(A) Representation of βCDR3aa networks from DPCD3−, DPCD3+, and CD8+. Each dot represents a single CDR3. Dots are connected (forming clusters) by edges defined by Levenshtein distance of ≤1 (one AA …
(A) Dotplot of thymocytes sorting. Cells from the different patients were sorted according to their phenotypes: CD3+CD4CD8+ for ThyCD8, CD3+CD4+CD8+ for DPCD3+ and CD3−CD4+CD8+ for DPCD3−. (B) …
βCDR3 network during thymopoiesis. Representation of the 18,000 most frequent βCDR3 networks from DPCD3+ and CD8+ thymocytes of eight donors (Pn).
(A, B) Clustered αCDR3s from DPCD3+ and CD8+ thymocytes. Analyses were performed on the first 18,000 most frequent αCDR3s per sample (n=6 for DPCD3+ and n=10 for CD8+ thymocytes). (A) Percentage of …
Mean percentages of public (black) or private (gray) βCDR3s in all, dispersed or clustered nodes (****p<0.0001, Mann–Whitney test, mean ± s.e.m, n=13). (B) Enrichment of public βCDR3s in the CD8+ …
Enrichment of public βCDR3s in CD8+ thymocytes versus DPCD3+.
(A) βCDR3 sharing between individuals. Pie charts represent the sharing between individuals before (DPCD3+) and after thymic selection (CD8+). Colours represent the dispersed (gray) or clustered …
(A) Barplots showing the mean percentages of CDR3s associated with pathogens within DPCD3+ and ThyCD8 cells and for dispersed or clustered CDR3s. (B) Mean generation probability of virus-specific …
Enrichment of virus-specific βCDR3s from databases in clustered CD8+ thymocytes.
(A) Enrichment of virus-specific βCDR3s in the CD8+ thymocyte repertoire. Representation of the generation probability as a function of βCDR3 connections in individuals (Pn). The contour plots …
(A) Network of clustered nodes from the first top ranking 18,000 CDR3s. For each individual, we plot CDR3s as viral-associated (red) either if they are in the public database (lines 1 and 2) or if …
(A) Network of tetramer-binding CDR3s from public database (VDJdb) identifying CDR3s with multiple viral specificities. Each dot represents a single CDR3. Dots are connected by an edge defined by a …
(A) Analysis of shared T-cell specificities with the GLIPH2 algorithm. 216,000 CDR3β sequences from the CD8 thymocytes and 32,496 sequences from VDJdb that are tetramer specific were analysed to …
List of peptides represented on the chord plot from Figure 4C.
(A) Heatmap of the binding score for different dextramers of different TCRs using the same CASSIRSSYEQYF βCDR3, in two donors. The recognition properties are remarkably similar whatever the βCDR3. …
(A) Six of the most expanded clonotypes were selected from the single-cell data set, of which three were specific to the Influenza_A0201 GILGFVFTL dextramer (A02_GILG9 specific), and the other three …
(A) Schematic representation of the in vitro cross-activation experiment. (B) In vitro activation of polyspecific T cells. Percentage of IFNγ producing emCD8+ cells after activation with …
List of the sequences of individual TCRs expressed and analyzed in vitro in Figure 5.
(A, B) CD8 were previously enriched from cytapheresis PBMC. Gating strategy of the sorting of Cytomegalovirus (A) or Epstein-Barr virus (B) dextramère positive effector memory CD8 (emCD8) from CD8 …
(A) PBMC were stimulated in vitro using Peptivator CMV pp65 (that consists mainly of 15-mer peptides with 11-amino acid overlap, covering the complete sequence of the pp65 protein) and cultured for …
Multi-other refers to multi-specific clonotypes without any differentially high binding to any of the dextramers. Finally, uni-GIL are uni-specific clonotypes that exclusively bind the A02-GIL …