were specific to COVID-19 samples (Supplementary Fig. 7a). Consistent with previous reports, monocytes in COVID-19 samples sharply upregulated interferon response genes63,64, but were correctly harmonized with healthy monocytes (Fig. 5b and Supplementary Fig. 7b). By matching shared cell types across disease states (while still allowing for the possibility of disease-specific subpopulations), this collection represents a valuable resource for identifying cell-type specific transcriptional changes that reproduce across multiple studies. We characterized cell-type specific responses for eight additional cell types, each of which exhibited a conserved interferon-driven response alongside the activation of cell type-specific response genes (Supplementary Fig. 8).
