Nugen ovation one direct system

cDNA synthesis and amplification was performed with the NuGEN Ovation One-Direct System (NuGEN, San Carlos, CA, USA). Total RNA was used for cDNA synthesis followed by whole transcriptome amplification by NuGEN's Ribo-SPIA® technology. The amplified single stranded DNA was purified with AMpure XP beads (Beckman, Indianapolis, IN, USA). Qualitative and quantitative analyses were performed on the Bioanalyzer and NanoDrop, respectively. 5 μg of the amplified DNA was used for biotinylation and fragmentation using the NuGEN Ovation Encore Biotin Module (Nugen, San Carlos, CA, USA). All samples were hybridized to Affymetrix GeneChip® Rhesus Macaque Genome Arrays (Affymetrix, Santa Clara, CA, USA). The probe arrays were washed, stained and scanned as described in the Affymetrix GeneChip® Expression Analysis Technical Manual. CEL files were extracted from the raw scanned images using the Affymetrix GeneChip® command console Software. Quality Control metrics were monitored on the Affymetrix Expression console software; discordant arrays were excluded from further downstream analyses.