Targeted lipidomics dataset of central nervous system and plasma from mice with experimental autoimmune encephalomyelitis
Description
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.
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Tissue and plasma samples were collected from SJL/J mice that were assigned to one of three experimental groups (control, EAE, or EAE treated with fingolimod) according to standardized protocols. After blood collection, plasma was isolated in K+EDTA tubes and immediately processed for centrifugation and separation. The brain regions (the cerebellum, the hippocampus, and the prefrontal cortex) were dissected and snap-frozen in liquid nitrogen. All samples were stored at −70°C until analysis. Lipid extraction was performed using liquid–liquid extraction protocols tailored to each lipid class. Endocannabinoids and related lipids were extracted using an ethyl acetate and hexane mixture (9:1, v/v), sphingolipids and ceramides were extracted using a chloroform, methanol, and hydrochloric acid mixture, and lysophosphatidic acids were extracted using butanol. Isotopically labeled internal standards were added during extraction to enable accurate quantification. The quantification of 62 lipid species was conducted on a QTRAP 5500 LC-MS/MS platform in targeted mode using validated chromatographic separation and mass spectrometric detection parameters. All steps were carried out blinded to treatment group.
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Funding
Deutsche Forschungsgemeinschaft
CRC1039 A03 (IT), Z01 (GG), LO 612/16-1 (JL)
Else Kröner-Fresenius-Stiftung
Translational Research Innovation Pharma (TRIP) graduate school