REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
ARID1A	Cell Signaling Technology	Cat# 12354; RRID:AB_2637010
ACO2	Abcam	Cat# ab129069; RRID:AB_11144142
SDHA	Abcam	Cat# ab14715; RRID:AB_301433
SDHB	Abcam	Cat# ab175225; RRID:AB_2904585
FH	Abcam	Cat# ab233394; RRID:AB_2892589
PKM	Abcam	Cat# ab150377; RRID:AB_2941747
FDX1	Proteintech Group Inc	Cat#12592-1-AP; RRID:AB_11182486
HIF-1 alpha	Abcam	Cat# ab179483; RRID:AB_2732807
α-tubulin	Abcam	Cat# ab7291; RRID:AB_2241126
Lipoic Acid	Abcam	Cat# ab58724; RRID:AB_880635
Total OXPHOS Human WB Antibody Cocktail	Abcam	Cat# ab110411; RRID:AB_2756818
ARID1A	Abcam	Cat# ab182560
Bacterial and virus strains
Toronto human knockout pooled library (TKOv3)	Addgene	Cat# 125517; RRID:Addgene_125517
pLenti-puro-ARID1A	Addgene	Cat# 39478; RRID:Addgene_39478
lentiCas9-Blast	Addgene	Cat# 52962; RRID:Addgene_52962
psPAX2	Addgene	Cat# 12260; RRID:Addgene_12260
pMD.2G	Addgene	Cat# 12259; RRID:Addgene_12259
Biological samples
Hepatocellular Carcinoma samples	This study	N/A
Chemicals, peptides, and recombinant proteins
IACS-010759	MedChemExpress	Cat# HY-112037
ferrostatin-1	MedChemExpress	Cat# HY-100579
Necrostatin-1	MedChemExpress	Cat# HY-15760
Z-VAD-FMK	MedChemExpress	Cat# HY-16658B
Ammonium tetrathiomolybdate(VI)	MedChemExpress	Cat# HY-W076067
Elesclomol	MedChemExpress	Cat# HY-12040
Puromycin	MedChemExpress	Cat# HY-B1743A
Hygromycin B	MedChemExpress	Cat# HY-B0490
Polybrene Infection	Sigma-Aldrich	Cat# TR-1003
Copper(II) chloride	Sigma-Aldrich	Cat# 7447-39-4
MitoBright LT Deep Red	Dojindo	Cat# MT12
TB Green® Premix Ex Taq™ II	Takara	Cat# RR820Q
Lipofectamine 2000 Transfection Reagent	Invitrogen	Cat# 11668019
13C-Glucose	Cambridge Isotopes Laboratories	Cat# CLM-1396
NEBNext® Ultra™ II Q5® Master Mix	New England Biolabs	Cat# M0544S
Critical commercial assays
Pyruvate Assay Kit	Abcam	Cat# ab65342
L-Lactate Assay Kit (Colorimetric)	Abcam	Cat# ab65331
Pyruvate Kinase Assay Kit	Abcam	Cat# ab83432
Seahorse XF Glycolysis Stress Test Kit	Agilent	Cat# 103015-100
Seahorse XF Cell Mito Stress Test Kit	Agilent	Cat# 103020-100
CUT&RUN Assay Kit	Cell Signaling Technology	Cat# 86652
TIANamp Genomic DNA Kit	TIANGEN	Cat# DP304
Presto Blue™ Cell Viability Reagent	Invitrogen™	Cat# A13262
DNA Library Prep Kit for Illumina Systems	Cell Signaling Technology	Cat# 56795
JC-1 MitoMP Detection Kit	Dojindo	Cat# MT09
Deposited data
ChIP-seq sequencing data	Raab et al.34	GSE69566
CHCC-HBV cohort proteomic data	Gao et al.21	https://doi.org/10.1016/j.cell.2019.08.052
ATAC sequencing data	This study	GSE228179
CUT&RUN sequencing data	This study	GSE228179
CRISPR/Cas9 screen sequencing data	This study	GSE228179
Experimental models: Cell lines
Hep3B	Cell Resource Center, IBMS, CAMS/PUMC	Cat# 1101HUM-PUMC000376
HepG2	Cell Resource Center, IBMS, CAMS/PUMC	Cat# 1101HUM-PUMC000035
293T	Cell Resource Center, IBMS, CAMS/PUMC	Cat# 1101HUM-PUMC000091
NCI-H1975	Cell Resource Center, IBMS, CAMS/PUMC	Cat# 1101HUM-PUMC000252
SNU449	ATCC	Cat# CRL-2234
Experimental models: Organisms/strains
NOD SCID	Charles River	N/A
NOG	Charles River	N/A
Oligonucleotides
ARID1A Knockout sgRNA sequences ARID1A-sg1: 5′- CAGCAGAACTC TCACGACCACGG -3’ (Exon 1)	This paper	N/A
ARID1A Knockout sgRNA sequences ARID1A-sg2: 5′- CCTGTTGACCATACCC GCTGGGG -3’ (Exon 3)	This paper	N/A
siRNA sequences	This paper	Table S1
Primer for qPCR or Cut&Run-qPCR	This paper	Table S1
Software and algorithms
GraphPad Prism 9	GraphPad	https://www.graphpad.com/
ImageJ (version 2.9.0)	NIH	https://ImageJ.nih.gov/ij/download.html
FlowJo (version 10.7.2)	BD Biosciences	https://www.flowjo.com/
GATK4	Broad institute	https://software.broadinstitute.org/gatk/
Fiji software	Schindelin et al.35	https://ImageJ.net/software/fiji/downloads
R (v4.1.1)	R	https://cran.r-project.org/
MAGeCK algorithm (v0.5.9.4)	Li et al.36	https://sourceforge.net/p/mageck/wiki/
GSEA (v4.1.0)	UC San Diego	https://www.gsea-msigdb.org/gsea/index.jsp
LAS X Office	Leica	https://www.leica-microsystems.com.cn/cn/products/microscope-software/p/leica-las-x-ls/downloads/