Tissue- and stage-specific cellular context regulates Wnt target gene expression subsequent to ß-catenin recruitment

The aim of our study is to identify direct target genes of Wnt/ß-catenin signaling operating in gastrula-stage X. tropicalis embryos. We characterized the genomic loci bound by the Wnt signaling downstream component ß-catenin in intact X. tropicalis gastrulae using ChIP-seq. We also determined the normal mRNA expression profile in control (uninjected and control-MO-injected) embryos and altered mRNA expression profiles in two experimental samples: embryos where endogenous wnt8a function was knocked down with wnt8a MO, and where we experimentally re-instated Wnt8a expression with a DNA construct (pCSKA-wnt8a) in the same wnt8a knock down. Overall design: For ChIP-seq, one ChIP DNA and one input control DNA samples pooled from three independent ChIP experiments using early gastrula embryos were sequenced. For RNA-seq, Twelve total RNA samples (triplicates of each experimental samples: uninjected, CoMO-injected, wnt8aMO-injected, wnt8aMO and pCSKA-wnt8a-coinjected) from early gastrula embryos were sequenced.