For the microarray analysis, the total RNA in each orbital adipose/connective tissue sample obtained from eight GO patients and six non-GO normal controls was extracted using a commercial reagent (TRI Reagent; Molecular Research Center, Cincinnati, OH, USA), according to the manufacturer's instructions. The quality and quantity of total RNA were assessed using a bioanalyzer (Agilent Bioanalyzer 2100; Agilent Technologies, Santa Clara, CA, USA). Starting with 250 ng of total RNA, the labeling process began by adding a poly(A) tail to each RNA strand using poly(A) polymerase, followed by ligation of biotin-labeled 3DNA dendrimer. Biotinylated RNA strands were hybridized at 48°C for 18 hours on a miRNA array (Affymetrix GeneChip miRNA 4.0 Array; Affymetrix, Santa Clara, CA, USA). The miRNA array (Affymetrix), with 2578 human mature miRNA, was washed and stained in an array cartridge system (Affymetrix Fluidics Station 450; Affymetrix). Amplified fluorescent signals were scanned using a commercial scanner (Affymetrix GeneChip Scanner 3000 7G; Affymetrix).
The arrays were analyzed using a scanner with associated software (Agilent). The miRNA expression levels were calculated with a commercial console (Expression Console 1.4; Affymetrix). Relative signal intensities for each miRNA were generated using the robust multi-array average algorithm. The data were processed based on the quantile normalization method using commercial software (GeneSpring GX 13.1; Agilent Technologies). This normalization method aims to achieve a consistent distribution of intensities for each of a set of arrays. The normalized and log-transformed intensity values were then analyzed using commercial software (Agilent Technologies). The fold changes in the miRNA expression between the GO and non-GO samples were calculated from the signal values. MicroRNA expression was considered significantly different if the fold change exceeded 1.5. Target prediction was performed using a cutoff at the 95% percentile using the TargetScan6.2 database in the public domain (
http://www.targetscan.org/).