Growth Protocol:	Protocols for maintenance of hPSCs and generation of lung cells were slightly modified from previous studies (Chen et al., 2019; Huang et al., 2014). Pancreatic endocrine cell differentiation was performed using INSGFP/W MEL-1 cells. Cells were cultured on Matrigel-coated 6-well plates in StemFlex medium (Gibco Thermo Fisher).; Protocols for maintenance of hPSCs and generation of lung cells were slightly modified from previous studies (Chen et al., 2019; Huang et al., 2014). Pancreatic endocrine cell differentiation was performed using INSGFP/W MEL-1 cells. Cells were cultured on Matrigel-coated 7-well plates in StemFlex medium (Gibco Thermo Fisher).; Protocols for maintenance of hPSCs and generation of lung cells were slightly modified from previous studies (Chen et al., 2019; Huang et al., 2014). Pancreatic endocrine cell differentiation was performed using INSGFP/W MEL-1 cells. Cells were cultured on Matrigel-coated 8-well plates in StemFlex medium (Gibco Thermo Fisher).; Protocols for maintenance of hPSCs and generation of lung cells were slightly modified from previous studies (Chen et al., 2019; Huang et al., 2014). Pancreatic endocrine cell differentiation was performed using INSGFP/W MEL-1 cells. Cells were cultured on Matrigel-coated 9-well plates in StemFlex medium (Gibco Thermo Fisher).; Protocols for maintenance of hPSCs and generation of lung cells were slightly modified from previous studies (Chen et al., 2019; Huang et al., 2014). Pancreatic endocrine cell differentiation was performed using INSGFP/W MEL-1 cells. Cells were cultured on Matrigel-coated 10-well plates in StemFlex medium (Gibco Thermo Fisher).; Protocols for maintenance of hPSCs and generation of lung cells were slightly modified from previous studies (Chen et al., 2019; Huang et al., 2014). Pancreatic endocrine cell differentiation was performed using INSGFP/W MEL-1 cells. Cells were cultured on Matrigel-coated 11-well plates in StemFlex medium (Gibco Thermo Fisher).
Treatment Protocol:	Mock infected versus SARS-CoV-2 infected
Extract Protocol:	Total RNA was extracted in TRIzol (Invitrogen) and DNase I treated using Directzol RNA Miniprep kit (Zymo Research) according to the manufacturer’s instructions.
Library Construction Protocol:	RNAseq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

Molecule Type:	Poly(A)+ RNA
Library Source:
Library Layout:	PAIRED
Library Strand:	Forward
Platform:	ILLUMINA
Instrument Model:	Illumina NovaSeq 6000
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	Case Detail	Control 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