TABLE 1.

Genes upregulated and downregulated by 4-h and 24-h treatment with IFN-α, IFN-β, and IFN-γa

TABLE 1.
  • a Microarray analysis of gene expression changes induced by 20 IU/ml of IFN-α and IFN-β or IFN-γ/ml in HCV replicon cells (I389neo/NS3-3′/wt). Total cellular RNA (10 μg) was used to synthesize double-stranded cDNA, which was subsequently used to generate biotin-labeled cRNA. Fragmented cRNA (20 μg) target was hybridized to a Hu6800 full-length GeneChip array (Affymetrix) at 45°C overnight. The chips were washed (Fluidics Station 400; Affymetrix) and stained with phycoerythrin-labeled streptavidin (Molecular Probes, Eugene, Oreg.) and then scanned on a Hewlett Packard/Agilent GeneArray scanner. Data was analyzed using the Affymetrix Data Mining Tool (version 3.0). The manufacturer recommended analyses to assess variability in array hybridization (efficiency and normalization), and cDNA synthesis efficiency were performed as previously described (9). Genes are listed by open reading frame (ORF) GenBank accession numbers or TIGR database HT number). Genes preferentially upregulated by IFN-γ are listed in red with fold changes highlighted in red, whereas genes preferentially upregulated by IFN-α and IFN-β are listed in blue with fold changes highlighted in blue. Genes not preferentially upregulated by all three IFNs are listed in black. Downregulated genes are listed in green. Bold numbers represent fold changes of >3.