TCR repertoire relatedness among recipient groups and across experiment locations. Two pairwise indices (JI and BC) were used to measure similarity between any 2 samples. One dot in the figure represents JI or BC between 2 samples. Boxplot and violin plots show the index values according to transplant groups and/or time points. Data shown in this figure are from TRA and TRB repertoire. (A) JI and BC of TCR repertoire between donor graft T cells and GI tract. In every transplant experiment, recipient mice shared 1 donor graft T-cell pool purified from several C57BL/6 mice (N = 5-10). A total of 5 donor TCR repertoire from graft T cells were used for relatedness calculation. We isolated the CD4 and CD8 memory and naive cells from the T-cell pool in 3 transplant experiments. GI tracts from every donor mouse were processed individually and used for TCR and relatedness analysis. The x-axis labels are given as follows: T means donor T-cell pool; CD4M represents CD4 memory T cells; CD4N is CD4 naive T cells; CD8M is CD8 memory; CD8N is CD8 naive; Gut means no separation of large and small intestines. (B) Donor TRA clone frequency distribution of 2 representative experiments across sites. Left: TRA from donor graft T cells; Right: TRA clones from GI tracts of representative donor mice. Pearson correlation of TCR from donor T cells is 0.86 (highly related); GI tract has only 0.21. Note: TRA clones from GI tracts were pooled from donor mice (N = 5) in 2 representative transplant experiments. (C) Relatedness of recipient mice between locations. JC and BC of TCR repertoire were measured between any pair of intragroup mice within 1 experiment, or across experiments (local or cross sites).