Extended Data Fig. 4: Manual annotation in the COVID-19 lung cell atlas.
From: COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets
a, b, Identification of main immune lineage annotations. a, UMAP of 106,792 sc/snRNA-Seq profiles after Harmony correction (as in Fig. 2a) coloured by expression of genes (colour bar, genes listed below) used to separate immune cell sub-lineages (Supplementary Methods). b, Differentially expressed (DE) genes between subclusters within each lineage. Expression (colour bar) of genes (rows) that are differentially expressed (Supplementary Methods) across the subclusters (columns) within each compartment. DE genes shown are a union of the following: (i) top 10 DE genes between clusters, (ii) DE genes above an AUC of 0.8 and 0.75 for B/Plasma cells, (iii) pseudo-bulk DE genes above a log(fold change) threshold (thresholds: endothelial = 4.2, T/NK = 3, myeloid = 4, B/plasma = 2) (label on top). c, Batch correction within lineage. Fraction of cells/nuclei (y axis) from different processing protocols (left) or different donors (right, n = 17) in each subcluster (x axis) after batch correction with Harmony53 within each lineage.
