To characterize the nature of gene regulatory networks for cell specification and differentiation, embryos from various developmental stages (0, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, and 30 hours post fertilization) of the sea urchin Hemincentrotus pulcherrimus were obtained from three different sets of parents (batches) and subjected to RNA sequencing.