Fig. 1

Transcriptomic profiling of the hypothalamus along EAE progression. A–C Heatmaps of normalized counts (Z-scores) for the significant differentially expressed genes (DEGs) in the hypothalamus between EAE and control mice at 10, 20, and 40 days post-immunization (dpi). Hierarchical clustering can differentiate the two experimental conditions in each cross-sectional comparison. In the heatmaps, each row represents a DEG and each column a sample. D–F Histograms showing the top 5 most enriched gene ontology (GO) terms among the significant DEGs at the different time points. G, H Most significant protein interaction MCODE networks associated with the DEGs at 10 and 40 dpi. I Validation of RNA-seq results by qRT-PCR on selected DEGs from each time point. All genes except Fabp7, Zfpm1 and Hmgcs1 show significant differences between EAE and control conditions. The data are expressed as log2 transformed fold change (log2FC) and plotted as means ± SEM (N = 3 per group from one EAE immunization). Differences between experimental groups were assessed by two-tailed Student’s t-test. *P ≤ 0.05, **P ≤ 0.01; ***P ≤ 0.005