Fig. 3.

Gene expression profile analysis in tonsil epithelial organoids. (A) Heatmap showing the gene expression pattern of the tonsil organoids (Org) cultured for 15 days and their matched tonsil crypt and surface (Surf) tissues from two donors 21–33 and 21–36. Gene expression levels (ranging from 2 to 20) were pseudo-temporally ordered and the samples were clustered based on the similarity of the gene expression pattern. (B) Pairwise Pearsons' correlation coefficients between samples (r). (C) Principal component analysis (PCA) plot of microarray samples. PCA scores on PC1 (88%) and PC2 (8%) are pointed with black, red and blue dots, accounting for crypt, surface and organoid samples, respectively, from the two donors. (D) Heatmaps showing differentially expressed genes (DEGs) in tonsil organoids compared to tonsil tissues (with > 4-fold changes). Upregulated genes are colored in red (left panel), while downregulated genes are in blue (right panel). (E) Gene ontology (GO) enrichment analysis of differentially expressed genes. The bar graphs indicate the top 10 upregulated (red) and downregulated (blue) GO biological processes in the tonsil epithelial organoids. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)