Growth Protocol:	Calu-3 cells were cultured in DMEM with 10% FBS and 1% penicillin/streptomycin
Treatment Protocol:	Prior to lysis, cells were seeded in 100mm dishes, and treated cells were infected with SARS-CoV-2 (MOI = 0.1). At 48 hpi, both mock and treated dishes for RPF, QTI, and mRNA-seq were treated with either 100 μg/ml cycloheximide (CHX) or 2 µg/ml harringtonine (Harr) for 10 min.
Extract Protocol:	For sRNA-seq, RNA was extracted using Trizol. For rest, cells were washed with PBS then lysed with lysis buffer (10 mM Tris-HCl (pH 7.4), 5 mM MgCl2, 100 mM KCl, 1% Triton X-100, 100 μg/ml CHX, 1 mM dithiothreitol, 0.2 U/μl RiboLock RNase inhibitor, and 1 × EDTA-free protease inhibitor cocktail). For RPF-seq and QTI-seq, lysates were treated with RNase I and ribosome protected fragments were isolated using illustra MicroSpin S-400 HR Columns (GE Healthcare).
Library Construction Protocol:	All of the libraries (mRNA-seq, RPF-seq, QTI-seq, and sRNA-seq) were constructed following the Illumina Truseq small RNA library preparation protocol (TruSeq Small RNA Library Prep Guide, Part # 15004197 Rev. G)

Molecule Type:	rRNA- RNA
Library Source:
Library Layout:	SINGLE
Library Strand:	Reverse
Platform:	ILLUMINA
Instrument Model:	Illumina HiSeq 2500
Strand-Specific:	Specific

Data Resource	GEN Sample ID	GEN Dataset ID	Project ID	BioProject ID	Sample ID	Sample Name	BioSample ID	Sample Accession	Experiment Accession	Release Date	Submission Date	Update Date	Species	Race	Ethnicity	Age	Age Unit	Gender	Source Name	Tissue	Cell Type	Cell Subtype	Cell Line	Disease	Disease State	Development Stage	Mutation	Phenotype	Condition Detail	Growth Protocol	Treatment Protocol	Extract Protocol	Library Construction Protocol	Molecule Type	Library Layout	Strand-Specific	Library Strand	Spike-In	Strategy	Platform	Instrument Model	Cell Number	Reads Number	Gbases	AvgSpotLen1	AvgSpotLen2	Uniq Mapping Rate	Multiple Mapping Rate	Coverage Rate