Fig 1

(A) Animal view, dorsal to right of mean pSmad5 intensities at mid-gastrula stage (8 hpf) WT (n = 4) and bmp7 mutant (n = 3) embryos. (B) Differential gene expression in WT and bmp7 mutants at 8 hpf using RNA-seq. Significantly up-regulated genes in WT compared to bmp7 mutants are shown in red, and significantly down-regulated genes are shown in blue. All other genes are shown in gray. A subset of known BMP-dependent genes is highlighted. See Table A in S1 Data for underlying data. (C) Schematic of method to isolate RNA for sequencing from CHX-treated bmp7 mutant embryos injected with BMP2/7 protein. (D) Representative image of pSmad5 intensities of all nuclei of an individual bmp7 mutant (n = 9) and bmp7 mutant injected with 10 pg of BMP2/7 protein (n = 9). Animal pole facing up. (E) Differential gene expression using RNA-seq of CHX-treated bmp7 mutants versus CHX-treated bmp7 mutants injected with BMP2/7 protein. Significantly up-regulated genes with BMP2/7 protein injection are shown in red, and significantly down-regulated genes are shown in blue. All other genes are shown in gray. A subset of BMP direct target genes is highlighted. See Table B in S1 Data for underlying data. (F) GO term analysis for biological processes of the 57 direct target genes. See Table C in S1 Data for underlying data. A.U. is arbitrary units. BMP, Bone Morphogenetic Protein; CHX, cycloheximide; DV, dorsal–ventral; GO, Gene Ontology; hpf, hours post fertilization; pSmad5, phosphorylated Smad5; RNA-seq, RNA sequencing; TGFβ, Transforming Growth Factor Beta; WT, wild-type.