Differential gene expression, differential chromatin gene scores and gene set enrichment analysis

Differential gene expression analyses were performed using the MAST implemented in FindMarkers from Seurat⁸¹. Analysis comparing tumour cluster 1 and tumour cluster 2 from Slide-tags snRNA-seq and comparing compartment-specific CD8⁺ T cells from Slide-tags multiome data used min.pct = 0.25 and log2fc.threshold = 0.25. Analysis comparing tumour cluster 1 and tumour cluster 2 from Slide-tags multiome data used min.pct = 0.1 and log2fc.threshold = 0.25. Gene Ontology biological process (GO_Biological_Process_2021) gene set enrichment analysis was performed using the Enrichr package (v.3.1) in R^82–84 on tumour cluster 2 enriched differentially expressed genes with log₂[FC] < −0.5 and P_adj < 0.05. Differential chromatin gene score analysis was conducted using the Wilcoxon rank-sum test implemented in FindMarkers from Seurat with min.pct = 0.1 and log2fc.threshold = 0.