Probe:	UI-M-AH1-agv-f-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	Ambiguous		Catnb-SHH E11.5-sagittal , Catnb-Shh E11.5-coronal	Staining is either absent or ubiquitous in the mantle 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: diencephalon lateral wall ventricular layer	Strong		Catnb-SHH E11.5-sagittal , Catnb-Shh E11.5-coronal	There is strong staining 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	Ambiguous		Catnb-Shh E11.5-coronal , Catnb-SHH E11.5-sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone and cortical plate of the cerebral cortex and in the mantle zone of the ganglionic eminences.
TS19: telencephalon ventricular layer	Strong	Non-Uniform	Catnb-Shh E11.5-coronal , Catnb-SHH E11.5-sagittal	There is strong staining in the ventricular zone of the ganglionic eminences and weak staining in the ventricular zone of the cerebral cortex.

Structure	Level	Pattern	Image	Note
TS20: cerebral cortex intermediate zone	Ambiguous		Catnb-SHH E12.5-sagittal , Catnb-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	Strong		Catnb-Shh E12.5-coronal , Catnb-SHH E12.5-sagittal	There is strong staining in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Catnb-SHH E12.5-sagittal , Catnb-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	Weak	Non-Uniform	Catnb-SHH E12.5-sagittal , Catnb-Shh E12.5-coronal	There is weak staining in the mantle zone of the supramam zone. Staining is either absent or ubiquitous in the mantle zone of the premam and mam zones and the TT.
TS20: diencephalon ventricular layer	Weak	Non-Uniform	Catnb-Shh E12.5-coronal , Catnb-SHH E12.5-sagittal	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.
TS20: ganglionic eminence	Strong	Non-Uniform	Catnb-SHH E12.5-sagittal , Catnb-Shh E12.5-coronal	There is strong 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	Strong	Non-Uniform	Catnb-SHH E12.5-sagittal , Catnb-Shh E12.5-coronal	There is strong staining in the mantle zone of the AVH. Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei and the anterior and posterior IDs.
TS20: hypothalamus ventricular layer	Strong	Non-Uniform	Catnb-Shh E12.5-coronal , Catnb-SHH E12.5-sagittal	There is strong staining in the VZ of the dorsal and ventral POAs, the PVH nucleus, the AVH and anterior ID and weaking staining in the posterior ID and the ARH nucleus. Staining is either absent or ubiquitous in the VZ of the VMH nucleus.
TS20: thalamus mantle layer	Ambiguous		Catnb-SHH E12.5-sagittal , Catnb-Shh E12.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Strong		Catnb-Shh E12.5-coronal , Catnb-SHH E12.5-sagittal	There is strong staining in the ventricular zone of the dorsal thalamus and prethalamus.

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

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