TCR sequence analysis
TCR sequencing was used to count clonotypes detected in more than two cells per sample. A cell’s clonotype was defined as the combined alpha and beta chain CDR3 nucleotide sequences for that cell. As it was not possible to deduce beta and alpha chain pairing for partitions with multiple beta chains, these partitions were treated as a single clone. To assess clonal enrichment, the proportion of cells having the same clone was compared between sample types for each clone. To determine whether clonal expansion of CD8 T cells may be driven by common antigen(s), we used the GLIP