REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
anti-biotin	ImmuneChem	Cat#ICP0615; RRID:AB_2893170
anti-S	Sino Biological Inc	Cat#40591-T62; RRID:AB_2893171
anti-N	Sino Biological Inc	Cat#40143-mm08; RRID:AB_2827978
anti-Myc	MBL Life Science	Cat#M047-3; RRID:AB_591112
anti-Flag	MBL Life Science	Cat#M185-3L; RRID:AB_11123930
anti-Flag-HRP	Sigma-Aldrich	Cat#A8592; RRID:AB_439702
anti-β-actin	Sigma-Aldrich	Cat#A5441; RRID:AB_476744
anti-p-STAT1-Y701	Abcam	Cat#ab29045; RRID:AB_778096
anti-H3K36me3	Cell Signaling Technology	Cat#4909; RRID:AB_1950412
anti-MAVS	Santa Cruz Biotechnology	Cat#SC-166583; RRID:AB_2012300
anti-ITGB1	Santa Cruz Biotechnology	Cat#SC-374429; RRID:AB_11012020
anti-Myc-HRP	Santa Cruz Biotechnology	Cat#SC-40 HRP; RRID:AB_2857941
anti-STAT1	Beyotime Biotechnology	Cat#AF2512; RRID:AB_2893172
anti-IRF3	Beyotime Biotechnology	Cat#AF2485; RRID:AB_2893173
anti-p-IRF3-S386	Beyotime Biotechnology	Cat#AF1594; RRID:AB_2893174
anti-SETD2	Abclonal	Cat#A3194; RRID:AB_2764980
anti-GAPDH	Proteintech	Cat#60004-1-Ig; RRID:AB_2107436
anti-rabbit IgG conjugated HRP	R&D Systems	Cat#HAF008; RRID:AB_357235
anti- mouse IgG conjugated HRP	R&D Systems	Cat#HAF007; RRID:AB_357234
Alexa fluor® 594-conjugated affinipure goat anti-rabbit IgG (H+L)	ImmunoResearch Laboratories Inc	Cat#111-585-003; RRID:AB_2338059
Bacterial and virus strains
DH5α	Tsingke Biotechnology Co.	Cat#TSV-A07
SeV	(Zheng et al., 2020)	PMID: 33372174
SARS-CoV-2	Peking Union Medical College	IPBCAMS-WH-01/2019
Chemicals, peptides, and recombinant proteins
Human IFN-alpha 1	Cell Signaling Technology	Cat#8927
Azacitidine	Selleck	Cat#S1782
Camptothecin	Selleck	Cat#S1288
Dasatinib	Selleck	Cat#S1021
Glycyrrhizic acid	Selleck	Cat#S2302
Melatonin	Selleck	Cat#S1204
Methotrexate	Selleck	Cat#S1210
Nicardipine	Selleck	Cat#S5255
Pemetrexed	Selleck	Cat#S1135
Sulfinpyrazone	Selleck	Cat#S4628
Streptavidin-HRP	Abcam	Cat#ab7403
Thimerosal	Selleck	Cat#S3646
Torasemide	Selleck	Cat#S1698
Verteporfin	Selleck	Cat#S1786
Critical commercial assays
Dual-Luciferase Reporter Assay Kit	Vazyme	DL101-01
Cell Counting Kit	Yeasen	40203ES60
Deposited data
PaxDB	(Wang et al., 2015)	PMID: 25656970
Multilevel proteomics data of SARS-CoV-2	(Stukalov et al., 2021)	PMID: 33845483
Raw data of mass spectrometry	This study	PXD022086
Experimental models: Cell lines
HEK293T	ATCC	Cat#CRL-11268
HEK293T-hACE2	(Wu et al., 2021b)	PMID: 34117209
HeLa-hACE2 cells	This study	N/A
MAVS-knockout HeLa-hACE2 cells	This study	N/A
Vero	ATCC	CCL-81
Oligonucleotides
See Table S6 for oligonucleotides
Recombinant DNA
pcDNA3.1-myc-TurboID	This study	N/A
pcDNA6B-TurboID-myc	This study	N/A
pCAG-TurboID-myc	This study	N/A
pCDH-CMV-MCS- EF1α-copGFP	System Biosciences	Cat#CD511B-1
pLP1	Thermofisher	Cat#K4975-00
pLP2	Thermofisher	Cat#K4975-00
pRK5-Myc-TBK1	(Meng et al., 2016)	PMID: 27125670
Software and algorithms
Clusterprofiler	(Yu et al., 2012)	http://www.bioconductor.org/packages/release/bioc/html/clusterProfiler.html
Enrichr	(Kuleshov et al., 2016)	https://maayanlab.cloud/Enrichr/
Mascot	Matrix Science	http://www.matrixscience.com/
PANDA	(Chang et al., 2019)	https://sourceforge.net/projects/panda-tools/
Pepdistiller	(Li et al., 2012)	http://sourceforge.net/projects/pepdistiller
Perl	Perl Core Team	http://www.perl.org
R	R Core Team	http://www.r-project.org
ReactomePA	(Yu and He, 2016)	http://www.bioconductor.org/packages/release/bioc/html/ReactomePA.html
REVIGO	(Supek et al., 2011)	http://revigo.irb.hr/
SAINTexpress	(Teo et al., 2014)	https://sourceforge.net/projects/saint-apms/files/