BMP signaling coordinates D-V patterning. (A) Experimental design. FG and HG (endoderm plus mesoderm) explants were dissected from DMSO (vehicle)- or DMH1-treated NF20 embryos and submitted for RNA-seq (in triplicate). (B) Venn diagram showing overlap of FG-enriched genes, HG-enriched genes and BMP-activated and BMP-repressed transcripts (log2 FC≥1, FDR≤5%); see Fig. S2B for details. (C) Expression heatmap clustering of FG endoderm-, FG mesoderm-, HG endoderm- and HG mesoderm-enriched transcripts in vehicle-treated (CONT) or DMH1-treated explants. (D) Different categories of BMP-activated (ACT) or BMP-repressed (REP) transcripts based on whether the gene is normally enriched in the endoderm, mesoderm or expressed in both (en=me). (E) In situ hybridization of vehicle control-treated, DMH1-treated or BMP2-injected stage NF20 embryos in mid-sagittal section (cdx2, sfrp5, cebpa and nkx2-5; anterior left and dorsal up) or cross-section (hrg and mnx1; dorsal up; white lines indicate expression domain); n>20 for each probe.