Probe:	UI-M-AL1-ahn-c-08-0-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	Moderate	Non-Uniform	Sema6a-Shh E11.5_sagittal , Sema6a-Shh E11.5_coronal , Sema6a-Shh-E11.5_sagittal-2	Staining is moderate in the MZ of prethalamus & AVH & weak in dorsal & ventral POAs, PVH nucleus, anterior & posterior IDs, premam zone & TT. Staining is either absent or ubiquitous in the MZ of dorsal thalamus, VMH & ARH nuclei & mam & supramam zones.
TS19: diencephalon lateral wall ventricular layer	Strong	Non-Uniform	Sema6a-Shh E11.5_coronal , Sema6a-Shh-E11.5_sagittal-2 , Sema6a-Shh E11.5_sagittal	Staining is strong in the VZ of posterior ID, moderate in the prethalamus, weak in the dorsal & ventral POAs, PVH nucleus, AVH & anterior ID & either absent or ubiquitous in the dorsal thalamus, VMH & ARH nuclei, premam, mam & supramam zones & TT.
TS19: telencephalon mantle layer	Moderate	Non-Uniform	Sema6a-Shh E11.5_sagittal , Sema6a-Shh-E11.5_sagittal-2 , Sema6a-Shh E11.5_coronal	There is moderate 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	Moderate		Sema6a-Shh-E11.5_sagittal-2 , Sema6a-Shh E11.5_coronal , Sema6a-Shh E11.5_sagittal	There is moderate staining in the ventricular zone of the cerebral cortex and the ganglionic eminences.

Structure	Level	Pattern	Image	Note
TS20: cerebral cortex intermediate zone	Ambiguous		Sema6a-Shh E12.5_coronal , Sema6a-Shh E12.5_sagittal , Sema6a-Shh-E12.5_sagittal-2	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS20: cerebral cortex ventricular layer	Moderate		Sema6a-Shh-E12.5_sagittal-2 , Sema6a-Shh E12.5_coronal , Sema6a-Shh E12.5_sagittal	There is moderate staining in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Sema6a-Shh E12.5_sagittal , Sema6a-Shh-E12.5_sagittal-2 , Sema6a-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	Non-Uniform	Sema6a-Shh E12.5_sagittal , Sema6a-Shh E12.5_coronal , Sema6a-Shh-E12.5_sagittal-2	There is strong staining in the mantle zone of the TT and moderate staining in the premam zone. Staining is either absent or ubiquitous in the mantle zone of the mam and supramam zones.
TS20: diencephalon ventricular layer	Ambiguous		Sema6a-Shh E12.5_sagittal , Sema6a-Shh E12.5_coronal , Sema6a-Shh-E12.5_sagittal-2	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	Sema6a-Shh-E12.5_sagittal-2 , Sema6a-Shh E12.5_sagittal , Sema6a-Shh E12.5_coronal	There is moderate 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	Strong	Non-Uniform	Sema6a-Shh E12.5_coronal , Sema6a-Shh-E12.5_sagittal-2 , Sema6a-Shh E12.5_sagittal	There is strong staining in the mantle zone of the PVH nucleus and the AVH and moderate staining in the anterior and posterior IDs and VMH nucleus. Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs and ARH nucleus.
TS20: hypothalamus ventricular layer	Moderate	Non-Uniform	Sema6a-Shh-E12.5_sagittal-2 , Sema6a-Shh E12.5_coronal , Sema6a-Shh E12.5_sagittal	There is moderate staining in the ventricular zone of the dorsal and ventral POAs, the PVH nucleus, the AVH and anterior and posterior IDs. Staining is either absent or ubiquitous in the ventricular zone of the VMH and ARH nuclei.
TS20: thalamus mantle layer	Strong	Non-Uniform	Sema6a-Shh E12.5_coronal , Sema6a-Shh-E12.5_sagittal-2 , Sema6a-Shh E12.5_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.
TS20: thalamus ventricular layer	Moderate		Sema6a-Shh-E12.5_sagittal-2 , Sema6a-Shh E12.5_coronal , Sema6a-Shh E12.5_sagittal	There is moderate staining in the ventricular zone of the dorsal thalamus and prethalamus.

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Moderate		Sema6a-Shh E14.5_sagittal , Sema6a-Shh E14.5_coronal , Sema6a-Shh-E14.5_sagittal-2	There is moderate staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Ambiguous		Sema6a-Shh E14.5_sagittal , Sema6a-Shh E14.5_coronal , Sema6a-Shh-E14.5_sagittal-2	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Moderate		Sema6a-Shh-E14.5_sagittal-2 , Sema6a-Shh E14.5_sagittal , Sema6a-Shh E14.5_coronal	There is moderate staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Ambiguous		Sema6a-Shh E14.5_coronal , Sema6a-Shh-E14.5_sagittal-2 , Sema6a-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	Sema6a-Shh-E14.5_sagittal-2 , Sema6a-Shh E14.5_sagittal , Sema6a-Shh E14.5_coronal	There is strong staining in the ventricular zone of the TT. Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS22: ganglionic eminence	Weak	Non-Uniform	Sema6a-Shh E14.5_coronal , Sema6a-Shh E14.5_sagittal , Sema6a-Shh-E14.5_sagittal-2	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	Sema6a-Shh-E14.5_sagittal-2 , Sema6a-Shh E14.5_sagittal , Sema6a-Shh E14.5_coronal	There is strong staining in the MZ of the PVH and VMH nuclei, moderate staining in the AVH and ARH nucleus and weak staining in the dorsal and ventral POAs. Staining is either absent or ubiquitous in the MZ of the anterior and posterior IDs.
TS22: hypothalamus ventricular layer	Strong	Non-Uniform	Sema6a-Shh-E14.5_sagittal-2 , Sema6a-Shh E14.5_sagittal , Sema6a-Shh E14.5_coronal	There is strong staining in the VZ of the dorsal POA, PVH nucleus and anterior and posterior IDs and moderate staining in the ventral POA, the AVH and the VMH nucleus. Staining is either absent or ubiquitous in the VZ of the ARH nucleus.
TS22: thalamus mantle layer	Strong	Non-Uniform	Sema6a-Shh E14.5_sagittal , Sema6a-Shh E14.5_coronal , Sema6a-Shh-E14.5_sagittal-2	There is strong staining in the mantle zone of the dorsal thalamus and moderate staining in the prethalamus.
TS22: thalamus ventricular layer	Strong	Non-Uniform	Sema6a-Shh E14.5_sagittal , Sema6a-Shh E14.5_coronal , Sema6a-Shh-E14.5_sagittal-2	There is strong staining in the ventricular zone of the dorsal thalamus. Staining is either absent or ubiquitous in the ventricular zone of the prethalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Ambiguous		Sema6a-Shh E16.5_coronal , Sema6a-Shh-E16.5_sagittal-2 , Sema6a-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	Strong		Sema6a-Shh E16.5_coronal , Sema6a-Shh-E16.5_sagittal-2 , Sema6a-Shh E16.5_sagittal	There is strong staining in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Sema6a-Shh-E16.5_sagittal-2 , Sema6a-Shh E16.5_coronal , Sema6a-Shh E16.5_sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Weak	Non-Uniform	Sema6a-Shh-E16.5_sagittal-2 , Sema6a-Shh E16.5_sagittal , Sema6a-Shh E16.5_coronal	There is weak staining in the mantle zone of the premam and mam zones. Staining is either absent or ubiquitous in the mantle zone of the supramam zone.
TS24: diencephalon ventricular layer	Strong	Non-Uniform	Sema6a-Shh E16.5_sagittal , Sema6a-Shh-E16.5_sagittal-2 , Sema6a-Shh E16.5_coronal	There is 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	Weak	Non-Uniform	Sema6a-Shh E16.5_coronal , Sema6a-Shh-E16.5_sagittal-2 , Sema6a-Shh E16.5_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.
TS24: hypothalamus mantle layer	Moderate	Non-Uniform	Sema6a-Shh E16.5_sagittal , Sema6a-Shh E16.5_coronal , Sema6a-Shh-E16.5_sagittal-2	There is moderate staining in the MZ of the dorsal POA and the PVH nucleus and weak staining in the ventral POA, the AVH, the DAH, the DMH and VMH nuclei and the PH. Staining is either absent or ubiquitous in the MZ of the SCH and ARH nuclei.
TS24: hypothalamus ventricular layer	Strong	Non-Uniform	Sema6a-Shh-E16.5_sagittal-2 , Sema6a-Shh E16.5_sagittal , Sema6a-Shh E16.5_coronal	There is strong staining in the ventricular zone of the PVH, DMH and VMH nuclei, the AVH, the DAH and the PH. Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs and the SCH and ARH nuclei.
TS24: thalamus mantle layer	Moderate		Sema6a-Shh E16.5_sagittal , Sema6a-Shh E16.5_coronal , Sema6a-Shh-E16.5_sagittal-2	There is moderate staining in the mantle zone of the dorsal thalamus and prethalamus.
TS24: thalamus ventricular layer	Strong	Non-Uniform	Sema6a-Shh-E16.5_sagittal-2 , Sema6a-Shh E16.5_sagittal , Sema6a-Shh E16.5_coronal	There is strong staining in the ventricular zone of the prethalamus. Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus.