Fig. 5
Technical evaluation of the gastroesophageal organoid scRNA-seq data. (a) Scatter plot showing the distribution of genes per cell (nFeature_RNA) relative to the percentage of mitochondrial genes (percent. mt). The dotted rectangle indicates the region of optimal quality threshold. A Pearson correlation coefficient of −0.3 was observed between nFeature_RNA and percent.mt. (b–d) Violin plots depicting the distribution of gene count (nFeature_RNA) (b), unique molecular identifier (UMI) count (nCount_RNA) (c), and the percentage of mitochondrial genes (percent.mt) (d) following the QC step. (e–g) Violin plots showing the distribution of gene count (nFeature_RNA) (e), unique molecular identifier (UMI) count (nCount_RNA) (f), and the percentage of mitochondrial genes (percent.mt) (g), similar to (b–d) but at the individual sample level. (h) UMAP visualization of gastroesophageal epithelial organoids showing the cellular subtypes; cells color-coded by epithelial cell type. (i) Feature plots depicting the absolute expression levels of squamous (Krt5/Krt13) and columnar (Krt8/Krt18) epithelia; Sq and Co represent squamous and columnar epithelia, respectively.
