REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse Anti-Pan-Cytokeratin (Clone AE1/AE3)	Agilent	Cat#M351529-2; RRID:AB_2132885
Rabbit Anti-Vimentin	Cell Signaling Technology	Cat#5741S; RRID:AB_10695459
Rabbit Anti-Cytokeratin 7 (Clone EPR1619Y)	Abcam	Cat#Ab68459; RRID:AB_1139824
Mouse Anti-Cytokeratin 20 (Clone Ks20.8)	Invitrogen	Cat#MA5-13263; RRID:AB_10981940
Rabbit Anti-Ki-67	Abcam	Cat#Ab15580; RRID:AB_443209
Mouse Anti-alpha Smooth Muscle Actin (clone 1A4)	Agilent	Cat#M085101-2; RRID:AB_2223500
Rabbit Anti-Periostin	Abcam	Cat#Ab14041;RRID:AB_2299859
Alexa Fluor 488 Goat Anti-Mouse IgG	Invitrogen	Cat#A-11029; RRID:AB_2534088
Alexa Fluor 633 Goat Anti-Mouse IgG	Invitrogen	Cat#A-21052; RRID:AB_2535719
Alexa Fluor 488 Goat Anti-Rabbit IgG	Invitrogen	Cat#A-11008; RRID:AB_143165
Alexa Fluor 568 Goat Anti-Rabbit IgG	Invitrogen	Cat#A-11036; RRID:AB_10563566
Biological samples
Human esophageal adenocarcinoma FFPE blocks	University Hospital Southampton, Department of Cellular Pathology	See Table 1
Chemicals, peptides, and recombinant proteins
DAPI	Sigma-Aldrich	Cat#D9542-5MG
Hanks' Balanced Salt Solution	ThermoFisher	Cat#14025092
Amphotericin B	ThermoFisher	Cat#15290026
Collagenase P	Sigma-Aldrich	Cat#11213865001
Primocin	InvivoGen	Cat#ant-pm-05
Penicillin-Streptomycin	ThermoFisher	Cat#15140122
Cultrex Basement Membrane Extract, Type 2, Pathclear	Bio-Techne	Cat#3532-005-02
Advanced DMEM/F12	ThermoFisher	Cat#12634010
HEPES	ThermoFisher	Cat#15630056
GlutaMAX	ThermoFisher	Cat#35050061
N-2 Supplement	ThermoFisher	Cat#17502048
B-27 Supplement	ThermoFisher	Cat#17504044
Recombinant Human Noggin	Peprotech	Cat#120-10C-500
Recombinant Human EGF	Peprotech	Cat#AF-100-15-1000
Recombinant Human FGF-10	Peprotech	Cat#100-26-1000
N-Acetylcysteine	Sigma-Aldrich	Cat#A9165-5g
Nicotinamide	Sigma-Aldrich	Cat#N0636-100g
A83-01	TOCRIS	Cat#2939-10mg
SB202190	Stem Cell Technologies	Cat#72634
Y-27632	Sigma-Aldrich	Cat#Y0503-5MG
TrypLE Express	ThermoFisher	Cat#12604013
Fructose	Sigma-Aldrich	Cat#F3510-100G
Glycerol	Sigma-Aldrich	Cat#G5516-500ML
Urea	Sigma-Aldrich	Cat#51456-500G
Zwittergent 3-10	Sigma-Aldrich	Cat#693021-5GM
Boric Acid	Sigma-Aldrich	Cat#B6768
Phalloidin-iFluor594	Abcam	Cat#176757
Triton X-100	Sigma-Aldrich	Cat#T8787-50ML
Bovine Serum Albumin	Sigma-Aldrich	Cat#A2153-10G
Agarose	Sigma-Aldrich	Cat#A9539-100G
4% Paraformaldehyde	ThermoFisher	Cat#I28800
Xylene, Reagent Grade	Sigma-Aldrich	Cat#214736
Eosin Y solution, Alcoholic	Sigma-Aldrich	Cat#HT110116
Mayer’s Hematoxylin	Agilent	Cat#S330930-2
Expert XTF Mounting Medium	CellPath	Cat#SEA-1900-00A
Alcian blue	Sigma-Aldrich	Cat#A3157-10G
Schiff’s Reagent	Sigma-Aldrich	Cat#3952016-500ML
Sirius Red F3B	Sigma-Aldrich	Cat#365548-5G
Saturated Aqueous Picric Acid	Sigma-Aldrich	Cat#P6744-1GA
Mowiol 4-88	Sigma-Aldrich	Cat#81381-50G
DABCO 33-LV	Sigma-Aldrich	Cat#290734-100ML
Dulbecco’s Modified Eagle’s Medium, High Glucose	Sigma-Aldrich	Cat#D6546
Critical commercial assays
RNeasy Mini Kit	Qiagen	Cat#74104
Deposited data
Bulk RNA-seq data	This paper	GSE277147
Microscopy data	This paper	https://doi.org/10.5281/zenodo.11639336
Experimental models: Cell lines
OESO-005	Gift from Dr. Matthew Garnett, Wellcome Sanger Institute, Cambridge, UK	Cell Model Passport ID: HCM-SANG-0290-C15
OESO-191	Gift from Dr. Matthew Garnett, Wellcome Sanger Institute, Cambridge, UK	Cell Model Passport ID: HCM-SANG-0543-C15
OESO-195	Gift from Dr. Matthew Garnett, Wellcome Sanger Institute, Cambridge, UK	Cell Model Passport ID: HCM-SANG-0546-C15
CAF1412	This paper	See Table 1
CAF669	This paper	See Table 1
L-Wnt3A	ATCC	Cat#CRL-2647; RRID:CVCL_0635
HA-R-Spondin1-FC 293T	R&D Systems	Cat#3710-001-01; RRID:CVCL_RU08
Software and algorithms
Imaris (v9.5.1)	Oxford Instruments	RRID:SCR_007370