Whole retinas were collected in Trizol and purified using the manufactures instructions (Invitrogen, Grand Island, NY, USA). Each sample consisted of three retinas in groups of either diabetic or control mice; three samples of each group were then run on the array. RNA was quantified using a Nanodrop spectrophotometer (Thermo Scientific, Waltham, MA, USA) and quality checked with the Total RNA Nano 6000 Assay Kit (Agilent Technologies, Victoria, Australia) and the Agilent Bioanalyser. All RNA integrity (RIN) values were 7 or higher. Synthesis of cRNA was performed using an Illumina TotalPrepTM RNA Amplification Kit (Ambion, Austin, TX, USA) according to the manufacturer's instructions. A total of 750 ng labeled cRNA was suspended in 5 μL RNase free water and hybridized to a BeadChip Array MouseRef-8 V2 (Illumina, San Diego, CA, USA) according to the manufacturer's instructions, followed by washing and staining with Streptavidin Cy-3 (GE Heathcare, Amersham, UK). The BeadChip was scanned with Bead Array Reader (Illumina) using Illumina Bead Studio software (Illumina).
The data were further analyzed in the ‘R' statistical environment. Transcripts that had a detection P value less than 0.05 in greater than 10% of the sample set were obtained using the LUMI R module. Following this, negative gene expression values (which do not have any biological meaning) were removed. Other experimental-, biological-, and machine-related variations were then eliminated by transforming data sets to Log2 scale values and normalizing using a Robust Spline Normalization (RSN) algorithm. In order to ensure the accuracy of the normalizing process, diagnostic plots were generated. Sample replicates clustering together and aligning to the same median value indicates correct normalization. Following the above procedure, Principle Component Analysis (PCA) was applied to the normalized microarray data sets. Samples were subject to differential expression analysis using the empirical Bayesian technique described in the LIMMA R package and a False Discovery Rate (FDR) correction was applied to the P values. Genes were considered differentially expressed if they had Benjamini-corrected FDR P values smaller than 0.05 together with a greater than 0.5 log 2-fold change (either positive or negative).