REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples
Patient-derived biopsy tissues	NIH/NCI Clinical Center	N/A
Chemicals, peptides, and recombinant proteins
RPMI 1640 Medium	Gibco	Cat# 11875
MACS Tissue Storage Solution	Miltenyi Biotech	Cat# 130-100-008
Cell Culture Freezing Medium	Gibco	Cat# 12648-010
1X Red Blood Cell Lysis Buffer	Invitrogen (Thermo-Fisher)	Cat# 00-4333-57
C Tubes	Miltenyi Biotech	Cat# 130-093-237
MACS Strainers (70μm)	Miltenyi Biotech	Cat# 130-095-823
Critical commercial assays
Tumor Dissociation Kit, Human	Miltenyi Biotech	Cat# 130-095-929
Chromium Single Cell 3′ Library & Gel Bead Kit v1 & v2	10x Genomics	Cat# PN-120237
Chromium Single Cell A Chip Kit	10x Genomics	Cat# PN-120236
Chromium Single Cell G Chip Kit	10x Genomics	Cat# PN-1000127
Chromium i7 Multiplex Kit	10x Genomics	Cat# PN-120262
Deposited data
scRNA-seq data	This paper	GEO: GSE229772
scRNA-seq data	Ma et al. 24	GEO: GSE151530
LCI (HCC)	Roessler et al. 45	GEO: GSE14520 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc = gse14520)
TCGA (HCC)	TCGA (https://portal.gdc.cancer.gov)	TCGA-LIHC
TIGER-LC (HCC)	TIGER-LC	GEO: GSE76297 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE76297)
Software and algorithms
Cell Ranger version 6.0.1	10x Genomics	https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest
Seurat version 4.1.0	Satija Lab	https://satijalab.org/seurat/
R version 3.4.3	The R Project for Statistical Computing	https://www.r-project.org/
GSEA version 4.1.0	Broad Institute	http://software.broadinstitute.org/gsea/index.jsp
InferCNV	GitHub	https://github.com/broadinstitute/inferCNV
GraphPad Prism version 9	GraphPad Software, San Diego, CA, USA	https://www.graphpad.com/
CASCADE	This paper	https://doi.org/10.5281/zenodo.10424656
Other
GentleMACS Dissociator	Miltenyi Biotech	130-093-235
Sequencer NextSeq 500	Illumina	N/A
Sequencer HiSeq 4000	Illumina	N/A
Sequencer NovaSeq 6000	Illumina	N/A