Antibody:	anti-HNF3b
Assay notes:	Two antibodies were described, but the one used in this assay was not specified. Either MGI:1338477 or MGI:5562562 could have been used.

Structure	Level	Pattern	Image	Note
TS13: future midbrain floor plate	Present		1Ab	Expression overlapped with Foxa1 to a large extent.

Structure	Level	Pattern	Image	Note
TS15: future midbrain floor plate	Present		1Ad
TS15: future midbrain	Present	Regionally restricted	1Ad	Expression in the ventral midbrain overlapped with Foxa1 to a large extent, except for a group of cells near the alar/basal boundary that only expresses Foxa2.

Structure	Level	Pattern	Image	Note
TS17: midbrain floor plate	Present		1Af
TS17: midbrain	Present	Regionally restricted	1Af	Expression in the ventral midbrain overlapped with Foxa1 to a large extent, except for a group of cells near the alar/basal boundary that only expresses Foxa2.

Structure	Level	Pattern	Image	Note
TS19: midbrain floor plate	Present		1Ah
TS19: midbrain	Present	Regionally restricted	1Ah	Expression in the ventral midbrain overlapped with Foxa1 to a large extent, except for a group of cells near the alar/basal boundary that only expresses Foxa2.

Structure	Level	Pattern	Image	Note
TS20: midbrain floor plate	Present		1Aj
TS20: midbrain	Present	Regionally restricted	1Aj	Expression in the ventral midbrain overlapped with Foxa1 to a large extent, except for a group of cells near the alar/basal boundary that only expresses Foxa2.

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

Structure	Level	Pattern	Image	Note
TS13: future midbrain floor plate	Present	Regionally restricted	2d	Expression in the conditional mutant is deleted from the ventral midbrain except in the medial floor plate.

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

Structure	Level	Pattern	Image	Note
TS15: future midbrain floor plate	Present	Regionally restricted	2h	Expression in the conditional mutant is deleted from the ventral midbrain except in the medial floor plate.

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

Structure	Level	Pattern	Image	Note
TS17: midbrain floor plate	Present	Regionally restricted	2l	Expression in the conditional mutant is deleted from the ventral midbrain except in the medial floor plate.

Structure	Level	Pattern	Image	Note
TS17: midbrain floor plate	Present	Regionally restricted	2n	Expression in the conditional mutant is deleted from the ventral midbrain except in the medial floor plate.

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

Structure	Level	Pattern	Image	Note
TS20: midbrain floor plate	Present	Regionally restricted	2r	Expression in the conditional mutant is deleted from the ventral midbrain except in the medial floor plate.

Structure	Level	Pattern	Image	Note
TS20: midbrain	Present	Regionally restricted	2t	Expression was detected in ventral midbrain, as in control.

Structure	Level	Pattern	Image	Note
TS20: midbrain floor plate	Present		2v

Structure	Level	Pattern	Image	Note
TS15: future midbrain	Present	Regionally restricted	S1_Foxa2 E9.25	Compared to an adjacent section, Foxa2 expression overlaps with Gli2 at E9.25.

Structure	Level	Pattern	Image	Note
TS15: future midbrain	Present	Regionally restricted	S1_Foxa2 E9.5

Structure	Level	Pattern	Image	Note
TS20: midbrain	Present	Regionally restricted	S1_Foxa2 E12.5	Compared to an adjacent section, the dorsal limit of Foxa2 expression abuts the ventral limit of Gli2 expression at E12.5.