Integrated multi-omics analysis of lung transcriptome and proteome shows strong tissue injury and innate immune responses upon severe SARS-CoV-2 infection. (A) Venn diagram of transcripts with matching Uniprot IDs and global lung proteome. (B) Percent associated genes of representative GO terms for 269 globally shared factors in unfiltered proteome and transcriptome. (C) Venn diagram of transcripts with matching Uniprot IDs and global lung proteome factors significantly altered in at least one time point (0, 2, 4, and 6 days). (D) Percent associated genes of representative GO terms for 132 significantly changed shared factors in at least one time point (0, 2, 4, and 6 days).