Figure 6.

SHH pathway dysregulation in trisomic NPCs. (A) Pairwise correlation analysis between the 1,000 DEX genes shows that gene clusters whose expression is primarily driven by differentiation day are tightly correlated in the center of the network. (B) Closer examination of genes in the RNA-seq dataset shows that there are significant differences in SHH signaling pathway expression in the trisomic tNPCs. (C) qRT-PCR validation of the SHH pathway genes from the RNA-seq dataset show dysregulation in both trisomic lines (WC^ts and ILD^ts) of differentiated tNPCs compared to their euploid controls (WC^eu and ILD^eu). n = 3–5 independently cultured wells. Data are shown as mean ± SD. *p-value < 0.05 with specific values in text.