REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
CDX2 (1:200)	BioGenex	Cat#MU392A-5U; RRID: AB_2650531
FOXF1 (1:200)	R&D	Cat#AF4798; RRID: AB_2105588
E-cadherin (1:100)	R&D	Cat#AF648; RRID: AB_355504
MUC2 (1:100)	Santa Cruz	Cat#Sc15334; RRID: AB_2146667
Chromogranin A (1:1000)	DiaSorin	Cat#SP-1
Villin (1:100)	Novus Biologicals	Cat#NBP1-85335; RRID: AB_11020888
Ki67 (1:50)	Novus Biologicals	Cat#NB600-1252; RRID: AB_2142376
alpha-Smooth Muscle Actin (1:150)	Novus Biologicals	Cat#NB600-531; RRID: AB_10000930
Vimentin (1:200)	Novus Biologicals	Cat#NB300-223; RRID: AB_10003206
Lysozyme (1:1000)	Sigma	Cat#HPA048284; RRID: AB_2680339
Sucrase Isomaltase (1:100)	Santa Cruz	Cat#Sc393424; RRID:AB_2891093
Wnt2b (1:500)	Invitrogen	Cat#710888
tdTomato (1:300)	SICGEN	Cat# AB8181 RRID: AB_2722750
GFP (1:100)	Santa Cruz	Cat# sc-9996 RRID: AB_627695
Alexa 488 donkey anti-rabbit IgG (1:200)	Invitrogen	Cat#A21206; RRID: AB_2535792
Alexa 488 goat anti-rabbit IgG (1:200)	Invitrogen	Cat#A11034; RRID: AB_2576217
Alexa 488 donkey anti-mouse IgG (1:200)	Invitrogen	Cat#A21202; RRID: AB_141607
Alexa 488 rabbit anti-goat IgG (1:200)	Invitrogen	Cat#A11078; RRID: AB_141838
Alexa 488 chicken anti-goat IgG (1:200)	Invitrogen	Cat#A21467; RRID: AB_2535870
Alexa 594 donkey anti-rabbit IgG (1:200)	Invitrogen	Cat#A21207; RRID: AB_141637
Alexa 594 chicken anti-goat IgG (1:200)	Invitrogen	Cat#A21468; RRID: AB_141859
Alexa 594 donkey anti-goat IgG (1:200)	Invitrogen	Cat#A11058; RRID: AB_2534105
Alexa 594 donkey anti-chicken IgG (1:200)	Jackson Immuno	Cat#703-585-155; RRID: AB_2340377
Alexa 594 donkey anti-chicken IgG (1:200)	Invitrogen	Cat#A78951; RRID: AB_2921073
Alexa 594 donkey anti-mouse IgG (1:200)	Invitrogen	Cat#A21203; RRID: AB_141633
Chemicals, peptides, and recombinant proteins
Recombinant murine EGF	Peprotech	Cat#31509
Recombinant mouse Noggin	R&D	Cat#1967
Recombinant mouse R-spondin1	R&D	Cat#3474-RS
A83-01	Tocris	Cat#2939
Recombinant Human IGF-1	BioLegend	Cat#590906
Nicotinamide	Sigma	Cat#N0636
Afamin/Wnt3a conditioned medium	MBL lifescience	Cat#J2-001
Activin A	Nacalai Tesque	Cat#18585-81
CHIR99021	Cayman Chemicals	Cat#13122
Recombinant human FGF4	Peprotech	Cat#100-31
Recombinant human BMP-4	R&D	Cat# 314-BP
Wnt-C59	Chemscene LLC	Cat#CS-1420
PIK90	Cayman Chemicals	Cat#10010749
Retinoic acid	Sigma Aldrich	Cat#R2625
Purmorphamine	Tocris Bioscience	Cat#4551
Y-27632	Fujifilm Wako Pure Chemical	Cat#253-00513
FGF-basic(154a.a.), Human, Recombinant	Peprotech	Cat#100-18B
Recombinant Human IGF-I	BioLegend	Cat#590906
Cellartis DEF-CS™ 500 culture system	Takara Bio	Cat#Y50101
Advanced DMEM/F12	Thermo Fisher	Cat#12634010
DMEM, high glucose	Thermo Fisher	Cat#11965-092
RPMI 1640 with L-Gln, liquid	Nacalai Tesque	Cat#30264-85
Embryonic stem cell Fetal Bovine Serum	Thermo Fisher	Cat#16141079
GlutaMAX™ Supplement	Thermo Fisher	Cat#35050-061
HEPES buffer	Nacalai Tesque	Cat#17557-94
Penicillin-Streptomycin Mixed Solution	Nacalai Tesque	Cat#26253-84
Matrigel Growth Factor Reduced	Corning	Cat#356231
N-2 supplement (100X)	Thermo Fisher	Cat#17502-048
B-27 Supplement (50X), serum free	Thermo Fisher	Cat#17504-044
B-27 Supplement (50X), minus vitamin A	Thermo Fisher	Cat#12587010
TrypLE Express Enzyme	Thermo Fisher	Cat#12604013
Accumax	Nacalai Tesque	Cat#17087-54
Hoechst 33342	Thermo Fisher	Cat#H3570
VECTASHIELD mounting medium with DAPI	VECTOR Laboratories	Cat#H1200
DAPI solution (1 mg/mL)	Nacalai Tesque	Cat#19178-91
The P3 Primary Cell 4D-Nucleofector X Kit S	Lonza	Cat#V4XP-3032
Critical commercial assays
RNAscope 2.5HD Assay-Red	Advanced Cell Diagnostics	Cat#322350
RNeasy Mini kit	QIAGEN	Cat#74106
QuantiTect Reverse Transcription Kit	QIAGEN	Cat#205313
Experimental models: Cell lines
Human induced pluripotent stem cell line: HiPS-RIKEN-2F	RIKEN BRC Cell Bank (Japan)	HPS0014
Human induced pluripotent stem cell line: PB001	Kindly gifted by Dr Hideki Masaki (Institute of Medical Science, the University of Tokyo)	N/A
Human induced pluripotent stem cell line: TkdA3-4	Institute of Medical Science, the University of Tokyo	N/A
Experimental models: Organisms/strains
NOD.Cg-Prkdcscid/Il2rgtm1wji/SzJ (NSG) mice	The Jackson Laboratory Japan	N/A
Oligonucleotides
RNAscope Probe-Hs-LGR5	Advanced Cell Diagnostics	Cat#311021
RNAscope Probe-Hs-RSPO3-01	Advanced Cell Diagnostics	Cat#429851
Primer: CDX2 Fwd: CTCGGCAGCCAAGTGAAAAC	This paper	N/A
Primer: CDX2 Rev: CTCCTTTGCTCTGCGGTTCT	This paper	N/A
Primer: FOXF1 Fwd: AGCAGCCGTATCTGCACCAGAA	This paper	N/A
Primer: FOXF1 Rev: CTCCTTTCGGTCACACATGCTG	This paper	N/A
Primer: β-actin Fwd: GGATGCAGAAGGAGATCACTG	This paper	N/A
Primer: β-actin Rev: CGATCCACACGGAGTACTTG	This paper	N/A
Recombinant DNA
PB-CMV-MCS-EF1-GreenPuro cDNA Cloning and Expression Vector	System Biosciences	Cat# PB513B-1
Super piggyBac Transposase expression vector	System Biosciences	Cat# PB200A-1
Software and algorithms
Prism 9	GraphPad Software; Dotmatics	N/A
CellSens	Olympus	N/A
R v4.3.3	R Foundation	N/A
ImageJ v1.54k	National Institute of Health	N/A
Other
EZSPHERE® 6-well plate	AGC Techno Glass Co. Ltd.	Cat#4810-900SP
EZ-BindShut® 96-well plate	AGC Techno Glass Co. Ltd.	Cat#4870-800SP
Org-SP plate	AGC Techno Glass Co. Ltd.	N/A
Ultra-low attachment 6-well plate	Corning	Cat#3471
CellPet 3D-iPS rotary suspension culture system	JTEC Corp.	CELLPET iPS/3S/MA-2.1
Culture vessel syringe (10 mL)	JTEC Corp.	CELLPET VES/S10/6
Culture vessel syringe (30 mL)	JTEC Corp.	CELLPET VES/S30/6
Culture vessel syringe (50 mL)	JTEC Corp.	CELLPET VES/S50/6
SUMILON STEMFULL 15mL Centrifuge tube	Sumitomo Bakelite Co., Ltd	Cat#MS-90150
SUMILON ProteoSave SS 50mL Centrifuge tube	Sumitomo Bakelite Co., Ltd	Cat#MS-52550
Beriplast P Combi-Set Tissue adhesion 0.5 mL	CSL Behring	N/A
VICRYL	ETHICON	J107G
All-in-one Fluorescence Microscope	KEYENCE	BZ-X810
Laser-scanning confocal microscope	Olympus	FLUOVIEW FV3000
Stereomicroscope system	OLYMPUS	SZX7
4D-NucleofectorR System	Lonza	N/A
StepOnePlus Real-Time PCR	Applied Biosystems	N/A