Probe:	IMAGE clone 5706335
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	Very strong	Non-Uniform	Vax1-Shh E11.5_coronal	There is very strong staining in the MZ of the AVH & anterior ID. Staining is either absent or ubiquitous in the MZ of the dorsal thalamus, prethalamus, dorsal & ventral POAs, the PVH, VMH & ARH nuclei, posterior ID, premam, mam & supramam zones & the TT.
TS19: diencephalon lateral wall ventricular layer	Very strong	Non-Uniform	Vax1-Shh E11.5_coronal	Staining is very strong in the VZ of the AVH & anterior ID & weak in the dorsal & ventral POAs. Staining is either absent or ubiquitous in the VZ of the dorsal thalamus, prethalamus, PVH, VMH & ARH nuclei, posterior ID, premam, mam & supramam zones & TT.
TS19: telencephalon mantle layer	Strong	Non-Uniform	Vax1-Shh E11.5_coronal	There is strong 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	Strong	Non-Uniform	Vax1-Shh E11.5_coronal	There is strong 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	Ambiguous		Vax1-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	Ambiguous		Vax1-Shh E12.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Vax1-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	Ambiguous		Vax1-Shh E12.5_coronal	Staining is either absent or ubiquitous in the mantle zone of the premam, mam and supramam zones and the TT.
TS20: diencephalon ventricular layer	Ambiguous		Vax1-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	Moderate	Non-Uniform	Vax1-Shh E12.5_coronal	There is moderate staining in the ventricular zone of the ganglionic eminences. Staining is either absent or ubiquitous in the mantle zone of the ganglionic eminences.
TS20: hypothalamus mantle layer	Very strong	Non-Uniform	Vax1-Shh E12.5_coronal	There is very strong staining in the mantle zone of the AVH and anterior ID. Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei and posterior ID.
TS20: hypothalamus ventricular layer	Very strong	Non-Uniform	Vax1-Shh E12.5_coronal	There is very strong staining in the VZ of the AVH and anterior ID, strong staining in the VMH and ARH nuclei and weak staining in the dorsal and ventral POAs. Staining is either absent or ubiquitous in the VZ of the PVH nucleus and posterior ID.
TS20: thalamus mantle layer	Ambiguous		Vax1-Shh E12.5_coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Ambiguous		Vax1-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		Vax1-Shh E14.5_coronal	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Ambiguous		Vax1-Shh E14.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Vax1-Shh E14.5_coronal	Staining is either absent or ubiquitous in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Ambiguous		Vax1-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	Vax1-Shh E14.5_coronal	There is weak 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 and the TT.
TS22: ganglionic eminence	Strong	Non-Uniform	Vax1-Shh E14.5_coronal	There is strong staining in the ventricular zone of the ganglionic eminences and moderate staining in the mantle zone of the ganglionic eminences.
TS22: hypothalamus mantle layer	Very strong	Non-Uniform	Vax1-Shh E14.5_coronal	There is very strong staining in the MZ of the anterior ID, moderate staining in the AVH & moderate, scattered staining in the VMH nucleus. Staining is either absent or ubiquitous in the MZ of dorsal & ventral POAs, the PVH & ARH nuclei & posterior ID.
TS22: hypothalamus ventricular layer	Very strong	Non-Uniform	Vax1-Shh E14.5_coronal	There is very strong staining in the VZ of the anterior ID, strong staining in the dorsal & ventral POAs & the AVH & moderate staining in the VMH nucleus. Staining is either absent or ubiquitous in the VZ of the PVH & ARH nuclei & the posterior ID.
TS22: thalamus mantle layer	Ambiguous		Vax1-Shh E14.5_coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS22: thalamus ventricular layer	Ambiguous		Vax1-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		Vax1-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		Vax1-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Vax1-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	Weak	Non-Uniform	Vax1-Shh E16.5_coronal	There is weak staining in the mantle zone of the premam zone. Staining is either absent or ubiquitous in the mantle zone of the mam and supramam zones.
TS24: diencephalon ventricular layer	Ambiguous		Vax1-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		Vax1-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS24: hypothalamus mantle layer	Strong	Non-Uniform	Vax1-Shh E16.5_coronal	There is strong staining in the MZ of the DAH and the SCH, DMH and VMH nuclei, strong, scattered staining in the AVH and weak staining in the dorsal POA. Staining is either absent or ubiquitous in the MZ of the ventral POA, PVH and ARH nuclei and the PH.
TS24: hypothalamus ventricular layer	Moderate	Non-Uniform	Vax1-Shh E16.5_coronal	There is moderate staining in the ventricular zone of the dorsal POA and the AVH and weak staining in the ventral POA. Staining is either absent or ubiquitous in the ventricular zone of the PVH, SCH, DMH, VMH and ARH nuclei, the DAH and the PH.
TS24: thalamus mantle layer	Ambiguous		Vax1-Shh E16.5_coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS24: thalamus ventricular layer	Ambiguous		Vax1-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.