KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-Cytokeratin 19 | Abcam | Cat# ab52625; RRID: AB_2281020 |
| AFP antibody | Proteintech | Cat# 14550-1-AP; RRID: AB_2223933 |
| Anti-Glypican 3 | Abcam | Cat# ab66596; RRID: AB_1141042 |
| Anti-Hepatocyte Specific Antigen | Abcam | Cat# ab75677; RRID: AB_1523754 |
| Anti-Cytokeratin 7 | Abcam | Cat# ab181598; RRID: AB_278382 |
| Nestin antibody | Santa Cruz Biotechnology | Cat# sc-23927; RRID: AB_627994 |
| Goat anti-Mouse secondary antibody | Abcam | Cat#ab6789; RRID: AB_955439 |
| Goat anti-Rabbit secondary antibody | Abcam | Cat#ab6721; RRID: AB_955447 |
| Biological Samples | ||
| Tumor, adjacent non-cancerous liver tissues and blood samples from patients diagnosed with cHCC-ICC | This paper | This paper (PKU_cHCC-ICC) |
| Critical Commercial Assays | ||
| PEN Membraneslide | Leica | Cat#11505158 |
| DNeasy Blood & Tissue Kit | Qiagen | Cat#69504 |
| GeneRead DNA FFPE Kit | Qiagen | Cat#180134 |
| QIAamp DNA Micro Kit | Qiagen | Cat#56304 |
| RNeasy Mini Kit | Qiagen | Cat#74106 |
| AllPrep DNA/RNA Micro Kit | Qiagen | Cat#80284 |
| NEBNext Ultra DNA Library Prep Kit for Illumina | New England Biolabs | Cat#E7645L |
| SureSelect All Exon V6 | Agilent Technologies | Cat#5190-8864 |
| NEBNext Ultra RNA Library Prep Kit for Illumina | New England Biolabs | Cat#E7530L |
| Deposited Data | ||
| cHCC-ICC WES data | This paper | EGA: EGAS00001003093 |
| cHCC-ICC WGS data | This paper | EGA: EGAS00001003093 |
| cHCC-ICC RNA-seq data | This paper | EGA: EGAS00001003093 |
| TCGA LIHC data | TCGA, 2017 | https://gdc.cancer.gov/ |
| TCGA CHOL data | Farshidfar et al., 2017 | https://gdc.cancer.gov/ |
| ICGC HCC data | Fujimoto et al., 2016 | https://dcc.icgc.org/ |
| ICGC CCA data | Jusakul et al., 2017 | https://dcc.icgc.org/ |
| Oligonucleotides | ||
| Primer1 for TERT promoter, Forward GCAGCACCTCGCGGTAGTGGCTG | This paper | N/A |
| Primer1 for TERT promoter, Reverse GCCGATTCGACCTCTCTCCGCTGGCC | This paper | N/A |
| Primer2 for TERT promoter, Forward CAGCGCTGCCTGAAACTCGC | This paper | N/A |
| Primer2 for TERT promoter, Reverse TGGCGTCCCTGCACCCTGG | This paper | N/A |
| Primers for mutation validation of single nucleus, see Table S5 | This paper | N/A |
| Software and Algorithms | ||
| BWA | Li et al., 2009 | http://bio-bwa.sourceforge.net/ |
| Samtools v0.1.19 | Li et al., 2009 | http://samtools.sourceforge.net/ |
| GATK v2.1–8 | McKenna et al., 2010 | https://software.broadinstitute.org/gatk/ |
| Mutect v1.1.4 | Cibulskis et al., 2013 | https://software.broadinstitute.org/cancer/cga/mutect |
| SnpEff 4.0 | Cingolani et al., 2012 | http://snpeff.sourceforge.net/about.html |
| Genomon | N/A | https://genomon-project.github.io/GenomonPages/ |
| EBCall | Shiraishi et al., 2013 | https://github.com/friend1ws/EBCall |
| ANNOVAR | Wang et al., 2010 | http://annovar.openbioinformatics.org/en/latest/user-guide/download/ |
| MutSigCV 1.4 | Lawrence et al., 2013 | https://software.broadinstitute.org/cancer/cga/mutsig_download |
| dNdScv | Martincorena et al. (2017) | https://github.com/im3sanger/dndscv |
| SigProfiler Mutational Signatures | Alexandrov et al., 2013 | https://ww2.mathworks.cn/matlabcentral/fileexchange/38724-sigprofiler |
| deConstructSigs | Rosenthal et al., 2016 | https://github.com/raerose01/deconstructSigs |
| mSigAct | Ng et al., 2017 | https://stm.sciencemag.org/content/suppl/2017/10/16/9.412.eaan6446.DC1 |
| MEGA5 | Tamura et al., 2011 | https://www.megasoftware.net/download_form |
| PyClone | Roth et al., 2014 | https://github.com/aroth85/pyclone |
| DNAcopy | Venkatraman et al., 2007 | https://bioconductor.org/packages/release/bioc/html/DNAcopy.html |
| Sequenza v2.1.1 | Favero et al., 2015 | http://www.cbs.dtu.dk/biotools/sequenza/ |
| CNVkit v0.9.2 | Talevich et al., 2016 | https://cnvkit.readthedocs.io/en/stable/ |
| GISTIC v2.0.23 | Mermel et al., 2011 | https://software.broadinstitute.org/cancer/cga/gistic |
| STAR | Dobin et al., 2013 | https://github.com/alexdobin/STAR |
| DESeq2 v1.22.2 | Love et al., 2014 | http://bioconductor.org/packages/release/bioc/html/DESeq.html |
| Gene Set Enrichment Analysis (GSEA) v3.0 | Subramanian et al., 2005 | http://software.broadinstitute.org/cancer/software/genepattern/ |
| pheatmap | N/A | https://www.rdocumentation.org/packages/pheatmap/versions/1.0.2 |
| survminer v0.4.3 | N/A | https://cran.r-project.org/web/packages/survminer/index.html |
| Chromas v2.3 | N/A | www.technelysium.com.au |
| Graphpad Prism7 | N/A | https://www.graphpad.com/ |
| Rstudio v3.5.1 | N/A | https://www.rstudio.com/products/rstudio/ |