Limited nutrient availability during development puts individuals at risk to develop complications later in life. Central in this early-life stress paradox lies developmental plasticity, a poorly understood mechanism that responds to environmental cues from early to late developmental stages. In this study, we introduce the zebrafish (Danio rerio) as a model to study the early-developmental responses to reduced nutrient availability and their outcome. To reduce nutrient availability, we partially remove the yolk during embryogenesis. Around 5 hours post-fertilization, we removed ~30% of the yolk (YD samples) or sham-punctured embryos (SP) with a Hamilton syringe system. At 8, 24 and 32 hours post-fertilization, we collected RNA from whole embryos and obtained transcriptome profiles by RNAseq.