Fig. 2: Spatial gene expression data identified various types of cells and regions in mouse lungs with super-infection. | Communications Biology

Fig. 2: Spatial gene expression data identified various types of cells and regions in mouse lungs with super-infection.

From: Influenza virus and Staphylococcus aureus super-infection disrupts spatially coordinated cellular immunity in the mouse lung

Fig. 2

A Unsupervised clustering of spot-level spatial gene expression identified different anatomical structures of the infected lung. B Spatial deconvolution with RCTD identified the proportion or density of detailed cell types. C Marker genes employed to identify different cell types and estimation of cell type proportions. D The deconvolution-estimated proportion of airway epithelial cells (left, sum of goblet, club, and ciliated cells) and immune cells (right, sum of all types of immune cells) in different manually annotated regions in the lung. E The final annotation of different regions combining both manual annotation and cell type proportions (See Methods).

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