Probe:	UI-M-AO1-aem-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	Weak	Non-Uniform	Ltbp1-Shh E11.5-coronal	There is weak staining in the mantle zone of the dorsal thalamus and prethalamus. Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH nucleus, the AVH and anterior and posterior IDs.
TS19: diencephalon lateral wall ventricular layer	Ambiguous		Ltbp1-Shh E11.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus, prethalamus, dorsal and ventral POAs, PVH nucleus, the AVH and anterior and posterior IDs.
TS19: telencephalon mantle layer	Ambiguous		Ltbp1-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	Weak	Non-Uniform	Ltbp1-Shh E11.5-coronal	There is weak staining in the ventricular zone of the ganglionic eminences. Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.

Structure	Level	Pattern	Image	Note
TS20: cerebral cortex intermediate zone	Moderate		Ltbp1-Shh E12.5-coronal	There is moderate staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS20: cerebral cortex ventricular layer	Moderate		Ltbp1-Shh E12.5-coronal	There is moderate staining in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Moderate		Ltbp1-Shh E12.5-coronal	There is moderate staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS20: diencephalon mantle layer	Ambiguous		Ltbp1-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		Ltbp1-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		Ltbp1-Shh E12.5-coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS20: hypothalamus mantle layer	Ambiguous		Ltbp1-Shh E12.5-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.
TS20: hypothalamus ventricular layer	Ambiguous		Ltbp1-Shh E12.5-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.
TS20: thalamus mantle layer	Strong	Non-Uniform	Ltbp1-Shh E12.5-coronal	There is strong 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		Ltbp1-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	Moderate	Scattered	Ltbp1-Shh E14.5-coronal	There is moderate, scattered staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Very strong		Ltbp1-Shh E14.5-coronal	There is very strong staining in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Moderate	Scattered	Ltbp1-Shh E14.5-coronal	There is moderate, scattered staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Ambiguous		Ltbp1-Shh E14.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the premam zone and the TT.
TS22: diencephalon ventricular layer	Very strong	Non-Uniform	Ltbp1-Shh E14.5-coronal	There is very strong staining in the ventricular zone of the premam zone. Staining is either absent or ubiquitous in the ventricular zone of the TT.
TS22: ganglionic eminence	Strong	Non-Uniform	Ltbp1-Shh E14.5-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.
TS22: hypothalamus mantle layer	Ambiguous		Ltbp1-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	Very strong	Non-Uniform	Ltbp1-Shh E14.5-coronal	There is very strong staining in the ventricular zone of the PVH, VMH and ARH nuclei and the AVH and strong staining in the dorsal POA. Staining is either absent or ubiquitous in the ventricular zone of the ventral POA and anterior and posterior IDs.
TS22: thalamus mantle layer	Moderate	Non-Uniform	Ltbp1-Shh E14.5-coronal	There is moderate staining in the mantle zone of the prethalamus. Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus.
TS22: thalamus ventricular layer	Ambiguous		Ltbp1-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		Ltbp1-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	Very strong		Ltbp1-Shh E16.5-coronal	There is very strong staining in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Ltbp1-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	Ambiguous		Ltbp1-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	Very strong	Non-Uniform	Ltbp1-Shh E16.5-coronal	There is very strong staining in the ventricular zone of the premam and mam zones. Staining is either absent or ubiquitous in the ventricular zone of the supramam zone.
TS24: ganglionic eminence	Ambiguous		Ltbp1-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS24: hypothalamus mantle layer	Ambiguous		Ltbp1-Shh E16.5-coronal	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	Ltbp1-Shh E16.5-coronal	There is very strong staining in the VZ of the PVH, DMH, VMH and ARH nuclei, the AVH, the DAH and the PH and moderate staining in the dorsal and ventral POAs. Staining is either absent or ubiquitous in the VZ of the SCH nucleus.
TS24: thalamus mantle layer	Ambiguous		Ltbp1-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		Ltbp1-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.