Multiplexed histology of COVID-19 post-mortem lung samples - Single-cell Mean Fluorescence Intensities

Data table containing single-cell mean fluorescence intensities (MFI) of all markers analyzed by multiplexed histology in all COVID-19 post-mortem lung samples and non-COVID-related pneumonia controls (14 lung samples, stratified based on disease duration into control, acute, chronic and prolonged). It contains information at the single-cell level about approx 50 proteins in around 40.000 lung cells. Data shown has been arcsin(h) transformed with a co-factor of 0.2. Additionally, cells expressing less than 0.15 MFI of all markers have been labeled as non-defined and excluded from the data set. Seurat package 4.0.0 was used in R to perform mean centering and scaling, followed by PCA, and reduced the dimensions of the data to the top 11 principal components. UMAP was initialized in this PCA space to visualize the data on reduced UMAP dimensions. The cells were clustered on PCA space using the SNN algorithm implemented as <em>FindNeighbors</em> and <em>FindClusters </em>with <em>n.epochs = 500</em> and default parameters (<em>res = 0.8</em>). We obtained 26 clusters that we merged to get relevant populations for our analysis based on canonical lineage markers. We ended up with 8 cell clusters that were manually annotated based on cell-type-specific markers found to be differentially expressed.