Clonal sharing among CD4 ⁺ T cells in the colon lamina propria. (A) UMAP plot illustrating the clonal size of each cell from CD (n = 3, CD Patient 1–3 in Table S1) and control (n = 3, Ctrl-Patient 1–3 in Table S1) colon samples. (B) Pie chart visualizing the distribution of TCR-sharing patterns among all CD4⁺ T cells from CD and control samples. The chart segments represent cells with TCRs shared by five or more cells, two to four cells, and TCRs unique to a single cell. Both the number of clones (top) and cells (bottom) are displayed. (C) Circos plot demonstrating the overlap of unique individual TCR clonotypes between each cluster. (D) Pie chart visualizing the distribution of TCR-sharing patterns among all cells from the T_RM_2 cluster of CD samples. The chart segments represent cells with TCRs shared within T_RM_2 by five or more cells, two to four cells, and TCRs unique to a single cell. Both the number of clones (left) and cells (right) are displayed. (E) UpSet plot showing the distribution of TCR-sharing patterns among cells from the T_RM_2 cluster of CD samples, highlighting TCR overlaps between T_RM_2 and other clusters. The numbers in parentheses indicate the number of clones in each T cell subset. (F) UMAP plot showcasing cells that share TCRs with T_RM_2 cells from the CD samples. The dots represent cells outside of the T_RM_2 cluster that share the same TCR as cells within T_RM_2, along with the T_RM_2 cells that have matching TCRs. The lines connect cells with common TCRs. (G) UMAP plot with RNA velocity vectors overlaid on cells, indicating predicted future states and dynamic transitions in the transcriptional landscape.