REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-E Cadherin antibody [HECD-1] - Intercellular Junction Marker	Abcam	Cat# ab1416; RRID:AB_300946
Recombinant Anti-Vimentin antibody [EPR3776] – Cytoskeleton Marker	Abcam	Cat# ab92547; RRID:AB_10562134
Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa fluor 555	Molecular Probes, Invitrogen	Cat# A21428; RRID:AB_141784
Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa fluor 647	Molecular Probes, Invitrogen	Cat# A21235; RRID:AB_2535804
Rabbit Anti-Human VE Cadherin Polyclonal Antibody, Unconjugated	Abcam	Cat# ab33168; RRID:AB_870662
ZO-1 Monoclonal Antibody (ZO1-1A12), Alexa Fluor 594	Thermo-Fisher	Cat# 339194 RRID:AB_2532188
Bacterial and virus strains
LentiBrite Histone-H2B-GFP Lentiviral Biosensor	Millipore	Cat#17-10229
Biological samples
Patient-derived sample: CAF000UE	Shannon M. Mumenthaler This paper	N/A
Patient-derived sample: CAF000U8	Shannon M. Mumenthaler This paper	N/A
Patient-derived sample: CAF000W8	Shannon M. Mumenthaler This paper	N/A
Patient-derived sample: CAF000US	Shannon M. Mumenthaler This paper	N/A
Patient-derived sample: ORG000US	Shannon M. Mumenthaler This paper	N/A
Chemicals, peptides, and recombinant proteins
Basement membrane extract (BME)	Cultrex	Cat#3533-005-02
Noggin	Tonbo	Cat#21-7075-U500
Epidermal growth factor (EGF)	Life Technologies	Cat#PHG0313
SB202190	Sigma Aldrich	Cat#S7067
TGF-β RI Kinase Inhibitor IV (A83-01)	Millipore	Cat#616454-2MG
Nicotinamide	Sigma Aldrich	Cat#N0636
B27	Gibco	Cat#17504-001
N-Acetyl-L-cysteine	Sigma Aldrich	Cat#A9165
N2	Gibco	Cat#17502-048
HEPES	Gibco	Cat#15630-080
GlutaMax	Gibco	Cat#35050-061
16% paraformaldehyde	Electron Microscopy Sciences	Cat#15710
Inulin-Fluorescein isothiocyanate (FITC, 2-5kDa)	Sigma Aldrich	Cat# F3272
Collagenase, Type II	Millipore	Cat#234155-100MG
Bovine hyaluronidase	MP Biomedicals	Cat#0210074080
Hoechst 33342 (nuclear dye)	Invitrogen	Cat# H1399
Saponin	Sigma Aldrich	Cat#84510
Bovine Serum Albumin	Millipore	Cat#260-500GM
InfinityLab Deactivator Additive	Agilent	Cat#5191-4506
EGM-2 Endothelial Cell Growth Medium-2 BulletKit	Lonza	Cat# CC-3162
DMEM	Gibco	Cat#10569-010
Eagle’s Minimum Essential Medium	Corning	Cat#10-009-CV
Advanced DMEM/F-12	Gibco	Cat#12634-010
Rat tail collagen type I	Corning	Cat# C354249
Matrigel	Corning	Cat#356231
ER-1	Emulate, Inc	Cat# Basic Research Kit
ER-2	Emulate, Inc	Cat# Basic Research Kit
Rat tail collagen IV	Sigma Aldrich	Cat# C5533
Cell Tracker Deep Red	Invitrogen	Cat# C34565
Gentle Cell Dissociation Reagent	STEMCELL Technologies	Cat#07174
TrypLE	Gibco	Cat#12605-028
LY-27632	Millipore	Cat#5.09228.0001
McCoy’s 5A (Modified) Media	Gibco	Cat#16600-082
DAPI	Sigma Aldrich	Cat# D9542
Critical commercial assays
RNAspin Mini RNA Isolation Kit	GE Healthcare	Cat#25-0500-71
Proteome Profiler Human XL Cytokine Array Kit	R&D Systems	Cat# ARY022B
Metabolomics QC Standard 2	Cambridge Isotope Laboratories, Inc	Cat# MSK-QC2
Metabolomics QC Standard 1	Cambridge Isotope Laboratories, Inc	Cat# MSK-QC1
iScript Reverse Transcription Supermix	Bio-Rad	Cat#1708841
iQ SYBR Green Master	Bio-Rad	Cat#1708880
Organ-on-Chip	Emulate, Inc	Basic Research Kit
Experimental models: cell lines
Human: RFP expressing Human umbilical vein endothelial cells	Angio-Proteomie	Cat# cAP-0001RFP
Human: Caco2 C2BBe1	ATCC	Cat# CRL-2102
Human: HCT116	ATCC	Cat# CCL-247
Human: HT29	ATCC	Cat# HTB-38
Human: CCD18Co	ATCC	Cat# CRL-1459
Oligonucleotides
Primers for analysis of gene-expression changes, see Table S11	Integrated DNA Technologies (IDT)	N/A
Software and algorithms
R statistical environment	https://www.R-project.org/	v4.0.2
VennDiagram R package	R statistical environment	v1.6.20
Harmony High-Content Imaging and Analysis Software	Perkin Elmer	N/A
Imaris image analysis	Imaris	N/A
Profinder	Agilent Technologies	N/A
Mass Profiler Professional (MPP)	Agilent Technologies	N/A
Ingenuity Pathway Analysis (IPA)	digitalinsights.qiagen. com	N/A
GraphPad Prism 8	GraphPad Software, Inc.	https://www.graphpad.com/
Mass Hunter	Agilent Technologies	N/A
Biorender	Biorender	https://biorender.com/
Other
Fluoroblok™ transwell inserts with PET membranes	Corning	#351152
Zoë ™ Culture Module	Emulate, Inc.	N/A
Orb™ Hub Module	Emulate, Inc.	N/A
Perkin Elmer Operetta High Content Screening (HCS) platform	Perkin Elmer	N/A
Perkin Elmer Operetta CLS High Content System	Perkin Elmer	N/A
Spectramax	Molecular Devices	N/A
Olympus FV3000	Olympus	N/A
Ultra high performance liquid chromatography (UHPLC) system 1290	Agilent Technologies	N/A
Quadrupole time of flight (Q-TOF 6545) mass spectrometer	Agilent Technologies	N/A
InfinityLab Poroshell 120 HILIC	Agilent Technologies	675775-924
ZORBAX RRHD Eclipse Plus C18	Agilent Technologies	959757-902