This PDF file includes:

• fig. S1. Knockdown efficiency of DUBs by sgRNAs.
  
• fig. S2. Identification of functional DUBs in antiviral response by FACS analysis and luciferase assay.
  
• fig. S3. Validation of identified DUB candidates in an overexpression system and by siRNA.
  
• fig. S4. DUBs interact with the key molecules in type I IFN signaling pathways and the induction of the indicated genes in sg_NT A549 and PBMCs after viral infection.
  
• fig. S5. Attenuated DUB expression in A549 cells and PBMCs affects virus-induced cytokine expression.
  
• fig. S6. Total ubiquitination and different linkages of ubiquitination of the key molecules in the type I IFN pathway are regulated by DUBs.
  
• fig. S7. USP5 inhibits type I IFN signaling and enhances viral replication through the promotion of STUB1-mediated RIG-I degradation.
  
• Legends for tables S1 to S3

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Other Supplementary Material for this manuscript includes the following:

• table S1 (Microsoft Excel format). Relative mRNA expression of DUBs in THP-1 monocytes or macrophages after VSV infection or IFN-β treatment for the indicated time points and the relative mRNA expression of DUBs in PBMCs after VSV infection, HSV-1 infection, or IFN-β treatment.
  
• table S2 (.pdf format). Summary of DUB expression patterns using different stimuli.
  
• table S3 (Microsoft Excel format). List of sgRNA sequences, qRT-PCR primer sequences, and siRNA sequences used in this study.