REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-SND1 antibody (rabbit)	Bethyl	Cat# A302-883A, RRID:AB_10631268
SARS-CoV-2 (COVID-19) NSP9 antibody (rabbit)	GeneTex	Cat# GTX135732, RRID:AB_2909871
SARS-CoV-2 (COVID-19) nucleocapsid antibody (rabbit)	GeneTex	Cat# GTX135357, RRID:AB_2868464
SARS-CoV-2 (COVID-19) NSP3 antibody (rabbit)	GeneTex	Cat# GTX135614, RRID:AB_2887505
Normal Rabbit IgG	Cell Signaling Technology	Cat# 2729, RRID:AB_1031062
Anti-SND1 antibody (mouse)	Proteintech	Cat# 60265-1-Ig, RRID:AB_2881386
Anti-SND1 antibody (rabbit)	Proteintech	Cat# 10760-1-AP, RRID:AB_2193410
Anti-dsRNA J2 antibody (mouse)	Jena Bioscience	RNT-SCI-10010200
Anti-FLAG (mouse)	Sigma-Aldrich	Cat# F3165, RRID:AB_259529
Anti-V5 (rabbit)	Abcam	Cat# ab9116, RRID:AB_307024
Anti-Actin (rabbit)	Sigma Aldrich	Cat# A2103, RRID:AB_476694
Bacterial and virus strains
SARS-CoV-2	Peterhoff et al.78	N/A
Chemicals, peptides, and recombinant proteins
Dynabeads Protein G	Thermo Fisher Scientific	10004D
T4 Polynucleotide Kinase	New England Biolabs	M0201L
FastAP Thermosensitive Alkaline Phosphatase	Thermo Fisher Scientific	EF0651
100% DMSO	Sigma-Aldrich	41639
50% PEG8000	New England Biolabs	B10045
T4 RNA ligase high concentration	New England Biolabs	M0437M
5 M NaCl	VWR International	A7006.1000
Proteinase K	New England Biolabs	P8107S
0.1 M DTT	Thermo Fisher Scientific	Y00147
Lithium Chloride	Merck Millipore	5922-500ML
Dodecyl maltoside	Carl Roth	CN26.5
Sodium dodecyl sulphate	Omnilab	APP A3942.1000
Sodium deoxycholate	Sigma-Aldrich	30970-25G
IGEPAL CA-630	Sigma-Aldrich	I8896-100ML
Complete EDTA-free protease inhibitor cocktail	Sigma Aldrich	11873580001
Murine RNase inhibitor	New England Biolabs	M0314L
Turbo DNase	Thermo Fisher Scientific	AM2239
EDTA	VWR International	A4892.1000
EGTA	Carl Roth	3054.1
Urea	Sigma-Aldrich	U0631
TCEP	Sigma-Aldrich	646547
16% Formaldehyde (w/v), Methanol-free	Thermo Fisher Scientific	28908
4',6-Diamidino-2-Phenylindole (DAPI)	Thermo Fisher Scientific	D1306
Fluoromount-G Mounting Medium	Thermo Fisher Scientific	00495802
Dynabeads MyOne Streptavidin C1	Thermo Fisher Scientific	65002
Dynabeads MyOne Silane	Thermo Fisher Scientific	37002D
AMPure XP beads	Beckmann Coulter	A63881
NHS-activated magnetic beads	Thermo Fisher Scientific	PIER88827
N-laroylsarcosine	VWR International	SAFSL7414-50ML
Benzonase	Merck Millipore	71206-3
RNase I	Thermo Fisher Scientific	AM2295
ExoSAP-IT	Thermo Fisher Scientific	78201.1.ML
SUPERase-In RNase Inhibitor	Thermo Fisher Scientific	AM2696
Trichloroacetic acid	Sigma-Aldrich	T0699-100ML
Lipofectamine 2000 transfection reagent	Thermo Fisher Scientific	11668019
FuGene HD transfection reagent	Promega	E2311
NuPAGE 4-12% Bis-Tris Protein Gels	Thermo Fisher Scientific	NP0335BOX
NuPAGE 3-8% Tris-Acetate Protein Gels	Thermo Fisher Scientific	EA0378BOX
AffinityScript reverse transcriptase	Agilent	600109
PowerUp SybrGreen master mix	Thermo Fisher Scientific	A25778
SsoAdvanced Universal SYBR Green Supermix	Biorad Laboratories	1725272
4-Thiouridine	Biosynth Carobsynth	NT06186
Iodoacetamide	Thermo Fisher Scientific	A39271
Buffer RLT	Qiagen	79261
Poly-A-Polymerase	Takara	2180A
ATP	New England Biolabs	N0437A
SMARTscribe Reverse Transcriptase	Takara	639538
Q5 Hot Start High-Fidelity 2x Master Mix	New England Biolabs	M0494L
Deoxynucleotide Mix	Agilent Technologies	200415
Lipofectamine RNAiMAX	Life Technologies	13778030
Anti-FLAG® M2 Magnetic Beads	Merck Millipore	M8823
Proteintech ChromoTek V5-Trap Magnetic Agarose	Proteintech	V5TMA
Triton-X 100	Sigma-Aldrich	T9284-100ML
RNase H	New England Biolabs	M0297L
4x LDS sample buffer	Thermo Fisher Scientific	B0007
QX200 ddPCR EvaGreen Supermix	BioRad	1864034
QX200 droplet generation oil for EvaGreen	BioRad	1864006
2′-deoxythymidine-3′,5′-bisphosphate	Biosynth	NT09781
SND1 recombinant protein	Origene	TP300059
NSP9 recombinant protein	Abcam	ab289608
Critical commercial assays
Pierce BCA Protein Assay Kit	Thermo Scientific	Cat# 23225
CellTiter-Glo® Luminescent Cell Viability Assay	Promega	G7571
Duolink in situ red starter kit	Sigma Aldrich	DUO92101-1KT
Duolink in situ detection reagents green	Sigma Aldrich	DUO92014-30RXN
HCR IHC + HCR RNA-FISH Kit	Molecular Instruments	N/A
Qubit dsDNA HS Kit	Thermo Fisher Scientific	Q32851
Direct-zol RNA MicroPrep	Zymo Research	R2063
RNA Clean & Concentrator-5	Zymo Research	R1015
Zymoclean Gel DNA Recovery Kit	Zymo Research	D4007
NEB Next rRNA Depletion Kit v2	New England Biolabs	E7400X
RED-MALEIMIDE 2nd Generation kit	NanoTemper Technologies	SKU: MO-L014
Deposited data
Illumina sequencing data	This paper	GEO: GSE217429
CoIP proteomics data	This paper	PRIDE: PXD037528
RAP-MS proteomics data	This paper	MassIVE: MSV000090682
Source code for quantification and statistical analysis	This paper	https://github.com/AlexGa/cRIP-eCLIP-workflow and https://doi.org/10.5281/zenodo.8304669
Experimental models: Cell lines
Human: Huh-7 cell line	Virology Diagnostics Unit at Institute of Virology and Immunobiology, University of Würzburg	N/A
Human: Calu-3 cell line	Virology Diagnostics Unit at Institute of Virology and Immunobiology, University of Würzburg	N/A
Human: A549ACE2 cell line	A. Pichlmair	N/A
African Green Monkey: Vero-E6-TMPRSS2 cell line	S. Pöhlmann	N/A
Human: HEK293T	U. Fischer	N/A
Oligonucleotides
RiL-19: /5Phos/rArGrArUrCrGrGrArArGrArGrCrArCrArCr GrUrC/3SpC3/	van Nostrand et al.41	N/A
AR17: CAGACGTGTGCTCTTCCGA	van Nostrand et al.41	N/A
Rand103Tr: /5Phos/NNNNNNNNNNAGATCGGAAGA GCGTCGTGT/3SpC3/	van Nostrand et al.41	N/A
Universal forward PCR primer: AATGATACGGCGACCACCGAGATCTACACTCTTTC CCTACACGACGCTCTTCCGATCT	van Nostrand et al.41; Illumina customer service letter	N/A
Barcoded reverse PCR primer: CAAGCAGAAGACGG CATACGAGATNNNNNNNNGTGACTGGAGTTCAGA CGTGTGCTCTTCCGATCT	van Nostrand et al.41; Illumina customer service letter	N/A
Biotinylated antisense probes	Schmidt et al.8	N/A
HCR probes NegativeSense_N	Molecular Instruments	PRK126
ON-TARGETplus Human SND1 (27044) siRNA - SMARTpool	Dharmacon	L-010657-01-0005
ON-TARGETplus Human ACE2 (59272) siRNA - SMARTpool	Dharmacon	L-005755-00-0005
ON-TARGETplus Non-targeting Pool	Dharmacon	D-001810-10-20
Template-switching oligo: Biotin/TACACGACGCTCTT CCGATCTrGrG + G	Basak et al.79	N/A
RT primer: CAGACGGCTCTTCCGATCTTTTTTTTTTTT TTTTTTTTTTTTTTTTTTTV-3′	This paper	N/A
RdRP Fwd qPCR primer: GTGARATGGTCATGTGTGGCGG	Corman et al.80	N/A
RdRP Rev qPCR primer: CARATGTTAAASACACTATTAGCATA	Corman et al.80	N/A
N Fwd qPCR primer: CACATTGGCACCCGCAATC	Corman et al.80	N/A
N Rev qPCR primer: GAGGAACGAGAAGAGGCTTG	Corman et al.80	N/A
18S rRNA Fwd qPCR primer: ATGGCCGTTCTTAGTTGGTG	Schmidt et al.8	N/A
18S rRNA Rev qPCR primer: GAACGCCACTTGTCCCTCTA	Schmidt et al.8	N/A
SARS-CoV-2 leader Fwd qPCR primer: CCCAGGTAACAAACCAACCAAC	This paper	N/A
SARS-CoV-2 ORF1a (gRNA) Rev qPCR primer: CTCGTTGAAACCAGGGACAAG	This paper	N/A
SARS-CoV-2 M (sgmRNA) Rev qPCR primer: GGTTCCATTGTTCAAGGAGCTT	This paper	N/A
SARS-CoV-2 N (sgmRNA) Rev qPCR primer: GTAATGCGGGGTGCATTTCG	This paper	N/A
Recombinant DNA
pLEX_307	David Root	Addgene plasmid #4139
SND1 (NM_014390) Human Tagged ORF Clone	Origene	RC200059
pDONR223 SARS-CoV-2 NSP9	Fritz Roth	Addgene plasmid #141263
pLEX-SND1	This paper	N/A
pLEX-SND1-FLAG	This paper	N/A
pLEX-NSP9-V5	This paper	N/A
CRISPR/Cas9 control plasmid	Santa Cruz Biotechnology	sc-418922
SND1 CRISPR/Cas9 KO plasmids	Santa Cruz Biotechnology	sc-403949
Software and algorithms
Spectrum Mill MS Proteomics Software	Broad Institute	https://proteomics.broadinstitute.org/millhome.htm
ImageJ	Schneider et al.81	https://imagej.nih.gov/ij/
R	The Comprehensive R Archive Network	https://cran.r-project.org/
Python	Python Programming Language	https://www.python.org/
BWA	Li and Durbin82	http://bio-bwa.sourceforge.net/bwa.shtml
Picard Tools	Broad Institute	https://broadinstitute.github.io/picard
Samtools	Li et al.83	http://samtools.sourceforge.net/
Bedtools	Quinlan and Hall84	https://github.com/arq5x/bedtools2/blob/master/docs/content/overview.rst
MACS2	Zhang et al.85	https://github.com/macs3-project/MACS
Trimmomatic	Bolger et al.86	http://www.usadellab.org/cms/index.php?page=trimmomatic
STAR	Dobin et al.87	https://github.com/alexdobin/STAR
IGV	Robinson et al.88	https://software.broadinstitute.org/software/igv/
Big-FISH	Imbert et al.89	https://big-fish.readthedocs.io/en/stable/
DAVID Bioinformatics Resources	https://david.ncifcrf.gov/	DAVID 6.8