Supplementary Table 1. The primers used for real-time PCR analysis of mRNA expression

GeneSymbol / Direction / Nucreotide sequence / product size (bp)
HMGCR / Forward / gtcattccagccaaggttgt / 228
Reverse / gggaccacttgcttccatta
SQLE / Forward / gtctccggaaagcagctatg / 191
Reverse / caggcttttcctgaacttgg
CYP51A1 / Forward / tggccagaactcctcagact / 185
Reverse / agctccaaatggcacatagg
TM7SF2 / Forward / ctggtcaatggcttccagtt / 248
Reverse / gccccacggaagatgtagta
NSDHL / Forward / gggtttgataatccccaggt / 194
Reverse / ccagcctctttgcaagtttc
EBP / Forward / gcctcagcacctaagactgg / 189
Reverse / atgaacccacacactgcaaa
Beta-actin / Forward / tttgcggtggacgatggaggggccggactc / 150
Reverse / acaatgaagatcaagatcattgctcctcct

Supplementary Table 2. Pathway analysis (1b and 2a replicon cells compared to cured cells, Fold change>1.2, delta=0.1)

Pathway ID* / Description / p-value / FDR
hsa04010 / MAPK signaling pathway / 0.00040 / 0.08
hsa00970 / Aminoacyl-tRNA biosynthesis / 0.00210 / 0.21
hsa00260 / Glycine, serine and threonine metabolism / 0.00361 / 0.21
hsa00100 / Biosynthesis of steroids / 0.00421 / 0.21
hsa01032 / Glycan structures - degradation / 0.00815 / 0.29
hsa04350 / TGF-beta signaling pathway / 0.00840 / 0.29

* KEGG pathway maps for each significant pathways are shown in the Supplementary Figures 2A through 2F.

Supplementary Table 3. Pathway analysis (cured-1b and -2a cells compared to Huh7 cells, Fold change>1.2, delta=0.1)

Pathway ID* / Description / p-value / FDR
hsa00100 / Biosynthesis of steroids / 0.000175 / 0.036
hsa00650 / Butanoate metabolism / 0.002568 / 0.203
hsa00900 / Terpenoid biosynthesis / 0.002983 / 0.203
hsa00363 / Bisphenol A degradation / 0.004465 / 0.228
hsa04350 / TGF-beta signaling pathway / 0.008429 / 0.251
hsa00150 / Androgen and estrogen metabolism / 0.008769 / 0.251
hsa04110 / Cell cycle / 0.008998 / 0.251
hsa00280 / Valine, leucine and isoleucine degradation / 0.009942 / 0.251
hsa00072 / Synthesis and degradation of ketone bodies / 0.011051 / 0.251
hsa00600 / Sphingolipid metabolism / 0.013283 / 0.271
hsa00380 / Tryptophan metabolism / 0.015524 / 0.288

* KEGG pathway maps for each significant pathways are shown in Figure 5 and the Supplementary Figures 3A through 3J.

Supplementary Table 4. Correspondence between the genes that were examined in the microarray analyses and enzymes that are presented in Figure 5 and 7.

Gene names / EGIDs
Figure 5 / hydroxymethylglutaryl-CoA reductase / 1.1.1.34
mevalonate kinase / 2.7.1.36
phosphomevalonate kinase / 2.7.4.2
diphosphomevalonate decarboxylase / 4.1.1.33
isopentenyl-diphosphate delta-isomerase / 5.3.3.2
geranylgeranyl-diphosphate synthase / 2.5.1.29
geranyltranstransferase / 2.5.1.10
geranyl-diphosphate synthase / 2.5.1.1
farnesyl-diphosphate farnesyltransferase / 2.5.1.21
squalene monooxygenase / 1.14.99.7
lanosterol synthase / 5.4.99.7
Delta24-sterol reductase / 1.3.1.72
sterol 14-demethylase / 1.14.13.70
Delta14-sterol reductase / 1.3.1.70
methylsterol monooxygenase / 1.14.13.72
sterol-4alpha-carboxylate 3-dehydrogenase / 1.1.1.170
3-keto-steroid reductase / 1.1.1.270
cholestenol delta-isomerase / 5.3.3.5
lathosterol oxidase / 1.14.21.6
7-dehydrocholesterol reductase / 1.3.1.21
Figure 7 / acetyl-CoA C-acetyltransferase / 2.3.1.9
acetyl-CoA acyltransferase / 2.3.1.16
3-hydroxyacyl-CoA dehydrogenase / 1.1.1.35
long-chain 3-hydroxyacyl-CoA dehydrogenase / 1.1.1.211
enoyl-CoA hydratase / 4.2.1.17
acyl-CoA oxidase / 1.3.3.6
glutaryl-CoA dehydrogenase / 1.3.99.7
acyl-CoA dehydrogenase / 1.3.99.-
butyryl-CoA dehydrogenase / 1.3.99.2
acyl-CoA dehydrogenase / 1.3.99.3
long-chain-acyl-CoA dehydrogenase / 1.3.99.13
carnitine O-palmitoyltransferase 1 / 2.3.1.21
long-chain acyl-CoA synthetase / 6.2.1.3

Supplementary Table 5. List of KEGG molecular pathways that showned significant differences between naïve and HCV-JFH1-infected cell lines.

Pathway ID / Description / p-value / FDR
hsa00910 / Nitrogen metabolism / 0.000114 / 0.023
hsa00471 / D-Glutamine and D-glutamate metabolism / 0.002494 / 0.223
hsa04360 / Axon guidance / 0.003282 / 0.223
hsa00550 / Peptidoglycan biosynthesis / 0.007640 / 0.285
hsa04350 / TGF-beta signaling pathway / 0.008085 / 0.285
hsa03320 / PPAR signaling pathway / 0.009913 / 0.285
hsa00900 / Terpenoid biosynthesis / 0.010902 / 0.285
hsa04610 / Complement and coagulation cascades / 0.011178 / 0.285