REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse anti-FXR	Santa Cruz	Cat#sc-25309;RRID:AB_628039
Mouse anti-PPARα	Santa Cruz	Cat#sc-398394;RRID:AB_2885073
Mouse anti-BrdU	Servicebio	Cat#GB12051
Mouse anti-Notch1	Santa Cruz	Cat#sc-376403;RRID:AB_11149738
Rabbit anti-Sox9	Millipore	Cat#AB5535;RRID:AB_2239761
Mouse anti-Hnf4α	Abcam	Cat#ab41898;RRID:AB_732976
Rabbit anti-GFP	Proteintech	Cat#50430-2-AP
Mouse anti-Ck19	Servicebio	Cat#GB12197
Rabbit anti-CK19	Abcam	Cat#ab52625;RRID:AB_2281020
Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody,Alexa Fluor 555	Invitrogen	Cat#A-21428;RRID:AB_2535849
Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody,Alexa Fluor 555	Invitrogen	Cat#A-21422;RRID:AB_2535844
Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody,Alexa Fluor 488	Invitrogen	Cat#A11001;RRID:AB_2534069
Mouse anti-GAPDH	Proteintech	Cat#60004-I-Ig
Biotin-conjugated Affinipure Goat Anti-Rabbit IgG(H+L)	Proteintech	Cat#SA00004-2
Biotin-conjugated Affinipure Goat Anti-Mouse IgG(H+L)	Proteintech	Cat#SA00004-1
Chemicals, peptides, and recombinant proteins
GW7647	Cayman	Cat#10008613
GW4064	MCE	Cat#HY-50108
tamoxifen	Sigma	Cat#T5648
DAPI	Abcam	Cat#104139
BrdU	Sigma	Cat#B5002
Critical commercial assays
Luminescent ATP Detection Assay Kit	Beyotime	Cat#S0027
Glycolysis Cell-based Assay Kit	Cayman	Cat#600450
Oxygen Consumption Rate Assay Kit 600800	Cayman	Cat#600800
electrophoretic mobility shift assay (EMSA) Kit	Beyotime	Cat#GS009
ChIP Assay kit	Beyotime	Cat#P2078
pGL3-basic vector	Promega	Cat#E1751
phRL-TK	Promega	Cat#E2241
Lipofectamine 2000	Invitrogen	Cat#11668019
dual-luciferase assay kit	Promega	Cat#E1910
GPT/ALT kit	Nanjing jiancheng	Cat#C009-2
GOT/AST kit	Nanjing jiancheng	Cat#C010-2
Hematoxylin and Eosin Staining Kit	Beyotime	Cat#C0105S
RNAscope Multiplex Fluorescent Reagent Kit v.2	Advanced Cell Diagnostics	Cat#323110
RNAscope® H202 and Protease Reagents	Advanced Cell Diagnostics	Cat#322381
Experimental models: Cell lines
HepG2	ATCC	Cat#HB-8065
Hep1-6	ATCC	Cat#CRL-1830
primary mouse hepatocytes	This paper	N/A
Experimental models: Organisms/strains
FXR−/− mice	Jackson Laboratory	strain name: B6.129X1(FVB)-Nr1h4tm1Gonz/J, stock number 007214
PPARα−/− mice	Jackson Laboratory	strain name: B6;129S4-Pparαtm1Gonz/J, stock number 008154
Sox9-CreERT2 mice	Jackson Laboratory	strain name: STOCK Tg (Sox9-cre/ERT2) 1Msan/J, stock number 018829
Rosa26-mTmG mice	Jackson Laboratory	B6.129(Cg)-Gt (ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo/J, stock number 007676
C57BL/6 mice	Laboratory Animal Center	N/A
Oligonucleotides
See Tables S1 and S2
Recombinant DNA
pGL3-basic-Sox9-promoter vector	This paper	N/A
pGL3-basic-Sox9- mutation vector	This paper	N/A
Software and algorithms
Image Pro Plus v.7	Image Pro Plus	https://image-pro-plus.software.informer.com/
GraphPad Prism 6	GraphPad Prism	https://www.graphpad.com/
Zen 2.3 lite	Carl Zeiss Microscopy	https://www.zeiss.com/microscopy/int/products/microscope-software.html