1：Experimental Design and Method Selection:

The study utilized an MPTP neurotoxin model of Parkinson's disease in mice. Mice were randomly allocated to groups for different durations of remote PBM pre-conditioning (2, 5, or 10 days) or sham treatment, followed by MPTP or saline injections. The experimental design included stereological cell counting, RNA microarray analysis, and pathway enrichment analysis to assess neuroprotection and molecular mechanisms.

2：Sample Selection and Data Sources:

Male BALB/c mice (n=62) were used, selected for light penetration through fur. Samples included brain tissues for immunohistochemistry and RNA extraction.

3：List of Experimental Equipment and Materials:

Equipment included a hand-held LED panel (WARP 10; Quantum Devices), freezing microtome (Leica SM2010R), stereology software (StereoInvestigator), microscope (Leitz Orthoplan), camera (QICAM Fast 1394), spectrophotometer (NanoDrop ND-1000), bioanalyzer (Agilent 2100), microarray system (Illumina MouseWG-6 v2.0 Expression BeadChips), and qPCR machine (Roche Lightcycler 480). Materials included antibodies (e.g., anti-TH, anti-FOS), kits (e.g., mirVana PARIS Kit, Illumina TotalPrep RNA Amplification Kit), and chemicals (e.g., MPTP, formalin).

4：0 Expression BeadChips), and qPCR machine (Roche Lightcycler 480). Materials included antibodies (e.g., anti-TH, anti-FOS), kits (e.g., mirVana PARIS Kit, Illumina TotalPrep RNA Amplification Kit), and chemicals (e.g., MPTP, formalin). Experimental Procedures and Operational Workflow:

4. Experimental Procedures and Operational Workflow: Mice were irradiated with 670nm light (50 mW/cm2, 90 seconds daily) on dorsum and hindlimbs with head shielded. After pre-conditioning, MPTP (25 mg/kg/day for 2 days) or saline was injected. Tissues were collected 7 days post-injection for immunohistochemistry (TH and FOS labeling) and RNA isolation. RNA was analyzed by microarray and validated by qRT-PCR. Data analysis included normalization, differential expression, and pathway enrichment using DAVID, GSEA, and IPA.

5：Data Analysis Methods:

Statistical analyses used one-way ANOVA with Sidak's test for cell counts and Student's t-test for qRT-PCR. Microarray data were normalized using Cubic Spline, Average, and Quantile methods, with pathway enrichment analysis performed using DAVID, GSEA, and IPA.