Fig. 1: TME of HGSOC at single-cell resolution.

a, Overview of the MSK SPECTRUM cohort and specimen collection workflow. b, UMAP plot of cells profiled by scRNA-seq coloured by patient. Cell types are highlighted with grey outlines. c, Patient specificity for each cell type (Methods). Ov, ovarian. d, Number of cells identified per cell type next to a UMAP plot with cells coloured by cell type. e, Number of cells profiled per tumour site next to a UMAP plot with cells coloured by tumour site. UQ, upper quadrant. f, Site-specific enrichment of cell type composition in scRNA-seq, H&E and mpIF data fitted using a GLM. GLMs for H&E and mpIF data were separated by tumour (T) and stroma (S) regions. The colour gradient indicates the log₂-transformed odds ratio (red, enrichment; blue, depletion), and sizes indicate the Bonferroni-corrected –log₁₀(P value). g, Cell type composition based on scRNA-seq data for CD45⁻ and CD45⁺ samples. Upper panels, absolute and relative cell type numbers; lower panels, box plot distributions of sample ranks with respect to tumour site. h, Cell type composition based on H&E with lymphocyte ranks in tumour and stroma. Panels are analogous to those in g. i, Cell type composition based on mpIF with CD8⁺ T cell ranks in tumour and stroma. Panels are analogous to those in g. For c and g–i, violin plots and box plots are shown as the median, top and bottom quartiles; whiskers correspond to 1.5× interquartile range (IQR). *P < 0.05, **P < 0.01.