Fig. 3
OXR1 is required for planar neural differentiation. a Immunocytochemical analyses of neurospheres from patient (OXR1ΔEx18) and healthy control (CTRL). Neurite outgrowth is visualized by antibody against neuron-specific class III beta-tubulin (Tuj1). Bar diagrams show quantification of the neurite (Tuj1+) covered area, the fluorescence intensity of covered area, and the longest neurite length by average of 5 longest neurites of each neurosphere (n = 15 independent neurospheres for each genotype). b Principal components analysis (PCA) showing the clustering of samples based on principal component 1 and 2 (PC1 and PC2). All samples are three different clones of each genotype derived from the monolayer neuronal differentiation experiment. Induced pluripotent stem cells (iPSC) were collected at day0, neural aggregates (NA) at day 2 (48 h after initiation of differentiation) and neurons (Neu) at day 20. c The violin plot shows the Log2FC distribution of DEGs in patient (OXR1ΔEx18) samples at each differentiation stage (Padj < 0.05). The medium values were indicated by red lines, the quartiles were indicated by blue lines. The discrepancy was analyzed by Wilcoxon Signed Rank Test at 95% confidence interval. All p values < 0.001. d Pathway enrichment analysis showing the core pathways involved in neural development by Gene Set Enrichment Analysis (GSEA, normalized enrichment score, |NES|≥ 1; nominal p value, (p) < 0.05; false discovery rate (FDR) ≤ 0.25). e Gene Ontology (GO) analysis by GSEA. The most underrepresented GO terms of biological processes in OXR1ΔEx18 neurons are relevant to neural development. The NES and FDR values were indicated next to each bar. f Heatmap showing z-score normalized read counts of the top ranked leading-edge genes in neurogenesis and differentiation that were differentially expressed in Neu_OXR1ΔEx18. g Heatmap showing z-score normalized read counts of the top ranked leading-edge genes in axon genesis and cell migration that were differentially expressed in Neu_OXR1ΔEx18