Probe:	MTF#182
Probe preparation:	Antisense labelled with digoxigenin RNA
Visualized with:	Alkaline phosphatase
Assay notes:	Two possible probes were referenced: MGI:3506052 and MGI:1315062. The probe used in this assay was not specified.

Structure	Level	Pattern	Image	Note
TS27: suprachiasmatic nucleus	Present	Widespread	1_Six3	Expression was detected throughout the entire suprachiasmatic nucleus.

Structure	Level	Pattern	Image	Note
TS28: suprachiasmatic nucleus	Present	Widespread	2A Six3	Expression was detected throughout the entire suprachiasmatic nucleus.

Structure	Level	Pattern	Image	Note
TS28: suprachiasmatic nucleus	Present	Widespread	2B Overlay , 2B Six3	The full rostral to caudal expression was observed throughout the suprachiasmatic nucleus.

Structure	Level	Pattern	Image	Note
TS28: suprachiasmatic nucleus	Present	Widespread		Expression was identical to that seen at P15.

Structure	Level	Pattern	Image	Note
TS28: suprachiasmatic nucleus	Present	Widespread		Expression was identical to that seen at P15.

Structure	Level	Pattern	Image	Note
TS28: suprachiasmatic nucleus	Present		3_Six3 2

Structure	Level	Pattern	Image	Note
TS28: suprachiasmatic nucleus	Present		3_Six3 6	Variation of expression was significantly different between mid-day peak (ZT6) and mid-night trough (ZT18).

Structure	Level	Pattern	Image	Note
TS28: suprachiasmatic nucleus	Present		3_Six3 10

Structure	Level	Pattern	Image	Note
TS28: suprachiasmatic nucleus	Present		3_Six3 14

Structure	Level	Pattern	Image	Note
TS28: suprachiasmatic nucleus	Present		3_Six3 18	Variation of expression was significantly different between mid-day peak (ZT6) and mid-night trough (ZT18).

Structure	Level	Pattern	Image	Note
TS28: suprachiasmatic nucleus	Present		3_Six3 22

Structure	Level	Pattern	Image	Note
TS28: suprachiasmatic nucleus	Present		3_Six3 26

Structure	Level	Pattern	Image	Note
TS22: hypothalamus	Present	Regionally restricted	4_Six3 E14.5	Expression was detected in both the presumptive suprachiasmatic nucleus region, as well as dorsal areas.

Structure	Level	Pattern	Image	Note
TS23: hypothalamus	Present	Regionally restricted	4_Six3 E15.5

Structure	Level	Pattern	Image	Note
TS25: suprachiasmatic nucleus	Present	Ubiquitous	4_Six3 E17.5	Staining encompassed the entire suprachiasmatic nucleus.

Structure	Level	Pattern	Image	Note
TS27: suprachiasmatic nucleus	Present	Ubiquitous	4_Six3 p0	Staining encompassed the entire suprachiasmatic nucleus.

Structure	Level	Pattern	Image	Note
TS25: hypothalamus	Present	Regionally restricted		Staining also marked cells more dorsal and lateral to the suprachiasmatic nucleus.

Structure	Level	Pattern	Image	Note
TS17: diencephalon floor plate	Present	Regionally restricted	6A E10.5 low mag , 6A E10.5 Six3	Expression marked a broad dorsoventral and rostrocaudal region of the developing floor plate.

Structure	Level	Pattern	Image	Note
TS19: diencephalon	Present	Regionally restricted	6A E11.5 Six3 , 6A E11.5 low mag	At E11.5, expression was restricted to more ventral regions of the early telencephalon/diencephalon but remained expressed within the developing hypothalamus and pituitary.
TS19: telencephalon	Present	Regionally restricted	6A E11.5 Six3 , 6A E11.5 low mag	At E11.5, expression was restricted to more ventral regions of the early telencephalon/diencephalon but remained expressed within the developing hypothalamus and pituitary.

Structure	Level	Pattern	Image	Note
TS20: diencephalon	Present	Regionally restricted	6A E12.5 low mag , 6A E12.5 Six3	Expression became more restricted but still surrounded the base of the third ventricle.

Structure	Level	Pattern	Image	Note
TS21: diencephalon	Present	Regionally restricted	6A E13.5 low mag , 6A E13.5 Six3	Expression became more restricted but still surrounded the base of the third ventricle.

Structure	Level	Pattern	Image	Note
TS19: diencephalon	Present	Regionally restricted	6D E11.5 Rostral 1 Six3	At E11.5, Six3 was restricted to more ventral regions of the early telencephalon/diencephalon but remained expressed within the developing hypothalamus and pituitary.
TS19: telencephalon	Present	Regionally restricted	6D E11.5 Rostral 1 Six3	At E11.5, Six3 was restricted to more ventral regions of the early telencephalon/diencephalon but remained expressed within the developing hypothalamus and pituitary.

Structure	Level	Pattern	Image	Note
TS19: diencephalon	Present	Regionally restricted	6D E11.5 2 Six3	At E11.5, Six3 was restricted to more ventral regions of the early telencephalon/diencephalon but remained expressed within the developing hypothalamus and pituitary.
TS19: telencephalon	Present	Regionally restricted	6D E11.5 2 Six3	At E11.5, Six3 was restricted to more ventral regions of the early telencephalon/diencephalon but remained expressed within the developing hypothalamus and pituitary.

Structure	Level	Pattern	Image	Note
TS19: diencephalon	Present	Regionally restricted	6D E11.5 3 Six3	At E11.5, Six3 was restricted to more ventral regions of the early telencephalon/diencephalon but remained expressed within the developing hypothalamus and pituitary.
TS19: telencephalon	Present	Regionally restricted	6D E11.5 3 Six3	At E11.5, Six3 was restricted to more ventral regions of the early telencephalon/diencephalon but remained expressed within the developing hypothalamus and pituitary.

Structure	Level	Pattern	Image	Note
TS19: diencephalon	Present	Regionally restricted	6D E11.5 4 Six3	At E11.5, Six3 was restricted to more ventral regions of the early telencephalon/diencephalon but remained expressed within the developing hypothalamus and pituitary.
TS19: telencephalon	Present	Regionally restricted	6D E11.5 4 Six3	At E11.5, Six3 was restricted to more ventral regions of the early telencephalon/diencephalon but remained expressed within the developing hypothalamus and pituitary.

Structure	Level	Pattern	Image	Note
TS19: diencephalon	Present	Regionally restricted	6D E11.5 Caudal 5 Six3	At E11.5, Six3 was restricted to more ventral regions of the early telencephalon/diencephalon but remained expressed within the developing hypothalamus and pituitary.
TS19: telencephalon	Present	Regionally restricted	6D E11.5 Caudal 5 Six3	At E11.5, Six3 was restricted to more ventral regions of the early telencephalon/diencephalon but remained expressed within the developing hypothalamus and pituitary.

Structure	Level	Pattern	Image	Note
TS21: diencephalon	Present	Regionally restricted	6D E13.5 Rostral 1 Six3	Expression became more restricted but still surrounded the base of the third ventricle.

Structure	Level	Pattern	Image	Note
TS21: diencephalon	Present	Regionally restricted	6D E13.5 2 Six3	Expression became more restricted but still surrounded the base of the third ventricle.

Structure	Level	Pattern	Image	Note
TS21: diencephalon	Present	Regionally restricted	6D E13.5 3 Six3	Expression became more restricted but still surrounded the base of the third ventricle.

Structure	Level	Pattern	Image	Note
TS21: diencephalon	Present	Regionally restricted	6D E13.5 4 Six3	Expression became more restricted but still surrounded the base of the third ventricle.

Structure	Level	Pattern	Image	Note
TS21: diencephalon	Present	Regionally restricted	6D E13.5 Caudal 5 Six3	Expression became more restricted but still surrounded the base of the third ventricle.

Structure	Level	Pattern	Image	Note
TS26: suprachiasmatic nucleus	Present		8A top Six3

Structure	Level	Pattern	Image	Note
TS26: hypothalamus	Absent		8A bottom Six3	This mutant sample showed complete bilateral loss of Six3 in the ventral anterior hypothalamus.

Structure	Level	Pattern	Image	Note
TS26: pituitary gland	Present		8B top Six3

Structure	Level	Pattern	Image	Note
TS26: diencephalon	Absent		8B bottom Six3	The pituitary gland was lost in the mutant.

Structure	Level	Pattern	Image	Note
TS26: zona incerta	Present		8B inset top

Structure	Level	Pattern	Image	Note
TS26: zona incerta	Absent		8B inset bottom

Structure	Level	Pattern	Image	Note
TS23: hypothalamus medial zone	Present	Regionally restricted	8C top Six3	Expression was detected in the early suprachiasmatic nucleus unilaterally in mice displaying partial Six3 deletion.

Structure	Level	Pattern	Image	Note
TS23: hypothalamus medial zone	Present	Regionally restricted	8C bottom Six3	A mutant with no loss of Six3 retained expression in the early suprachiasmatic nucleus.