Probe:	UI-M-BH3-asa-g-02-0-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	Nova1-Shh E11.5_coronal , Nova1-Shh E11.5_sagittal	Staining is strong in the MZ of the PVH nucleus, premam, mam & supramam zones & TT & moderate in posterior ID. Staining is either absent or ubiquitous in the MZ of dorsal thalamus, prethalamus, dorsal & ventral POAs, VMH & ARH nuclei, AVH & anterior ID.
TS19: diencephalon lateral wall ventricular layer	Ambiguous		Nova1-Shh E11.5_coronal , Nova1-Shh E11.5_sagittal	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	Strong	Non-Uniform	Nova1-Shh E11.5_coronal , Nova1-Shh E11.5_sagittal	There is strong staining in the mantle zone of the ganglionic eminences. Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone and cortical plate of the cerebral cortex
TS19: telencephalon ventricular layer	Ambiguous		Nova1-Shh E11.5_coronal , Nova1-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		Nova1-Shh E12.5_coronal , Nova1-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		Nova1-Shh E12.5_coronal , Nova1-Shh E12.5_sagittal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Nova1-Shh E12.5_sagittal , Nova1-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	Strong		Nova1-Shh E12.5_sagittal , Nova1-Shh E12.5_coronal	There is strong staining in the mantle zone of the premam, mam and supramam zones and the TT.
TS20: diencephalon ventricular layer	Ambiguous		Nova1-Shh E12.5_sagittal , Nova1-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	Moderate	Non-Uniform	Nova1-Shh E12.5_sagittal , Nova1-Shh E12.5_coronal	There is moderate 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	Very strong	Non-Uniform	Nova1-Shh E12.5_coronal , Nova1-Shh E12.5_sagittal	There is very strong staining in the mantle zone of the ventral POA and PVH nucleus and strong staining in the anterior and posterior IDs. Staining is either absent or ubiquitous in the mantle zone of the dorsal POA, the VMH and ARH nuclei and the AVH.
TS20: hypothalamus ventricular layer	Ambiguous		Nova1-Shh E12.5_coronal , Nova1-Shh E12.5_sagittal	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	Nova1-Shh E12.5_sagittal , Nova1-Shh E12.5_coronal	There is strong staining in the mantle zone of the prethalamus and moderate staining in the dorsal thalamus.
TS20: thalamus ventricular layer	Ambiguous		Nova1-Shh E12.5_sagittal , Nova1-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		Nova1-Shh E14.5_coronal , Nova1-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		Nova1-Shh E14.5_sagittal , Nova1-Shh E14.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Nova1-Shh E14.5_coronal , Nova1-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	Strong	Non-Uniform	Nova1-Shh E14.5_sagittal , Nova1-Shh E14.5_coronal	There is strong staining in the mantle zone of the mam and supramam zones and the TT and moderate staining in the premam zone.
TS22: diencephalon ventricular layer	Ambiguous		Nova1-Shh E14.5_coronal , Nova1-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	Moderate	Non-Uniform	Nova1-Shh E14.5_sagittal , Nova1-Shh E14.5_coronal	There is moderate 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	Nova1-Shh E14.5_sagittal , Nova1-Shh E14.5_coronal	There is strong staining in the MZ of the AVH and anterior and posterior IDs, moderate staining in the dorsal and ventral POAs and weak staining in the VMH nucleus. Staining is either absent or ubiquitous in the MZ of the PVH and ARH nuclei.
TS22: hypothalamus ventricular layer	Moderate	Non-Uniform	Nova1-Shh E14.5_sagittal , Nova1-Shh E14.5_coronal	There is moderate staining in the ventricular zone of the AVH. Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei and anterior and posterior IDs.
TS22: thalamus mantle layer	Strong	Non-Uniform	Nova1-Shh E14.5_coronal , Nova1-Shh E14.5_sagittal	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.
TS22: thalamus ventricular layer	Moderate		Nova1-Shh E14.5_sagittal , Nova1-Shh E14.5_coronal	There is moderate staining in the ventricular zone of the dorsal thalamus and prethalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Ambiguous		Nova1-Shh E16.5_coronal , Nova1-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		Nova1-Shh E16.5_sagittal , Nova1-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Nova1-Shh E16.5_sagittal , Nova1-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	Strong		Nova1-Shh E16.5_coronal , Nova1-Shh E16.5_sagittal	There is strong staining in the mantle zone of the premam zone.
TS24: diencephalon ventricular layer	Ambiguous		Nova1-Shh E16.5_sagittal , Nova1-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam zone.
TS24: ganglionic eminence	Weak	Non-Uniform	Nova1-Shh E16.5_sagittal , Nova1-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	Strong	Non-Uniform	Nova1-Shh E16.5_coronal , Nova1-Shh E16.5_sagittal	There is strong staining in the MZ of the AVH, the DAH, the DMH, VMH and ARH nuclei and the PH and moderate staining in the dorsal and ventral POAs and the PVH nucleus. Staining is either absent or ubiquitous in the MZ of the SCH nucleus.
TS24: hypothalamus ventricular layer	Ambiguous		Nova1-Shh E16.5_sagittal , Nova1-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	Strong	Non-Uniform	Nova1-Shh E16.5_sagittal , Nova1-Shh E16.5_coronal	There is strong staining in the mantle zone of the prethalamus and moderate staining in the dorsal thalamus.
TS24: thalamus ventricular layer	Moderate	Non-Uniform	Nova1-Shh E16.5_coronal , Nova1-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.