mRNA profile of zebrafish periderm at 4-somite stage

In order to compare the transcriptome and tissue-specific nucleosome free regions of zebrafish periderm cells at 4-somite stage, we isolated the RNA from sorted GFP-positive cells of Tg(krt4:GFP) embryos and perform low-input RNA-seq. This study revealed periderm-specific transcriptome at 4-somite stage. Moreover, comparing with ATAC-seq from the same tissue, we confirmed the correlation between gene expression and nearby chromatin accessibility. GFP-positive embryos were harvested from three independent incross of Tg(krt4:GFP). Embryos were dissociated and sorted with FACS. For each batch, 2000 GFP-positive and 2000 GFP-negative cells were collected and subjected to RNA-seq.