Probe:	UI-M-BH0-akg-a-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	Lsamp-Shh E11.5-coronal , Lsamp-Shh E11.5-sagittal	Staining is strong in the MZ of the supramam zone, moderate in dorsal POA, weak in AVH, anterior ID, VMH & ARH nuclei & premam zone & either absent or ubiquitous in dorsal thalamus, prethalamus, ventral POA, PVH nucleus, posterior ID, TT & mam zone.
TS19: diencephalon lateral wall ventricular layer	Weak	Non-Uniform	Lsamp-Shh E11.5-sagittal , Lsamp-Shh E11.5-coronal	There is weak staining in the VZ of the prethalamus & PVH nucleus. Staining is either absent or ubiquitous in the VZ of the dorsal thalamus, dorsal & ventral POAs, the VMH & ARH nuclei, the AVH, anterior & posterior IDs, premam, mam & supramam zones & TT.
TS19: telencephalon mantle layer	Moderate	Non-Uniform	Lsamp-Shh E11.5-coronal , Lsamp-Shh E11.5-sagittal	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	Non-Uniform	Lsamp-Shh E11.5-sagittal , Lsamp-Shh E11.5-coronal	There is moderate, scattered staining in the ventricular zone of the ganglionic eminences. Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.

Structure	Level	Pattern	Image	Note
TS20: cerebral cortex intermediate zone	Ambiguous		Lsamp-Shh E12.5-sagittal , Lsamp-Shh E12.5-coronal2 , Lsamp-Shh E12.5-coronal	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS20: cerebral cortex ventricular layer	Ambiguous		Lsamp-Shh E12.5-coronal , Lsamp-Shh E12.5-sagittal , Lsamp-Shh E12.5-coronal2	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Lsamp-Shh E12.5-coronal2 , Lsamp-Shh E12.5-sagittal , Lsamp-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	Lsamp-Shh E12.5-coronal2 , Lsamp-Shh E12.5-sagittal , Lsamp-Shh E12.5-coronal	There is strong staining in the mantle zone of the supramam zone and moderate staining in the premam and mam zones. Staining is either absent or ubiquitous in the mantle zone of the TT.
TS20: diencephalon ventricular layer	Ambiguous		Lsamp-Shh E12.5-sagittal , Lsamp-Shh E12.5-coronal2 , Lsamp-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	Strong	Non-Uniform	Lsamp-Shh E12.5-sagittal , Lsamp-Shh E12.5-coronal , Lsamp-Shh E12.5-coronal2	There is strong staining in the mantle zone of the ganglionic eminences and weak staining in the ventricular zone of the ganglionic eminences.
TS20: hypothalamus mantle layer	Strong	Non-Uniform	Lsamp-Shh E12.5-coronal2 , Lsamp-Shh E12.5-sagittal , Lsamp-Shh E12.5-coronal	There is strong staining in the MZ of the PVH nucleus and anterior ID, moderate staining in the VMH and ARH nuclei and weak staining in the dorsal POA and posterior ID. Staining is either absent or ubiquitous in the MZ of the ventral POA and the AVH.
TS20: hypothalamus ventricular layer	Strong	Non-Uniform	Lsamp-Shh E12.5-coronal , Lsamp-Shh E12.5-coronal2 , Lsamp-Shh E12.5-sagittal	There is strong staining in the VZ of the ventral POA, moderate staining in the dorsal POA and weak staining in the anterior and posterior IDs. Staining is either absent or ubiquitous in the VZ of the PVH, VMH and ARH nuclei and the AVH.
TS20: thalamus mantle layer	Ambiguous		Lsamp-Shh E12.5-coronal2 , Lsamp-Shh E12.5-sagittal , Lsamp-Shh E12.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Weak		Lsamp-Shh E12.5-coronal , Lsamp-Shh E12.5-sagittal , Lsamp-Shh E12.5-coronal2	There is weak staining in the ventricular zone of the dorsal thalamus and prethalamus.

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

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