Updated project metadata. To identify the proteome alterations in human epithelial cells upon SARS-CoV-2 infection, we performed an in vitro experiment, where we infected lung-adenocarcinoma cultured human airway epithelial cells (Calu-3) with an isolate of the ancestral variant and alpha variant of SARS-CoV-2 in two separate experiments. Samples were then collected 3 hours, 1 day, 3 days, and 7 days post infection. In parallel, for comparison, we collected samples on the same days from non-infected cells and cells treated with SARS-CoV-2 virus (of the corresponding variant) inactivated by ultraviolet radiation. All conditions were performed in biological triplicates and we performed phosphoproteomics analysis with high-pH fractionation and LC-MS/MS. Cell culture specifics Human lung adenocarcinoma Calu3 cells (ATCC, HTB-55) were grown in minimum essential medium (MEM) supplemented with 20% FBS, HEPES, L-glutamin, 100 U/ml penicillin, and 100 mg/ml streptomycin at 37°C and 5% CO2. The SARS-CoV-2 variants were propagated on Vero E6 cells and titrated via end point dilution assay. For UV-inactivation, the virus stock was incubated under UV-light for 3 x 1.5 min. Complete inactivation was confirmed via infection attempt and no live virus could be detected after the treatment. Cells were infected with active or UV-inactivated SARS-CoV-2 in complete MEM at a multiplicity of infection (MOI) of 1. After two  hours of incubation the virus solution was removed, the cells were washed, and fresh growth medium was added. Before the infection, the active and inactivated virus were treated with Trypsin at 1:100 dilution for one hour at 37°C.  Before sample collection at the indicated time points, the cells were washed thoroughly. Cells were lysed in lysis buffer containing 1mM DTT and boiled at 95°C for five minutes.