Characterization of cuprizone mouse model at single-cell and spatial transcriptomics level[Spatial Transcriptomics]

We generated a comprehensive dataset utilizing the cuprizone model. This dataset encompasses bulk RNA-seq, single-nucleus RNA-seq (snRNA-seq), and spatial transcriptomics, with the aim of investigating the molecular changes linked to the cuprizone-induced demyelination phenotype. Integration of these omics dataset allowed us to investigate the changes occurring at both the single-cell and spatial levels, thereby enabling a deeper understanding of the cellular dynamics and molecular interactions associated with the cuprizone-induced demyelination phenotype. In the cuprizone (CPZ) group, male mice aged 6-8 weeks were administered a 0.3% Cuprizone diet for 4 weeks to induce demyelination in the brain (n = 3). In the recovery group, mice were administered CPZ diet for 4-weeks and then switched to a control diet for an additional 2 weeks (n = 3). In the control group, mice received the control diet throughout the entire 6-week study period (n = 4). At 4 (CPZ) and 6 weeks (Control and Recovery), mice were euthanized by carbon dioxide (CO2) inhalation, and their brains were subsequently dissected. Each brain was cut sagittally to separate left and right hemispheres, one brain hemisphere was trimmed into three coronal segments and embedded in OCT for snRNA-seq or spatial transcriptomic study, the other hemisphere was snap frozen for bulk RNA-seq study (Figure 1). To enrich for sequencing of cells from the corpus collosum and cortex, only the top half of the coronal section was collected for snRNA-seq, which includes the dorsal cortex, CC, and hippocampus.