Probe:	UI-M-BH1-akz-e-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	Ambiguous		0610007R22Rik-Shh E11.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus, the prethalamus, the PVH, VMH and ARH nuclei, the AVH, the anterior and posterior IDs, the premam, mam and supramam zones and the tubermammilary terminal.
TS19: diencephalon lateral wall ventricular layer	Ambiguous		0610007R22Rik-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	Ambiguous		0610007R22Rik-Shh E11.5-coronal	Staining is either absent or ubiquitous in the intermediate zone and cortical plate of the cerebral cortex and in the mantle zone of the ganglionic eminences.
TS19: telencephalon ventricular layer	Ambiguous		0610007R22Rik-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		0610007R22Rik-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		0610007R22Rik-Shh E12.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		0610007R22Rik-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	0610007R22Rik-Shh E12.5-coronal	There is weak staining in the mantle zone of the premam and supramam zones. Staining is either absent or ubiquitous in the mantle zone of the TT and the mam zone.
TS20: diencephalon ventricular layer	Ambiguous		0610007R22Rik-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	Ambiguous		0610007R22Rik-Shh E12.5-coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS20: hypothalamus mantle layer	Strong	Non-Uniform	0610007R22Rik-Shh E12.5-coronal	There is strong staining in the mantle zone of the ventral POA, the PVH nucleus and the anterior and posterior IDs. Staining is either absent or ubiquitous in the dorsal POA, the VMH and ARH nuclei and the AVH.
TS20: hypothalamus ventricular layer	Ambiguous		0610007R22Rik-Shh E12.5-coronal	Staining is either absent or ubquitous 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	Weak	Non-Uniform	0610007R22Rik-Shh E12.5-coronal	There is weak staining in the mantle zone of the prethalamus. Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus.
TS20: thalamus ventricular layer	Ambiguous		0610007R22Rik-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		0610007R22Rik-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		0610007R22Rik-Shh E14.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		0610007R22Rik-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	Strong	Non-Uniform	0610007R22Rik-Shh E14.5-coronal	There is strong staining in the premam and mam zones and the TT and weak staining in the supramam zone.
TS22: diencephalon ventricular layer	Ambiguous		0610007R22Rik-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		0610007R22Rik-Shh E14.5-coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS22: hypothalamus mantle layer	Moderate	Non-Uniform	0610007R22Rik-Shh E14.5-coronal	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 anterior and posterior IDs.
TS22: hypothalamus ventricular layer	Ambiguous		0610007R22Rik-Shh E14.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH, VMH, ARH nuclei, the AVH, the anterior and posterior IDs.
TS22: thalamus mantle layer	Ambiguous		0610007R22Rik-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		0610007R22Rik-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		0610007R22Rik-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		0610007R22Rik-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		0610007R22Rik-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	Very strong		0610007R22Rik-Shh E16.5-coronal	There is very strong staining in the mantle zone of the premam, mam and supramam zones.
TS24: diencephalon ventricular layer	Ambiguous		0610007R22Rik-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam , mam and supramammillar zones.
TS24: ganglionic eminence	Ambiguous		0610007R22Rik-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS24: hypothalamus mantle layer	Very strong	Non-Uniform	0610007R22Rik-Shh E16.5-coronal	There is very strong staining in the mantle zone of the dorsal and ventral POAs, the PVH, SCH, DMH, VMH and ARH nuclei and the PH. Staining is either absent or ubiquitous in the mantle zone of the AVH and the DAH.
TS24: hypothalamus ventricular layer	Very strong	Non-Uniform	0610007R22Rik-Shh E16.5-coronal	There is very strong staining in the ventricular zone of the DAH. Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH, SCH, DMH, VMH and ARH nuclei and the AVH and the PH.
TS24: thalamus mantle layer	Ambiguous		0610007R22Rik-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		0610007R22Rik-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.