Probe:	UI-M-BH3-aun-a-06-0-UI.s1
Probe preparation:	Antisense labelled with digoxigenin RNA
Visualized with:	Alkaline phosphatase

Structure	Level	Pattern	Image	Note
TS19: diencephalon	Present		S7_m	This annotation was inferred from the data presented in Supp. Table 4.

Structure	Level	Pattern	Image	Note
TS20: diencephalon	Present		S7_n	This annotation was inferred from the data presented in Supp. Table 4.

Structure	Level	Pattern	Image	Note
TS22: hypothalamus	Present	Regionally restricted	S7_o	Expression is present in the developing suprachiasmatic nucleus.

Structure	Level	Pattern	Image	Note
TS24: hypothalamus	Present	Regionally restricted	S7_p	Expression is present in the developing suprachiasmatic nucleus.

Structure	Level	Pattern	Image	Note
TS19: diencephalon lateral wall mantle layer	Moderate	Non-Uniform	Id4-Shh E11.5-coronal , Id4-Shh E11.5-sagittal	Staining is moderate in the MZ of the dorsal thalamus & weak in the prethalamus, dorsal & ventral POAs, AVH, anterior ID & mam zone. Staining is either absent or ubiquitous in the MZ of PVH, VMH & ARH nuclei, posterior ID, premam & supramam zones & TT.
TS19: diencephalon lateral wall ventricular layer	Ambiguous		Id4-Shh E11.5-coronal , Id4-Shh E11.5-sagittal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus, the prethalamus, dorsal and ventral POAs, the PVH, VMH and ARH nuclei, the AVH, the anterior and posterior IDs, the premam, mam and supramam zones and the TT.
TS19: telencephalon mantle layer	Moderate	Non-Uniform	Id4-Shh E11.5-coronal , Id4-Shh E11.5-sagittal	There is moderate staining in the mantle zone of the ganglionic eminences. Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone and cortical plate of the cerebral cortex.
TS19: telencephalon ventricular layer	Moderate		Id4-Shh E11.5-sagittal , Id4-Shh E11.5-coronal	There is moderate staining in the ventricular zone of the cerebral cortex and the ganglionic eminences.

Structure	Level	Pattern	Image	Note
TS20: cerebral cortex intermediate zone	Ambiguous		Id4-Shh E12.5-sagittal , Id4-Shh E12.5-coronal	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS20: cerebral cortex ventricular layer	Strong		Id4-Shh E12.5-sagittal , Id4-Shh E12.5-coronal	There is strong staining in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Id4-Shh E12.5-sagittal , Id4-Shh E12.5-coronal	Staining is either absent or ubiquitous in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS20: diencephalon mantle layer	Weak	Non-Uniform	Id4-Shh E12.5-sagittal , Id4-Shh E12.5-coronal	There is weak staining in the mantle zone of the mam zone. Staining is either absent or ubiquitous in the mantle zone of the premam and supramam zones and the TT.
TS20: diencephalon ventricular layer	Ambiguous		Id4-Shh E12.5-coronal , Id4-Shh E12.5-sagittal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones and the TT.
TS20: ganglionic eminence	Moderate		Id4-Shh E12.5-coronal , Id4-Shh E12.5-sagittal	There is moderate staining in the ventricular and mantle zones of the ganglionic eminences.
TS20: hypothalamus mantle layer	Moderate	Non-Uniform	Id4-Shh E12.5-coronal , Id4-Shh E12.5-sagittal	There is moderate staining in the mantle zone of the dorsal and ventral POAs and the anterior ID and weak staining in the PVH nucleus. Staining is either absent or ubiquitous in the mantle zone of the VMH and ARH nuclei, the AVH and posterior ID.
TS20: hypothalamus ventricular layer	Ambiguous		Id4-Shh E12.5-coronal , Id4-Shh E12.5-sagittal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei, the AVH and anterior and posterior IDs.
TS20: thalamus mantle layer	Very strong	Non-Uniform	Id4-Shh E12.5-sagittal , Id4-Shh E12.5-coronal	There is very strong staining in the mantle zone of the dorsal thalamus. Staining is either absent or ubiquitous in the mantle zone of the prethalamus.
TS20: thalamus ventricular layer	Ambiguous		Id4-Shh E12.5-sagittal , Id4-Shh E12.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Ambiguous		Id4-Shh E14.5-coronal , Id4-Shh E14.5-sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Very strong		Id4-Shh E14.5-coronal , Id4-Shh E14.5-sagittal	There is very strong staining in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Id4-Shh E14.5-coronal , Id4-Shh E14.5-sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Moderate	Non-Uniform	Id4-Shh E14.5-sagittal , Id4-Shh E14.5-coronal	There is moderate staining in the mantle zone of the mam zone. Staining is either absent or ubiquitous in the mantle zone of the premam and supramam zones and the TT.
TS22: diencephalon ventricular layer	Ambiguous		Id4-Shh E14.5-sagittal , Id4-Shh E14.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones and the TT.
TS22: ganglionic eminence	Weak		Id4-Shh E14.5-coronal , Id4-Shh E14.5-sagittal	There is weak staining in the ventricular and mantle zones of the ganglionic eminences.
TS22: hypothalamus mantle layer	Weak	Non-Uniform	Id4-Shh E14.5-sagittal , Id4-Shh E14.5-coronal	There is weak staining in the mantle zone of the dorsal and ventral POAs and weak, scattered staining in the VMH nucleus. Staining is either absent or ubiquitous in the mantle zone of the PVH and ARH nuclei, the AVH and anterior and posterior IDs.
TS22: hypothalamus ventricular layer	Ambiguous		Id4-Shh E14.5-coronal , Id4-Shh E14.5-sagittal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei, the AVH and anterior and posterior IDs.
TS22: thalamus mantle layer	Very strong	Non-Uniform	Id4-Shh E14.5-sagittal , Id4-Shh E14.5-coronal	There is very strong staining in the mantle zone of the dorsal thalamus. Staining is either absent or ubiquitous in the mantle zone of the prethalamus.
TS22: thalamus ventricular layer	Ambiguous		Id4-Shh E14.5-sagittal , Id4-Shh E14.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Ambiguous		Id4-Shh E16.5-coronal , Id4-Shh E16.5-sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Moderate		Id4-Shh E16.5-sagittal , Id4-Shh E16.5-coronal	There is moderate staining in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Id4-Shh E16.5-coronal , Id4-Shh E16.5-sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Strong	Non-Uniform	Id4-Shh E16.5-coronal , Id4-Shh E16.5-sagittal	There is strong staining in the mantle zone of the mam zone. Staining is either absent or ubiquitous in the mantle zone of the premam and supramam zones.
TS24: diencephalon ventricular layer	Ambiguous		Id4-Shh E16.5-sagittal , Id4-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS24: ganglionic eminence	Moderate	Non-Uniform	Id4-Shh E16.5-coronal , Id4-Shh E16.5-sagittal	There is moderate staining in the mantle zone of the ganglionic eminences. Staining is either absent or ubiquitous in the ventricular zone of the ganglionic eminences.
TS24: hypothalamus mantle layer	Very strong	Non-Uniform	Id4-Shh E16.5-sagittal , Id4-Shh E16.5-coronal	There is very strong staining in the MZ of the SCH nucleus, moderate staining in the DAH and weak staining in the dorsal and ventral POAs. Staining is either absent or ubiquitous in the MZ of the PVH, DMH, VMH and ARH nuclei, the AVH and the PH.
TS24: hypothalamus ventricular layer	Weak	Non-Uniform	Id4-Shh E16.5-sagittal , Id4-Shh E16.5-coronal	There is weak staining in the ventricular zone of the dorsal and ventral POAs. Staining is either absent or ubiquitous in the ventricular zone of the PVH, SCH, DMH, VMH and ARH nuclei, the AVH, the DAH and the PH.
TS24: thalamus mantle layer	Very strong		Id4-Shh E16.5-coronal , Id4-Shh E16.5-sagittal	There is very strong staining in the mantle zone of the dorsal thalamus and prethalamus.
TS24: thalamus ventricular layer	Ambiguous		Id4-Shh E16.5-coronal , Id4-Shh E16.5-sagittal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.