Maternal and zygotic factors sequentially shape the tissue regionalization of chromatin landscapes in early vertebrate embryos

ChIP-seq and RNA-seq analyses to understand the establishment of the cis-regulatory mark H3K4me1 during early embryogenesis. We examined the spatial regionalization of H3K4me1 marking across the early Xenopus tropicalis embryo. We performed H3K4me1 ChIP-seq in ectoderm, mesoderm and endoderm samples [note that the endoderm samples were previously released in GSE118024]. Subsequently, we performed H3K4me1 ChIP-seq alpha-amanitin treated embryos (ectoderm, mesoderm and endoderm) and Otx1/Vegt/Foxh1 knockdown embryos (endoderm). We also performed single embryo RNA-seq on 15 individual embryos from 3 clutches to compare the expression variation genes with or without H3K4me1 marking.