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. 2019 Dec 20;12:316. doi: 10.3389/fnmol.2019.00316

FIGURE 3.

FIGURE 3

Single cell and single nucleus transcriptome profiles reveal common novel cell type-specific genes in the adult stria vascularis. (A) Feature plots for P30 SV scRNA-Seq data demonstrate expression of novel markers for 4 main SV cell types: marginal cells (Abcg1, Heyl), intermediate cells (Nrp2, Kcnj13), basal cells (Sox8, Nr2f2), and spindle/root cells (P2rx2, Kcnj16). Maximum expression (normalized counts) is noted in the black outlined gray box for each gene in the lower left corner of each feature plot. Spindle/root cell clusters are delineated by red circles. (B) Grid violin plot of scRNA-Seq dataset demonstrates expression of novel marker genes amongst SV cell types. Normalized counts were scaled to a range of 0–1 using min-max scaling. (C) Feature plots for P30 SV snRNA-Seq data demonstrate expression of novel markers for 4 main SV cell types: marginal cells (Abcg1, Heyl), intermediate cells (Nrp2, Kcnj13), basal cells (Sox8, Nr2f2), and spindle/root cells (P2rx2, Kcnj16). Maximum expression (normalized counts) is noted in the black outlined gray box for each gene in the lower left corner of each feature plot. Spindle/root cell clusters are delineated by red circles. (D) Grid violin plot of snRNA-Seq dataset demonstrates expression of novel marker genes amongst SV cell types. Normalized counts were scaled to a range of 0 to 1 using min-max scaling. (E) Validation of known gene expression was performed using single molecule fluorescent in situ hybridization (smFISH). Novel marginal cell-specific transcript (Abcg1, Heyl) expression in red is demonstrated in and around the marginal cell nuclei on the apical surface of the marginal cells. Novel intermediate cell-specific transcript (Nrp2, Kcnj13) expression in red is co-expressed with Kcnj10 and Cd44 transcripts in green, respectively. Novel basal cell-specific transcript (Sox8, Nr2f2) expression in red is localized to the basal cell layer. Yellow dashed lines in the images with only the DAPI labeling for nuclei demarcate the respective cell layers (marginal, intermediate and basal cell layers). (F) Novel spindle/root cell-specific transcripts, P2rx2 (in red) and Kcnj16 (in green) are co-expressed with Slc26a4 transcripts to spindle and root cells (left panel). The same image without the Slc26a4 (blue) channel (center panel) and without DAPI (right panel) are shown. Note the slightly different distributions in P2rx2 (red) versus Kcnj16 (green) transcripts amongst spindle and root cells, respectively. Yellow dashed lines demarcate the SV, spindle cells (SpC) and root cells (RC) in the spiral prominence (SP). DAPI (4′,6-diamidino-2-phenylindole). All scale bars 10 μm.