Gene Expression Data from the Hippocampus of Mice Subjected to Tail Suspension Test

This study investigates the functional effects of pine needle (PN) extract on depressive-like behavior in a tail suspension test model. Gene expression profiling was conducted in the hippocampus of control, LPS-induced, and LPS plus PN-treated mice to explore the potential neuroprotective effects of PN. Total RNA was extracted from the hippocampus using an ISOGEN (Nippon Gene Co. Ltd., Tokyo, Japan) following the manufacturer's instructions. Total RNA concentration was determined using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA).Microarray analysis was performed on RNA samples extracted from the hippocampus of mice subjected to the TST, control (water treatment), LPS groups and 50 mg/kg PN administration groups. The Clariom S assay Mouse system (Thermo Fisher Scientific K.K., Tokyo, Japan) was used for triplicate RNA samples from each group. According to the user manual, cDNA for microarray analysis was generated using a GeneChip WT Plus Reagent kit (Thermo Fisher Scientific K.K.). The samples were hybridized using a Clariom S GeneChip Microarray Kit for mouse (Thermo Fisher Scientific K.K.). After washing and staining, images were captured, and raw intensity data were generated using a GeneChip Scanner 3000 (Thermo Fisher Scientific K.K.).Raw image data processing and normalization were performed using Transcriptome Analysis Console (TAC) software version 4.0.2 (Thermo Fisher Scientific, MA, USA) following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. The gene-level analysis was then performed employing the Limma Bioconductor package included with TAC 4.0.2. A one-way ANOVA was applied to identify the differentially expressed genes (DEGs), followed by an empirical Bayes correction to enhance the statistical reliability of the results.A detected above background (DABG) cutoff of 0.05 was set to refine the analysis further to eliminate non-significant signals. Additionally, the positive vs. negative area under the curve (AUC) value was conservatively set at greater than or equal to 0.7 to focus on genes with strong discriminatory potential.The final selection of DEGs was based on stringent filter criteria, requiring a p-value of less than 0.05 (calculated using one-way between-subject ANOVA). −1.2 > linear fold change > 1.2.