Probe:	UI-M-AQ1-aec-a-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	Cspg3-Shh E11.5-coronal	There is moderate staining in the MZ of the dorsal thalamus, prethalamus, dorsal & ventral POAs, posterior ID, mam & supramam zones & TT. Staining is either absent or ubiquitous in the MZ of the PVH, VMH & ARH nuclei, the AVH, anterior ID & premam zone.
TS19: diencephalon lateral wall ventricular layer	Ambiguous		Cspg3-Shh E11.5-coronal	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	Cspg3-Shh E11.5-coronal	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	Ambiguous		Cspg3-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	Ambiguous		Cspg3-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		Cspg3-Shh E12.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Cspg3-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	Strong		Cspg3-Shh E12.5-coronal	There is strong staining in the mantle zone of the premam, mam and supramam zones and the TT.
TS20: diencephalon ventricular layer	Ambiguous		Cspg3-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	Strong	Non-Uniform	Cspg3-Shh E12.5-coronal	There is strong 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	Strong	Non-Uniform	Cspg3-Shh E12.5-coronal	There is strong staining in the mantle zone of the dorsal and ventral POAs, the PVH nucleus, the anterior and posterior IDs and the VMH nucleus. Staining is either absent or ubiquitous in the mantle zone of the AVH and the ARH nucleus.
TS20: hypothalamus ventricular layer	Strong	Non-Uniform	Cspg3-Shh E12.5-coronal	There is strong staining in the ventricular zone of the posterior ID. 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 ID.
TS20: thalamus mantle layer	Strong	Non-Uniform	Cspg3-Shh E12.5-coronal	There is strong staining in the mantle zone of the dorsal thalamus and moderate staining in the prethalamus.
TS20: thalamus ventricular layer	Ambiguous		Cspg3-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		Cspg3-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		Cspg3-Shh E14.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Cspg3-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		Cspg3-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	Ambiguous		Cspg3-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		Cspg3-Shh E14.5-coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS22: hypothalamus mantle layer	Ambiguous		Cspg3-Shh E14.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei, the AVH and anterior and posterior IDs.
TS22: hypothalamus ventricular layer	Moderate	Non-Uniform	Cspg3-Shh E14.5-coronal	There is moderate staining in the ventricular zone of the PVH nucleus and weak staining in the anterior and posterior IDs. Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the AVH and the VMH and ARH nuclei.
TS22: thalamus mantle layer	Ambiguous		Cspg3-Shh E14.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS22: thalamus ventricular layer	Moderate	Non-Uniform	Cspg3-Shh E14.5-coronal	There is moderate 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
TS24: cerebral cortex intermediate zone	Weak		Cspg3-Shh E16.5-coronal	There is weak staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Ambiguous		Cspg3-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Weak		Cspg3-Shh E16.5-coronal	There is weak staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Ambiguous		Cspg3-Shh E16.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the premam zone.
TS24: diencephalon ventricular layer	Very strong		Cspg3-Shh E16.5-coronal	There is very strong staining in the ventricular zone of the premam zone.
TS24: ganglionic eminence	Weak	Non-Uniform	Cspg3-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	Cspg3-Shh E16.5-coronal	There is moderate staining in the mantle zone of the VMH nucleus. 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	Very strong	Non-Uniform	Cspg3-Shh E16.5-coronal	There is very strong staining in the ventricular zone of the dorsal and ventral POAs, the PVH, DMH and VMH nuclei, the AVH, the DAH and the PH. Staining is either absent or ubiquitous in the ventricular zone of the SCH and ARH nuclei.
TS24: thalamus mantle layer	Weak	Non-Uniform	Cspg3-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	Very strong	Non-Uniform	Cspg3-Shh E16.5-coronal	There is very strong staining in the ventricular zone of the prethalamus and strong staining the dorsal thalamus.