REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Human ACE-2 Antibody	R & D Systems	#AF933 RRID:AB_355722
CDX2	Biogenex	#MU392A-UC RRID:AB_2650531
Cytokeratin-20	Santa Cruz	#sc-56522 RRID:AB_831485
FOXJ1	Thermo Fisher Scientific	#14-9965-82 RRID:AB_1548835
Acetyl-α-Tubulin	Cell Signaling	#5335 RRID:AB_2798556
acetyl-alpha tubulin	Sigma-Aldrich	#MABT868 RRID:AB_2819178
MUC5AC	Thermo Fisher Scientific	#MA5-12178 RRID:AB_10978001
P63	Biocare	#CM 163 A RRID:AB_10582730
SARS-CoV/SARS-CoV-2 Nucleocapsid Antibody	Sino Biological	#40143-R001 RRID:AB_2827974
Ki67 Antibody (SP6)	THERMO FISHER	#RM-9106-S1 RRID:AB_2314700
Donkey anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488	Thermo Fisher Scientific	#A-21202 RRID:AB_141607
Donkey anti-Rabbit IgG (H+L) Secondary Antibody, Alexa Fluor 594 conjugate	Thermo Fisher Scientific	#A-21207 RRID:AB_141637
Donkey anti-Rabbit IgG (H+L) Secondary Antibody, Alexa Fluor 647 conjugate	Thermo Fisher Scientific	#A-31573 RRID:AB_2536183
Donkey anti-Goat IgG (H+L) Secondary Antibody, Alexa Fluor 647	Thermo Fisher Scientific	#A-31571 RRID:AB_162542
Donkey anti-Goat IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 647	Thermo Fisher Scientific	#A-21447 RRID:AB_141844
DAPI	Santa Cruz	#sc-3598
Chemicals, peptides, and recombinant proteins
Y-27632	MedchemExpress	#HY-10583
CHIR99021	Cayman Chemical	#13122
Retinoic acid	Sigma Aldrich	#R2625-500MG
LDN 193189 hydrochloride - DM 3189 hydrochloride	Axon Medchem	#Axon 1509
L-Ascorbic acid	Sigma Aldrich	#A4544-100G
SB431542	R&D Systems	#1614/50
Dorsomorphin dihydrochloride	R&D Systems	#3093/50
IWP2	R&D Systems	#3533/50
Dexamethasone	Sigma-Aldrich	#D4902
8-Bromo-cAMP	Sigma-Aldrich	#B5386
IBMX	Sigma-Aldrich	#I5879
A83-01	Tocris Bioscience	#2939
DMH1	Tocris Bioscience	#4126
GW6471	Selleck	#S2798
Xanthohumol	MedchemExpress	#HY-N1067
Chetomin	Sigma-Aldrich	#C9623
ND-646	MedchemExpress	#HY-101842
TOFA	MedchemExpress	#HY-101068
Activin A	R&D Systems	#338-AC-500/CF
Recombinant Human FGF-10 Protein	Peprotech	#100-26-500UG
Recombinant Human bFGF Protein	Peprotech	#100-18B-500UG
Recombinant Human BMP-4 Protein	R & D Systems	#314-BP
Recombinant Human EGF	Peprotech	#AF-100-15-500UG
Recombinant Human BMP-2	Peprotech	#AF-120-02
Recombinant Human FGF-4	Peprotech	#AF-100-31
Deposited data
scRNA-seq	This paper	GEO: GSE160231
RNA-seq	This paper	GEO: GSE160231
Metabolism Profiling	This paper	NMDR: ST001921
Experimental models: Cell lines
hESC line H1	WiCell	0043
RUES2	WiCell	0013
293T	ATCC	#CRL-11268
Vero E6	ATCC	#CRL-1586
Software and algorithms
Code for data analysis	This paper	zenodo: https://zenodo.org/record/5533014
Cell Ranger	10X Genomics	https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome
Scran	Lun et al., 2016	https://bioconductor.org/packages/release/bioc/html/scran.html
Rstudio	Rstudio	https://www.rstudio.com/
Seurat R package v3.1.0	Butler et al., 2018	https://satijalab.org/seurat/
DAVID6.8	LHRI	https://david.ncifcrf.gov/home.jsp
Adobe illustrator CC2017	Adobe	https://www.adobe.com/products/illustrator.html
Graphpad Prism 6	Graphpad software	https://www.graphpad.com
ToppCell Atlas	Toppgene	https://toppgene.cchmc.org/
Other
StemFlex	GIBCO Thermo Fisher	#A3349401
mTeSR1 Complete Kit	Stem Cell Technologies	#85850
F12	GIBCO Thermo Fisher	#31765035
Penicillin-Streptomycin (5,000 U/mL)	GIBCO Thermo Fisher	#15070063
IMDM	GIBCO Thermo Fisher	#21056023
GlutaMAX Supplement	Thermo Fisher Scientific	#35050079
Accutase	StemCell Technologies, Inc.	# 07920
ReleSR	StemCell Technologies, Inc.	# 05872
B27	Thermo Fisher Scientific	# A3582801
Matrigel	Corning	#354234
N2 supplement-B	Stem Cell Technologies	#7156
DMEM/F12	Thermo Fisher Scientific	# 10565018
Advanced DMEM/F-12	GIBCO Thermo Fisher	# 12-634-028
RPMI 1640	GIBCO Thermo Fisher	#10-040-CV
Monothioglycerol	Sigma Aldrich	#M6145
PneumaCult-Ex Plus Medium	StemCell Technologies, Inc.	#05040
PneumaCult-ALI Medium	StemCell Technologies, Inc.	#05001