Fig. 4
Tcf4-deficient cells leave the Paneth cell lineage and acquire gene expression characteristics of goblet cells. Single-cell RNA-seq data of Defa6-tdTom cells from the small intestine of different Tcf7l2 genotypes. A Left, UMAP visualization of scRNA-seq clustering of Defa6-tdTom cells from the small intestine (jejunum) of mice with the wt (Tcf7l2wt/wt, sample 1) or knockout Tcf7l2 (Tcf7l2flox/flox, sample 2) cells. Cell cycle analysis of Defa6-tdTom cells combined from both samples is shown in the inset. The cell clusters are numbered according to the amount of cells in the merged dataset. Cell types were assigned based on the genes specifically expressed in each cluster (see Additional file 5: Supplementary Table S5 for a complete list of genes). B UMAP feature plots showing the expression patterns of the different marker genes. The plots were derived from the merged dataset. Additional cell type markers are shown in Additional file 8: Supplementary Figure S5. Ace2, angiotensin-converting enzyme 2; Clca1, chloride channel accessory 1; Krt20, cytokeratin 20; Mptx2, mucosal pentraxin 2; Sox9, sex-determining region Y (SRY)-box 9. C Violin plots showing the expression level of epithelial cell adhesion molecule (EpCAM) gene as well as genes of the Tcf/Lef family in both Defa6-tdTom scRNA-seq samples. The expression levels of Axin2 and Sp5, which indicate the status of Wnt signaling, are also shown in the identified cell clusters from panel A. D Frequency of cell types in the clusters of the two scRNA-seq samples. The percentages are plotted so that the total number of cells in a respective sample is 100%. Three cell types most changed between Tcf7l2 wt and knockout samples are indicated by the gray dotted boxes. Lef1, lymphoid enhancer-binding factor 1