Fig. 5

CDR3 protein sequences cluster by tissue site within an individual. A Comparing edit distance by tissue and subset. tSNE projections of TCR clones based exclusively on the edit distances between CDR3 amino acid (protein) sequences. Shown are 250 non-overlapping clones that were randomly chosen from each of the three most extensively sampled donors, D324, D383, and D466 (see Methods). Each clone (dot) is colored according to its tissue origin (upper) or subset identity (lower). TCM, central memory; TEM, effector memory; TEMRA, terminal effector; TRM, resident memory; Bld, blood; BM, bone marrow; LN, lung lymph node; Spl, spleen. B Hierarchy of TCR repertoire similarity. Average CDR3 edit distances in amino acid (left) and V gene Kullback-Leibler (KL) divergence (right) are computed for samples by donor, lineage (CD4 or CD8), tissue, subset, and biological replicates from separate DNA aliquots from the same sample (see Methods). A total of 500 clones were randomly chosen from all tissue donor samples for each analysis. Average values and standard errors for each measure were computed. Differences between neighboring samples were computed using a two-sided unpaired t test. * p < 0.05; ** p < 0.01; *** p < 0.001