REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-DNA	Millipore	Cat #CBL186; RRID: AB_93367
Anti-HSP60	Novus	Cat #NBP1-77397; RRID: AB_11004596
Anti-Flavivirus group antigen [D1-4G2-4-15 (4G2)]	GeneTex	Cat #GTX57154; RRID: AB_2887950
Anti-Flavivirus group antigen [D1-4G2-4-15 (4G2)]	Millipore	Cat #MAB10216-I; RRID: AB_827205
Anti-DENV NS3 protein	GeneTex	Cat #GTX124252; RRID: AB_11171668
Anti-human NANOG	R & D	Cat #AF1997; RRID: AB_355097
Anti-OCT-3/4 Antibody	Santa Cruz	Cat #sc-5279; RRID: AB_628051
Anti-SOX2 (D6D9)	Cell Signaling	Cat #3579; RRID: AB_2195767
TRA-1-60 Monoclonal Antibody	BD Biosciences	Cat #560071; RRID: AB_1645604
TRA-1-81 (Podocalyxin) Monoclonal Antibody	Thermo Scientific	Cat #14-8883-82; RRID: AB_891614
Anti-FOXJ1	Thermo Fisher Scientific	Cat #14-9965-82; RRID: AB_1548835
Anti-Acetyl-α-Tubulin (Lys40) (D20G3)	Cell Signaling	Cat #5335S; RRID: AB_10544694
Anti-MAP2 antibody	Abcam	Cat #ab5392; RRID: AB_2138153
Anti-E-Cadherin (4A2)	Cell Signaling	Cat #14472S; RRID: AB_2728770
Anti-SARS-CoV/SARS-CoV-2 Nucleocapsid	SinoBiological	Cat #40143-R001; RRID: AB_2827974
Anti-NDUFA4 antibody	Abcam	Cat #ab129752; RRID: AB_11155881
Anti-β actin	Thermo Fisher Scientific	Cat # MA1-140; RRID: AB_2536844
Anti-STEM121 human antigen	Takara	Cat #Y40410; RRID: AB_2801314
Anti-Mucin 5AC antibody	Abcam	Cat #ab3649; RRID: AB_2146844
Anti- IFN-alpha/beta R1	R & D	Cat #AF245; RRID: AB_355270
Anti- IFN-alpha/beta R2	R & D	Cat #MAB4015; RRID: AB_2122619
Donkey anti-Mouse IgG (H + L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488	Thermo Fisher Scientific	Cat #A-21202; RRID: AB_141607
Donkey anti-Mouse IgG (H + L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 594	Thermo Fisher Scientific	Cat #A-21203; RRID: AB_141633
Donkey anti-Rabbit IgG (H + L) Secondary Antibody, Alexa Fluor 594 conjugate	Thermo Fisher Scientific	Cat #A-21207; RRID: AB_141637
Donkey anti-Rabbit IgG (H + L) Secondary Antibody, Alexa Fluor 647 conjugate	Thermo Fisher Scientific	Cat #A-31573; RRID: AB_2536183
Donkey anti-Mouse IgG (H + L) Secondary Antibody, Alexa Fluor 647	Thermo Fisher Scientific	Cat #A-31571; RRID: AB_162542
680RD Donkey anti-Mouse IgG Secondary Antibody	Li-Cor	Cat #926–68072; RRID: AB_10953628
800CW Donkey anti-Rabbit IgG Secondary Antibody	Li-Cor	Cat #926–32213; RRID: AB_621848
DAPI	Thermo Fisher Scientific	Cat# D1306; RRID:AB_2629482
Bacterial and virus strains
Zika Virus (Strain: MR 766)	ZeptoMetrix	Cat# 0810521CF
Zika Virus (Strain: PRVABC59)	ZeptoMetrix	Cat# 0810525CF
SARS-CoV-2 Isolate USA-WA1/2020	BEI Resources	Cat# NR-52281
Dengue virus type 2	ATCC	Cat# VR-1584
Biological samples
Patient samples	This paper	N/A
Chemicals, peptides, and recombinant proteins
Y-27632	MedchemExpress	#HY-10583
CHIR99021	Cayman Chemical	#13122
Retinoic acid	Sigma Aldrich	#R2625-500MG
L-Ascorbic acid	Sigma Aldrich	#A4544-100G
SB431542	R&D Systems	#1614/50
Dorsomorphin dihydrochloride	R&D Systems	#3093/50
Dexamethasone	Sigma-Aldrich	#D4902
Potassium cyanide	Sigma-Aldrich	#60178
8-Bromo-cAMP	Sigma-Aldrich	#B7880
IBMX	Sigma-Aldrich	#I5879
DAPT	R&D Systems	#2634
Activin A	R&D Systems	#338-AC-500/CF
Recombinant Human bFGF Protein	Peprotech	#100-18B-500UG
Recombinant Human BMP-4 Protein	R & D Systems	#314-BP
Recombinant Human FGF-10 Protein	R&D Systems	#345-FG-250
Critical commercial assays
TruSeq Stranded mRNA LP	Illumina	#20020594
Seahorse XF Cell Mito Stress Test Kit	AGILENT TECHNOLOGIES	#103015-100
Deposited data
RNA-seq	This Paper	GEO: GSE182376, GSE203401
Experimental models: Cell lines
293T	ATCC	#CRL-11268
Vero E6	ATCC	#CRL-1586
iPSC cell lines	Paull et al., 2015	N/A
Software and algorithms
Rstudio	Rstudio	https://rstudio.com
Seurat R package v3.1.4	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/product/photoshop.html
Graphpad Prism 9	Graphpad software	https://www.graphpad.com