Single cell RNA-seq analysis of the transcriptomic profiles of endothelial cells and immune cells from the brain, spinal cord (SC), dorsal cranial dura, and spinal dura of naïve and EAE mice at the onset and peak of the disease

To understand transcriptomic changes in different CNS compartments following EAE, we sorted DAPI- viable CD31+ endothelial cells and CD45+ immune cells from the brain, SC, dorsal cranial dura, and spinal dura of naïve mice and MOG35-55-induced EAE mice at the onset (10 days post-immunization (dpi), EAE10) and peak (14 dpi, EAE14) of the disease by flow cytometry and performed scRNA-seq analysis. We analyzed in total 12 samples, aiming at sequencing 10,000 cells with an average depth of 50,000 reads per cell for every sample.