Extended Data Fig. 3: Quality control of scRNA-seq data and cell type abundance profiled by scRNA-seq, H&E and mpIF.

a, UMAPs of cells profiled by scRNA-seq coloured by different QC metrics: log₂ transformed number of UMIs and genes, fraction of mitochondrial reads, cell cycle phase. b, Distributions of QC metrics per cell type. Box plots show the median, top and bottom quartiles; whiskers correspond to 1.5× IQR. c, Absolute and relative cell type compositions of CD45⁻ (top) and CD45⁺ (bottom) sorted samples based on scRNA-seq, separated by patient, ranked by fraction of ovarian cancer cells and T cells respectively. d, Absolute and relative cell type compositions based on H&E, ranked by lymphocyte fractions for tumour-rich (top) and stroma-rich (bottom) compartments. Panel analogous to c. e, Absolute and relative cell type compositions based on mpIF, ranked by CD8⁺ T cell fractions in tumour-rich (top) and stroma-rich (bottom) compartments. Panel analogous to c. Colour legends for c–e are shown along the bottom of the figure. f, Correlation between the fraction of lymphocytes in tumour and stroma regions of H&E slides (left panel) and the fraction of CD8⁺ and CD68⁺ cells in mpIF slides (right panel).