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. 2022 Oct 6;29(10):1475–1490.e6. doi: 10.1016/j.stem.2022.09.008
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