Abi software version 2

Total RNA was extracted from different tissues (0.1 g liver or tissues indicated in Supplementary information, Figure S1D), cells (1 × 10⁶) or serum (0.1 ml) using Trizol or Trizol LS reagent (Invitrogen). Quantitative RT-PCR analyses with One-step QuantiTect SYBR Green Kit (Qiagen, CA, USA) of the indicated genes were performed as previously described^{14 (link)} in an ABI 7500 (ABI, CA, USA).The internal standard HCV RNA was synthesized by in vitro transcription (MEGAscript T7, Ambion, TX, USA) from pJFH-1 plasmid and quantified by a commercial kit (path-HCV, PrimerDesign, UK) at 1.1 × 10¹⁰ copies/ml. Serial dilutions of the internal standard HCV RNAs were spiked in ICR sera and liver homogenates to determine the linear range of detection and the limit of detection, using One-step QuantiTect SYBR Green Kit. The limit of detection of HCV RNA by this method is defined as the lowest concentration at which 95% of HCV RNA are detected^{53 (link)}, i.e., 500 copies/ml (serum) and 100 copies/mg (liver), respectively. Nested PCR was performed to detect HCV negative strand^{16 (link)} (see Supplementary information, Table S6 for primers). Quantitative RT-PCR analyses were carried out similarly for mRNA levels of IFNα4, IFNβ1, ISGs, miR-122, apoE, CypA and IL-28 (see Supplementary information, Table S6 for primers). Data were analyzed with ABI software version 2.0.3 (Applied Biosystems).