Fig. 1

Single-cell transcriptome analyses uncover cell composition of ileum tissues in piglets. a Schematic of the sample collection, scRNA-seq, and cross-species analytic workflow. b t-Stochastic neighbor embedding (t-SNE) plots of all cell clusters obtained from NSPs and PWPs (n = 3), showing 24 distinct cell types identified from the first clustering. EC, enterocyte (Im: immature, Ma: mature); ESC, epithelial secretory cell; ProgC, progenitor cell; TAC, transient-amplifying cell; Macro, macrophage; DC, dendritic cell; Mono, monocyte; Mes, mesenchyme. c Heatmap showing the differential expression of cell type-specific genes in intestinal structural and immune cells. d t-SNE plots showing expression levels of canonical markers for various intestinal epithelial and immune cell populations. The expression intensity is indicated by the purple color. The expression scale is normalized by the logNormalize method in Seurat. e Violin plots depicting expression levels of representative marker genes across Macro, DC, Mono, and ESC clusters. The y-axis shows the normalized gene expression values. See Additional file 1: Table S1 for all marker genes. f t-SNE plots with single cells colored according to their cell-cycle phase. g Histogram showing cell-cycle quantity of epithelial, stromal, and immune cell subsets in piglet ileum mucosa