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Gene/Clone	Species	Stage	Anatomy Item	Experimenter
sox17b.1	xenopus

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Experiment details for sox17b.1

Dynamic in vivo binding of transcription factors to cis-regulatory modules of cer and gsc in the stepwise formation of the Sp...

Dynamic in vivo binding of transcription factors to cis-regulatory modules of cer and gsc in the stepwise formation of the Spemann-Mangold organizer.

Gene	Clone	Species	Stages	Anatomy
sox17b.1.S		laevis	NF stage 9	endoderm , vegetal
sox17b.1.S		laevis	NF stage 10	endoderm , vegetal
sox17b.1.S		laevis	NF stage 10.5	mesoderm , blastopore lip , prechordal plate , upper blastopore lip , lower blastopore lip , [+] endoderm

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Fig. S6. Detailed comparison of expression domains between organizer-expressing genes in early X. laevis embryogenesis. mRNA localizations of organizer-expressing genes as well as other genes for comparison as indicated on the left were visualized by whole-mount in situ hybridization using bisected embryos from the early blastula to neural stages as indicted on the top. Arrows indicate mRNA localization in the BCNE region (green), the presumptive mesoderm or mesoderm (yellow), the presumptive endoderm or endoderm (magenta) and the prechordal plate (black). Arrowheads indicate the blastopore. (A) Stage 8 to 10.5. Maternal vegt mRNA was detected at the early blastula (stage 8) in the entire presumptive endoderm region, whereas zygotic vegt mRNA was seen in the presumptive mesoderm region at mid stage 9 thereafter, as has been reported (Stennard et al., 1999). sia and later gsc start to be expressed in the BCNE region. mix1 expression is already seen at mid-stage 9 in the presumptive endodermal region except for the central region, then expands to the central endoderm and mesodermal region during the late blastula (late stage 9) to the early gastrula stage (stage 10), and gradually decreased from the central region. Both chd and gsc are co-expressed at the late blastula (stage 9) and early gastrula stages (stages 10 and 10.5) in the region overlapping with the sia expression domain. At stage 10/10.5, both chd and gsc expression patterns expand to the dorsal endoderm based on the observation shown in supplementary material Fig. S7. cer expression starts in a central region of the dorsovegetal region (indicated by a magenta arrow), though very weakly, at stage 9 (mid blastula) and expands to the entire dorsal endoderm (indicated by a magenta arrow) and the anterior dorsal mesoderm at stages 10 and 10.5 (supplementary material Fig. S7). The lim1 and otx2 genes are expressed at a mid period of stage 9 in the marginal zone. It seems to start in an endodermal region and expand to the dorsal mesoderm (supplementary material Fig. S7). (B) Colocalization of gsc and vegt or cer and sia. Embryos were bisected along the dorsal-ventral axis. Each counterpart of embryo was treated with whole-mount in situ hybridization for the indicated probe. The data show that gsc expression corresponds to zvegt in the dorsal mesoderm region at mid-blastula stage, while cer and sia are co-expressed in the dorsal endoderm at the mid-blastula stage. (C) Expression pattern at the late gastrula to early neurula stage. Arrows indicate mRNA localization in the prechordal plate. mix1 expression ceased before the late gastrula stage. Note that lim1 mRNA disappears from the prechordal plate (indicated by an arrow at stage 15) and later the notochord, but the Lim1 protein persists at least to the tailbud stage (stage 28; supplementary material Fig. S5N).

Gene	Clone	Species	Stages	Anatomy
sox17b.1.S		laevis	NF stage 10.5	endoderm

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Fig. S8. Assignment of expression domains of organizer genes. The mesoderm (green line) is discriminated from the endoderm according to the size of cells, and from the ectoderm based on the fate map of yellow and red cells, as shown by Bauer et al. (Bauer et al., 1994). Arrowhead indicates dorsal blastopore; bc, blastocoel.