Fig. 2: Region-specific differences in HC gene expression. | Nature Communications

Fig. 2: Region-specific differences in HC gene expression.

From: Novel environment exposure drives temporally defined and region-specific chromatin accessibility and gene expression changes in the hippocampus

Fig. 2

A Heatmap of row-normalized z-scores from bulk RNA-seq and snRNA-seq expression across all regions and major cell types, respectively. Each bulk and snRNA-seq column represents a biological replicate (n = 5, n = 2, respectively) separated by region. Bulk RNA-seq CA1-, CA3-, and DG-enriched genes were determined by k-means clustering. Significant genes were defined as DESeq2 Padj < 0.05 (using a two-sided Wald test with Benjamini-Hochberg multiple hypothesis correction) and Fold Change |FC | > 2. B Merged genome browser tracks (top), box and whisker plots (bottom left) of bulk RNA-seq DSEq2 depth-normalized counts, and violin plots (bottom right) of snRNA-seq counts for Gabrg3 (CA1-enriched), Chgb (CA3-enriched), and C1ql3 (DG-enriched). Box plots are shown as median ± IQR (whiskers = 1.5*IQR). Violin plots are shown with mean as a dash. C Schematic of region-enriched synaptic genes in CA1, CA3, and DG based on differential gene expression analysis and Gene Ontology.

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