Additional Supporting Information may be found in the online version of this article.

DVDY_22192_sm_SuppFig1.tif3713KSupp. Fig. S1. Continuous expression of Sox9 in WT trachea after chondrogenesis. A: Immunostaining of Sox9 on E17.5 wild-type trachea shows its clear expression in cartilages (arrow, 100×). B: Sox9 expression is undetectable in mesenchyme of the Shh−/− tracheo-esophageal tube at E17.5 (arrow, 100×). Blue, DAPI background; red, Sox9; Tr, trachea; TE, tracheo-esophageal tube.
DVDY_22192_sm_SuppFig2.tif3932KSupp. Fig. S2. Bmp4 and Noggin expression in trachea of WT and Shh−/− embryos. A,B: Immunofluorescent staining of Bmp4 on E11.5 wild-type tracheal (A) and Shh−/− tracheo-esophageal tube sections (B) show the significant loss of Bmp4 expression in Shh−/− foregut (B), and its expression in wild-type ventral tracheal mesenchyme (A) (200×). C,D: Immunofluorescent staining of Noggin on wild-type (C) and Shh−/− sections (D) show Noggin expression in dorsal mesenchyme of wild-type trachea (C), which is also significantly reduced, if present, in the Shh−/− tracheo-esophageal tube (D) (200×).

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