Extended Data Fig. 9: GeoMx WTA DSP analysis of lung biopsy samples reveals region- and inflammation-specific expression programs.
From: COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets
a, Region selection. Serial sections of lung biopsy samples (five donors, D13–17; image depicts serial sections of D14) processed with GeoMx WTA DSP with four-colour staining (DNA, CD45, CD68, PanCK), RNAscope with probes against (SARS-CoV-2 S gene (used to derive semiquantitative viral load scores), ACE2, TMPRSS2), H&E staining and immunohistochemistry (IHC) with anti-SARS-CoV-2 S-protein. Scale bar, 100 μm. b–d, Region- and inflammation-specific expression programs. b, The first two principal components (PCs, x and y axes) from lung ROI gene expression profiles from donors D13–17, spanning normal-appearing alveoli (green; D14 = 6 AOIs, D15 = 2 AOIs, D16 = 5 AOIs, D17 = 4 AOIs); inflamed alveoli (magenta; D13 = 14 AOIs, D14 = 18 AOIs, D15 = 7 AOIs, D16 = 3 AOIs, D17 = 8 AOIs); bronchial epithelium (blue; D14 = 2 AOIs, D15 = 1 AOI, D16 = 2 AOIs, D17 = 3 AOIs) and arterial blood vessels (black; D13 = 2 AOIs, D15 = 3 AOIs). c, GSEA score (circle size, legend) of the enrichment of the IFNγ pathway in each normal-appearing (green; 6 AOIs) and inflamed (magenta; 18 AOIs) alveolar AOIs (dot) from the section of donor D14 (in a), placed in their respective physical coordinates on the tissue section (as in a). d, Expression (colour bar, log2(counts per million)) of IFNγ pathway genes (rows) from normal-appearing (green, n = 6) and inflamed (magenta, n = 18) alveoli AOIs (columns) from D14 lung biopsy.
