Probe:	UI-M-CC1-bac-f-09-0-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		4921524J17Rik-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	Moderate	Scattered	4921524J17Rik-Shh E11.5-coronal	There is moderate, scattered 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 and premam, mam and supramam zones and the TT.
TS19: telencephalon mantle layer	Ambiguous		4921524J17Rik-Shh E11.5-coronal	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	Moderate	Scattered	4921524J17Rik-Shh E11.5-coronal	There is moderate, scattered staining in the ventricular zone of the cerebral cortex and the ganglionic eminences.

Structure	Level	Pattern	Image	Note
TS20: cerebral cortex intermediate zone	Weak		4921524J17Rik-Shh E12.5-coronal	There is weak staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS20: cerebral cortex ventricular layer	Weak		4921524J17Rik-Shh E12.5-coronal	There is weak staining in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Weak		4921524J17Rik-Shh E12.5-coronal	There is weak staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS20: diencephalon mantle layer	Ambiguous		4921524J17Rik-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		4921524J17Rik-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	Weak	Non-Uniform	4921524J17Rik-Shh E12.5-coronal	There is weak 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	Weak	Non-Uniform	4921524J17Rik-Shh E12.5-coronal	There is weak staining in the mantle zone of the dorsal and ventral POAs. Staining is either absent or ubiquitous in the mantle zone of the PVH, VMH and ARH nuclei, the AVH and anterior and posterior IDs.
TS20: hypothalamus ventricular layer	Weak	Non-Uniform	4921524J17Rik-Shh E12.5-coronal	There is weak staining in the ventricular zone of the dorsal and ventral POAs, the PVH nucleus, the AVH and anterior and posterior IDs. Staining is either absent or ubiquitous in the ventricular zone of the VMH and ARH nuclei.
TS20: thalamus mantle layer	Ambiguous		4921524J17Rik-Shh E12.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Weak		4921524J17Rik-Shh E12.5-coronal	There is weak staining in the ventricular zone of the dorsal thalamus and prethalamus.

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Strong		4921524J17Rik-Shh E14.5-coronal	There is strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Ambiguous		4921524J17Rik-Shh E14.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Strong		4921524J17Rik-Shh E14.5-coronal	There is strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Ambiguous		4921524J17Rik-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		4921524J17Rik-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	Weak	Non-Uniform	4921524J17Rik-Shh E14.5-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.
TS22: hypothalamus mantle layer	Weak	Non-Uniform	4921524J17Rik-Shh E14.5-coronal	There is weak staining in the mantle zone of the dorsal and ventral POAs and the AVH. Staining is either absent or ubiquitous in the mantle zone of the PVH, VMH and ARH nuclei and the anterior and posterior IDs.
TS22: hypothalamus ventricular layer	Ambiguous		4921524J17Rik-Shh E14.5-coronal	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	Weak	Non-Uniform	4921524J17Rik-Shh E14.5-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.
TS22: thalamus ventricular layer	Ambiguous		4921524J17Rik-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	Strong		4921524J17Rik-Shh E16.5-coronal	There is strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Ambiguous		4921524J17Rik-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Strong		4921524J17Rik-Shh E16.5-coronal	There is strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Ambiguous		4921524J17Rik-Shh E16.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the premam , mam and supramam zones.
TS24: diencephalon ventricular layer	Ambiguous		4921524J17Rik-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS24: ganglionic eminence	Weak	Non-Uniform	4921524J17Rik-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	Weak	Non-Uniform	4921524J17Rik-Shh E16.5-coronal	There is weak staining in the mantle zone of the DMH nucleus. Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH, SCH, VMH and ARH nuclei, the AVH, the DAH and the PH.
TS24: hypothalamus ventricular layer	Ambiguous		4921524J17Rik-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	Weak	Non-Uniform	4921524J17Rik-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	Ambiguous		4921524J17Rik-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.