Probe:	UI-M-BH0-akb-b-12-0-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		Gli3-Shh E11.5-sagittal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus, 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	Non-Uniform	Gli3-Shh E11.5-sagittal	Staining is strong in the VZ of premam zone & TT, moderate in dorsal thalamus & prethalamus, weak & scattered in dorsal & ventral POAs & PVH nucleus & either absent or ubiquitous in AVH, anterior & posterior IDs, VMH & ARH nuclei & mam & supramam zones.
TS19: telencephalon mantle layer	Ambiguous		Gli3-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	Very strong		Gli3-Shh E11.5-sagittal	There is very strong staining in the ventricular zone of the cerebral cortex and the ganglionic eminences.

Structure	Level	Pattern	Image	Note
TS20: cerebral cortex intermediate zone	Ambiguous		Gli3-Shh E12.5-coronal , Gli3-Shh E12.5-sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS20: cerebral cortex ventricular layer	Strong		Gli3-Shh E12.5-coronal , Gli3-Shh E12.5-sagittal	There is strong staining in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Gli3-Shh E12.5-sagittal , Gli3-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	Ambiguous		Gli3-Shh E12.5-sagittal , Gli3-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	Strong	Non-Uniform	Gli3-Shh E12.5-sagittal , Gli3-Shh E12.5-coronal	There is strong staining in the ventricular zone of the premam zone. Staining is either absent or ubiquitous in the ventricular zone of the mam and supramam zones and the TT.
TS20: ganglionic eminence	Strong	Non-Uniform	Gli3-Shh E12.5-sagittal , Gli3-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	Ambiguous		Gli3-Shh E12.5-sagittal , Gli3-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	Moderate	Non-Uniform	Gli3-Shh E12.5-sagittal , Gli3-Shh E12.5-coronal	There is moderate, scattered staining in the VZ of the dorsal and ventral POAs and the PVH nucleus and weak staining in the AVH. Staining is either absent or ubiquitous in the VZ of the anterior and posterior IDs and the VMH and ARH nuclei.
TS20: thalamus mantle layer	Ambiguous		Gli3-Shh E12.5-coronal , Gli3-Shh E12.5-sagittal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Moderate	Scattered	Gli3-Shh E12.5-sagittal , Gli3-Shh E12.5-coronal	There is moderate, scattered staining in the ventricular zone of the dorsal thalamus and prethalamus.

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Ambiguous		Gli3-Shh E14.5-sagittal , Gli3-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	Very strong		Gli3-Shh E14.5-sagittal , Gli3-Shh E14.5-coronal	There is very strong staining in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Gli3-Shh E14.5-coronal , Gli3-Shh E14.5-sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Ambiguous		Gli3-Shh E14.5-coronal , Gli3-Shh E14.5-sagittal	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	Non-Uniform	Gli3-Shh E14.5-coronal , Gli3-Shh E14.5-sagittal	There is strong staining in the ventricular zone of the premam zone. Staining is either absent or ubiquitous in the ventricular zone of the mam and supramam zones and the TT.
TS22: ganglionic eminence	Ambiguous		Gli3-Shh E14.5-coronal , Gli3-Shh E14.5-sagittal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS22: hypothalamus mantle layer	Ambiguous		Gli3-Shh E14.5-sagittal , Gli3-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	Weak	Non-Uniform	Gli3-Shh E14.5-sagittal , Gli3-Shh E14.5-coronal	There is weak staining in the ventricular zone of the dorsal POA. Staining is either absent or ubiquitous in the ventricular zone of the ventral POA, the PVH, VMH and ARH nuclei, the AVH and anterior and posterior IDs.
TS22: thalamus mantle layer	Strong	Non-Uniform	Gli3-Shh E14.5-coronal , Gli3-Shh E14.5-sagittal	There is strong 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	Moderate	Non-Uniform	Gli3-Shh E14.5-sagittal , Gli3-Shh E14.5-coronal	There is moderate staining in the ventricular zone of the prethalamus. Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Ambiguous		Gli3-Shh E16.5-coronal , Gli3-Shh E16.5-sagittal	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		Gli3-Shh E16.5-sagittal , Gli3-Shh E16.5-coronal	There is very strong staining in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Gli3-Shh E16.5-sagittal , Gli3-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		Gli3-Shh E16.5-coronal , Gli3-Shh E16.5-sagittal	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	Gli3-Shh E16.5-coronal , Gli3-Shh E16.5-sagittal	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 mam and supramam zones.
TS24: ganglionic eminence	Very strong	Non-Uniform	Gli3-Shh E16.5-sagittal , Gli3-Shh E16.5-coronal	There is very strong staining in the ventricular zone of the ganglionic eminences. Staining is either absent or ubiquitous in the mantle zone of the ganglionic eminences.
TS24: hypothalamus mantle layer	Ambiguous		Gli3-Shh E16.5-coronal , Gli3-Shh E16.5-sagittal	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	Moderate	Non-Uniform	Gli3-Shh E16.5-sagittal , Gli3-Shh E16.5-coronal	There is moderate staining in the VZ of the ARH nucleus and weak staining in the dorsal and ventral POAs, the PVH nucleus and the AVH. Staining is either absent or ubiquitous in the VZ of the DAH, the SCH, DMH and VMH nuclei and the PH.
TS24: thalamus mantle layer	Strong	Non-Uniform	Gli3-Shh E16.5-sagittal , Gli3-Shh E16.5-coronal	There is strong 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	Moderate	Non-Uniform	Gli3-Shh E16.5-coronal , Gli3-Shh E16.5-sagittal	There is moderate staining in the ventricular zone of the prethalamus. Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus.