Probe:	UI-M-CG0p-bqm-d-06-0-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	Strong	Non-Uniform	Zic3-Shh E11.5_sagittal , Zic3-Shh E11.5_coronal	Staining is strong in the MZ of the dorsal thalamus, prethalamus & ventral POA & moderate in the dorsal POA & AVH. Staining is either absent or ubiquitous in the MZ of the PVH, VMH & ARH nuclei, anterior & posterior IDs, premam, mam & supramam zones & TT.
TS19: diencephalon lateral wall ventricular layer	Strong	Non-Uniform	Zic3-Shh E11.5_coronal , Zic3-Shh E11.5_sagittal	Staining is strong in the VZ of the dorsal thalamus & moderate in the prethalamus, dorsal & ventral POAs & AVH. Staining is either absent or ubiquitous in the VZ of the PVH, VMH & ARH nuclei, anterior & posterior IDs, premam, mam & supramam zones & TT.
TS19: telencephalon mantle layer	Ambiguous		Zic3-Shh E11.5_sagittal , Zic3-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	Ambiguous		Zic3-Shh E11.5_coronal , Zic3-Shh E11.5_sagittal	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		Zic3-Shh E12.5_coronal , Zic3-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	Ambiguous		Zic3-Shh E12.5_coronal , Zic3-Shh E12.5_sagittal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Zic3-Shh E12.5_coronal , Zic3-Shh E12.5_sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS20: diencephalon mantle layer	Ambiguous		Zic3-Shh E12.5_sagittal , Zic3-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		Zic3-Shh E12.5_coronal , Zic3-Shh E12.5_sagittal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones and the TT.
TS20: ganglionic eminence	Strong	Non-Uniform	Zic3-Shh E12.5_coronal , Zic3-Shh E12.5_sagittal	There is strong staining in the mantle zone of the ganglionic eminences. Staining is either absent or ubiquitous in the ventricular zone of the ganglionic eminences.
TS20: hypothalamus mantle layer	Ambiguous		Zic3-Shh E12.5_coronal , Zic3-Shh E12.5_sagittal	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	Strong	Non-Uniform	Zic3-Shh E12.5_sagittal , Zic3-Shh E12.5_coronal	There is strong staining in the ventricular zone of the dorsal and ventral POAs and the AVH. Staining is either absent or ubiquitous in the ventricular zone of the PVH, VMH and ARH nuclei and anterior and posterior IDs.
TS20: thalamus mantle layer	Strong		Zic3-Shh E12.5_coronal , Zic3-Shh E12.5_sagittal	There is strong staining in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Strong	Non-Uniform	Zic3-Shh E12.5_sagittal , Zic3-Shh E12.5_coronal	There is strong staining in the ventricular zone of the dorsal thalamus and moderate staining in the prethalamus.

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Ambiguous		Zic3-Shh E14.5_coronal , Zic3-Shh E14.5_sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Ambiguous		Zic3-Shh E14.5_coronal , Zic3-Shh E14.5_sagittal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Zic3-Shh E14.5_coronal , Zic3-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		Zic3-Shh E14.5_coronal , Zic3-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	Ambiguous		Zic3-Shh E14.5_coronal , Zic3-Shh E14.5_sagittal	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	Zic3-Shh E14.5_coronal , Zic3-Shh E14.5_sagittal	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	Strong	Non-Uniform	Zic3-Shh E14.5_coronal , Zic3-Shh E14.5_sagittal	There is strong staining in the mantle zone of the dorsal POA and the AVH. Staining is either absent or ubiquitous in the mantle zone of the ventral POA, the PVH, VMH and ARH nuclei and anterior and posterior IDs.
TS22: hypothalamus ventricular layer	Strong	Non-Uniform	Zic3-Shh E14.5_coronal , Zic3-Shh E14.5_sagittal	There is strong staining in the ventricular zone of the AVH and weak staining in the ventral POA. Staining is either absent or ubiquitous in the mantle zone of the ventral POA, the PVH, VMH and ARH nuclei and anterior and posterior IDs.
TS22: thalamus mantle layer	Strong	Non-Uniform	Zic3-Shh E14.5_sagittal , Zic3-Shh E14.5_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.
TS22: thalamus ventricular layer	Very strong	Non-Uniform	Zic3-Shh E14.5_coronal , Zic3-Shh E14.5_sagittal	There is very strong staining in the ventricular zone of the dorsal thalamus and moderate staining in the prethalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Ambiguous		Zic3-Shh E16.5_coronal , Zic3-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	Ambiguous		Zic3-Shh E16.5_sagittal , Zic3-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Zic3-Shh E16.5_sagittal , Zic3-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		Zic3-Shh E16.5_sagittal , Zic3-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		Zic3-Shh E16.5_coronal , Zic3-Shh E16.5_sagittal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS24: ganglionic eminence	Ambiguous		Zic3-Shh E16.5_sagittal , Zic3-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		Zic3-Shh E16.5_sagittal , Zic3-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	Ambiguous		Zic3-Shh E16.5_coronal , Zic3-Shh E16.5_sagittal	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	Ambiguous		Zic3-Shh E16.5_coronal , Zic3-Shh E16.5_sagittal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS24: thalamus ventricular layer	Ambiguous		Zic3-Shh E16.5_sagittal , Zic3-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.