Fig. 2

Identification of Shh-regulated genes in cNCCs in vitro. a Volcano plot showing the linear fold change (SHH/Veh) (x-coordinate) and –log₁₀ FDR p-value (y-coordinate) of each differentially expressed gene. Black dots represent significant differentially expressed genes (FDR p-value < 0.01), and grey dots mark genes with non-significant changes. The bona fide Shh target genes Gas1 (negatively regulated) and Gli1 (positively regulated) are labeled and marked with X’s. b RT-PCR validated the downregulation of Gas1 and upregulation of Gli1 in SHH-activated cNCCs (t-test, ** p-value < 0.015, ***** p-value < 0.00001). c Hierarchical clustering heat map of 2749 significant differentially expressed genes (FDR p-value < 0.01) between vehicle- and SHH-treated cNCCs shows the robust differential expression and high level of consistency within treatments for the in vitro model. Heat map represents log₁₀ signal intensity for each gene in each condition, which are then clustered by biological response. Yellow represents genes with higher expression while blue represents genes with lower expression. N = 4 biological replicates (1–4)