Fig. 3
Heterogeneity of immune cell subtypes in ileum tissues of piglets. a t-SNE plot showing representations of B cell subclusters. MBC, memory B cell; ASC, antigen-secreting cells; GCB, germinal-center B cell; TC, transitory cell. b t-SNE plot showing representations of T cell subclusters. Th, T helper; Tn, T naïve; Tfh, T follicular helper; TCM, T central memory; Treg, T regulatory; CTL cytotoxic T lymphocytes. c Violin plots showing canonical marker genes across T cell subtypes. d Dot plot showing the scaled expression of signature genes for each B cell subtype, colored by the average gene expression. Dot sizes reflect the percentage of cells in each cluster expressing the corresponding gene. See Additional file 7: Table S5 for all marker genes. e Pseudotime-ordered analysis of T cell subtypes from NSP (middle panel) and PWP (down panel). T cell subpopulations are marked by the colors in the top panel. The distribution of cell density with various state is shown at the top. f Pseudotime-ordered analysis of B cell subtypes. Each subpanel corresponds to a previously identified cell type (a). g t-SNE plot showing cell counts for B cell subtypes from NSPs and PWPs. Dashed line, differences in ASC2 cell numbers between NSPs and PWPs. h Changes in cell proportions of B cell subtypes. Error bars: SEM; *FDR < 0.025, Wald test. i t-SNE plot showing T cell subtype counts from NSPs and PWPs. Dashed line, differences in Th17 and CTL cell numbers between NSPs and PWPs. j Changes in cell proportions for T cell subtypes. Error bars: SEM; *FDR<10−4, Wald test