Oat (Avena sativa L.) genome resources are less abundant than for wheat and barley, but next generation sequencing (NGS) technologies have great potential to accelerate new genome information for oat in a cost-effective manner. We are employing RNA-Seq to develop a gene expression atlas of developing oat seeds sampled at four developmental stages. In total approximately 360 million quality-filtered Illumina 100 base paired-end reads were obtained for this project. We are using the Trinity software package for de novo assembly to generate non-redundant transcript assemblies; the resultant reference gene set will be a powerful new tool for analyzing gene expression relevant to the nutritional value of oat. Tocols (vitamin E) are of particular interest due to their health benefits, but their accumulation during oat seed development is poorly understood. Thus seed tocol composition was quantified at the same stages sampled for RNA-Seq. Tocotrienols were the most abundant tocol in whole seeds, but embryos contained higher concentrations of tocopherols. The accumulation kinetics of different tocols varied over time, indicating that enzymes of tocol biosynthesis are differentially regulated during oat seed development. Thus we will employ our RNA-Seq data to monitor the expression of genes of tocol biosynthesis. Our findings will advance our understanding of the molecular regulation of tocol accumulation in oat, and the gene expression atlas will add a significant new resource for an array of oat improvement efforts.