Targeted lipidomics dataset of central nervous system and plasma from mice with experimental autoimmune encephalomyelitis

This dataset contains quantitative lipidomic profiles of plasma and central nervous system (CNS) tissues (i.e., cerebellum, hippocampus, and prefrontal cortex) collected from SJL/J mice in a preclinical neuroinflammation model. The study population includes three groups: (1) controls, (2) mice with experimental autoimmune encephalomyelitis (EAE), and (3) EAE mice treated with fingolimod (FTY720). Each tissue sample was analyzed for 62 lipid variables, including lysophosphatidic acids, ceramides, sphingoid bases, and endocannabinoids, using targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS).
The dataset is organized into three CSV files: a raw quantitative data matrix with missing values; a log₁₀-transformed, imputed version of the same matrix; and a comprehensive metadata file. The metadata includes experimental group assignments, sample identifiers, and tissue type, enabling flexible stratification and downstream analysis. Missing values were imputed using random forest–based approaches. The sample handling, lipid extraction, and quantification protocols followed standardized procedures.