Extended Data Fig. 6: Profiling of lung tissue with targeted spatial transcriptomics using GeoMx.

a, Experimental design of GeoMx dataset. b, Representation of the procedure of choosing a ROI within the lung tissue to capture with GeoMx. c, Enrichment of cell-type-specific gene set signatures for various cell types that match the IMC data, across disease groups. d, Comparison of the estimated changes in cell-type abundance with IMC (x axis) and gene set signatures in GeoMx (y axis). e, Viral load, dependent on the time of death relative to the onset of COVID-19 symptoms in an independent cohort. COVID-19 samples were categorized into ‘early’ or ‘late’ death depending on whether death occurred before or after 15 days after the onset of symptoms, respectively. f, Schematic of the cohort of patients for whom GeoMx data are available (in total, 5 patients and 231 ROIs). g, Estimated fractions of cell-type composition, using the CYBERSORT program, between early and late COVID-19 from the original publication²⁵. h, Comparison of the estimated changes in cell-type abundance with IMC (x axis) and GeoMx (y axis) between late and early COVID-19. In d, h, r, Pearson coefficient, P, its two tailed P value; shaded area indicates 95th confidence interval. In c, g, **P < 0.01; *P < 0.05, two-sided Mann–Whitney U-test, pairwise between groups, Benjamini–Hochberg FDR adjustment.