Fig. 5
RAGE-Seq on a human lymph node. a t-SNE analysis of 6027 lymph node cells generated from short-read sequencing data. Number of cells: B-cell naive, 853; B-cell memory, 738; CD4 effector memory (EM), 1069; CD4 central memory (CM) 1, 1069; CD4 CM 2, 226; CD4 T follicular helper cell (TfH), 142; CD4 T regulatory cell (Treg), 740; CD8 CM, 487; CD8 effector (EFF), 405; Plasmablast, 28; Innate-like, 144; Doublets, 86; Epithelial, 13. b Assignment of productive TCR and BCR chains to each population identified in a. NR, no receptor. c Characterization of full-length IGH mRNA sequences assigned to individual naïve (n = 401) or memory B cells (n = 283) from the lymph node or plasmablasts (P, n = 15) from a matched tumor (Supplementary Fig. 6). Mutation rate (%) measures the percentage of nucleotides in the V region mutated from germline. d Assignment of TCRγ chains, TCRδ chains and invariant TCR chains associated with MAIT and GEM T cells to the T-cell populations of the lymph node in a. 92 T cells were assigned TCRγ chains alone, 14 T cells were assigned TCRδ chains alone and 11 T cells were assigned paired TCRγ and TCRδ chains. 10 T cells were assigned MAIT-associated TCR chains and two T cells assigned GEM-associated TCR chains (see Methods). e Visualisation of the lymph node t-SNE plot in a for cells assigned paired BCR (n = 689) or paired TCR (n = 705) chains and amongst these cells those clones that are expanded. Clones were considered expanded if a paired TCR or BCR sequence was found in more than one cell. Different colors denote each expanded clone. 13 T-cell expanded clones and 13 B-cell expanded clones were identified. Each clone was represented by two cells
