Single-nucleus RNA-seq of peripheral blood mononuclear cells from multiple sclerosis patients and healthy controls

Multiple sclerosis (MS) is a chronic immune-mediated disease of the central nervous system marked by neuroinflammation and demyelination. Emerging evidence suggests that circulating immune cells contribute to disease activity, heterogeneity of clinical course, and treatment response. Here we provide single-nucleus transcriptomes of peripheral blood mononuclear cells (PBMCs) from individuals with MS and healthy controls. The dataset enables cell-type–resolved interrogation of peripheral immune states associated with MS, including comparisons of cell-state frequencies and gene-expression programs between groups, exploration of inflammatory pathways and ligand–receptor interactions, and discovery of candidate biomarkers. This resource supports integrative analyses with external MS cohorts and facilitates hypothesis generation on mechanisms of immune dysregulation in MS. Whole blood was collected from patients diagnosed with multiple sclerosis and from healthy control donors. PBMCs were isolated by Ficoll density-gradient centrifugation. Nuclei were extracted from PBMCs (10x Genomics protocol CG000365) and loaded on a Chromium Next GEM controller for single-nucleus capture and library construction using the Single Cell 3′ v3.1 Dual Index kit. Libraries were sequenced on an Illumina instrument. Resulting data were processed to obtain per-cell (nucleus) UMI count matrices for downstream analyses and group comparisons (MS vs control).