Extended Data Fig. 5: Single cell RNA sequencing annotation; (Corresponds to Fig. 3).

a, Schematic visualisation of representative DEN-induced tumours under the dissection microscope, before and after microdissection using punch biopsy tool. b, Image composite depicting sample collection strategy for scRNA-seq. Squamous oesophagus and forestomach (outlined in red) first underwent tumour marking and were then peeled to separate epithelial (Ep) and Stromal (Str) compartments. This was followed by sample biopsying, where tumours and size-matched control biopsies (adjacent tissue as internal control, DEN; untreated tissue as external control, Control) were micro-dissected for scRNA-seq. c, UMAP representing cell cluster distribution as defined by Seurat. d, UMAP cell distribution of cell-types identified using label transfer from ref. ⁷³. e, Heatmap showing expression of representative marker genes used for curated cell type annotation across the 22 clusters. Log-transformed normalised expression levels were averaged by cluster for each gene and scaled across all cells belonging to each group. Scale bar denotes expression range (scale: -4 to 6). f, UMAPs showing expression of representative genes for each cell type identified. Colour bars of UMAPs indicate log-transformed normalised expression levels. g, UMAP cell distribution representing identified cell types in each condition. Illustration in a) was created in BioRender; Alcolea, M. https://BioRender.com/l73dcie (2026).