Supplementary Materials and Methods
Moksiskaan analysis
Moksiskaan [22] is a data integration platform that contains gene, pathway and drug data
obtained from Ensembl [45], KEGG [26], Gene Ontology [46], SPIA [23], SNPs3D [47],
PathwayCommons [48], PINA [49] and COSMIC [50]. We used these data to identify
cellular connections between the differentially expressed genes (Fig. S1b), and to relate
them to the existing drugs (Fig. S1c), diseases and known cancer mutations.
Reverse transcriptase-polymerase chain reaction
RNA isolated from the tumor tissue was analysed using a two-step reverse transcriptasepolymerase chain reaction (RT-PCR). Qiagen QuantiTect Reverse Transcription Kit
(205311, Hilden, Germany) was first used to synthesize cDNA, which included genomic
DNA wipeout, and concentrations of the cDNAs were balanced to 100 ng/μl using
NanoDrop 2000 Spectrophotometer (Thermo Scientific, Waltham, WA). The primers
were designed to overlap exon-intron boundaries in order to eliminate the bias of possible
genomic
DNA
contamination.
The
primers
used
were:
MxA
(5’-
TACCAGACTCCGACACGAGT-3’ and 5’-GTGATGTTCAGCATGTGTCAGT-3’),
IFI27 (5’-TCTGGCTGAAGTTGAGGATC-3’ and 5’-GATAGTTGGCTCCTCGCTG3’),
IFI6
(5’-GGAGGCAGGTAAGAAAAAGT-3’
and
5’-
TGTCTATCACTCTCCCCAAC-3’) and β-actin (5’-CGAGGCCCAGAGCAAGACA-3’
and 5’-CACAGCTTCTCCTTAATGTCACG-3’), which produced 1106 bp, 502 bp, 607
bp, and 482 bp PCR products, respectively. Briefly, 50 ng cDNA was added to PCR
mixture containing 0.2 μl DyNAzyme II DNA Polymerase (Finnzymes, Espoo, Finland),
1.5 μl 10x buffer (F-511; Finnzymes), 0.6 μl of 10 mM deoxynucleoside triphosphates, 1
μl of each 10 μM primer in a final volume of 15 μl. The thermocycler conditions used
were 54°C for 30 min for reverse transcription, 95°C for 15 min for activation of the
DNA polymerase, and then 35 cycles of 94°C for 45 s, 54°C for 45 s for annealing, and
72°C for 45 s, followed by an extension of 10 min at 72°C. PCR products were run on
agarose gel.
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