REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
CD31 Ax488 (for FACS isolation)	Biolegend	Cat#303109 (WM59); RRID:AB_493075
CD45 Ax488 (for FACS isolation)	Biolegend	Cat#103121 (30-F11); RRID:AB_493532
EpCAM BV650 (for FACS isolation)	Biolegend	Cat#324226 (9C4); RRID:AB_2562735
CD24 BV421 (for FACS isolation)	Biolegend	Cat#311122 (ML5); RRID:AB_2561691
CD133 APC (for FACS isolation)	Miltenyi Biotech	Cat#130-098-829 (AC133); RRID:AB_2660883
αSMA	Sigma-Aldrich	Cat#A2547; RRID:AB_476701
AE2	Abcam	Cat#Ab140953
ALB	Abcam	Cat#Ab2406; RRID:AB_303048
CD45	R&D	Cat#MAB114; RRID:AB_357485
CK19	Novocastra	Cat#NCL-CK19: RRID:AB_563799
EpCAM	Abcam	Cat#Ab32392; RRID:AB_732181
EpCAM (mouse specific)	Abcam	Cat#Ab221552
CD133	Abcam	Cat#Ab19898; RRID:AB_470302
CD24	Biolegend	Cat#101803; RRID:AB_312836
GFP	Abcam	Cat#Ab13970; RRID:AB_300798
HMGB1	Abcam	Cat#Ab18256; RRID:AB_444360
HNF4α	R&D	Cat#PP-H1415-00; RRID:AB_2263954
Human Mitochondria	Merck	Cat#MAB1273; RRID:AB_94052
Ki67	Abcam	Cat#Ab16667; RRID:AB_302459
LGR5	Abcam	Cat#Ab75732; RRID:AB_1310281
MRP2	Thermo Fisher Scientific	Cat#MA532687; RRID:AB_2809964
PCNA	Abcam	Cat#Ab29; RRID:AB_303394
P53	Abcam	Cat#Ab26; RRID:AB_303198
P21	Santa Cruz	Cat#SC-471; RRID:AB_632123
STEM121	Takara	Cat#Y40410; RRID:AB_2801314
Sox9	Merck	Cat#AB5535; RRID:AB_2239761
ZO-1	Santa Cruz	Cat#SC-33725; RRID:AB_628459
Biotinylated Anti-Rabbit IgG (H+L) (secondary Ab)	Vector Lab.	Cat#BA-1000; RRID:AB_2313606
Biotinylated Anti-Mouse IgG (H+L) (secondary Ab)	Vector Lab.	Cat#BA-9200; RRID:AB_2336171
Biotinylated Anti-Rat IgG (H+L) (secondary Ab)	Vector Lab.	Cat#BA-9400; RRID:AB_2336202
Anti-Mouse IgG(H+L)-555 (secondary Ab)	Thermo Fisher Scientific	Cat#A31570; RRID:AB_2536180
Anti-Rabbit IgG(H+L)-488 (secondary Ab)	Thermo Fisher Scientific	Cat#A21206; RRID:AB_2535792
Anti-Rabbit IgG(H+L)-555 (secondary Ab)	Thermo Fisher Scientific	Cat#A31572; RRID:AB_162543
Anti-Rat IgG(H+L)-555 (secondary Ab)	Thermo Fisher Scientific	Cat#A21434; RRID:AB_141733
Mouse IgG (Isotype Control)	Vector Lab.	Cat#I-2000; RRID:AB_2336354
Rat IgG (Isotype Control)	Vector Lab.	Cat#I-4000; RRID:AB_2336356
Rabbit IgG (Isotype Control)	Vector Lab.	Cat#I-1000 RID:AB_2336355
Biological samples
Human livers unsuitable for donation preserved at 4°C in University of Wisconsin preservation fluid	NHS Organ Donation	Project No. 2015/0408 (LREC) 15/SS/0218
Chemicals, peptides, and recombinant proteins
Belzer MPS UW Machine Perfusion Solution	Bridge-to-life	Cat#BTLBUW-1000
Formaldehyde	VWR	Cat#9713.901
Methanol	Fisher Scientific	Cat#M/3900/17
Isopropanol	VWR	Cat#20842.323
Chloroform	Sigma-Aldrich	Cat#C2432
Glacial Acetic acid	Fisher Scientific	Cat#10365020
KCl	GIBCO	Cat#529552
NaCl	Sigma-Aldrich	Cat#S5886
EDTA	Sigma-Aldrich	Cat#E6758
EGTA	Sigma-Aldrich	Cat#E4378
Trizma® base	Sigma-Aldrich	Cat#93362
Triton X	Sigma-Aldrich	Cat# T8787
Tween-20	Sigma-Aldrich	Cat#P1379
Phosphate Buffer Saline (PBS)	Sigma-Aldrich	Cat#D8537
Hanks Balanced Salt Solution	GIBCO	Cat#14025-050
Advanced DMEM/F-12	GIBCO	Cat#12634010
StemMACS MSC Culture medium	Miltenyi Biotec	Cat#130-091-680
Liver Digest Media	GIBCO	Cat#17703034
Liver Perfusion Media	GIBCO	Cat#17701038
Penicillin /Streptomycin	GIBCO	Cat#15140-122
Glutamine	GIBCO	Cat#25030-024
Bovine Fetal Calf Serum	GIBCO	Cat# 10270106
L-Glutamine	GIBCO	Cat# 25030081
Versene 1:5000 (1x)	Thermo Fisher Scientific	Cat# 15040-033
TryPLE Express	GIBCO	Cat#12604-013
Dispase	STEMCELL technologies	Cat#07913
Liberase MNP-S GMP grade	Roche	Cat#06297790001
Percoll	Sigma-Aldrich	Cat#P1644
CellBanker 2	Amsbio	Cat#11891
HEPES pH7	GIBCO	Cat#15630-056
A-83-01	Sigma-Aldrich	Cat#SML0788
B27 Supplement	GIBCO	Cat#12587010
N2 Supplement	GIBCO	Cat#15630-056
Forskolin	Tocris	Cat#1099
Nicotinamide	Sigma-Aldrich	Cat#N0636
Human EGF	Peprotech	Cat#AF-100-15-100
Human FGF-10	Peprotech	Cat#100-26-100
Human HGF	Peprotech	Cat#100-39
Human BMP-7	Peprotech	Cat#120-03
Human FGF-19	Peprotech	Cat#100-32
rhWnt-3a	R&D	Cat#5036-WN/CF
Gastrin	Tocris	Cat#3006
N-Acetylcysteine (NAC)	Sigma-Aldrich	Cat#A9165
Dexamethasone	Sigma-Aldrich	Cat#D2915
Human R-Spondin 1	Peprotech	Cat#120-38
Y27632	Sigma-Aldrich	Cat#Y0503
Noggin	Peprotech	Cat#120-10c
DAPT	Sigma-Aldrich	Cat#D5942
Corning Matrigel GFP Basement Membrane Matrix	Corning	Cat#354230
Biolaminin 521 LN	BioLamina AB	Cat#LN521
Polycaprolactone (avg. Mn. 80000)	Sigma-Aldrich	Cat#440744
Human Platelet Lysate	STEMCELL technologies	Cat#06960
Tamoxifen	Sigma-Aldrich	Cat#T5648
Sunflower seed oil	Sigma-Aldrich	Cat#S5007
Carprofen	Pfizer	Cat#
Ketamine	Pfizer	Cat#
Medetomidine	Orion Pharma	Cat#
Heparin Sodium Salt	Sigma-Aldrich	Cat# H3149
Glutaraldehyde	Sigma-Aldrich	Cat#g6257
Protein Block	Abcam	Cat#Ab64226
Halt Protease Inhibitor	Thermo Fisher Scientific	Cat#78430
BLOXALL block (peroxidase-alkaline phosphatase)	Vector Lab.	Cat#Sp-6000
Avidin/Biotin block	Thermo Fisher Scientific	Cat#004303
Vectastain ABC reagent R.T.U.	Vector Laboratories	Cat#PK-7100
DAB+ Chromogen System	Dako	Cat#K3468
Picric Acid	Sigma-Aldrich	Cat#P6744
Fast Green	Sigma-Aldrich	Cat#F7258
Direct Red	Sigma-Aldrich	Cat#365548
Oil Red O	Sigma-Aldrich	Cat#O0625
Fluorescein Diacetate (FDA)	Thermo Fisher Scientific	Cat#F7378
Propidium Iodide	Sigma-Aldrich	Cat#P4170
Methylene Blue	Sigma-Aldrich	Cat#M4159
DAPI	Sigma-Aldrich	Cat#D9542
Fluoromount-G, with DAPI	Thermo Fisher Scientific	Cat#00-4959-52
DPX mountant media	Sigma-Aldrich	Cat#06522
CliniMACS CD133 microbeads	Miltenyi Biotec	Cat#172-01
Critical commercial assays
BCA protein assay	Thermo Fisher Scientific	Cat#23227
MycoAlert Assay Control set	Lonza	Cat#LT07-518
SYTOX-AAAdvanced Dead Cell Stain Kit	Thermo Fisher Scientific	Cat# S10349
Cell Titer-Blue	Promega	Cat#G8080
Human Albumin ELISA kit	Alpha Diagnostic	Cat#1190
SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian	Takara Bio	Cat#634411
DNA HS kit	Agilent	Cat#23225
Poly-A mRNA magnetic isolation module	NEB	Cat#E7490
NEBNEXT Ultra II Directional RNA Library Prep Kit	NEB	Cat#E6440
RNeasy Micro kit	QIAGEN	Cat#74004
RNeasy Mini kit	QIAGEN	Cat#74106
QuantiTect Reverse Transcription Kit	QIAGEN	Cat#205313
QuantiFast SYBR Green PCR kit	QIAGEN	Cat#204056
V-PLEX Proinflammatory Panel 1 mouse kit	Meso Scale Diagnostic	Cat#K15048D-1
V-PLEX Cytokine Panel 1 Mouse Kit	Meso Scale Diagnostic	Cat#K15245D
AMPure XP beads	Beckman Coulter	Cat#A63880
Deposited data
hBEC seq analysis	This paper	GEO: GSE155498
Experimental models: Cell lines
Human Mesenchymal Stem Cells (hMSC) isolated from liposuction waste and visceral adipose tissue	Scottish National Blood Transfusion service	N/A
Experimental models: Organisms/strains
Mouse line: K19CreERTMDM2fl/fl Rag2−/−Il2rg−/−	This paper	N/A
Oligonucleotides
Primers for mouse genotyping	This paper	Table S2
QIAGEN primers for RT-qPCR (Human)	This paper	Table S6
QIAGEN primers for RT-qPCR (Mouse)	This paper	Table S6
Software and algorithms
FlowJo (v10.7.1)	Becton Dickinson	N/A
Columbus Image Analysis	Perkin Elmer	N/A
TIBCO Spotfire software	Tibco software Inc	N/A
FastQC (v.0.11.9)	Andrews, 2010	https://www.bioinformatics.babraham.ac.uk/projects/fastqc
MultiQC (v.1.3.dev0)	Ewels et al., 2016	N/A
Cutadapt (v.1.16)	Martin, 2011	N/A
STAR (v.2.7.1a)	Dobin et al., 2013	N/A
Rsubread Bioconductor package (v.2.0.1)	Liao et al., 2019	N/A
DESeq2 (v.1.26.0)	Love et al., 2014	N/A
GSEA PreRanked (v.4.0.3)	Subramanian et al., 2005	N/A
MSigDB Hallmark Gene Set	Liberzon et al., 2015
Gene Ontology project	Ashburner et al., 2000	http://geneontology.org/
AmiGO tool (v.2.5.13)	Carbon et al., 2009	http://amigo.geneontology.org/amigo
ArrayExpress (E-MTAB-8495)	Sampaziotis et al., 2021	N/A
OSCA Bioconductor workflow	Amezquita et al., 2020	N/A
EmptyDrops	Lun et al., 2019	N/A
Q-Imaging, Image Pro premier software	Media Cybernetics	QCAM version
Fiji ImageJ	GNU General Public License	https://imagej.net/software/fiji/
Prism software version 5.0a	GraphPad	https://www.graphpad.com/support/prism-5-updates/
Other
Tibbs Cannulas	DTR Medical	Cat#TAC20SO
Vicryl 6/0	Ethicon	Cat#W9981
GentleMACS C-tubes	Miltenyi Biotec	Cat#130-093-237
Disposable sterile scalpels	Swann-Morton	Cat#0503
Cell strainer 70 um	Fisher Scientific	Cat#22363548
12 well Suspension Culture plate	Greiner Bio-One	Cat# 665102
Corning Cell Culture Flasks	Corning	Cat#CLS431081
RM1 + 0.1% DDC (P)	Special Diets Services	Cat#824943
Rat and Mouse No. 1 Maintenance (RM1) diet	Special Diets Services	Cat#801151