Figure 3. Validation of the RNA-seq approach using RT-PCR.

(A) Differential gene expression between control sample (NT) and samples depleted of Shoc2 (LV1). The differential expression (log₂fold change for LV1 samples compared to NT) is plotted against the log count per million for each gene. Each point represents a single ID of the reference transcriptome. Of 853 differentially expressed genes, 317 were upregulated (solid circle) and 536 were downregulated (open circle) (Fold change > 1.5, FDR <0.05).

(B) Fourteen differentially expressed genes were arbitrary selected from a range of upregulated and downregulated genes. Levels of expression were quantified by RT-PCR and the results were compared to those obtained by the RNA-seq approach. The log₂fold change in gene expression of RT-PCR and RNA-seq approach were closely correlated (R² = 0.85), indicating the accuracy of the RNA-seq analysis (C).