Antibody:

anti-Shh (H-160; sc9024)

Structure	Level	Pattern	Image	Note
TS13: future midbrain floor plate	Present		1Aa

Structure	Level	Pattern	Image	Note
TS15: future midbrain floor plate	Present		1Ac
TS15: future midbrain	Present	Regionally restricted	1Ac	Expression was detected in the ventral midbrain that extends to near the alar/basal boundary.

Structure	Level	Pattern	Image	Note
TS17: midbrain floor plate	Present		1Ae
TS17: midbrain	Present	Regionally restricted	1Ae	Expression was detected in the ventral midbrain that extends to near the alar/basal boundary.

Structure	Level	Pattern	Image	Note
TS19: midbrain floor plate	Absent		1Ag

Structure	Level	Pattern	Image	Note
TS20: midbrain floor plate	Absent		1Ai

Structure	Level	Pattern	Image	Note
TS13: future midbrain	Present	Regionally restricted	2a	Expression was detected in ventral midbrain.

Structure	Level	Pattern	Image	Note
TS13: future midbrain floor plate	Present	Regionally restricted	2c	Expression was severely reduced in the conditional knockout embryos. Expression was detected only in residual Foxa2-positive cells in the medial floor plate.

Structure	Level	Pattern	Image	Note
TS15: future midbrain	Present	Regionally restricted	2e	Expression was detected in ventral midbrain.

Structure	Level	Pattern	Image	Note
TS15: future midbrain floor plate	Present	Regionally restricted	2g	Expression was severely reduced in the conditional knockout embryos. Expression was detected only in residual Foxa2-positive cells in the medial floor plate.

Structure	Level	Pattern	Image	Note
TS15: future midbrain	Present	Regionally restricted		Expression was similar to control.

Structure	Level	Pattern	Image	Note
TS17: midbrain	Present	Regionally restricted	2i	Expression was detected in ventral midbrain.

Structure	Level	Pattern	Image	Note
TS17: midbrain floor plate	Present	Regionally restricted	2k	In the posterior midbrain, expression was severely reduced in the conditional knockout embryos. Expression was detected only in residual Foxa2-positive cells in the medial floor plate.

Structure	Level	Pattern	Image	Note
TS17: midbrain	Present	Regionally restricted	2m	In the anterior midbrain, expression was similar to control.

Structure	Level	Pattern	Image	Note
TS20: midbrain	Present	Regionally restricted	2o	Expression was detected in ventral midbrain.

Structure	Level	Pattern	Image	Note
TS20: midbrain	Present	Regionally restricted	2q	At E12.5, expression in the conditional knockout was similar to control in the entire midbrain.

Structure	Level	Pattern	Image	Note
TS20: midbrain	Present	Regionally restricted	2s	Expression was similar to control.

Structure	Level	Pattern	Image	Note
TS20: midbrain floor plate	Present		2u	Expression in the midbrain of the double mutant embryo was only in the floor plate.

Structure	Level	Pattern	Image	Note
TS15: future midbrain	Present		S1_Shh E9.25

Structure	Level	Pattern	Image	Note
TS15: future midbrain	Present		S1_Shh E9.5

Structure	Level	Pattern	Image	Note
TS20: midbrain	Present	Regionally restricted	S1_Shh E12.5	Compared to an adjacent section, there is a gap between Shh and Gli2 expression in the ventral midbrain.