Fig. 5: Fetal Vγ9Vδ2 and nonVγ9Vδ2 γδ thymocytes show similar effector programming.

γδ TCR CDR3 region was amplified from cDNA of fetal thymic sc RNA-seq libraries (n = 6). CDR3 data and transcriptomes were matched via cellular barcodes. A UMAP plot (left) and bar plots (center and right) displaying TRGV gene segment usage. Cells without TRG-detected chain are displayed as light gray dots in the UMAP. B UMAP plot (left) and dot plot (right) displaying Vγ9Vδ2 cells (left) and percentage of Vγ9Vδ2 cells (center and right); Vγ9Vδ2 T cells are identified based on the sc TCR (CDR3) data. C Paired dot plot indicating the % of Vγ9Vδ2 thymocytes in the immature (CD1a⁺) and mature (CD1a⁻) subsets evaluated at protein level from 9 different subjects. D Dot plots indicating the % of Vγ9Vδ2 and nonVγ9Vδ2 thymocytes in the distinct effector clusters, at transcriptomic level (left panel) and at protein level (right panel). E Volcano plot illustrating differentially expressed genes between Vγ9Vδ2 and nonVγ9Vδ2 thymocytes. Cell populations were sorted from different subjects than the ones used in the sc experiment (n = 3, age = 17 wk, 17 wk, and 19 wk of gestation). F Paired dot plots displaying number of N additions, nucleotide length and publicity levels of TRDV2-containing CDR3 sequences from Vγ9Vδ2 and nonVγ9Vδ2 thymocytes. Data in A was analyzed with ordinary two-ANOVA followed by Sidak’s multiple comparison test, in B, C groups were compared by two-tailed paired t-test, while in D groups were compared by Ordinary one-way ANOVA with Tukey’s multiple comparisons test as Post Hoc test. Error bars in D correspond to the SEM of 6 (right panel) and 9 subjects (right panel). “I-M” group: immature/maturing. “EFF” group: effector. “EFF” group: effector. “T1”, “T3”, and “T2” groups: Type 1, Type 3, and Type 2-like. Source data are provided as a Source data file. See also Supplementary Fig. 8.