REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Goat anti-mouse IgG-HRP	Thermo Fisher Scientific	Cat#31430; RRID:AB_228307
Anti-FLAG M2 magnetic beads	Millipore Sigma	Cat#M8823; RRID:AB_2637089
Anti-Renilla Luciferase antibody	Millipore Sigma	Cat#MAB4400; RRID:AB_95116
Anti-β actin mouse monoclonal antibody	Cell Signaling Technology	Cat#12262; RRID:AB_2566811
Anti-FLAG M2 mouse monoclonal antibody	Millipore Sigma	Cat#F1804; RRID:AB_262044
Bacterial and virus strains
Escherichia coli (Migula) Castellani and Chalmers	ATCC	Cat#29417
Chemicals, peptides, and recombinant proteins
Pseudo-UTP	APExBio	Cat#B7972
N1-Methylpseudo-UTP	APExBio	Cat#B8049
tRNA from E. coli MRE 600	Roche	Cat#10109541001
Passive Lysis Buffer	Promega	Cat#E1941
M-MLV Reverse Transcriptase	Promega	Cat#M1701
AMV Reverse Transcriptase	Promega	Cat#M5101
EasyTag™ L-[35S]-Methionine	PerkinElmer	Cat#NEG709A500UC
ATP, [γ-32P]	PerkinElmer	Cat#NEG002A100UC
3′-O-Me-m7G(5’)ppp(5′)G RNA Cap Structure Analog	NEB	Cat#S1411S
MEGAscript T7 Transcription Kit	Invitrogen	Cat#AM1334
T4 RNA Ligase 2, truncated	NEB	Cat#M0242S
T4 Polynucleotide Kinase	NEB	Cat#M0201S
CircLigase ssDNA Ligase	Lucigen	Cat#CL4111K
Nuclease P1 from Penicillium citrinum	Millipore Sigma	Cat#N8630
Calf Intestinal Phosphatase	NEB	Cat#M0290
Critical commercial assays
Dual-Luciferase Reporter Assay System	Promega	Cat#E1910
Wheat Germ Extract	Promega	Cat#L4380
Deposited data
Mass Spectrometry Data	This Study	ProteomeXchange: PXD029291
NGS Data for reverse transcriptase error	This Study	GEO: GSE186464
Mendeley Data	This Study	https://doi.org/10.17632/m5sjksybcn.1
Experimental models: Cell lines
Flp-In-T-REx-293	Thermo Fisher Scientific	Cat#R78007; RRID:CVCL_U427
Oligonucleotides
/5Phos/AGATCGGAAGAGCGTCGTGTAG GGAAAGAGT GTAGATCTCGGTGGTCG C/iSp18/CACTCA/iSp18/TTCAGACGTG TGCTCTTCCGATCTATTGATGGTG CCTACAG	IDT	N/A
5′rAppCTGTAGGCACCATCAAT/3ddC/3′	Millipore Sigma	N/A
5′-CAGAGGAGGUAAAA AAAUGUACUUGUACAAA-3′	Millipore Sigma	N/A
5′-CAGAGGAGGUAAAA AAAUGYACUUGUACAAA-3′	Dharmacon	N/A
5′ CAGAGGAGGUAAAAAA AUG m1YAC UUG UACAAA 3′	Genelink	N/A
Recombinant DNA
Pfizer-Spike_pUC57	GenScript; See Table S1 for sequence and primers	N/A
Dual Luciferase Reporter	This Work; See Table S1 for sequence and primers	N/A
Software and algorithms
Proteome Discoverer	Thermo Fisher Scientific	Cat#OPTON-31040; RRID:SCR_014477
GraphPad Prism	GraphPad	RRID:SCR_002798
deepSNV	Bioconductor	RRID:SCR_006214
ImageQuant TL	Cytiva	RRID:SCR_018374
Scaffold	Proteome Software	RRID:SCR_014345
MSnbase	Bioconductor	RRID:SCR_019317
FastQC	N/A	RRID:SCR_014583
Samtools	N/A	RRID:SCR_002105
NGmerge	N/A
Cutadapt	N/A	RRID:SCR_011841
BBMap	N/A	RRID:SCR_016965
Image Lab	Bio-Rad	RRID:SCR_014210
SkyLine	University of Washington	RRID:SCR_014080