Fig. 3: Transcriptomic characterization of gastric tissues and tissue-derived organoids from different stages of development.

a Principal component analysis (PCA) of RNA-sequencing samples from organoids (triangles) and fetal gastric epithelial tissues (circles) at different stages of development. Edge color identifies the biological replicates or patients within the same group of samples. Stages of fetal tissues or derived gastric organoids: early fetal (PCW 8–15), late fetal (week 17–20), and pediatric. b, c Expression of typical gastric markers in organoids (b) and gastric epithelium (c) at different stages of development. Black circles indicate single data points. Black error bar: mean ± SD (n = 4 for organoids biological replicates, n = 3 for biological replicates tissues). CPM: counts per million. Horizontal lines above the bar plots highlight DEGs between the indicated conditions. d Results of hierarchical clustering of organoid gene expression. The selected genes were previously shown to define the six stomach cellular subtypes identified in Gao et al.²⁸ by single-cell RNA-seq, as indicated on top of each plot. Genes whose name is preceded by an asterisk (*) are differentially expressed genes (DEGs) between any pair of conditions. e Pseudo-temporal profiles of gene expression according to differential expression analysis. DEGs were clustered according to a flat, increasing, or decreasing profile between pairs of time points. Data were scaled respect to the first time point. Red lines: average profile of each cluster. Gray lines: profile of each gene in the cluster. Blue digits: cluster identification number. f Selected categories from Reactome enrichment analysis of genes in the clusters displayed in e. Gray bars: graphical representation of the values of the adjusted p-value (always <0.01), corrected by Benjamini–Hochberg method, from the right-sided hypergeometric test. Full results are displayed in the Supplementary Information.