REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse monoclonal anti-Human/Rat/Hamster ACE2	Biotechne	Cat #MAB9332
Mouse monoclonal SARS-CoV/SARS-CoV-2 Nucleocapsid	Sino Biological	Cat #40143-MM05; RRID:AB_2827977
Alexa Fluor® 647 AffiniPure Donkey Anti-Mouse IgG (H + L)	Jackson ImmunoResearch	Cat #715-605-150; RRID:AB_2340862
Monoclonal ANTI-FLAG M2 antibody	Sigma Aldrich	Cat #F1804; RRID:AB_262044
Rabbit monoclonal HA-Tag (C29F4)	Cell Signaling Technology	Cat #3724S; RRID:AB_1549585
Rabbit polyclonal GAPDH (0411) Antibody	SantaCruz Biotechnology	Cat #sc-47724; RRID:AB_627678
Peroxidase AffiniPure Donkey anti-Rabbit IgG	Jackson ImmunoResearch	Cat #711-035-152; RRID:AB_10015282
Rabbit anti-mouse Immunoglobulins/HRP	Dako	Cat #P0260; AB_2636929
Rabbit monoclonal anti-ILF3	Abcam	Cat #Ab 92355; RRID:AB_2049804
Rabbit monoclonal anti-QKI	Abcam	Cat #Ab 126742; RRID:AB_11129508
Rabbit monoclonal anti-HNRNPA2B1	Abcam	Cat #Ab 259894
Rabbit monoclonal anti-SFPQ	Abcam	Cat #Ab 177149
Bacterial and virus strains
SARS-CoV-2 isolate 220_95	Isolated from patient (Onodi et al., 2021)	EPI_ISL_469284
Chemicals, peptides, and recombinant proteins
32% Paraformaldehyde (formaldehyde) aqueous solution	Electron Microscopy Sciences	Cat #15714
DMSO	Sigma-Aldrich	Cat #D5879
Triton X-100	Sigma-Aldrich	Cat #T9284
Artemisinin	Sigma-Aldrich	Cat #361593
(S)-(+)-Campthotecin	Sigma-Aldrich	Cat #C9911
Cerulenin	Sigma-Aldrich	Cat #C2389
Dabigatran	Sigma-Aldrich	Cat #SML2370
Geldanamycin from Streptomyces hygroscopicus	Sigma-Aldrich	Cat #G3381
Phenethyl isothiocyanate	Sigma-Aldrich	Cat #253731
Remdesivir	Selleckchem	Cat #SE-S8932
Sunitinib malate	Sigma-Aldrich	Cat #PZ0012
MyOne C1 beads	Thermo Fisher Scientific	Cat #65001
50 mM D-biotin	Thermo Fisher Scientific	Cat #B20656
SUPERase-in	Thermo Fisher Scientific	Cat #AM2696
NA-Deoxycholate	Sigma Merck	Cat #30970
N-Laurosylsarcosine sodium salt	Sigma Merck	Cat #L7414
EDTA ULTROL grade	Sigma Merck	Cat #324504
Trichloroacetic acid	Sigma Merck	Cat #T0699
Proteinase K	Qiagen	Cat #19133
TRizol LS Reagent	Thermo Fisher Scientific	Cat #10296028
Dynabeads Protein G	Thermo Fisher Scientific	Cat #10004D
3XFLAG peptide	Sigma Merck	Cat #F4799
HA peptide	Sigma Merck	Cat #11666975001
GlycoBlue Coprecipitant	Thermo Fisher Scientific	Cat #AM9515
Lipofectamine RNAiMax Transfection Reagent	Thermo Fisher Scientific	Cat #13778150
Lipofectamine 3000 Transfection Reagent	Thermo Fisher Scientific	Cat #L3000015
Bolt 4–12% Bis-Tris plus	Thermo Fisher Scientific	Cat #NW04122BOX
Bolt 10% Bis-Tris plus	Thermo Fisher Scientific	Cat #NW00100BOX
2X Laemmli Sample Buffer	Biorad	Cat #1610737
Critical commercial assays
CellTiter-Glo® 2.0 Assay	Promega	Cat #G9242
Profection® Mammalian Transfection System	Promega	Cat #E1200
Luna® Universal One-Step RT-qPCR Kit	New England Biolabs	Cat #E3005E
Maxima First Strand cDNA Synthesis Kit	Thermo Fisher Scientific	Cat #K1671
Experimental models: Cell lines
Lenti-X 293T	Takara Bio	Cat #632180
Lenti-X 293T-ACE2	This manuscript	N/A
A549	ATCC	Cat #CCL-185
A549-ACE2	This manuscript	N/A
Vero E6	ATCC	Cat #CRL-1586
Oligonucleotides
ChIRP tilling oligos, see Table S1	This paper	N/A
E_Sarbeco Forward: ACA GGT ACG TTA ATA GTT AAT AGC GT	Corman et al., (2020)	N/A
E_Sarbeco Reverse: ATA TTG CAG CAG TAC GCA CAC A	Corman et al., (2020)	N/A
EWSR1 HA Forward: TAA ACT ATG AAT TCA GGA TGG CGT CCA CGG ATT ACA GTA CCT ATA GCC AAG CTG CAG CGC AGC AGG GC	This paper	N/A
EWSR1 HA Reverse: ATA GTT TAG CGG CCG CTC AAG CGT AAT CTG GAA CAT CGT ATG GGT ATC CTC CAG CGG CCG AGT AGG GCC GAT CTC TGC GC	This paper	N/A
ACE2 Forward: CCG CTC GAG CGG GCC ATG TCA AGC TCT TCC TGG CTC	This paper	N/A
ACE2 Reverse: ATA AGA ATG CGG CCG CTT AAA AGG AGG TCT GAA CAT CAT CAG TG	This paper	N/A
ON-TARGETplus Human ILF3 siRNA - SMARTpool	Horizon Discovery	Cat #L-012442-00
ON-TARGETplus Human HNRNPA2B1 siRNA -SMARTpool	Horizon Discovery	Cat #L-011690-01
ON-TARGETplus Human QKI siRNA - SMARTpool	Horizon Discovery	Cat #L-024905-01
ON-TARGETplus Human SFPQ siRNA - SMARTpool	Horizon Discovery	Cat #L-006455-00
ON-TARGETplus Human CTSL siRNA SMART Pool	Horizon Discovery	Cat #L-005841-00
ON-TARGETplus Non-targeting Pool	Horizon Discovery	Cat #D-001810-10-05
QKI sgRNA targeting sequence: GGATCTTCAACCACCTCGAG	This paper	N/A
Recombinant DNA
pLVX-EF1alpha-IRES-Puro	Takara Bio	Cat #631988
pLVX-ACE2	This manuscript	N/A
MGC Human EWSR1 Sequence-Verified cDNA	Horizon Discovery	Cat #MHS6278-202759357
3xFlag SFPQ_pUC57-mini Plasmid	Genscript	N/A
3xFlag QKI_pUC57 Plasmid	Genscript	N/A
3xFlag ILF3_pUC57-Mini Plasmid	Genscript	N/A
3xFlag HNRNPA2B1_pUC57 Plasmid	Genscript	N/A
3xFlag HSPB1_pUC57 Plasmid	Genscript	N/A
3xFlag GFP_pUC57 Plasmid	Genscript	N/A
3xFlag TRIM28_pUC57-mini Plasmid	Genscript	N/A
Software and algorithms
Attune NxT	Thermo Fisher Scientific	Version 2.6
FlowJo	Tree Star	Version 10.0.8
Prism	GraphPad Software	Version 7.0d
Serial Cloner	SerialBasics	Version 2.6.1
ClueGo	Cytoscape	Version 2.5.7
Genamania	Cytoscape	Version 3.5.2
Other
Attune NxT	Thermo Fisher Scientific	N/A
TriStar2 LB 942	BERTHOLD Technologies	N/A
LightCycler 480	Roche	N/A