Extended Data Fig. 3: Transcriptomics analysis.
a, Principal component analysis (PCA) of RNA-sequencing samples from Fundus (blue), Body (green), and Antrum (red) SRA (rhomboids) versus MRA (triangles). (n = 3, patient 1). b, Principal component analysis (PCA) of RNA-sequencing samples from Fundus (blue), Body (green), and Antrum (red) MRA (triangles). (n = 3, patient 1). c, Volcano plots of DEGs between organoids and MRA of Fundus, Body, and Antrum regions (n = 3, patient 1). d, Volcano plots of DEGs between SRA and MRA of Fundus, Body, and Antrum regions. (n = 3, patient 1). e, Expression of CLDN23 and PHGR1 in organoids, SRA and MRA in Fundus (blue), Body (green), and Antrum (red). Circles indicate single data points, mean ±SD (n = 6, patient 2,3,4) CPM: counts per million. f, RT-qPCR for ATP4Bwhole MRA at progressive days during MRA formation, normalized to day 10. Mean and single datapoints displayed (n = 3). FLO (foetal lung organoids) were used as a negative control. g, Hierarchical clustering of receptors that are differentially expressed genes (DEGs) between organoids and MRA in the three regions intersected among 4 patients. Color bar indicates centered log2(CPM + 1). Patient 1: |fold change | >2, FDR < 0.01), patients 2, 3, and 4: |fold change | >1.5, FDR < 0.05). h, RT-qPCR for ligands and receptors in organoids (n = 2), MRA (n = 6), and organoids grown from MRA (n = 4) as labelled (patient 1). Single datapoints displayed, mean±SD. One way ANOVA i, Hierarchical clustering of receptors that are differentially expressed genes (DEGs) between SRA and MRA in the three regions intersected among 4 patients. Colorbar indicates centered log2(CPM + 1). Patient 1: |fold change | >2, FDR < 0.01), patients 2, 3, and 4: |fold change | >1.5, FDR < 0.05).
