Fig. 1

Single-cell isolation and unbiased clustering of the cochlear stria vascularis. A-B: The image shows mouse cochlea (A) and isolated stria vascularis (B). The bony labyrinth is opened at the apex to access the membranous labyrinth (SV, stria vascularis; SLg, spiral ligament). C: Representative picture of isolated single cells. Note: the varied morphology. (a), (b) and (c) are Kcnj10-expressing cells. (d), (e) and (f) are Slc26a4-expressing cells. Scale bar: 10 μm. D: Principal component analysis (PCA). Heatmaps of PCs 1–4 show differentially expressed genes. PCs 1–4 were later used for unbiased clustering. X-axis, cells; Y-axis, genes ordered by PCA score. E: Violin plot showing the number of unique genes detected per cell (top), and the percentage of mitochondrial counts (bottom) (group 1, pink; 2, green; 3, cyan; 4, purple). Each dot represents an individual cell. F: UMAP clustering displays four distinct clusters. G: Venn diagram showing the number of shared genes unique to each cell type. H: Schematic representation of the ion transporters and junctions in the cochlear SV. The marginal cell layer (spindle and marginal cells) expresses tight junctions (Cldn9, Cldn7, Cldn3). Between the marginal and basal cell layers is the intermediate cell (IMC) layer with K⁺ channels (Kcnj10), Na⁺/K⁺-ATPase (Atp1b3), and gap junctions (Gjb6). The marginal cell (MC) transports K⁺ into endolymph (E) using K⁺ channels (Kcne1/Kcnq1), Na⁺/K⁺-ATPase (Atp1a1 and Atp1b2), and NKCC1 co-transporters (Slc12a2). The spindle cell (SC) expresses pendrin (Slc26a4) to maintain endolymph pH (G, gap junctions; OS, outer sulcus; RC, root cell; SLg, spiral ligament; SP, spiral prominence; T, tight junctions). I: Violin plots of ion transporters and junctions shown in (H). The ROC AUC score of each gene is indicated under the name of the gene. (*, deafness-causing genes, the complete list of deafness-causing genes is available in supplementary table S1)