The Metabolome and Transcriptome of Early Drosophila Development at Single Embryo Resolution J. Eduardo Perez-Mojica, Ryan D. Sheldon, Adelheid Lempradl Van Andel Institute, Grand Rapids, United States Early embryonic development involves transformative events such as zygotic genome activation (ZGA) and cell lineage specification. These events lay the foundation for animal development and impact phenotypic variation. However, little is known of how metabolism integrates with these events. While novel low input genome wide techniques have facilitated seminal studies addressing associated transcriptome and epigenome changes, technologies required to characterize the metabolome have been lagging behind. We have successfully established a method to perform single embryo transcriptomics and metabolomics. Pseudotemporal ordering using the single embryo mRNA-seq data establishes a developmental timeline of transcription at unprecedented resolution and facilitate the assembly of the accompanying metabolic results into a detailed developmental trajectory. Here we provide an unbiased assessment of the early embryo metabolome and transcriptome during the early stages of development, including important events such as zygotic genome activation, germ layer (ectoderm, endoderm and mesoderm) determination and the onset of gastrulation. Together our data provide for the first time an integrative picture of transcription and metabolism during early embryonic development at exceptional resolution.