Antibody:	Anti-Lmx1a
Assay notes:	Two antibodies were described; either MGI:7431210 or MGI:7431211 were used in this assay.

Structure	Level	Pattern	Image	Note
TS20: rhombic lip	Present	Regionally restricted	1C , 1e' , 1E , 1e'''	Many Lmx1a+/Atoh1- cells were noted. Rare Lmx1a/Atoh1 double positive cells were seen.

Structure	Level	Pattern	Image	Note
TS24: rhombic lip	Present	Regionally restricted	1g' , 1F , 1g''' , 1G	Many Lmx1a+/Atoh1- cells were noted. Rare Lmx1a/Atoh1 double positive cells were seen.

Structure	Level	Pattern	Image	Note
TS20: rhombic lip	Present		1H

Structure	Level	Pattern	Image	Note
TS20: rhombic lip	Present		1I	Expression was still seen in the mutant.

Structure	Level	Pattern	Image	Note
TS24: rhombic lip	Present		1J

Structure	Level	Pattern	Image	Note
TS24: rhombic lip	Present		1K	Expression was still seen in the mutant.

Structure	Level	Pattern	Image	Note
TS26: rhombic lip	Present		3E

Structure	Level	Pattern	Image	Note
TS26: metencephalon	Present	Regionally restricted	3F	Virtually no rhombic lip was detected in these embryos. A few immunopositive cells were occasionally found in the area corresponding to the mutant rhombic lip.

Structure	Level	Pattern	Image	Note
TS20: cortical hem	Present		6C

Structure	Level	Pattern	Image	Note
TS20: cortical hem	Present		6E

Structure	Cell Type	Level	Pattern	Image	Note
TS21: cerebellum	cerebellum glutamatergic neuron	Present	Regionally restricted	S1C , S1A	Expression was detected in the nuclear transitory zone, which co-expressed beta-galactosidase.
TS21: cerebellum		Present	Regionally restricted	S1C , S1A	Expression was detected in c3 cells, which are beta-galactosidase-negative.

Structure	Level	Pattern	Image	Note
TS24: cerebellum	Present		S1F , S1E
TS24: rhombic lip	Present		S1F , S1E

Structure	Cell Type	Level	Pattern	Image	Note
TS27: cerebellum vermis		Present	Regionally restricted	S1I , S1H , S1G	At P3, numerous immunopositive cells were detected in the posterior vermis.
TS27: cerebellum internal granule cell layer	unipolar brush cell	Present	Regionally restricted	S1H , S1I , S1G	The vast majority of Lmx1a+ cells in the internal granule layer coexpress the unipolar brush cell marker Eomes.

Structure	Level	Pattern	Image	Note
TS17: hindbrain roof plate	Present	Regionally restricted	s2A	Expression was detected in the fourth ventricle roof plate.

Structure	Level	Pattern	Image	Note
TS17: hindbrain roof plate	Present	Regionally restricted	s2B	Expression was detected in the fourth ventricle roof plate.

Structure	Level	Pattern	Image	Note
TS21: cerebellum	Present	Regionally restricted	s2C	Expression was detected in the c3 region. Some coexpression was noted with GFP.
TS21: choroid plexus	Present		s2C	Coexpression was noted with GFP.
TS21: rhombic lip	Present		s2C	Coexpression was noted with GFP.

Structure	Level	Pattern	Image	Note
TS21: cerebellum	Present	Regionally restricted	s2G , s2E	Expression was detected in the c3 region. Some coexpression was noted with GFP.

Structure	Level	Pattern	Image	Note
TS21: cerebellum	Present	Regionally restricted	s2H	Expression in the c3 region was not changed in the mutant. Some coexpression was noted with GFP.
TS21: choroid plexus	Present		s2H	Coexpression was noted with GFP.
TS21: rhombic lip	Present		s2H	Coexpression was noted with GFP.

Structure	Level	Pattern	Image	Note
TS21: cerebellum	Present	Regionally restricted	s2J , s2L	Expression in the c3 region was not changed in the mutant. Some coexpression was noted with GFP.

Structure	Cell Type	Level	Pattern	Image	Note
TS27: cerebellum	unipolar brush cell	Present		s2M
TS27: choroid plexus		Present		s2M

Structure	Cell Type	Level	Pattern	Image	Note
TS27: cerebellum	unipolar brush cell	Absent		s2O
TS27: choroid plexus		Present		s2O

Structure	Level	Pattern	Image	Note
TS21: choroid plexus	Present		S3C , S3A	Coexpression with Cre-GFP was noted.
TS21: rhombic lip	Present		S3C , S3A	Coexpression with Cre-GFP was noted.

Structure	Level	Pattern	Image	Note
TS21: choroid plexus	Present		S3F , S3D	Coexpression with Cre-GFP was noted.
TS21: rhombic lip	Present		S3F , S3D	Coexpression with Cre-GFP was noted.

Structure	Level	Pattern	Image	Note
TS24: choroid plexus	Present		S3J , S3H	Coexpression with Cre-GFP was noted.
TS24: rhombic lip	Present		S3J , S3H	Coexpression with Cre-GFP was noted.

Structure	Level	Pattern	Image	Note
TS24: choroid plexus	Present		S3M , S3K	Coexpression with Cre-GFP was noted.
TS24: rhombic lip	Present		S3M , S3K	Coexpression with Cre-GFP was noted.

Structure	Level	Pattern	Image	Note
TS21: rhombic lip	Present		S5A , S5C	Some Lmx1a+/Atoh1+ cells were noted.

Structure	Level	Pattern	Image	Note
TS21: rhombic lip	Present		S5F , S5D	Many more Lmx1a+ cells coexpress Atoh1 in dreher rhombic lip than in wild type.

Structure	Level	Pattern	Image	Note
TS17: cortical hem	Present		S7D , S7B	Virtually all Lmx1a+ cells in the cortical hem were GFP+.

Structure	Level	Pattern	Image	Note
TS17: cortical hem	Present		S7E , S7G	Virtually all Lmx1a+ cells in the cortical hem were GFP+ in dreher mice at E10.5.

Structure	Level	Pattern	Image	Note
TS20: choroid plexus	Present		S7H
TS20: cortical hem	Present		S7H

Structure	Level	Pattern	Image	Note
TS20: choroid plexus	Present		S7J , S7L	Virtually all Lmx1a+ cells were GFP+.
TS20: cortical hem	Present		S7J , S7L	Virtually all Lmx1a+ cells were GFP+.

Structure	Level	Pattern	Image	Note
TS20: choroid plexus	Present		S7M
TS20: cortical hem	Present		S7M

Structure	Level	Pattern	Image	Note
TS20: choroid plexus	Present		S7O , S7Q	Virtually all Lmx1a+ cells were GFP+ in dreher mice. No ectopic expression of Lmx1a was detected in the mutant telencephalon.
TS20: cortical hem	Present		S7O , S7Q	Virtually all Lmx1a+ cells were GFP+ in dreher mice. No ectopic expression of Lmx1a was detected in the mutant telencephalon.

Structure	Level	Pattern	Image	Note
TS17: cortical hem	Present	Regionally restricted	S8A , S8C	The lateral limit of the expression domain in the cortical hem was indicated. The expression domain did not overlap with the Lhx2 domain significantly.

Structure	Level	Pattern	Image	Note
TS17: cortical hem	Present	Regionally restricted	S8D , S8F	The lateral limit of the expression domain in the cortical hem was indicated. In the mutant, the Lhx2 expression domain extended medially and included almost the entire cortical hem with significant overlap with the Lmx1a expression domain.