Extended Data Fig. 9: Neuron layer GO analysis, pathological group enrichment and RNAScope validation.
From: Repeated head trauma causes neuron loss and inflammation in young athletes
a. UMAP depicting excitatory neurons colored by layer subtype. b,c. Heatmap showing GO analysis of (b) excitatory layer and (c) inhibitory layer up and downregulated DEGs. n = 28 individuals. Statistics generated with GSEA and single-tailed hypergeometric test with Benjamini-Hochberg multiple hypothesis correction. d. Bar plots of excitatory neuron layer proportions by pathological group. Bar represents mean, dots represent individual samples, error bars show standard error of the mean. Statistical analysis performed by ANOVA with Bonferroni correction. Tests were two tailed. n = 28 individuals. e. UMAP showing inhibitory neurons colored by layer subtype. f. Bar plots of inhibitory neuron layer proportions by pathological group. Bar represents mean, dots represent individual samples, error bars show standard error of the mean. Statistical analysis performed by ANOVA with Bonferroni correction. Tests were two tailed. n = 28 individuals. g. Representative image showing RNAScope in situ hybridization of CUX2/LAMP5 image analysis with correct anatomical layer-wise distribution. White squares showing HALO identification of double-positive cells. Scale bar = 1 mm. h. Representative image of Nissl+ staining and neuronal masking using HALO AI. Top box is the raw image and bottom box is AI generated mask over neurons. Scale bar = 50 µm.
