Fig. 4: Type 1, type 3, and type 2-like γδ thymocytes are enriched for public CDR3 features upon maturation. | Nature Communications

Fig. 4: Type 1, type 3, and type 2-like γδ thymocytes are enriched for public CDR3 features upon maturation.

From: Identification of distinct functional thymic programming of fetal and pediatric human γδ thymocytes via single-cell analysis

Fig. 4

γδTCR CDR3 regions were amplified from cDNA of fetal thymus 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 TRDV gene segment usage. Cells without TRD chain detected are displayed as light gray dots in the UMAP. “Others” groups: TRDV4, TRDV6, TRDV7, and TRAV38-2DV8 variable chains. Percentages displayed in bar plots correspond to the mean value of the 6 thymic samples. B UMAP plot (left) and dot plots (center and right) display number of N additions (UMAP) and mean number of N additions (bar plots) in cells with TRDV2-containing CDR3 sequences. UMAP upper limit of the color scale represents sequences containing 10 or more N additions. C UMAP plot (left) and dot plots (center and right) display CDR3 nucleotide (nt) length (UMAP) and mean CDR3 nt length (dot plots) in cells with TRDV2-containing CDR3 sequences. UMAP lower/upper limits of the color scale represents sequences containing 54/44 or more/less nucleotides, and they were established based on 0.8/0.2 quantile calculated on all the TRDV2 CDR3 chains. D UMAP plot (left) and dot plots (center and right) display CDR3 publicity levels (UMAP) and mean CDR3 publicity values (dot plots) in cells with TRDV2-containing CDR3 sequences. Cells with a publicity level of 0 (navy blue color in UMAP) have a private TRDV2 sequence which is only present in one sc TCR-seq library. “Immature/Maturing” group: c1,c2,c5,c7,c8,c9,c10,c11 in Fig. 2A. “Effector” group: c3,c4,c6 clusters in Fig. 1A. “Type 1”, “Type 3”, and “Type 2-like”: c4, c3, and c6, respectively, in Fig. 1A (A–D). Bar plots/Dot plots are means ± SEM. Data in A was analyzed with ordinary two-ANOVA followed by Sidak’s multiple comparison test, in B, C, D I-M and EFF values were compared by Wilcoxon-matched pairs signed-rank test, while T1, T2, and T3 groups were compared by Ordinary one-way ANOVA with Tukey’s multiple comparisons test as Post Hoc test. Source data are provided as a Source data file. See also Supplementary Figs. 6 and 7.

Back to article page