Fig. 4: Innate T cells are clonally selected during development.
From: Single-cell RNA sequencing identifies shared differentiation paths of mouse thymic innate T cells
a Graphs show the distribution of CDR3α/γ (top) and CDR3β/δ (bottom) lengths of iNKT, MAIT, and γδ T cells, presented as the number of cells for each length. Canonical (top left, orange) and non-canonical (top right, turquoise) TCRα are shown together in iNKT and MAIT cells. The relative amino acid composition is shown for the most common length by using the WebLogo application (hydrophilic, blue; neutral, green; and hydrophobic, black). b Bar plots show the ordered number of cells for each clonotype repeated 3 or more in iNKT (left), MAIT (middle), and γδ T cells (right), colored by each subset (iNKT) or their UMAP regions (MAIT and γδ T). Each bar represents an individual clonotype from Supplementary data 2. c Normalized number of clonotypes (y-axis) within each type of innate T cells (colored lines) plotted over the number of cells having the identical clonotype. d Line plots show the Shannon equitability indexes of clonotypes for the indicated subset of cell cluster in iNKT (left), MAIT (middle), and γδ T cells (right). e t-SNE plot of γδ T cells colored by cells having the most abundant single clonotype from Supplementary data 2. f Graph shows percentage of cells having non-canonical TCRα subchain for each subset of iNKT. g Venn diagram shows the non-canonical TCRα and/or non-oligoclonal TCRβ usage of MAIT cells. Numbers indicate number of cells with each combination. Graphs show distribution of total cells or MAITs with non-canonical TCRα or non-canonical TCRα except 89 cells in Venn diagram in each MAIT cluster. Numbers in parentheses indicate total number of cells analyzed in each graph. Source data are provided as a Source Data file.
