Extended Data Fig. 5: Latent Semantic Index (LSI) projection of gastric organoids onto gastric tissue dataset.
From: Deterministic evolution and stringent selection during preneoplasia
a–b, UMAP visualizations coloured according to culture (left) and time point (right) for Donors 2 and 3 depicting 9,031 and 8,591 cells, respectively. c–d, Dotplot depicting the expression of selected marker genes for individual cultures and time points. Coloured bars highlight marker genes associated with normal gastric and intestinal cell types, genes up-regulated in the gene expression profiling interactive analysis (GEPIA) of GC, and others of functional relevance. Pit mucosal cells: MUC5AC, TFF1 – dark yellow; Gland mucosal cells: MUC6, TFF2 – light blue; Proliferative cells: MKI67 – purple; Neck-like cells: PGC, LYZ – orange; Mucosal stem cells: OLFM4 – turquoise; Enterocytes: FABP1, VIL1 – olive; Goblet cells: TFF3, WFDC2, MUC5B, CDX2 – green; GEPIA top 12 genes: CEACAM5, CEACAM6, CLDN3, CLDN4, CLDN7, REG4, MUC3A, MUC13, PI3, UBD, AOC1, CDH17 – black; Other: TP53, APC, CDKN2A, FHIT – red. e, The reference gastric tumour-normal dataset (Sathe et al.) for the LSI projection is shown with key cellular populations coloured according to their expression phenotype, as denoted in the legend. This panel is identical to that shown in Fig. 4c. f–h, Showing the LSI projection of individual cultures for donors 1, 2 and 3.
