Probe:	UI-M-BH3-asf-b-05-0-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	Gfra1-Shh E11.5-coronal , Gfra1-Shh E11.5-sagittal	Staining is strong in the MZ of dorsal thalamus, prethalamus, VMH & ARH nuclei & mam zone & weak in dorsal POA, PVH nucleus & AVH. Staining is either absent or ubiquitous in the MZ of ventral POA, anterior & posterior IDs, premam & supramam zones & TT.
TS19: diencephalon lateral wall ventricular layer	Strong	Non-Uniform	Gfra1-Shh E11.5-sagittal , Gfra1-Shh E11.5-coronal	There is strong staining in the VZ of the mam zone. Staining is either absent or ubiquitous in the VZ of the dorsal thalamus, prethalamus, dorsal & ventral POAs, the PVH, VMH & ARH nuclei, the AVH, anterior & posterior IDs, premam & supramam zones & TT.
TS19: telencephalon mantle layer	Ambiguous		Gfra1-Shh E11.5-sagittal , Gfra1-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		Gfra1-Shh E11.5-sagittal , Gfra1-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	Ambiguous		Gfra1-Shh E12.5-coronal , Gfra1-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		Gfra1-Shh E12.5-sagittal , Gfra1-Shh E12.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Gfra1-Shh E12.5-sagittal , Gfra1-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	Gfra1-Shh E12.5-coronal , Gfra1-Shh E12.5-sagittal	There is strong staining in the mantle zone of the TT and mam zone and moderate staining in the supramam zone. Staining is either absent or ubiquitous in the mantle zone of the premam zone.
TS20: diencephalon ventricular layer	Strong	Non-Uniform	Gfra1-Shh E12.5-coronal , Gfra1-Shh E12.5-sagittal	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 TT and supramam zone.
TS20: ganglionic eminence	Ambiguous		Gfra1-Shh E12.5-sagittal , Gfra1-Shh E12.5-coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS20: hypothalamus mantle layer	Strong	Non-Uniform	Gfra1-Shh E12.5-sagittal , Gfra1-Shh E12.5-coronal	There is strong staining in the MZ of the VMH nucleus, moderate staining in the dorsal and ventral POAs, the AVH and posterior ID and weak staining in the PVH nucleus. Staining is either absent or ubiquitous in the MZ of the anterior ID and ARH nucleus.
TS20: hypothalamus ventricular layer	Ambiguous		Gfra1-Shh E12.5-coronal , Gfra1-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		Gfra1-Shh E12.5-coronal , Gfra1-Shh E12.5-sagittal	There is strong staining in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Ambiguous		Gfra1-Shh E12.5-sagittal , Gfra1-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		Gfra1-Shh E14.5-sagittal , Gfra1-Shh E14.5-coronal	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Ambiguous		Gfra1-Shh E14.5-coronal , Gfra1-Shh E14.5-sagittal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Gfra1-Shh E14.5-coronal , Gfra1-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	Very strong	Non-Uniform	Gfra1-Shh E14.5-coronal , Gfra1-Shh E14.5-sagittal	There is very strong staining in the mantle zone of the mam zone and strong staining in the TT and supramam zone. Staining is either absent or ubiquitous in the mantle zone of the premam zone.
TS22: diencephalon ventricular layer	Very strong	Non-Uniform	Gfra1-Shh E14.5-coronal , Gfra1-Shh E14.5-sagittal	There is very strong staining in the ventricular zone of the mam zone and strong staining in the premam zone. Staining is either absent or ubiquitous in the ventricular zone of the TT and supramam zone.
TS22: ganglionic eminence	Ambiguous		Gfra1-Shh E14.5-sagittal , Gfra1-Shh E14.5-coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS22: hypothalamus mantle layer	Strong	Non-Uniform	Gfra1-Shh E14.5-sagittal , Gfra1-Shh E14.5-coronal	There is strong staining in the MZ of dorsal & ventral POAs & the AVH, moderate staining in the VMH nucleus & moderate, scattered staining in the ARH nucleus. Staining is either absent or ubiquitous in the MZ of the PVH nucleus & anterior & posterior IDs.
TS22: hypothalamus ventricular layer	Ambiguous		Gfra1-Shh E14.5-coronal , Gfra1-Shh E14.5-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.
TS22: thalamus mantle layer	Strong		Gfra1-Shh E14.5-coronal , Gfra1-Shh E14.5-sagittal	There is strong staining in the mantle zone of the dorsal thalamus and prethalamus.
TS22: thalamus ventricular layer	Ambiguous		Gfra1-Shh E14.5-sagittal , Gfra1-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	Ambiguous		Gfra1-Shh E16.5-coronal , Gfra1-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		Gfra1-Shh E16.5-sagittal , Gfra1-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Gfra1-Shh E16.5-coronal , Gfra1-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	Strong	Non-Uniform	Gfra1-Shh E16.5-coronal , Gfra1-Shh E16.5-sagittal	There is strong staining in the mantle zone of the mam zone, moderate staining in the premam zone and weak, scattered staining in the supramam zone.
TS24: diencephalon ventricular layer	Moderate	Non-Uniform	Gfra1-Shh E16.5-sagittal , Gfra1-Shh E16.5-coronal	There is moderate staining in the ventricular zone of the mam zone. Staining is either absent or ubiquitous in the ventricular zone of the premam and supramam zones.
TS24: ganglionic eminence	Moderate	Non-Uniform	Gfra1-Shh E16.5-sagittal , Gfra1-Shh E16.5-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.
TS24: hypothalamus mantle layer	Strong	Non-Uniform	Gfra1-Shh E16.5-coronal , Gfra1-Shh E16.5-sagittal	There is strong staining in the MZ of the SCH & DMH nuclei & the PH, moderate staining in the dorsal & ventral POAs, the AVH & DAH & weak, scattered staining in the PVH & ARH nuclei. Staining is either absent or ubiquitous in the MZ of the VMH nucleus.
TS24: hypothalamus ventricular layer	Ambiguous		Gfra1-Shh E16.5-sagittal , Gfra1-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	Very strong	Non-Uniform	Gfra1-Shh E16.5-coronal , Gfra1-Shh E16.5-sagittal	There is very strong staining in the mantle zone of the prethalamus and moderate staining in the dorsal thalamus.
TS24: thalamus ventricular layer	Ambiguous		Gfra1-Shh E16.5-sagittal , Gfra1-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.