Genespring 14.9 gx software

TIFF multiscan images from SureScan Microarray Scanner (Agilent Technologies, USA) were processed using Feature Extraction Software 11.5 (Agilent Technologies, USA). In this software also, the image processing was performed and acquired files with spot intensities for every microarray field (corresponding to one condition). The raw data underwent quality control, normalization, and statistical analysis in GeneSpring 14.9 GX software for gene expression analysis and Agilent Genomic Workbench 7.0.4.0 for DNA methylation analysis.

After IF-MF exposure, whole brains and livers were extracted from the mice, soaked with RNA later^® (Thermo Fisher Scientific, San Jose, CA, USA), and stored at −80 °C. Total RNA was extracted and confirmed for quality (purity, concentration, and degradation). The differential expression of transcripts was assessed in the organs between IF-MF- and sham-exposed mice by using GeneChip^® Mouse Gene 2.0 ST Array (Affymetrix, Santa Clara, CA, USA), which covered 35,240 probe sets. Data were analyzed with GeneSpring 14.9 GX software (Agilent Technologies, Palo Alto, CA, USA). The differential expression of transcripts was analyzed using multiple comparison testing with moderated t-testing, with a false discovery rate (FDR) adjusted p-value cutoff <0.05 [12 (link)] in sham-exposed mice. The fold change cutoff was set to >2.0 or 1.5. Ten mice in the 90A_exposure group were analyzed five by five in 90A_1 and 90A_2 exposure because only five mice could be used per experimental group and also to remove the inter-experimental error.