REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-TRIM28 antibody	Santa Cruz Biotechnology	Catalog # sc-515790
anti-TRIM33 antibody	Abcam	Catalog # ab47062; RRID:AB_956365
anti-EHMT1 antibody	Cell Signaling Technology	Catalog # 35005S; RRID:AB_2799068
anti-EHMT2 antibody	Abcam	Catalog # ab185050; RRID: AB_2792982
anti-VPS35 antibody	Santa Cruz Biotechnology	Catalog # sc-374372; RRID: AB_10988942
anti-SARS-CoV-2 N antibody	Abcam	Catalog # 33717; RRID: AB_2941972
anti-tubulin antibody	Merck	Catalog # T5168
anti-H3 antibody	Cell Signaling Technology	Catalog # 4499
anti-H3K9me2 antibody	Cell Signaling Technology	Catalog # 4658; RRID:AB_10544405
anti-SARS-CoV-2 S antibody	Abcam	Catalog # ab272504; RRID: AB_2847845
anti-ERGIC53 antibody	Santa Cruz Biotechnology	Catalog # sc-365158; RRID: AB_10709004
anti-HCoV-229E nucleoprotein antibody	Sino Biological, Beijing	Catalog # 40640-T62
Peroxidase AffiniPure™ Donkey Anti-Mouse IgG (H + L)	Jackson Immuno Research	Catalog # 715-035-150; RRID: AB_2340770
Peroxidase AffiniPure™ Donkey Anti-Rabbit IgG (H + L)	Jackson Immuno Research	Catalog # 711-035-152; RRID: AB_10015282
Goat anti-Mouse IgG (H + L) Cross-Adsorbed Secondary Antibody, Alexa Fluor™ 555	Thermo Fisher Scientific	Catalog # A-11034; RRID: AB_2576217
Goat anti-Rabbit IgG (H + L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor™ 488	Thermo Fisher Scientific	Catalog # A-21422; RRID: AB_2535844
Bacterial and virus strains
SARS-CoV-2/UT-NCGM02/Human/2020/Tokyo (EPI_ISL_418809)	The University of Tokyo	N/A
Chemicals, peptides, and recombinant proteins
UNC0642	MedChemExpress	Catalog # HY-13980
DAPI (4′,6-diamidino-2-phenylindole, dihydrochloride)	Thermo Fisher Scientific	Catalog #D1306
Dimethyl Sulfoxide, Nuclease and Protease tested	Nacalai Tesque	Catalog # 08904-14
Dulbecco’s modified Eagle’s medium (DMEM), high glucose	Thermo Fisher Scientific	Catalog # 11965118
Fetal calf serum (FCS)	Thermo Fisher Scientific	Catalog # 10270106
Penicillin-Streptomycin Mixed Solution	Nacalai Tesque	Catalog # 09367-34
Puromycin(solution)	INVIVOGEN	Catalog # ant-pr-1
Critical commercial assays
Primer/Probe N2	NIHON GENE RESEARCH LABORATORIES, INC	N/A
LDH cytotoxicity assay kit	Nacalai Tesque	Catalog # 18250-35
Experimental models: Cell lines
Human: A549	ATCC	Catalog # CCL-185
African green monkey: VeroE6/TMPRSS2	National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan	Catalog # JCRB1819
293T/17	ATCC	Catalog # CRL-11268
Experimental models: Organisms/strains
Syrian hamsters: Slc:Syrian	Japan SLC Inc	N/A
Oligonucleotides
sgRNA targeting sequence for target genes, see Table S4	This paper	N/A
Primers used for RT-qPCR, see Table S5	This paper	N/A
Recombinant DNA
pKLV2-EF1a-Cas9Bsd-W	Addgene	Catalog # 68343
pKLV2-U6gRNA5(BbsI)-PGKpuro2ABFP-W	Addgene	Catalog # 67974
The Human CRISPR Library v.3	Addgene	Catalog # 67989
pcDNA3	Thermo Fisher Scientific	Catalog # A-150228
Software and algorithms
MAGeCK v0.5.9.5	Li et al.56	https://anaconda.org/bioconda/mageck
ImageJ	Open source	N/A
Prism 10 software	GraphPad	N/A
Other
96-well cell culture plates	Corning	Catalog # 3596
12-well cell culture plates	Corning	Catalog # 3513
Fusion Solo instrument	Vilber-Lourmat	N/A
CFX96	Bio-Rad	N/A
Ti-E inverted microscope with a C1 confocal laser scanning system	Nikon	N/A
Eclipse TE-2000-U inverted microscope	Nikon	N/A
HT-7700 instrument	Hitachi	N/A