Fig. 5: Imputation of cell populations identified in murine esophageal epithelium in 3D murine esophageal organoids.

a Schematic overview of experimental design of single cell RNA-Sequencing (scRNA-Seq) from murine esophageal organoids established from mice (n = 3 independent experiments) and cultured for 15 days. Scale bar, 100 µm. b Seurat’s Uniform Manifold Approximation and Projection (UMAP) was used to visualize cell clusters within the epithelial dataset. c Prediction scores (based on confidence scale ranging from 0 to 1) of each cell population identified in organoids using classifications derived from murine esophageal epithelial scRNA-Seq dataset. Color intensity reflects the relative confidence that the predicted cluster identity is accurate with purple indicating cells with highest prediction confidence. d Average natural log fold change (FC) of individual genes in indicated cell population from murine 3D organoids as compared to the murine esophageal epithelial dataset. Genes marked as significant (indicated in red) have p < 0.05. e Comparison of proportions of each epithelial cluster in murine epithelial dataset (n = 10 animals) and 3D organoids (n = 3 independent experiments). Indicated p values in (d, e) were determined using Wilcoxon signed-rank test without adjustment for multiple comparisons. Each individual scatter point represents proportion indicated, box indicates quartiles, whiskers indicate minima and maxima. Mean is indicated by line striking through box. Source data are provided as a Source Data file.