Fig. 3: Identification of marker genes for supporting cells, hair cells, and their subtypes.
From: Revealing heterogeneity and damage response in the adult human utricle
a Volcano plot showing differentially expressed genes enriched in hair cells and supporting cells identified using a two-sided Wilcoxon rank-sum test. The top differentially expressed genes are labelled (Padj < 0.05, log2 FC > |1 |). b Dot plot showing the percentage of cells expressing representative markers for hair cells (teal, type I; pink, type II) and supporting cells (grey box), with the dot colour indicating average gene expression. c Enriched type II (pink) and type I (teal) hair cell genes are identified using a two-sided Wilcoxon rank-sum test. Arrowhead indicates the validated gene CALB1. d Dot plot illustrating the relative expression of a subset of marker genes across all clusters, indicating specificity for type I (teal) or II (pink) hair cells. Supplementary Data 2b, c contain the complete gene lists for (a, c). e UMAP plots of hair cell subtypes as well as CALB1 (magenta), SOX2 (green), and cells coexpressing both markers (white) in the type II hair cell cluster. Percentage of transcript counts are reported, proportions are calculated as the fraction of cells with normalized expression greater than zero relative to the total number of cells in each cluster shown in the inset in Fig. 2a; 19 is the total number of type II hair cells. Schematic of CALB1 expression was created with gEAR using a scalable vector graphic file derived from a cropped and inverted image of Fig. 1a. Immunofluorescences (20x magnification) in a human utricle section demonstrate the expression of hair cell type II-specific marker CALB1 (magenta). MYO7A (yellow) was used as a pan-HC marker, and SOX2 (green) was used to label hair cell type II and supporting cells. Some hair cells (MYO7A+) also express CALB1 and SOX2, visible in the merge panel, n > 3. Scale bar = 25 μm.
