Fig. 3

Volcano plots and GO analysis at different time points. a Volcano plot demonstrating proteins differentially regulated in RTT compared to iCTR at each time point of neuronal development. Each data point represents a single quantified protein. The x-axis represents the log2-fold change in abundance (RTT/iCTR) and y-axis the − log10 (p value). Threshold for significant proteins is chosen for p value cut-off (0.1) and fold change ≥ 1.3. Proteins in blue indicate for downregulation and in red indicate for upregulation in RTT. Arrow in day 22 points for SOX2 expression, and asterisk points for SOX9 expression. b Gene Ontology analysis of the significant proteins on their biological function at each time point of neuronal differentiation. Red indicates the upregulated and blue the downregulated biological processes. The numbers indicate the genes enriched for each term. c Western blot analysis showing SOX9 and SOX2 expression in iCTR NES lines at D22. Significant increase in SOX9 expression in RTT samples, and SOX2 shows a trend towards decrease in RTT samples