Figure 3

Figure 3. RNA sequencing analysis of slc38a9 mutant zebrafish. (A) Principal component analysis (PCA) plot of four wild type and slc38a9 mutant RNA-seq datasets. Principal component 1 (PC1), principal component 2 (PC2), and principal component 3 (PC3) were used for analysis. (B) Volcano plot of differential expression analysis of slc38a9 mutant and control larvae showing the relationship between −log10(padj) and log2FoldChanges. The red dot shows upregulated genes, the green dot shows downregulated genes, and the blue dot shows an unchanged gene. (C) Gene ontology (GO) analysis of differentially expressed genes in biological processes (red column), cellular component (green column), and molecular function (blue column). (D) The directed acyclic graph (DAG) of biological process. The lower terms are more specific, while the upper terms are more general. (E) Average heart rate of 60 hpf WT and slc38a9 mutant zebrafish larvae. Data shown are mean ± SEM, n = 10. * p < 0.05. (F) Correlation between qRT-PCR and RNA-seq results for select DEGs. The fold change values derived from the RNA-seq analysis of DEGs are compared with those obtained by qRT-PCR determined by 2^−ΔΔCT. The reference line indicates the expected linear relationship.