library_construction_protocol: Brains were isolated following perfusion with DPBS. The brainstem, thalamus, and hypothalamus—regions characterized by robust CD4⁺ T cell infiltration and activated microglia—were dissected and dissociated for 30 minutes at 37°C using the Adult Brain Dissociation Kit (Miltenyi Biotec) and gentle MACSTM Octo Dissociator with Heaters (Miltenyi Biotec) followed by the protocol provided in the kit. The resulting cell suspension was passed through a 70-µm strainer, and debris and red blood cells were removed according to the kit protocol. The pellet was sequentially depleted of myelin using Myelin Removal Beads v2 (Miltenyi Biotec) and dead cells using the Dead Cell Removal Kit serum albumin. After the cell viability was confirmed more than 80%, Single-cell 3' cDNA libraries were prepared at the DNA Services laboratory of the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign. Cells were processed into individually barcoded cDNA libraries using the 5' GEM-X scRNA library platform from 10X Genomics (Pleasanton, CA, USA) following the manufacturer's protocol, with a target of 10,000 cells per library. The 10X Chromium instrument encapsulated single cells into Gel Bead Emulsions (GEMs) to barcode mRNA from individual cells. Following double-stranded cDNA synthesis, barcoded libraries compatible with Illumina sequencing chemistry were constructed. Each library was quantified using Qubit, and the average fragment size was assessed with an AATI Fragment Analyzer (Advanced Analytics, Ames, IA, USA).