Fig. 4: Cortical transcriptomic signature at 1 month after HF-HI.

RNA-seq analysis 1 month after HF-HI. a Heatmap with all significantly differentially expressed genes (DEG) (515 upregulated and 393 downregulated) of sham and HF-HI cortical genes identified by RNA-seq show clustering by group. Color scale bar values represent Z value (normalized standard deviations from the mean) for expression relative to the overall mean expression (n = 7 sham, 8 HF-HI). b Volcano plots show the spread of these significantly differentially expressed genes. c Directionality dot plot of gene sets obtained by functional enrichment of significantly altered genes in HF-HI mice, using cellular components (CC) from gene ontology (GO) focusing on synaptic components show that these synaptic families are being modulated, appearing as significant categories in both the up- and downregulated CC. Node size corresponds to the number of genes in each ontology term. Color of each dot is the gene ratio compared to the total gene number. d, e Heatmaps displaying the top differentiated genes in learning or memory and synaptic signaling biological process (BP) categories show that genes in these categories are being modulated by HF-HI, and not just downregulated. Color scale bar values represent Z value (normalized standard deviations from the mean) for expression relative to the overall mean expression. Individual samples are listed below each heatmap. f Venn diagram demonstrating overlap of all significantly DEGs at 24 h and 1 month after HF-HI. Venn diagram demonstrating the overlap of synapse CC genes at 24 h and 1 month post HF-HI. g Venn diagram demonstrating the overlap of synaptic signaling BP genes between the 24 h and 1 month time points with a heatmap demonstrating the Log 2 fold change and directionality of the 39 conserved genes.