Probe:	UI-M-BH0-ajx-b-04-0-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	Strong	Non-Uniform	Zfp462-Shh E11.5_coronal	There is strong, scattered staining in the MZ of the dorsal thalamus and prethalamus and weak staining in the dorsal and ventral POAs. Staining is either absent or ubiquitous in the MZ of the PVH nucleus, the AVH and anterior and posterior IDs.
TS19: diencephalon lateral wall ventricular layer	Strong	Non-Uniform	Zfp462-Shh E11.5_coronal	Staining is strong & scattered in the VZ of the dorsal thalamus & prethalamus, moderate in the AVH & anterior & posterior IDs & moderate & scattered in the dorsal & ventral POAs. Staining is either absent or ubiquitous in the VZ of the PVH nucleus.
TS19: telencephalon mantle layer	Strong	Non-Uniform	Zfp462-Shh E11.5_coronal	There is strong staining in the postmitotic neurons in the intermediate zone and cortical plate of the cerebral cortex and moderate staining in the mantle zone of the ganglionic eminences.
TS19: telencephalon ventricular layer	Ambiguous		Zfp462-Shh E11.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex and the ganglionic eminences.

Structure	Level	Pattern	Image	Note
TS20: cerebral cortex intermediate zone	Strong		Zfp462-Shh E12.5_coronal	There is strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS20: cerebral cortex ventricular layer	Strong		Zfp462-Shh E12.5_coronal	There is strong staining in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Strong		Zfp462-Shh E12.5_coronal	There is strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS20: diencephalon mantle layer	Moderate	Non-Uniform	Zfp462-Shh E12.5_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.
TS20: diencephalon ventricular layer	Moderate	Non-Uniform	Zfp462-Shh E12.5_coronal	There is moderate staining in the ventricular zone of the mam zone. Staining is either absent or ubiquitous in the ventricular zone of the premam and supramam zones and the TT.
TS20: ganglionic eminence	Strong	Non-Uniform	Zfp462-Shh E12.5_coronal	There is strong staining in the ventricular zone of the ganglionic eminences and weak staining in the mantle zone.
TS20: hypothalamus mantle layer	Strong	Non-Uniform	Zfp462-Shh E12.5_coronal	There is strong staining in the mantle zone of the AVH and weak staining in the anterior and posterior IDs. Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs and the PVH, VMH and ARH nuclei.
TS20: hypothalamus ventricular layer	Strong	Non-Uniform	Zfp462-Shh E12.5_coronal	There is strong staining in the ventricular zone of the dorsal and ventral POAs and the AVH and weak staining in the PVH and VMH nuclei and anterior and posterior IDs. Staining is either absent or ubiquitous in the ventricular zone of the ARH nucleus.
TS20: thalamus mantle layer	Weak	Non-Uniform	Zfp462-Shh E12.5_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.
TS20: thalamus ventricular layer	Strong	Non-Uniform	Zfp462-Shh E12.5_coronal	There is strong staining in the ventricular zone of the dorsal thalamus. Staining is either absent or ubiquitous in the ventricular zone of the prethalamus.

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Very strong		Zfp462-Shh E14.5_coronal	There is very strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Ambiguous		Zfp462-Shh E14.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Very strong		Zfp462-Shh E14.5_coronal	There is very strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Ambiguous		Zfp462-Shh E14.5_coronal	Staining is either absent or ubiquitous in the mantle zone of the premam, mam and supramam zones and the TT.
TS22: diencephalon ventricular layer	Weak	Non-Uniform	Zfp462-Shh E14.5_coronal	There is weak staining in the ventricular zone of the premam and mam zones and the TT. Staining is either absent or ubiquitous in the ventricular zone of the supramam zone.
TS22: ganglionic eminence	Ambiguous		Zfp462-Shh E14.5_coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS22: hypothalamus mantle layer	Very strong	Non-Uniform	Zfp462-Shh E14.5_coronal	There is very strong staining in the mantle zone of the AVH and weak staining in the ventral POA. Staining is either absent or ubiquitous in the mantle zone of the dorsal POA, the PVH, VMH and ARH nuclei and anterior and posterior IDs.
TS22: hypothalamus ventricular layer	Very strong	Non-Uniform	Zfp462-Shh E14.5_coronal	There is very strong staining in the VZ of the AVH, moderate staining in the dorsal and ventral POAs and weak staining in the PVH and VMH nuclei and anterior and posterior IDs. Staining is either absent or ubiquitous in the VZ of the ARH nucleus.
TS22: thalamus mantle layer	Moderate	Non-Uniform	Zfp462-Shh E14.5_coronal	There is moderate 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	Moderate		Zfp462-Shh E14.5_coronal	There is moderate staining in the ventricular zone of the dorsal thalamus and prethalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Very strong		Zfp462-Shh E16.5_coronal	There is very strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Ambiguous		Zfp462-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Very strong		Zfp462-Shh E16.5_coronal	There is very strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Weak		Zfp462-Shh E16.5_coronal	There is weak staining in the mantle zone of the premam, mam and supramam zones.
TS24: diencephalon ventricular layer	Strong	Non-Uniform	Zfp462-Shh E16.5_coronal	There is strong staining in the ventricular zone of the premam zone. Staining is either absent or ubiquitous in the ventricular zone of the mam and supramam zones.
TS24: ganglionic eminence	Weak	Non-Uniform	Zfp462-Shh E16.5_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.
TS24: hypothalamus mantle layer	Moderate	Non-Uniform	Zfp462-Shh E16.5_coronal	There is moderate staining in the mantle zone of the ventral POA, the AVH, the DAH and the SCH nucleus and weak staining in the dorsal POA, VMH nucleus and the PH. Staining is either absent or ubiquitous in the mantle zone of the PVH, DMH and ARH nuclei.
TS24: hypothalamus ventricular layer	Ambiguous		Zfp462-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	Strong	Non-Uniform	Zfp462-Shh E16.5_coronal	There is strong staining in the mantle zone of the dorsal thalamus and weak staining in the prethalamus.
TS24: thalamus ventricular layer	Ambiguous		Zfp462-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.