REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and Virus Strains
SARS-CoV2 (USA WA1/2020)	BEI Resources	NR52281
BL21	NEB	C2527I
Chemicals, Peptides, and Recombinant Proteins
XBA1	NEB	R0145S
NOTI	NEB	R3189S
STUI	NEB	R0187S
Fugene HD	Promega	E2311
Cy3-UTP	Sigma	PA53026
Cy5-UTP	Sigma	PA55026
DNaseI	NEB	M0303L
Millenium RNA ladder	ThermoFisher Scientific	AM7151
TRIzol LS	ThermoFisher Scientific	10296028
Lysozyme	Fisher Scientific	BP535-10
Roche EDTA-free protease inhibitor cocktail	Millipore Sigma	11873580001
HisPur™ Cobalt Resin	ThermoFisher Scientific	89965
RNaseA	QIAGEN	19101
Atto 488 NHS ester	Millipore Sigma	41698
100X/1.49 NA oil	Cargille Lab	16241
(R)-(+)-α-Lipoic acid	Sigma-Aldrich	07039
1,6-Hexanediol	Sigma Aldrich	240117
Kanamycin	Millipore Sigma	60615-25G
5-Nitroisatoic Anhydride (5NIA)	AstaTech	69445
Recombinant SARS-CoV-2 Nucleocapsid Protein with C-terminal His-tag	Ray Biotech	QHD43423
Recombinant 6xHis-TEV-Nucleocapsid Y109A protein	this paper	N/A
Recombinant 6xHis-TEV-Nucleocapsid protein	this paper	N/A
Recombinant Nucleocapsid protein	this paper	N/A
Critical Commercial Assays
HiScribe™ T7 High Yield RNA Synthesis Kit	NEB	E2040S
1.8 × Mag-Bind TotalPure NGS SPRI beads	Omega Bio-tek	M1378-01
SuperScript II Reverse Transcriptase	Invitrogen	18064-022
RNeasy MinElute columns	QIAGEN	74204
Illustra G-50 microspin columns	GE Healthcare	GE27-5330-01
NEBNext second-strand synthesis reaction	NEB	B6117S
Nextera XT	Illumina	FC-131-1024
Amicon Ultra-4, PLGC Ultracel-PL Membrane, 10 kDa	Merck	UFC801024
Deposited Data
Raw and analyzed data	This paper	GEO: GSE162569
Experimental Models: Cell Lines
Vero E6	ATCC	CRL-1586
HEK293	ATCC	CRL-1573
HEK293T	ATCC	CRL-11268
Oligonucleotides
Sal-N-protein-fw: acgcatcgtcgacATGTCTGATAATGG ACC-CCAAAATCAG	IDT	N/A
Not1-N-protein-rev: tatctatgcggccgc TTAGGCCTGAGTTGAGTCAGC	IDT	N/A
Recombinant DNA
pJet	ThermoFisher Scientific	K1231
pET30b-6xHis-TEV-Nucleocapsid	This paper	N/A
pET30b-6xHis-TEV-Nucleocapsid Y109A	This paper	N/A
Nucleocapsid GFP Spark	Sino biological	VG40588-ACGLN
Plasmid pUC57-2019-ncov	This paper	N/A
pJet- 5′ end	This paper	N/A
pJet-frameshifting region	This paper	N/A
pJet- PS region	This paper	N/A
pJet- Anti-Sense-5′ end	This paper	N/A
pJet- Anti-Sense-frameshifting region	This paper	N/A
Software and Algorithms
ImageJ	Schneider et al., 2012	https://imagej.nih.gov/ij/
ShapeMapper2	Busan and Weeks, 2018	https://github.com/Weeks-UNC/shapemapper2
RNAStructure	Reuter and Mathews, 2010	https://rna.urmc.rochester.edu/RNAstructure.html
Superfold	Smola et al., 2015	https://github.com/Weeks-UNC/Superfold
VARNA	Darty et al., 2009	http://varna.lri.fr/index.php?lang=en&page=home&css=varna
ImageTank	O’Shaughnessy et al., 2019	https://www.visualdatatools.com/ImageTank/
Matplotlib	Hunter, 2007	https://matplotlib.org/
SciPy	Virtanen et al., 2020	https://www.scipy.org/
FRESCo	Sealfon et al., 2015	https://www.broadinstitute.org/fresco/running-fresco
Muscle 3.8.31	Edgar, 2004	https://www.drive5.com/muscle/
RAxML version 8.2.12 with the GTRGAMMA model of nucleotide evolution	Stamatakis, 2014	https://cme.h-its.org/exelixis/web/software/raxml/
RNAz 2.1	Gruber et al., 2010	https://www.tbi.univie.ac.at/software/RNAz/
Scikit-learn	Pedregosa et al., 2011	https://scikit-learn.org/
ggplot2 3.1.1	Wickham, 2016	https://ggplot2.tidyverse.org
Genome Viewer	Robinson et al., 2011	http://software.broadinstitute.org/software/igv/
Other
SARS-CoV-2 sequence	NC_045512	https://www.ncbi.nlm.nih.gov/nuccore/1798174254
Severe acute respiratory syndrome coronavirus 2 isolate 2019-nCoV WHU01	MN988668.1	https://www.ncbi.nlm.nih.gov/nuccore/MN988668.1