Probe:	MGC clone 7686
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	Wifl-Shh E11.5	There is strong staining in the MZ of the prethalamus. Staining is either absent or ubiquitous in the MZ of the dorsal thalamus, dorsal & ventral POAs, the PVH, VMH & ARH nuclei, the AVH, anterior & posterior IDs, premam, mam & supramam zones & the TT.
TS19: diencephalon lateral wall ventricular layer	Ambiguous		Wifl-Shh E11.5	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	Very strong	Non-Uniform	Wifl-Shh E11.5	There is very strong 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	Very strong	Non-Uniform	Wifl-Shh E11.5	There is very strong staining in the ventricular zone of the cerebral cortex. Staining is either absent or ubiquitous in the ventricular zone of the ganglionic eminences.

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