Fig. 3: Mesenchymal cells correlate with brain organoids morphology.
From: Deciphering brain organoid heterogeneity by identifying key quality determinants
A Illustration of the strategy for gene expression analysis. B Venn diagram, indicating the number of differentially expressed genes when organoids are compared by expert evaluation (‘Expert’s evaluation), k-means clustering of five top correlating clusters (‘Cluster_5’) or the determined Feret diameter threshold (‘Feret’). The overlap of all three analyses is depicted in red. C Gene Ontology analysis of differentially expressed genes common across three comparisons. The x-axis represents the Gene Ratio, while the y-axis displays the Gene Ontology (GO) terms associated with Biological Processes. The color scale indicates the adjusted p-value, and the size of the circles reflects the number of genes associated with each GO term. D Stacked bar chart illustrating the cellular composition of organoids calculated with deconvolution analysis. Further variables are color encoded below (sex, hPSC type, expert evaluation group, group in k-means clustering, group in Feret diameter thresholding). Annotation coding for cell types is shown at the bottom of the graph. Each stack represents an individual organoid. The mesenchymal cell’s coefficient of variation (MC CV) for each is presented as a percentage under the cell line name. E Boxplot of predicted fraction of mesenchymal cells in organoids by quality rating. Middle line represents median, individual measures as dots. Statistical significance shown on top (Wilcoxon rank-sum test). F Boxplot of predicted fraction of mesenchymal cells in organoids by cluster in k-means. Middle line represents median, individual measures as dots. Statistical significance shown on top (Wilcoxon rank-sum test). G Boxplot of predicted fraction of mesenchymal cells in organoids by Feret threshold of 3050 µm. Middle line represents median, individual measures as dots. Statistical significance shown on top (Wilcoxon rank-sum test). H Scatter plot of Mesenchymal cells (MC) and Feret diameter. Spearman r = 0.66, p = 3.18 × 10−10.
