Fig. 6
Tracking lymphocytes across a matched lymph node and tumor. a t-SNE analysis of patient matched tumor (n = 2493, see Supplementary Fig. 6) and lymph node (see Fig. 5). Cells expressing a shared receptor chain sequence found in both the tumor and lymph node datasets are highlighted and grouped by receptor chain type. The most frequent TCRβ (n = 10), TCRγ (n = 13) and immunoglobulin light chain (n = 20) sequence is highlighted. b Integrated t-SNE analysis of tumor and lymph node datasets (see Methods, n = 8,520). Cells assigned paired TCR chains or paired immunoglobulin heavy chains are highlighted. Seven TCR chain sequences found in both tumor and lymph node datasets (single chains; SC) are shown (across n = 30 cells) and six (every clonotype except SC2) are found in the highlighted box containing the CD8 effector cluster of both lymph node and tumor datasets. c Heat-map of differentially expressed genes (n = 1,328; P < 0.01, Wilcoxon signed-rank test) within the CD8 effector cluster highlighted in b. 50 ‘non-shared cells’ were randomly chosen for visualisation purposes. d, e Dotplot illustrating the top 65 genes differentially expressed between d all shared clonotypes (SC) and non-shared clonotypes (No SC) or e the top three most frequent shared clonotypes (SC7, SC6, and SC3) and non-shared clonotypes. LN lymph node, TU tumor, SC shared clonotype
