Probe:	UI-M-AJ0-aau-b-05-0-UI.s1
Probe preparation:	Antisense labelled with digoxigenin RNA
Visualized with:	Alkaline phosphatase
Assay notes:	These specimens were also hybridized with a fluorescein-labeled Shh probe MGI:2110655; detected with TBT/BCIP. The results are reported in Supp. Table 4, whose legend includes a key to the abbreviations used and more fully details the regions examined.

Structure	Level	Pattern	Image	Note
TS19: diencephalon lateral wall mantle layer	Moderate	Non-Uniform	Ype14-Shh E11.5_coronal	Staining is moderate in the MZ of the dorsal thalamus, prethalamus, dorsal POA, PVH nucleus & anterior & posterior IDs, weak in the premam zone & either absent or ubiquitous in the ventral POA, the AVH, VMH & ARH nuclei, the TT & mam & supramam zones.
TS19: diencephalon lateral wall ventricular layer	Moderate	Non-Uniform	Ype14-Shh E11.5_coronal	Staining is moderate in the VZ of anterior & posterior IDs & VMH nucleus & weak in AVH & premam zone. Staining is either absent or ubiquitous in the VZ of dorsal thalamus, prethalamus, dorsal & ventral POAs, PVH & ARH nuclei, mam & supramam zones & TT.
TS19: telencephalon mantle layer	Moderate	Non-Uniform	Ype14-Shh E11.5_coronal	There is moderate staining in the postmitotic neurons in the intermediate zone and cortical plate of the cerebral cortex. Staining is either absent or ubiquitous in the mantle zone of the ganglionic eminences.
TS19: telencephalon ventricular layer	Weak	Non-Uniform	Ype14-Shh E11.5_coronal	There is weak staining in the ventricular zone of the ganglionic eminences. Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.

Structure	Level	Pattern	Image	Note
TS20: cerebral cortex intermediate zone	Moderate		Ype14-Shh E12.5_coronal	There is moderate staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS20: cerebral cortex ventricular layer	Ambiguous		Ype14-Shh E12.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Moderate		Ype14-Shh E12.5_coronal	There is moderate staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS20: diencephalon mantle layer	Moderate	Non-Uniform	Ype14-Shh E12.5_coronal	There is moderate staining in the mantle zone of the TT and the mam zone and weak staining in the premam zone. Staining is either absent or ubiquitous in the mantle zone of the supramam zone.
TS20: diencephalon ventricular layer	Ambiguous		Ype14-Shh E12.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones and the TT.
TS20: ganglionic eminence	Weak	Non-Uniform	Ype14-Shh E12.5_coronal	There is weak staining in the mantle zone of the ganglionic eminences. Staining is either absent or ubiquitous in the ventricular zone of the ganglionic eminences.
TS20: hypothalamus mantle layer	Moderate	Non-Uniform	Ype14-Shh E12.5_coronal	There is moderate staining in the mantle zone of the dorsal and ventral POAs and weak staining in the anterior and posterior IDs and the VMH nucleus. Staining is either absent or ubiquitous in the mantle zone of the PVH and ARH nuclei and the AVH.
TS20: hypothalamus ventricular layer	Weak	Non-Uniform	Ype14-Shh E12.5_coronal	There is weak staining in the ventricular zone of the anterior and posterior IDs. Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei and the AVH.
TS20: thalamus mantle layer	Very strong	Non-Uniform	Ype14-Shh E12.5_coronal	There is very strong staining in the mantle zone of the dorsal thalamus and strong staining in the prethalamus.
TS20: thalamus ventricular layer	Ambiguous		Ype14-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	Moderate		Ype14-Shh E14.5_coronal	There is moderate staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Ambiguous		Ype14-Shh E14.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Moderate		Ype14-Shh E14.5_coronal	There is moderate staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Strong	Non-Uniform	Ype14-Shh E14.5_coronal	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 and the TT.
TS22: diencephalon ventricular layer	Ambiguous		Ype14-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	Ambiguous		Ype14-Shh E14.5_coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS22: hypothalamus mantle layer	Moderate	Non-Uniform	Ype14-Shh E14.5_coronal	There is moderate staining in the mantle zone of the ventral POA. Staining is either absent or ubiquitous in the mantle zone of the dorsal POA, the PVH, VMH and ARH nuclei, the AVH and anterior and posterior IDs.
TS22: hypothalamus ventricular layer	Weak	Non-Uniform	Ype14-Shh E14.5_coronal	There is weak staining in the ventricular zone of the anterior and posterior IDs. Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei and the AVH.
TS22: thalamus mantle layer	Very strong	Non-Uniform	Ype14-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		Ype14-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		Ype14-Shh E16.5_coronal	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Ambiguous		Ype14-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Ype14-Shh E16.5_coronal	Staining is either absent or ubiquitous in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Moderate	Non-Uniform	Ype14-Shh E16.5_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.
TS24: diencephalon ventricular layer	Ambiguous		Ype14-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS24: ganglionic eminence	Ambiguous		Ype14-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS24: hypothalamus mantle layer	Ambiguous		Ype14-Shh E16.5_coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH, SCH, DMH, VMH and ARH nuclei, the AVH, the DAH and the PH.
TS24: hypothalamus ventricular layer	Ambiguous		Ype14-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH, SCH, DMH, VMH and ARH nuclei, the AVH, the DAH and the PH.
TS24: thalamus mantle layer	Weak	Non-Uniform	Ype14-Shh E16.5_coronal	There is weak staining in the mantle zone of the dorsal thalamus. Staining is either absent or ubiquitous in the mantle zone of the prethalamus.
TS24: thalamus ventricular layer	Ambiguous		Ype14-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.