Fig. 3

Inulin diet affects distribution and transcriptional profile of colon epithelial cell populations. A Heatmap showing up- or downregulated genes in the colon epithelial cells of both dietary groups after transcriptome analysis. DESeq statistical test with significance threshold p < 0.05 (n = 3). B Volcano plot displaying up- (blue) and downregulated (red) genes in the inulin diet group. C Significant enriched terms identified from KEGG Pathway analysis of the significantly up- and downregulated genes. D t-SNE plot with defined cell populations in colon epithelium summarizing data from single-cell RNA-Seq analysis of inulin diet fed mice and controls. E Heatmap of colon epithelial cell cluster markers colored by relative gene expression. Cell types are indicated by colored bars on top matching colors in (D). Select markers for each cluster are shown on the right of the heatmap. F Proportion of the absorptive, proliferative or secretory epithelial cell types in both dietary groups. T-test was used to calculate p-values and corrected by Benjamini- Hochberg false discovery rates. * p < 0.05. G Proportion of the 9 defined cell populations in both dietary groups. T-test was used to calculate p-values and corrected by Benjamini–Hochberg false discovery rates. * p < 0.05. H Frequency of cells expressing S or G2/M phase cell-cycle genes in total and in the main intestinal epithelial populations (EEC and Tuft cells were excluded because their numbers were very low). Results were analyzed using Fisher’s exact test. *p < 0.05, ***p < 0.001, ****p < 0.0001