Fig. 3: Gastric assembloid bulk RNA-seq analysis.
a,b, PCA of RNA-seq samples from fundus (blue), body (green) and antrum (red) organoids (squares), SRAs (rhomboids) and MRAs (triangles). Panel a also includes the results for tissue (circles) (n = 3 for both; patient 1). c, Expression of typical gastric markers in organoids, SRAs, MRAs and tissue in the fundus (blue), body (green) and antrum (red). The circles indicate single data points and the error bars represent means ± s.d. (n = 3; patient 1). d,e, Chord diagrams displaying ligand–receptor analysis in organoids versus MRAs (d) and in SRAs versus MRAs (e). The fundus, body and antrum are represented in blue, green and orange, respectively. Receptors are noted with a purple bar and ligands with a green one. Upregulated genes are reported in red, downregulated genes are in blue and non-differentially expressed genes are in black (|fold change| > 1.5; false discovery rate (FDR) < 0.05). The external bar plots show the proportion of expression in the antrum, body and fundus of MRAs for every gene. For each of the ligand–receptor couples considered, at least one of the two genes of the couple was differentially expressed (only upregulated) across the four patients analysed at |fold change| > 2 and FDR < 0.01 (n = 9; patient 1 in triplicate; patients 2, 3 and 4 in duplicate).
