REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit anti-Ki67	Thermo Scientific	Cat# RM-9106-S1 ; RRID: AB_149792
Goat anti-LCT	Santa Cruz Biotechnology	Cat# sc-240614, RRID: AB_10917595
Goat anti-Sucrase-Isomaltase	Santa Cruz Biotechnology	Cat# sc-27603, RRID: AB_2188721
Goat anti-Chr-A	Santa Cruz Biotechnology	Cat# sc-1488, RRID: AB_2276319
Rabbit anti-FABP2	Abcam	Cat# ab89195, RRID: AB_2041190
Rabbit anti-EPCAM	Sigma-Aldrich	Cat# HPA026761, RRID: AB_1848198
Goat anti-Vimentin	R&D Systems	Cat# AF2105, RRID: AB_355153
Mouse anti-Mucin 5AC	Abcam	Cat# ab79082, RRID: AB_1603327
Goat anti-DPP4	R&D Systems	Cat# AF954, RRID: AB_355739
Mouse anti-CDX2	BioGenex	Cat# AM392, RRID: AB_2650531
Rabbit anti-ASBT (anti-SLC10A2)	Sigma-Aldrich	Cat# HPA004795, RRID: AB_1856953
Rabbit anti-Mucin2	Santa Cruz Biotechnology	Cat# sc-15334, RRID: AB_2146667
Goat anti-SOX9	R&D Systems	Cat# AF3075, RRID: AB_2194160
Rabbit anti-SM22	Abcam	Cat# ab14106, RRID: AB_443021
Rabbit anti-PDX1	Epitomics, Inc	Cat# 3470-1, RRID: AB_10703013
Goat anti-E-Cadherin	R&D Systems	Cat# AF748, RRID: AB_355568
Mouse anti-E-Cadherin	BD Transduction Laboratories	Cat# 610181, RRID: AB_397580
Goat anti-Sox2	Santa Cruz Biotechnology	Cat# sc-17320, RRID: AB_2286684
Rabbit anti-PDGFRa	Cell Signaling Technology	Cat#3164S, RRID: AB_2162351
Mouse anti-SMA	Sigma-Aldrich	Cat# C6198, RRID: AB_476856
Donkey anti-goat 488	Jackson Immuno	Cat# 705-545-147, RRID: AB_2336933
Donkey anti-goat 647	Jackson Immuno	Cat# 705-605-147, RRID: AB_2340437
Donkey anti-goat Cy3	Jackson Immuno	Cat# 705-165-147, RRID: AB_2307351
Donkey anti-mouse 488	Jackson Immuno	Cat# 715-545-150, RRID: AB_2340846
Donkey anti-mouse 647	Jackson Immuno	Cat# 715-606-151, RRID: AB_2340866
Donkey anti-mouse Cy3	Jackson Immuno	Cat# 715-165-150, RRID: AB_2340813
Donkey anti-rabbit 488	Jackson Immuno	Cat# 711-545-152, RRID: AB_2313584
Donkey anti-rabbit 647	Jackson Immuno	Cat# 711-605-152, RRID: AB_2492288
Donkey anti-rabbit Cy3	Jackson Immuno	Cat# 711-165-152, RRID: AB_2307443
Biological samples
Human fetal tissue samples, ages 7-21 post-conceptional weeks	University of Washington Laboratory of Developmental Biology	N/A
Human adult duodenum samples, age 45 and 50 years	University of Michigan Hospital	N/A
Chemicals, peptides, and recombinant proteins
Activin A	R&D	Cat#338-AC
EGF	R&D	Cat#236-EG
Noggin-Fc	Purified from conditioned media; Heijmans et al., 2013	N/A
R-Spondin 1	Conditioned media; Ootani et al., 2009	N/A
FGF4	Purified in house; Sugawara et al., 2014	N/A
CHIR99021	ApexBio	Cat#A3011
B27 supplement	Life Technologies	Cat#17504044
HEPES	Life Technologies	Cat#15630080
GlutaMAX	Life Technologies	Cat#35050061
Red Blood Cell Lysis Buffer	Roche	Cat#11814389001
NRG1	R&D	Cat#5898-NR-050
Alginic acid sodium salt, low viscosity	Alfa Aesar	Cat#11420828
Critical commercial assays
RNAscope Multiplex Fluorescent Reagent Kit v2	ACD	Cat#323100
RNAscope 2.5 HD Reagent Kit- Brown	ACD	Cat#322300
Neural Tissue Dissociation Kit (P)	Miltenyi	Cat#130-092-628
Deposited data
Raw and analyzed data	This work	E-MTAB-10187, E-MTAB-10268
Raw and analyzed data	Miller et al., 2020	E-MTAB-8221
Raw and analyzed data	Holloway et al., 2021	E-MTAB-9489
Raw and analyzed data	Holloway et al., 2020	E-MTAB-9228, E-MTAB-9363
Raw and analyzed data	Pijuan-Sala et al., 2019	E-MTAB-6967
Raw and analyzed data	Fujii et al., 2018	GSE119969
Experimental models: Cell lines
H9-WT	WiCell	Cat#WA09; RRID:CVCL_9773
H9-CDX2-CON	Derived from H9; Kumar et al., 2019	N/A
H9-CDX2-KO	Derived from H9; Kumar et al., 2019	N/A
Oligonucleotides
RNAscope Probe Hs-LGR5	ACD	Cat#311021
RNAscope Probe Hs-OLFM4	ACD	Cat#311041
RNAscope Probe Hs-DLL1	ACD	Cat#532631
RNAscope Probe Hs-F3-C2	ACD	Cat#407611-C2
RNAscope Probe Hs-WNT2	ACD	Cat#584071
RNAscope Probe Hs-SALL1	ACD	Cat#514331
RNAscope Probe Hs-SP5	ACD	Cat#406541
RNAscope Probe Hs-NKX2.3	ACD	Cat#581651
Software and algorithms
R (version 3.6.0)	N/A	https://www.r-project.org
Cell Ranger	N/A	https://github.com/10XGenomics/cellranger
Seurat (version 3.1)	Butler et al., 2018	https://github.com/satijalab/seurat
simspec	He et al., 2020	https://github.com/quadbiolab/simspec
SPRING	Weinreb et al., 2018	https://github.com/AllonKleinLab/SPRING
e1071	N/A	https://github.com/cran/e1071
presto	N/A	https://github.com/immunogenomics/presto
uwot	N/A	https://github.com/jlmelville/uwot
RANN	N/A	https://github.com/jefferislab/RANN
CellPhoneDB (version 2.0)	Efremova et al., 2020	https://github.com/Teichlab/cellphonedb
destiny	Angerer et al., 2016	https://github.com/theislab/destiny
splines	N/A	https://github.com/cran/splines
Quadprog	N/A	https://github.com/cran/quadprog
novoSpaRc	Nitzan et al., 2019	https://github.com/rajewsky-lab/novosparc
igraph	N/A	https://github.com/igraph/rigraph
MNN	Haghverdi et al., 2018	https://rdrr.io/github/LTLA/batchelor/
pySCENIC	Aibar et al., 2017	https://github.com/aertslab/pySCENIC
Other
TSA Plus Cyanine 3	Akoya Biosciences	Cat#NEL744001KT
TSA Plus Cyanine 5	Akoya Biosciences	Cat#NEL745E001KT
Corning® Matrigel® (GFR) Basement Membrane Matrix	Corning	Cat#354230
Corning® Matrigel® Basement Membrane Matrix	Corning	Cat#354234
Interactive web browser GutTubeR	This paper	http://guttuber.iob.ch/app/
Data S1 and supporting raw data analysis	This paper; Mendeley Data	https://doi.org/10.17632/x53tts3zfr.1