Wnt signaling promotes the HG transcriptional program and represses the FG transcriptional program. (A) Experimental design. FG and HG (endoderm plus mesoderm) explants were dissected from DMSO-treated, BIO-treated and Tg(hsp70:dkk1) NF20 embryos and submitted for RNA-seq (in triplicate). (B) Venn diagram illustrates overlap of FG-enriched, HG-enriched, Wnt-activated and Wnt-repressed genes (log2 FC≤−1 or ≥1, FDR≤5%); see Fig. S4A for details. (C) Unsupervised clustering of FG- and HG-enriched genes, showing that BIO-treated FG has an expression profile similar to the HG control. (D) Scatter plot showing log2 FC in expression between control, BIO-treated and Tg(hsp70:dkk1) FG and HG explants. Transcripts are colored based on the normal control expression; FG=HG refers to transcripts expressed similarly in FG and HG, whereas those in black are not normally expressed in FG or HG. (E) Different categories of Wnt-activated (ACT) or Wnt-repressed (REP) transcripts grouped based on whether the gene is normally enriched in the endoderm, mesoderm or expressed in both endoderm and mesoderm (en=me). (F) In situ hybridization of control, Tg(hsp70:dkk1) or BIO-treated embryos in mid-sagittal section; anterior is left and dorsal up. Anterior genes are gata4, cebpa and tbx1 and posterior genes are cdx2 and msx1; n>20 for each probe.