Probe:	UI-M-AN1-aff-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	Sez6-Shh E11.5_coronal , Sez6-Shh E11.5_sagittal	There is strong staining in the MZ of the dorsal thalamus, prethalamus, dorsal & ventral POAs, the PVH nucleus, the AVH, posterior ID, premam, mam & supramam zones & TT. Staining is either absent or ubiquitous in the MZ of anterior ID & VMH & ARH nuclei.
TS19: diencephalon lateral wall ventricular layer	Strong	Non-Uniform	Sez6-Shh E11.5_coronal , Sez6-Shh E11.5_sagittal	There is strong staining in the VZ of the dorsal POA. Staining is either absent or ubiquitous in the VZ of the dorsal thalamus, the prethalamus, ventral POA, the PVH, VMH & ARH nuclei, the AVH, anterior & posterior IDs, premam, mam & supramam zones & TT.
TS19: telencephalon mantle layer	Strong	Non-Uniform	Sez6-Shh E11.5_sagittal , Sez6-Shh E11.5_coronal	There is strong staining in the mantle zone of the ganglionic eminences and moderate staining in the postmitotic neurons in the intermediate zone and cortical plate of the cerebral cortex.
TS19: telencephalon ventricular layer	Ambiguous		Sez6-Shh E11.5_sagittal , Sez6-Shh E11.5_coronal	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	Strong		Sez6-Shh E12.5_sagittal , Sez6-Shh E12.5_coronal	There is strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS20: cerebral cortex ventricular layer	Ambiguous		Sez6-Shh E12.5_coronal , Sez6-Shh E12.5_sagittal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Strong		Sez6-Shh E12.5_coronal , Sez6-Shh E12.5_sagittal	There is strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS20: diencephalon mantle layer	Strong	Non-Uniform	Sez6-Shh E12.5_coronal , Sez6-Shh E12.5_sagittal	There is strong staining in the mantle zone of the premam zone and the TT and moderate staining in the supramam zone. Staining is either absent or ubiquitous in the mantle zone of the mam zone.
TS20: diencephalon ventricular layer	Ambiguous		Sez6-Shh E12.5_sagittal , Sez6-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	Sez6-Shh E12.5_sagittal , Sez6-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	Strong	Non-Uniform	Sez6-Shh E12.5_coronal , Sez6-Shh E12.5_sagittal	There is strong staining in the mantle zone of the dorsal POA, PVH nucleus, the AVH and posterior ID and weak staining in the anterior ID. Staining is either absent or ubiquitous in the mantle zone of the ventral POA and VMH and ARH nuclei.
TS20: hypothalamus ventricular layer	Strong	Non-Uniform	Sez6-Shh E12.5_sagittal , Sez6-Shh E12.5_coronal	There is strong staining in the ventricular zone of the dorsal POA and weak staining in the VMH nucleus. Staining is either absent or ubiquitous in the ventricular zone of the ventral POA, the PVH and ARH nuclei, the AVH and anterior and posterior IDs.
TS20: thalamus mantle layer	Strong		Sez6-Shh E12.5_coronal , Sez6-Shh E12.5_sagittal	There is strong staining in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Ambiguous		Sez6-Shh E12.5_sagittal , Sez6-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	Very strong		Sez6-Shh E14.5_coronal , Sez6-Shh E14.5_sagittal	There is very strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Ambiguous		Sez6-Shh E14.5_sagittal , Sez6-Shh E14.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Very strong		Sez6-Shh E14.5_sagittal , Sez6-Shh E14.5_coronal	There is very strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Strong	Non-Uniform	Sez6-Shh E14.5_sagittal , Sez6-Shh E14.5_coronal	There is strong staining in the mantle zone of the premam and the TT and weak staining in the mam and supramam zones.
TS22: diencephalon ventricular layer	Ambiguous		Sez6-Shh E14.5_coronal , Sez6-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		Sez6-Shh E14.5_coronal , Sez6-Shh E14.5_sagittal	There is weak staining in the ventricular and mantle zones of the ganglionic eminences.
TS22: hypothalamus mantle layer	Strong	Non-Uniform	Sez6-Shh E14.5_sagittal , Sez6-Shh E14.5_coronal	There is strong staining in the MZ of the anterior and posterior IDs, moderate staining in the PVH nucleus and weak staining in the dorsal and ventral POAs, AVH and VMH nucleus. Staining is either absent or ubiquitous in the MZ of the ARH nucleus.
TS22: hypothalamus ventricular layer	Moderate	Non-Uniform	Sez6-Shh E14.5_sagittal , Sez6-Shh E14.5_coronal	There is moderate staining in the ventricular zone of the PVH nucleus. Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the VMH and ARH nuclei, the AVH and anterior and posterior IDs.
TS22: thalamus mantle layer	Strong		Sez6-Shh E14.5_coronal , Sez6-Shh E14.5_sagittal	There is strong staining in the mantle zone of the dorsal thalamus and prethalamus.
TS22: thalamus ventricular layer	Ambiguous		Sez6-Shh E14.5_sagittal , Sez6-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	Very strong		Sez6-Shh E16.5_coronal , Sez6-Shh E16.5_sagittal	There is very strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Ambiguous		Sez6-Shh E16.5_coronal , Sez6-Shh E16.5_sagittal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Very strong		Sez6-Shh E16.5_coronal , Sez6-Shh E16.5_sagittal	There is very strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Strong	Non-Uniform	Sez6-Shh E16.5_sagittal , Sez6-Shh E16.5_coronal	There is strong staining in the mantle zone of the premam zone and weak staining in the mam and supramam zones.
TS24: diencephalon ventricular layer	Ambiguous		Sez6-Shh E16.5_coronal , Sez6-Shh E16.5_sagittal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS24: ganglionic eminence	Weak	Non-Uniform	Sez6-Shh E16.5_coronal , Sez6-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	Strong	Non-Uniform	Sez6-Shh E16.5_sagittal , Sez6-Shh E16.5_coronal	There is strong staining in the mantle zone of the ventral POA and the PH and weak staining in the dorsal POA and VMH nucleus. Staining is either absent or ubiquitous in the mantle zone of the PVH, SCH, DMH and ARH nuclei, the AVH and the DAH.
TS24: hypothalamus ventricular layer	Strong	Non-Uniform	Sez6-Shh E16.5_sagittal , Sez6-Shh E16.5_coronal	There is strong staining in the VZ of the dorsal POA, the AVH, the DMH nucleus and the PH, moderate staining in the PVH nucleus and weak staining in the ventral POA. Staining is either absent or ubiquitous in the VZ of the DAH and SCH, VMH and ARH nuclei.
TS24: thalamus mantle layer	Strong	Non-Uniform	Sez6-Shh E16.5_coronal , Sez6-Shh E16.5_sagittal	There is strong staining in the mantle zone of the prethalamus and moderate staining in the dorsal thalamus.
TS24: thalamus ventricular layer	Ambiguous		Sez6-Shh E16.5_sagittal , Sez6-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.