Tissue-specific transcriptomes reveal gene expression trajectories in two maturing skin epithelial layers in zebrafish embryos

We purified (FACS) and profiled (RNA-Seq) zebrafish embryo skin cells vs. nonskin cells at three early developmental stages. At two of the stages, we further purified and profiled two distinct epithelial layers of the skin: the periderm and basal cells. Our comprehensive expression analysis provides the first reported transcriptomes of these two cell types, reveals gene expression dynamics in space and time, and identifies common and distinct features of epithelial maturation in the two layers. Given the conserved nature of skin development, we believe our study to be of interest to those studying skin in other vertebrates. Overall design: At each of 20 SS, 52 hpf, and 72 hpf, we used krt4:dsRed transgenic zebrafish embryos and FACS to prepare and run two RNA-Seq conditions: all skin vs. nonskin1, with two replicates for each condition. At each of 52 hpf and 72 hpf, we used krt4:dsRed;krt5:GFP transenic zebrafish embryos and FACS to prepare and run three RNA-Seq conditions: periderm vs. basal cells vs. nonskin2, with two replicates for each condition, except 52 hpf nonskin2 has only one replicate.