Genechip human genome u133 hg u133 plus 2.0 array

Gene expression analysis was performed in triplicate (three sham, three nsEP exposed and three heat-shock treated) using the Affymetrix GeneChip^® Human Genome U133 (HG-U133) plus 2.0 Array that contains 54,675 probe sets. Briefly, two micrograms of RNA were used for preparation of biotin-labeled targets (cRNA) using MessageAmp^™-based protocols (Ambion, Inc., Austin, TX). Labeled cRNA was fragmented (0.5 μg/μL per reaction) and used for array hybridization and washing. The cRNA was mixed with a hybridization cocktail, heated to 99°C for 5 min and then incubated at 45°C for 5 min. Hybridization arrays were conducted for 16 h in an Affymetrix Model 640 hybridization oven (45°C, and 60 rpm). Arrays were washed and stained on an FS450 Fluidics station and were scanned on a GeneChip^® Scanner 3000 7G. Image signal data, detection calls and annotations were generated for every gene using the Affymetrix Statistical Algorithm MAS 5.0 (GeneChip^® Operating Software v1.3). A log2 transformation was conducted and a Student’s t-test was performed for comparison of the nsEP exposed samples to the two control groups (sham and heat-shocked). We conducted multiple testing correction—Benjamini and Hochberg—to determine the false discovery rate, and statistically significant genes were identified using Bonferroni correction procedures.