This dataset provides gene expression levels of single cell and pooled embryos as part of a study on zygotic genome activation in Ciona embryogenesis. The single cell RNA-seq data suggested that Cyclin B3 was a key mediator of this process. This was confirmed by performing RNA-seq on pooled RNA isolated from embryos where Cyclin B3 was knocked down (using morpholinos) or overexpressed (using mRNA injections). Overall design: 93 single cell transcriptomes consisting of cells from 4-, 8-, and 16-cell stage embryos. Each stage was performed in triplicate. 21 pooled embryo transcriptomes from total RNA of pooled embryos from 4- 8- and 16-cell stages for controls and embryos where Cyclin B3 has been knocked down (using morpholinos) as well as 16-cell embryos where Cyclin B3 has been overexpressed. All samples were performed in triplicate.