library_construction_protocol: Cells were harvested 5 hours post infection by a PBS wash followed by incubation of 15 min with ice-cold EDTA (5mM) and analyzed by flow cytometry (BD FACS Aria III) under continuous cooling at 4°C. Bystanders and infected cells were sorted into 1.7ml low–bind tubes containing 25μl of lysis buffer (0.1% Triton in RNase-free water), placed immediately on dry ice and stored in minus 80. Bulk samples were processed for libraries generation according to the Cel-seq protocol (Hashimshony et al., 2016) library strategy: CEL-seq