RNA-seq Analysis of AP2M1 and FCHO2 KO

RNA-seq was performed at the Centre for PanorOmic Science in the LKS Faculty of Medicine, HKU. Briefly, A549-ACE2-Cas9 cells were infected with AP2M1_sgRNA, FCHO2_sgRNA or safe harbor_sgRNA. On day 9 post infection, total mRNA was extracted using TaKaRa MiniBEST Universal RNA extraction kit (9767, TaKaRa) following manufacturer protocol. The complementary DNA library was prepared using KAPA mRNA HyperPrep kit and sequenced on an Illumina NovaSeq 6000 system. Three replicates were sampled for each group. Transcripts abundance was quantified using Kallisto^{73 (link)}. Then, gene abundance was quantified using tximport^{74 (link)}. DESeq2 was used to identify differentially expressed genes (DEGs)^{75 (link)}. Genes with fold change >1.2 or <0.8 and P_adj < 0.05 were defined as DEGs (Supplementary Data). GO enrichment analysis was performed on DEGs identified from either AP2M1 KO or FCHO2 KO samples using the R (v.2021.09.2 + 382) package clusterProfiler (v.4.4.4).