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. 2020 Dec 9;11:6319. doi: 10.1038/s41467-020-20139-7

Fig. 6. Intrapulmonary heterogeneity of SARS-CoV-2 host response.

Fig. 6

a Selection of ROIs. Left) SARS-CoV-2 RNA-ISH staining was used to guide ROI selection of viral positive and viral negative regions. (Scale bar = 2 mm). Right) multi-color immunofluorescence staining for CD45/red, CD68/yellow, PanCK/green, and DNA/blue were used in parallel to select ROIs. (Scale bar = 2 mm). Example ROIs are shown in insets. (Scale bar = 100 μm). b Distribution of immune subsets and relationship with viral location. Rows show estimates from distinct cell types; columns show distinct tissues. Point position shows the physical location of regions within each tissue. Point size shows a cell type’s estimated proportion of cells in a region. Point color denotes whether a region was classified SARS-CoV-2 positive or negative by RNA-ISH. c tSNE clustering of geometric ROIs highlights two primary clusters exist within the data irrespective of SARS-CoV-2 RNA-ISH status of ROI or patient viral load. d Differential expression analysis of clusters identified by tSNE analysis. Target genes colored by significance and association with tSNE clusters. Targets with FDR < 0.05 are shown in gray. Genes shown in red are associated with higher expression cluster labeled ‘active’ in panel (c); genes shown in blue are associated with higher expression in the cluster labeled ‘inactive’. e Unsupervised clustering analysis of interferon stimulated genes cluster across ROIs. Annotation by patient sample identifier and SARS-CoV-2 RNA-ISH positivity in the ROI as performed by GeoMx Digital Spatial Profiler. Source data are provided as a Source data file.