Journal: iScience

Article Title: Cellular heterogeneity and patterning strategies as revealed by upper respiratory epithelium single cell atlas

doi: 10.1016/j.isci.2025.112845

Figure Lengend Snippet: scRNA-seq of the upper respiratory epithelium reveal compartmental and cellular heterogeneity (A) Schematic illustration of cell isolation and scRNA-seq workflow. (B) Dotplot showing top markers for each cluster. Using default Seurat dotplot settings (Methods), percentage expressed was plotted from 0% to 75% detected and the color bar shows the average of scaled normalized expression values across cells in a given cluster. (C) UMAP plots of integrated upper airway scRNA-Seq data from adult WT B6 mice ( n = 8 biological repeats, 4 male, 4 female). (D and E) Schematic illustration of macro-anatomical regions of the upper airway with compartmental epithelial cell type diversity. (F–J) Feature plots with RNAscope validation of Tmprss11a (pharyngolaryngeal) (H), Nkx2-1 (tracheobronchial) (I), Dmbt1 (seromucous glands) (J) exhibiting pan-epithelial regional markers in coronal sections. (G) H&E-stained upper airway. DAPI is in blue. All images 20× magnification. Scale bar represents 500 μm. H&E, hematoxylin and eosin; AC, arytenoid cartilage; CC, cricoid cartilage; TC, tracheal cartilage; SSE, stratified squamous epithelium; SG, subglottis; SMG, submucosal gland.

Article Snippet: All staining procedures were performed using the RNAscope Fluorescent Multiplex Kit V2 (Advanced Cell Diagnostics, no. 323100) following the manufacturer’s instructions.

Techniques: Cell Isolation, Expressing, RNAscope, Biomarker Discovery, Staining

Journal: iScience

Article Title: Cellular heterogeneity and patterning strategies as revealed by upper respiratory epithelium single cell atlas

doi: 10.1016/j.isci.2025.112845

Figure Lengend Snippet: Genome-wide profiling revealed signatures of stratified squamous epithelium along basal-luminal axis with extensive Keratin diversity along proximal-distal axis (A) Integrated UMAP plot highlighting laryngeal surface epithelial cells. (B and C) Feature plots with RNAscope validation of basal-to-luminal canonical markers for laryngeal SSE. (D) Schematic illustration of KRT diversity along the proximal-to-distal upper respiratory axis. (E) Schematic illustration of cranial view of larynx to display coronal sections (red/yellow dashed lines) attained for analysis. (F and F′) Immunofluorescent coronal serial sections with insets of dorsal upper airway epithelium displaying regional KRT expression along various epithelium subtypes. Red line indicates transition zone from SSE to pseudostratified. (G and H) Diversity of KRT expression to SSE of tracheal hillocks and laryngeal VF tissue. DAPI is in blue. All images 20× magnification. Scale bar represents 100 μm (C, G, and H) and 500 μm (F). Epi, epiglottis; AE, aryepiglottic fold; SG, subglottis; AC, arytenoid cartilage; CC, cricoid cartilage; TC, tracheal cartilage; SSE, stratified squamous epithelium; KRT, keratin; SMG, submucosal gland.

Article Snippet: All staining procedures were performed using the RNAscope Fluorescent Multiplex Kit V2 (Advanced Cell Diagnostics, no. 323100) following the manufacturer’s instructions.

Techniques: Genome Wide, RNAscope, Biomarker Discovery, Expressing

Journal: iScience

Article Title: Cellular heterogeneity and patterning strategies as revealed by upper respiratory epithelium single cell atlas

doi: 10.1016/j.isci.2025.112845

Figure Lengend Snippet: scRNA-seq of the upper respiratory epithelium reveal compartmental and cellular heterogeneity (A) Schematic illustration of cell isolation and scRNA-seq workflow. (B) Dotplot showing top markers for each cluster. Using default Seurat dotplot settings (Methods), percentage expressed was plotted from 0% to 75% detected and the color bar shows the average of scaled normalized expression values across cells in a given cluster. (C) UMAP plots of integrated upper airway scRNA-Seq data from adult WT B6 mice ( n = 8 biological repeats, 4 male, 4 female). (D and E) Schematic illustration of macro-anatomical regions of the upper airway with compartmental epithelial cell type diversity. (F–J) Feature plots with RNAscope validation of Tmprss11a (pharyngolaryngeal) (H), Nkx2-1 (tracheobronchial) (I), Dmbt1 (seromucous glands) (J) exhibiting pan-epithelial regional markers in coronal sections. (G) H&E-stained upper airway. DAPI is in blue. All images 20× magnification. Scale bar represents 500 μm. H&E, hematoxylin and eosin; AC, arytenoid cartilage; CC, cricoid cartilage; TC, tracheal cartilage; SSE, stratified squamous epithelium; SG, subglottis; SMG, submucosal gland.

Article Snippet: RNAscope® Multiplex Fluorescent Reagent Kit V2 , Advanced Cell Diagnostics , Cat#323100.

Techniques: Cell Isolation, Expressing, RNAscope, Biomarker Discovery, Staining

Journal: iScience

Article Title: Cellular heterogeneity and patterning strategies as revealed by upper respiratory epithelium single cell atlas

doi: 10.1016/j.isci.2025.112845

Figure Lengend Snippet: Genome-wide profiling revealed signatures of stratified squamous epithelium along basal-luminal axis with extensive Keratin diversity along proximal-distal axis (A) Integrated UMAP plot highlighting laryngeal surface epithelial cells. (B and C) Feature plots with RNAscope validation of basal-to-luminal canonical markers for laryngeal SSE. (D) Schematic illustration of KRT diversity along the proximal-to-distal upper respiratory axis. (E) Schematic illustration of cranial view of larynx to display coronal sections (red/yellow dashed lines) attained for analysis. (F and F′) Immunofluorescent coronal serial sections with insets of dorsal upper airway epithelium displaying regional KRT expression along various epithelium subtypes. Red line indicates transition zone from SSE to pseudostratified. (G and H) Diversity of KRT expression to SSE of tracheal hillocks and laryngeal VF tissue. DAPI is in blue. All images 20× magnification. Scale bar represents 100 μm (C, G, and H) and 500 μm (F). Epi, epiglottis; AE, aryepiglottic fold; SG, subglottis; AC, arytenoid cartilage; CC, cricoid cartilage; TC, tracheal cartilage; SSE, stratified squamous epithelium; KRT, keratin; SMG, submucosal gland.

Article Snippet: RNAscope® Multiplex Fluorescent Reagent Kit V2 , Advanced Cell Diagnostics , Cat#323100.

Techniques: Genome Wide, RNAscope, Biomarker Discovery, Expressing