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. C-ter, International license (which was not certified by peer review) is the author/funder. It is made available under a Supplemental Material and Method Cloning. SARS-CoV-2 viral proteins coding sequences were cloned into pcDNA5 FRT

, BirA*Flag vectors by Gateway cloning (as in 1 ) using our collection of Gateway-compatible entry clones as templates 2 (see Supplemental table 4 for sequences), Flp-In? T-REx? HEK293 cells

, BioID samples were prepared as in 3 . Briefly, Flp-In? T-REx? HEK293 cells were grown in Dulbecco's Modified Eagle's Medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS, GlutaMAX? and Penicillin-Streptomycin (1x). Using the Flp-In system (Invitrogen), p.5

, three independent replicates of two 150 cm2 plates of sub-confluent (60%) cells were incubated for 24 hrs in complete media supplemented with 1 µg/ml tetracycline (Sigma), 50 µM biotin (Thermo Fisher Scientific). Cells were collected and pelleted (300 x g, 3 min), washed twice with PBS, and dried pellets were snap frozen, FRT/TO BirA*Flag-viral bait protein sequence plasmid. After selection (DMEM + 10% FBS + P/S + 200 ?g/ml hygromycin B), vol.1

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, Over 1 is considered as either enrichment or gain (if absent from the basal condition), between 1 and -1 corresponds to unchanged, and below -1 shows decreased or lost hits. When no value is indicated, it corresponds to interactions not detected in the poly(I:C) and the corresponding basal condition. The reported interactions columns display the bait-prey pairs previously identified in the literature (see tab D for details and references and main of all coronaviruses across the literature, with corresponding techniques and references. E. Comparative ToppCluster analysis (see Supplemental Method) output of all bait interactomes obtained in basal condition (union of N-and C-terminally tagged viral bait proteins BioID results). F. Input list for the analysis presented in E. G. Same as E, but with hits increased or gained after poly(I:C) treatment. H. Input enriched or gained interactors after poly(I:C) for the ToppCluster analysis presented in G. I. Raw output of the Perseus analysis of MaxQuant LFQ results. Columns G-JA: log2 transformed LFQ intensities for all biological replicates and conditions, the 'Indegree' column. The pand q-values are extracted from the Perseus statistical analysis of MaxQuant data (Tab H for details, 2015.

, Supplemental Table 2. Metascape custom annotation of all high confidence proximal interactors. The cell