Single-nucleus RNA sequencing analysis of normal-appearing brains from RRMS and SPMS patients

snRNA-seq reveals that normal-appearing brain regions from RRMS and SPMS patients have divergent cell type-specific gene expression profiles, with clinical ramifications for approved sphingosine 1-phosphate (S1P) receptor modulators. Post-mortem prefrontal cortices (BA10) from donors who suffered from RRMS or SPMS were cryo-sectioned at 300 µm and were processed for nuclei isolation. Single-nucleus capture (target capture of 5,000 nuclei per sample) and library preparation was conducted using Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3 (10x Genomics) and Chromium Single Cell B Chip Kit (10X Genomics) according to the manufacturer's instruction. Single-nucleus libraries were sequenced on the Illumina NovaSeq 6000 machine at GENEWIZ, Inc. Raw FASTQ files were input into the cellranger count pipeline (Cell Ranger V3.0.2, 10x Genomics) to align reads to the GRCh38 human genome.