Reagent/Resource	Reference or Source	Identifier or Catalog Number
Experimental Models
HEK Flp‐In™ 293 T‐Rex cell	Life Technologies	B6.129P2Gpr37tm1Dgen/J
HEK293	ATCC®	CRL‐1573™
Calu‐1	ATCC®	HTB‐54
U2‐OS	ATCC®	HTB‐96™
Recombinant DNA
pOG44 Flp‐Recombinase Expression Vector	Life Technologies	V600520
Gateway™ pDONR221™	Thermo Fisher Scientific	12536017
MAC‐tag‐N destination vector	Addgene	108078
MAC‐tag‐C destination vector	Addgene	108077
MAC‐GFP	Addgene	139636
pDEST40	Thermo Fisher Scientific	12274015
pcDNA5/FRT/TO	Invitrogen™	V652020
Antibodies
Anti‐HA Tag Antibody	Biolegend	PRB‐101C
Goat anti‐Mouse IgG (H + L) Highly Cross‐Adsorbed Secondary Antibody, Alexa Fluor Plus 488	Thermo Fisher Scientific	A32723
Alexa Fluor594‐conjugated secondary antibody	Thermo Fisher	A32740
Alexa Fluor‐488‐conjugated secondary antibody	Thermo Fisher	A‐11001
Anti‐alpha Tubulin antibody	Abcam	ab7291
Goat anti‐mouse IgG H&L (HRP)	Abcam	97023
anti‐V5 antibody	Invitrogen	37‐7500
Alexa Fluor 594‐conjugated phalloidin	Thermo Fisher	A32740
Rabbit anti‐SARS‐CoV2 N protein		Rusanen et al (2021)
Alexa Fluor goat anti‐rabbit IgG 488	Invitrogen	A11008
Alexa Fluor goat anti‐mouse IgG 568	Invitrogen	A11004
α‐tubulin monoclonal antibody	Abcam	ab184613
Chemicals, enzymes and other reagents
Gateway™ LR Clonase™ Enzyme Mix	Life Technologies	11791043
DMEM	Life Technologies	41965062
HEPES	Sigma	7365‐45‐9
Hoechst	Lifetech	33342
IGEPAL (electrophoresis reagent) CA630	Sigma	9002‐93‐1
Amersham™ ECL™ Prime	Cytiva	RPN2232
FuGENE® 6 Transfection Reagent	Promega	E2691
Pierce™ BCA Protein assay	Thermo Fisher Scientific	23225
Penicillin–streptomycin	Life Technologies	15140130
Formic Acid, ≥95%	Sigma	64‐18‐6
Tris(2‐carboxyethyl)phosphine (TCEP)	Sigma‐Aldrich	51805‐45‐9
Ammonium bicarbonate (AMBIC)	Sigma‐Aldrich	1066‐33‐7
N,N‐Dimethylformamide	Sigma	68‐12‐2
Sodium chloride	Merck	7647‐14‐5
Iodoacetamide (IAA)	Sigma‐Aldrich	64‐69‐7
Ethylenediamine, ≥ 99.5%	Sigma	107‐15‐3
Hygromycin B	Invitrogen	10687010
Laemmli sample buffer	Bio‐Rad	1610737
Sodium dodecyl sulfate	Sigma	151‐21‐3
Triton X‐100	Sigma	X100‐500
Phenylmethanesulfonylfluoride (PMSF) > 98.5%	Sigma	329‐98‐6
water MS‐grade	Merck	7732‐18‐5
Trypsin‐EDTA	Gibco	25200‐56
Sequencing Grade Trypsin	Promega	V5113
Strep‐Tactin® Sepharose® 50% (vol/vol) suspension	IBA life sciences	2‐1201‐010
Bio‐Spin® Chromatography Columns	Bio‐Rad	732‐6008
Sodium fluoride	Sigma	7681‐49‐4
Protease inhibitor cocktail	Sigma‐Aldrich	P8340/P2745
Biotin	Thermo Fisher Scientific	29129
Benzonase® Nuclease	Santa Cruz Biotechnology	sc‐202391
Tetracycline hydrochloride	Sigma‐Aldrich	T3383‐25G
ECL Western Blotting Detection Reagent	GE Healthcare	RPN2209
DRAQ5	Thermo Fisher	62251
DAPI, 4’,6‐diamidino‐2‐phenylindole, dihydrochloride	Sigma	D9542
DAPI, 4’,6‐diamidino‐2‐phenylindole, dihydrochloride	Santa Cruz	sc‐3598
RPMI medium	Sigma	R0883‐1L
Methotrexate	Selleck Chemicals	CL‐14377, CAS: 59‐05‐2
Compound XL413	Selleck Chemicals	BMS‐863233,1169562‐71‐3
Restore Plus Stripping buffer	Thermo Fisher	46430
Fetal bovine serum (FBS)	Gibco	10270‐106
Skimmed milk powder	Valio	D1‐5824
Ribavirin	Sigma‐Aldrich	36791‐04‐5
TWEEN®20	Sigma‐Aldrich	P1379‐250ML
Pure nitrocellulose membrane 0.45 μm	Perkin‐Elmer	NBA085C001EA
SDS‐PAGE gel	Bio‐Rad	4561096
Bradford reagent	Bio‐Rad	500‐0006
Software
Cytoscape v3.4.0	http://www.cytoscape.org	Shannon et al (2003)
nSolver™ 4.0	Nanostring Technologies
SlideBook	3I Intelligent Imaging Innovations
ImageJ	https://imagej.net/software/fiji/
SCT BIAS software	Single‐Cell‐Technologies	Daly et al (2020)
Xcalibur 2.0.7 SP1	Thermo Fisher
MaxQuant version 1.6.0.16	https://www.maxquant.org/	Cox and Mann (2008)
Significance Analysis of INTeractome 3.6.0	http://saint‐apms.sourceforge.net/Main.html	Choi et al (2011), Choi et al (2012)
Proteome Discoverer	Thermo Fisher
Prism 9.2	GraphPad Software
Harmony 4.9	PerkinElmer
Other
Easy‐nLC II Liquid Chromatography system	Thermo Fisher Scientific	LC120
Q Exactive™ Hybrid Quadrupole‐Orbitrap™ Mass Spectrometer	Thermo Fisher Scientific	IQLAAEGAAPFALGMAZR
Electrospray ionization sprayer	Thermo Fisher
Fluorescence microscope	Leica	Leica TCS SP8 STED
Turbo transfer system	Bio‐Rad
Nanostring nCounter®	NanoString Technologies, Seattle, USA
NanoString nCounter gene expression platform	NanoString Technologies, Seattle, USA
nCounter Prep Station	NanoString Technologies, Seattle, USA
Intelligent Imaging Innovations (3i) Marianas inverted spinning disk microscope	Yokogawa	Yokogawa CSU‐X1 M1 5,000 rpm
Leica Stellaris 8 Falcon microscope	Leica
Opera Phenix spinning‐disk confocal microscope	PerkinElmer
C‐18 Macro Spin Colum	Nest Group	800‐347‐6378
Bio‐Dot® Microfiltration System	Bio‐Rad	1703938
iBright Imaging Systems	Thermo Fisher
Acoustic liquid handler Echo 550	Labcyte
RNeasy® Mini Kit	Qiagen, Hilden, Germany	74004