Figure 3

Verification of RNA-Seq with quantitative RT-PCR. The log₂ (expression relative to actin and ubiquitin in test tissue by qRT-PCR/expression relative to actin and ubiquitin in pollen by qRT-PCR) is plotted on the y-axis and the log₂ (expression in test tissue by RNA-Seq(FPKM)/expression in pollen by RNA-Seq(FPKM)). Although the slopes of the lines are not equal to one, the R² values show good correlation between measurements using both types of data with the lowest correlation for the embryo sac samples. For RNA-Seq values expression values were from B73 Pollen, B73 Seedling, combined W23-B73 Embryo Sac, and combined W23-B73 Ovules-without-embryo Sacs. For RT-PCR expression values only W23 Embryo Sac and Ovules-without-embryo Sacs were used.