Pathway studio explore 1

Microarray hybridization probes were generated from isolated RNA samples. Double-stranded cDNA was synthesized from 100 ng of total RNA using the GeneAtlas 3′ IVT Express Kit (Affymetrix, Inc.). Biotin-labeled aRNA was synthesized by in vitro transcription and purified. 10 μg of purified aRNA was then fragmented using the GeneAtlas 3′ IVT Express Kit and was hybridized to the Affymetrix HG-U219 (Affymetrix) for 16 h at 45°C. The chips were washed and stained in the GeneAtlas Fluidics Station 400 (Affymetrix) and then imaged in the GeneAtlas Imaging Station (Affymetrix). The Partek Express software (Affymetrix) served for the data analysis by running comparisons of gene expression in treated and control cells based on mathematical algorithms. The generated data (significant fold change in gene expression) was then analyzed using the Pathway Studio Explore 1.1 software (Affymetrix).

The global gene expression changes in B16F10 cells were analyzed following the protocol for the Affymetrix MG-430 PM Array Strip (Affymetrix, Santa Clara, CA, USA). Partek Express Software (Affymetrix) was used to analyze the data, by running comparisons of gene expression in treated and control cells based on mathematical algorithms. The generated data (significant fold change in gene expression) was then analyzed using the Pathway Studio Explore 1.1 software (Affymetrix). The DNA microarray data comply with MIAME guidelines, and have been deposited in the ArrayExpress database at EMBI-EBI (www.ebi.ac.uk/arrayexpress), under the reference number E-MTAB-8836.