Undamaged hepatocytes and damaged hepatocytes were isolated by liver perfusion and gravity purification. The Sox9+ reprogrammed hepatocytes were isolated by sorting the RFP+ damaged hepatocytes in the BD influx cell sorter based on size/granularity and RFP expression. For isolating of biliary epithelia cells (BECs), the Ck19CreERT2:RFP reporter mice were treated with three individual oral gavage of tamoxifen (150mg/kg) under resting condition. The BECs were isolated by sorting RFP+ NPCs in the BD influx cell sorter based on size/granularity and RFP expression.Nuclei isolated from 20,000 counted cells were used for transposition reaction with transposase (Vazyme Biotech). Libraries were prepared with NEBNext High-Fidelity 2x PCR Master Mix (New England Labs Cat #M0541)with 12 cycles