ALT Schematic of the Perturb-seq workflow to study SARS-CoV-2 host factors (Fig. 1A of the paper): A sgRNA library targeting host factors of SARS-CoV-2 is delivered to Calu-3 cells stably expressing the CRISPRi machinery. The cells are then infected with SARS-CoV-2 and analyzed by single-cell RNA-seq, analyzing the expression of host and viral genes in 27k individual cells, and monitoring how perturbation of host factors changes the progression of infection and the activity of antiviral pathways.