Fig. 6: Experimental design, sample clustering, and response to damage using bulk RNA-seq. | Nature Communications

Fig. 6: Experimental design, sample clustering, and response to damage using bulk RNA-seq.

From: Revealing heterogeneity and damage response in the adult human utricle

Fig. 6: Experimental design, sample clustering, and response to damage using bulk RNA-seq.

a Schematic of the damage paradigm experimental design. Created in BioRender. Luca, E. (https://BioRender.com/kw809th). b PCA of bulk RNA-seq samples; control (C, teal) and gentamicin-treated (T, orange), n = 3 per condition. c Dendrogram illustrates the hierarchical relationship within the two groups and between the two conditions (control and gentamicin treated), Padj < 0.05. Each column represents an individual biological sample, and each row a gene. Euclidean distances were computed, and hierarchical cluster analysis was performed using Ward clustering. The heatmap displays 47 differentially expressed genes (DESeq2, FDR < 0.05) between control and gentamicin-treated utricles, including five highlighted transcription factors. Colour scale represents gene expression value (magenta-downregulation, yellow-upregulation). Arrowhead indicates validated gene SLPI. See Supplementary Data 4a for the gene list.

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