SRX18046773 GSM6689418_r1 SRP404912 PRJNA895043 SRS15553170 GSM6689418 GSM6689418 OTHER GENOMIC other Macro-dissected HCC were weighted and equal amounts (≈1mg each) from three different mice of intermediate- (n=3) and end-stage (n=3) HCC-bearing mice. Genomic DNA was extracted quantified on the Nanodrop 2000 (Thermofisher). A max of 2000 ng of double stranded genomic DNA were fragmented by Covaris shearing to obtain fragment sizes of 200-300 bp. Samples were purified using 2X Agencourt AMPure XP PCR Purification beads according to manufacturer's instructions (Beckman Coulter, cat no A63881). The sheared DNA samples were quantified and qualified on a BioAnalyzer system using the DNA7500 assay kit (Agilent Technologies cat no. 5067- 1506). With an input of maximum 1 μg sheared DNA, library preparation for Illumina sequencing was performed using the KAPA HTP Prep Kit (KAPA Biosystems, KK8234). During library amplification 4 PCR cycles were used to obtain enough yield for the exome capture. After library preparation, the libraries were cleaned up using 1X AMPure XP beads. All DNA libraries are analyzed on a BioAnalyzer system using the DNA7500 chips for determining the concentration. A single pool of six samples were created using 142ng of each indexed sample. The pool treated with Mouse COT (Invitrogen, ref 18440-016) and xGen universal Blocking Oligo's (IDT, cat no 1075475) before being captured with a SeqCap ES Share Developer Mouse probe (Roche, ref 08333025001), following the Hypercap Target Enrichment (Roche, ref 08286370001) with the probe incubation for 20 hours. After capture the pool was amplified using 10 PCR cycles and purified with Ampure XP beads. The pool was diluted to a final concentration of 10nM and subjected to paired-end 75bp sequencing on an Illumina Nextseq 550, according to manufacturer's instructions. NextSeq 550 SRX18046774 GSM6689419_r1 SRP404912 PRJNA895043 SRS15553171 GSM6689419 GSM6689419 OTHER GENOMIC other Macro-dissected HCC were weighted and equal amounts (≈1mg each) from three different mice of intermediate- (n=3) and end-stage (n=3) HCC-bearing mice. Genomic DNA was extracted quantified on the Nanodrop 2000 (Thermofisher). A max of 2000 ng of double stranded genomic DNA were fragmented by Covaris shearing to obtain fragment sizes of 200-300 bp. Samples were purified using 2X Agencourt AMPure XP PCR Purification beads according to manufacturer's instructions (Beckman Coulter, cat no A63881). The sheared DNA samples were quantified and qualified on a BioAnalyzer system using the DNA7500 assay kit (Agilent Technologies cat no. 5067- 1506). With an input of maximum 1 μg sheared DNA, library preparation for Illumina sequencing was performed using the KAPA HTP Prep Kit (KAPA Biosystems, KK8234). During library amplification 4 PCR cycles were used to obtain enough yield for the exome capture. After library preparation, the libraries were cleaned up using 1X AMPure XP beads. All DNA libraries are analyzed on a BioAnalyzer system using the DNA7500 chips for determining the concentration. A single pool of six samples were created using 142ng of each indexed sample. The pool treated with Mouse COT (Invitrogen, ref 18440-016) and xGen universal Blocking Oligo's (IDT, cat no 1075475) before being captured with a SeqCap ES Share Developer Mouse probe (Roche, ref 08333025001), following the Hypercap Target Enrichment (Roche, ref 08286370001) with the probe incubation for 20 hours. After capture the pool was amplified using 10 PCR cycles and purified with Ampure XP beads. The pool was diluted to a final concentration of 10nM and subjected to paired-end 75bp sequencing on an Illumina Nextseq 550, according to manufacturer's instructions. NextSeq 550 SRX18046775 GSM6689420_r1 SRP404912 PRJNA895043 SRS15553172 GSM6689420 GSM6689420 OTHER GENOMIC other Macro-dissected HCC were weighted and equal amounts (≈1mg each) from three different mice of intermediate- (n=3) and end-stage (n=3) HCC-bearing mice. Genomic DNA was extracted quantified on the Nanodrop 2000 (Thermofisher). A max of 2000 ng of double stranded genomic DNA were fragmented by Covaris shearing to obtain fragment sizes of 200-300 bp. Samples were purified using 2X Agencourt AMPure XP PCR Purification beads according to manufacturer's instructions (Beckman Coulter, cat no A63881). The sheared DNA samples were quantified and qualified on a BioAnalyzer system using the DNA7500 assay kit (Agilent Technologies cat no. 5067- 1506). With an input of maximum 1 μg sheared DNA, library preparation for Illumina sequencing was performed using the KAPA HTP Prep Kit (KAPA Biosystems, KK8234). During library amplification 4 PCR cycles were used to obtain enough yield for the exome capture. After library preparation, the libraries were cleaned up using 1X AMPure XP beads. All DNA libraries are analyzed on a BioAnalyzer system using the DNA7500 chips for determining the concentration. A single pool of six samples were created using 142ng of each indexed sample. The pool treated with Mouse COT (Invitrogen, ref 18440-016) and xGen universal Blocking Oligo's (IDT, cat no 1075475) before being captured with a SeqCap ES Share Developer Mouse probe (Roche, ref 08333025001), following the Hypercap Target Enrichment (Roche, ref 08286370001) with the probe incubation for 20 hours. After capture the pool was amplified using 10 PCR cycles and purified with Ampure XP beads. The pool was diluted to a final concentration of 10nM and subjected to paired-end 75bp sequencing on an Illumina Nextseq 550, according to manufacturer's instructions. NextSeq 550 SRX18046776 GSM6689421_r1 SRP404912 PRJNA895043 SRS15553173 GSM6689421 GSM6689421 OTHER GENOMIC other Macro-dissected HCC were weighted and equal amounts (≈1mg each) from three different mice of intermediate- (n=3) and end-stage (n=3) HCC-bearing mice. Genomic DNA was extracted quantified on the Nanodrop 2000 (Thermofisher). A max of 2000 ng of double stranded genomic DNA were fragmented by Covaris shearing to obtain fragment sizes of 200-300 bp. Samples were purified using 2X Agencourt AMPure XP PCR Purification beads according to manufacturer's instructions (Beckman Coulter, cat no A63881). The sheared DNA samples were quantified and qualified on a BioAnalyzer system using the DNA7500 assay kit (Agilent Technologies cat no. 5067- 1506). With an input of maximum 1 μg sheared DNA, library preparation for Illumina sequencing was performed using the KAPA HTP Prep Kit (KAPA Biosystems, KK8234). During library amplification 4 PCR cycles were used to obtain enough yield for the exome capture. After library preparation, the libraries were cleaned up using 1X AMPure XP beads. All DNA libraries are analyzed on a BioAnalyzer system using the DNA7500 chips for determining the concentration. A single pool of six samples were created using 142ng of each indexed sample. The pool treated with Mouse COT (Invitrogen, ref 18440-016) and xGen universal Blocking Oligo's (IDT, cat no 1075475) before being captured with a SeqCap ES Share Developer Mouse probe (Roche, ref 08333025001), following the Hypercap Target Enrichment (Roche, ref 08286370001) with the probe incubation for 20 hours. After capture the pool was amplified using 10 PCR cycles and purified with Ampure XP beads. The pool was diluted to a final concentration of 10nM and subjected to paired-end 75bp sequencing on an Illumina Nextseq 550, according to manufacturer's instructions. NextSeq 550 SRX18046777 GSM6689422_r1 SRP404912 PRJNA895043 SRS15553174 GSM6689422 GSM6689422 OTHER GENOMIC other Macro-dissected HCC were weighted and equal amounts (≈1mg each) from three different mice of intermediate- (n=3) and end-stage (n=3) HCC-bearing mice. Genomic DNA was extracted quantified on the Nanodrop 2000 (Thermofisher). A max of 2000 ng of double stranded genomic DNA were fragmented by Covaris shearing to obtain fragment sizes of 200-300 bp. Samples were purified using 2X Agencourt AMPure XP PCR Purification beads according to manufacturer's instructions (Beckman Coulter, cat no A63881). The sheared DNA samples were quantified and qualified on a BioAnalyzer system using the DNA7500 assay kit (Agilent Technologies cat no. 5067- 1506). With an input of maximum 1 μg sheared DNA, library preparation for Illumina sequencing was performed using the KAPA HTP Prep Kit (KAPA Biosystems, KK8234). During library amplification 4 PCR cycles were used to obtain enough yield for the exome capture. After library preparation, the libraries were cleaned up using 1X AMPure XP beads. All DNA libraries are analyzed on a BioAnalyzer system using the DNA7500 chips for determining the concentration. A single pool of six samples were created using 142ng of each indexed sample. The pool treated with Mouse COT (Invitrogen, ref 18440-016) and xGen universal Blocking Oligo's (IDT, cat no 1075475) before being captured with a SeqCap ES Share Developer Mouse probe (Roche, ref 08333025001), following the Hypercap Target Enrichment (Roche, ref 08286370001) with the probe incubation for 20 hours. After capture the pool was amplified using 10 PCR cycles and purified with Ampure XP beads. The pool was diluted to a final concentration of 10nM and subjected to paired-end 75bp sequencing on an Illumina Nextseq 550, according to manufacturer's instructions. NextSeq 550 SRX18046778 GSM6689423_r1 SRP404912 PRJNA895043 SRS15553175 GSM6689423 GSM6689423 OTHER GENOMIC other Macro-dissected HCC were weighted and equal amounts (≈1mg each) from three different mice of intermediate- (n=3) and end-stage (n=3) HCC-bearing mice. Genomic DNA was extracted quantified on the Nanodrop 2000 (Thermofisher). A max of 2000 ng of double stranded genomic DNA were fragmented by Covaris shearing to obtain fragment sizes of 200-300 bp. Samples were purified using 2X Agencourt AMPure XP PCR Purification beads according to manufacturer's instructions (Beckman Coulter, cat no A63881). The sheared DNA samples were quantified and qualified on a BioAnalyzer system using the DNA7500 assay kit (Agilent Technologies cat no. 5067- 1506). With an input of maximum 1 μg sheared DNA, library preparation for Illumina sequencing was performed using the KAPA HTP Prep Kit (KAPA Biosystems, KK8234). During library amplification 4 PCR cycles were used to obtain enough yield for the exome capture. After library preparation, the libraries were cleaned up using 1X AMPure XP beads. All DNA libraries are analyzed on a BioAnalyzer system using the DNA7500 chips for determining the concentration. A single pool of six samples were created using 142ng of each indexed sample. The pool treated with Mouse COT (Invitrogen, ref 18440-016) and xGen universal Blocking Oligo's (IDT, cat no 1075475) before being captured with a SeqCap ES Share Developer Mouse probe (Roche, ref 08333025001), following the Hypercap Target Enrichment (Roche, ref 08286370001) with the probe incubation for 20 hours. After capture the pool was amplified using 10 PCR cycles and purified with Ampure XP beads. The pool was diluted to a final concentration of 10nM and subjected to paired-end 75bp sequencing on an Illumina Nextseq 550, according to manufacturer's instructions. NextSeq 550