Fig. 3

Bulk RNA-seq differential expression analyses and quantitative PCR on embryonic tissues. A Principal component analysis of the seven RNA-seq samples that primarily cluster based on their sex at this early stage of development when pigmentation is not visible yet. B Volcano plot depicting statistically significant gene expression changes between wild-type and Motley embryonic dorsal skin samples in terms of log2 fold-change (x-axis) and negative log10 of adjusted p-value (y-axis). In cyan, the genes significantly upregulated in Motley, and in red, the ones significantly downregulated (cutoff adjusted p-value: 0.05). The ten genes with a log2 fold-change > 1 are labeled. LOC117667003 is ryncolin-3, LOC117678171 is calcium-activated potassium channel subunit beta-2 (KCNMB2), LOC132709993 is an uncharacterized protein C2orf72-like, and LOC117667077 is an uncharacterized protein. C Expression levels of CLCN2 in Transcripts per Million in Motley, Stripe, and wild-type samples. Despite that the samples are from two different clutches (Motley 1 with wild-type and Motley 2 with Stripe), we observe similar levels of expression for all Motley samples from the two crosses. The expression in Stripe is similar to the wild-type expression. D Gene expression ratio of CLCN2 in the embryonic skin, the brain, and a body part compared to the wild-type for three genotypes. The CLCN2 expression is significantly downregulated in the Motley embryonic skin sample, compared to the heterozygous and the wild-type, based on a Welch’s t-test. The three asterisks denote a p-value < 0.001 and “ns” a p-value > 0.05. The error bars correspond to the standard deviations