Figure 3
Organoids are composed of epithelial and fibroblast cell types. (a) tSNE projection of 1961 cells from gastric organoids. Cells are grouped into six clusters based on transcriptome profiles and were colored accordingly. (b) The expression of cell type specific genes, Epcam, Col1a1, Foxq1, Acta2, Mki67, Stmn1, Foxj1, and Krt5 are displayed on violin plots and tSNE projection. The expression level of violin plot is the natural log of the normalized UMI counts. (c) The heatmap of top 15 cluster specific genes in 200 cells (or less) from each cluster. Yellow - high expression. Purple - low/no expression. Each row represents a gene, and each column represents a single cell. (d) Stem cell marker Lgr5 is expressed in both epithelial and fibroblast cells. Lgr5 mRNA is detected in both epithelial and fibroblast cell clusters on the tSNE map (top). Raw Lgr5 counts in Epithelial and Fibroblast cell clusters (bottom). (e) The expression of lineage specific transcriptional factors, Klf5 (top) and Hoxa5 (bottom), on violin plots and tSNE maps. Epi – Epithelial, Fib – Fibroblast. The expression level of violin plot is the raw UMI counts * Bonferroni adjusted p value < 0.001.
