Single cell RNA-seq of SARS-CoV-2 infected organoids. (A) UMAP projection of cells from single cell sequencing.(B) Monocle trajectory analysis resulted in four distinct states of cells from the organoid. (C) The four major clusters consisted of the following: (1) Neural progenitor, outer radial glia like cells; (2) intermediate progenitor, interneurons; (3) neurons; and (4) cortical neurons. (D) Monocle projection of individual clusters. (E) Heatmap of commonly used genes for identification of cell subtypes in human brain organoids.(F) UMAP projection of organoids depending on infection status. (G) Percentage of infected cells in each cluster.(H) UMAP heatmap of SARS-CoV-2 transcript + cells separated by infection status. (I) Correlation between % change of cell population versus % of cells infected in each cluster. Single cell data were produced by two separate organoids (see F) to ensure reproducibility.