Fig. 4

Application of collagen sphere to human colon. A Microscopic images of human colonic organoids cultured in Matrigel with WRN conditioned medium (left) and in COL with recombinant medium (right) are shown. Scale bars, 300 μm (left) and 200μm (right). B Principal component analysis of RNA-seq data from Matrigel organoids (MG) and collagen spheres (COL) derived from 3 different human colonic samples is shown. The plot represents 17,500 genes after discarding genes with low expression levels (<count16). Sample origins are indicated underneath the plot. C A volcano plot of DEGs (padj<0. 05, FC≥2) between MG and COL with DEGs indicated. Each plot indicates the average log 2-fold change (x-axis) and log 10 of 1/adjusted p value (y-axis) of triplicate samples of each condition. D Immunofluorescence images of YAP (green) of human colonic organoids in MG (top panel) and COL (bottom panel) are shown. Images are counterstained with DAPI (blue). A dashed square is enlarged in adjacent images for YAP, DAPI, and Merge. Scale bar, 50 μm. E, F Top 20 GO-TERM (BP direct) (E) and KEGG pathway (F) in upregulated gene set in COL compared to MG is shown. G, H Venn diagram depicting the overlap of COL gene set (804 genes; red and yellow) or MG gene set (682 genes; blue and yellow) with inflammatory gene set (p<0.05, FC≥2; adapted from ref [29]) (2221 genes; brown and yellow) (G) or fetal gene set (adapted from ref [30]) (323 genes; green and yellow) (H) is shown. The overlap is indicated with a number of genes (yellow). The p value of statistical significance is indicated