Whole-genome gene expression profiles were analyzed using the Mouse Gene Expression 4x44K v2 Microarray (Agilent Technologies, Tokyo, Japan), which detects 39,430 Entrez Gene RNAs. Total RNA was first isolated with TRIzol reagent (ThermoFisher Scientific, Waltham, MA, USA) from whole brains of four male mice in each group with the Ctrl or Trp− diet. Total RNA was determined using an Agilent 2100 Bioanalyzer. Total RNA was then applied to Cy3-labeled cRNA synthesis, which was performed with a Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions. Finally, Cy3-labeled cRNA was hybridized to the microarray and detected using an Agilent SureScan Microarray Scanner (Agilent Technologies).
Microarray image data were extracted to ProcessedSignal using Feature Extraction 11.5.1.1 software (Agilent Technologies). GeneSpring GX v14.5 software (Agilent Technologies) was used for subsequent data processing. Gene expression with a statistically significant difference (P < 0.05) and an absolute value of log2 fold change > 1.2 between groups was exported to the dataset. Gene ontology and pathway analyses were performed using BaseSpace (Illumina KK, Tokyo, Japan) and MetaCore v6.30 build 68780 (Clarivate Analytics Japan, Tokyo, Japan), respectively.
Microarray image data were extracted to ProcessedSignal using Feature Extraction 11.5.1.1 software (Agilent Technologies). GeneSpring GX v14.5 software (Agilent Technologies) was used for subsequent data processing. Gene expression with a statistically significant difference (P < 0.05) and an absolute value of log2 fold change > 1.2 between groups was exported to the dataset. Gene ontology and pathway analyses were performed using BaseSpace (Illumina KK, Tokyo, Japan) and MetaCore v6.30 build 68780 (Clarivate Analytics Japan, Tokyo, Japan), respectively.