KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibody | ||
| AFP | Cell Signaling Technologies | Cat#: 4448; RRID:AB_10897327 |
| β-actin | Sigma | Cat#: A5316; RRID:AB_476743 |
| β-catenin (H-102) | Santa Cruz | Cat#: SC-7199; RRID:AB_634603 |
| CD8 | eBioscience | Cat#: 14-0032-81; RRID:AB_467052 |
| CK19 | DSHB | Cat#: Troma-III; RRID:AB_2133570 |
| Clec4f | BioLegend | Cat#: 156804; RRID:AB_2814082 |
| Erk1/2 | Cell Signaling Technologies | Cat#: 4695; RRID:AB_390779 |
| F4/80 | eBioscience | Cat#: 14-4801-82; RRID:AB_467558 |
| Gapdh | Cell Signaling Technologies | Cat#: 5172 |
| Glutamine Synthetase | Cell Signaling Technologies | Cat#: 3886 |
| Histone 3 | Cell Signaling Technologies | Cat#: 4499P; RRID:AB_10544537 |
| HNF4a | Santa Cruz | Cat#: sc-8987; RRID:AB_2116913 |
| Ki67 | eBioscience | Cat#: 14-5698-80; RRID:AB_10853185 |
| MYC | abcam | Cat#: ab32072; RRID:AB_731658 |
| p-c-Myc (S62) | abcam | Cat#: ab51156; RRID:AB_869189 |
| p-c-Myc (T58) | abcam | Cat#: ab28842; RRID:AB_731667 |
| PCNA | Santa Cruz | Cat#: 7907; RRID:AB_2160375 |
| p-Erk1/2 | Cell Signaling Technologies | Cat#: 4370; RRID:AB_2315112 |
| p-β-catenin (S33/37/T41) | Cell Signaling Technologies | Cat#: 9561; RRID:AB_331729 |
| Shp2 | Santa Cruz | Cat#: sc-7384; RRID:AB_628252 |
| FACS antibodies | ||
| Life/Dead Aqua Stain | ThermoFisher | Cat#: L34957 |
| CD45 – PerCP | Biolegend | Cat#: 147706; RRID:AB_2563538 |
| Ly6c – PE | Biolegend | Cat#: 128008; RRID:AB_1186132 |
| F4/80 - BV421 | Biolegend | Cat#: 123124; RRID:AB_893475 |
| CD11c – APC | Biolegend | Cat#: 117309; RRID:AB_313778 |
| MHCII - APC Cy7 | Biolegend | Cat#: 107628; RRID:AB_2069377 |
| CD11b - BV605 | Biolegend | Cat#: 101257; RRID:AB_2565431 |
| TCRβ - BV421 | Biolegend | Cat#: 109226; RRID:AB_1027649 |
| NK1.1 – APC | Biolegend | Cat#: 108710; RRID:AB_313397 |
| CD8a - PE Cy7 | Biolegend | Cat#: 100722; RRID:AB_312761 |
| CD19 - APC Cy7 | Biolegend | Cat#: 115530; RRID:AB_830707 |
| CD4 - BV605 | Biolegend | Cat#: 100451; RRID:AB_2564591 |
| CD69 - BV711 | Biolegend | Cat#: 104537; RRID:AB_2566120 |
| Commercial assays | ||
| Pico-Sirius Red Stain Kit | American MasterTech | Cat#: KTPSRPT |
| Mayer’s Hematoxylin | Electron Microscopy Services | Cat#: 2617303 |
| TUNEL | Takara | Cat#: MK500; RRID:AB_2800362 |
| RNAScope 2.5 HD Assay - Red | ACDBio | Cat#: 322360, 3223650 |
| Nuclear Extraction Kit | abcam | Cat#: ab113474 |
| Dead Cell Removal Kit | Miltenyi Biotech | Cat#: 130-090-101 |
| Oligonucleotides | ||
| See Table S4 | ||
| Software and algorithms | ||
| FlowJo 10.6.2 | BD | https://www.flowjo.com |
| Graphpad Prism 5.0 | Graphpad | https://www.graphpad.com/scientific-software/prism/ |
| ImageJ / FIJI | ImageJ, FIJI team | https://imagej.net/software/fiji |
| Cellranger v3.0.2 | 10x Genomics | https://www.10xgenomics.com/ |
| STAR | Dobin et al., 2013 | https://github.com/alexdobin/STAR |
| R | The R Foundation | https://www.r-project.org/ |
| Seurat | Butler et al., 2018; Stuart et al., 2019 | https://github.com/satijalab/seurat |
| Python 3 | Python Software Foundation | https://www.python.org/ |
| MAGIC | van Dijk et al., 2018 | https://github.com/KrishnaswamyLab/MAGIC |
| Experimental models: Organisms | ||
| Mouse: SKO (Albumin-Cre; Shp2 f/f) | Bard-Chapeau et al., 2006 | N/A |
| Mouse: BKO(Albumin-Cre; β-catenin f/f) | Liang et al., 2018 | N/A |
| Mouse: SBKO(Albumin-Cre; Shp2 f/f; β-catenin f/f) | This paper | N/A |
| Deposited data | ||
| Single Cell RNA-sequencing data | GEO Repository | GSE157561 |
| Public datasets analyzed | ||
| TCGA-LIHC project | cBioPortal | NA |
| GSE14520 dataset | GEO Repository | GSE14520 |