Probe:	UI-M-CD1-azu-e-09-0-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	Ambiguous		Epha3-Shh E11.5-coronal , Epha3-Shh E11.5-sagittal	Staining is either absent or ubiquitous in the mantle 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: diencephalon lateral wall ventricular layer	Strong	Non-Uniform	Epha3-Shh E11.5-sagittal , Epha3-Shh E11.5-coronal	Staining is strong in the VZ of the prethalamus, dorsal & ventral POAs, PVH nucleus, posterior ID, premam, mam & supramam zones & TT & weak in dorsal thalamus. Staining is either absent or ubiquitous in the VZ of the AVH, anterior ID & VMH & ARH nuclei.
TS19: telencephalon mantle layer	Ambiguous		Epha3-Shh E11.5-sagittal , Epha3-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	Strong		Epha3-Shh E11.5-sagittal , Epha3-Shh E11.5-coronal	There is strong staining in the ventricular zone of the cerebral cortex and the ganglionic eminences.

Structure	Level	Pattern	Image	Note
TS20: cerebral cortex intermediate zone	Ambiguous		Epha3-Shh E12.5-coronal , Epha3-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	Very strong		Epha3-Shh E12.5-coronal , Epha3-Shh E12.5-sagittal	There is very strong staining in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Epha3-Shh E12.5-coronal , Epha3-Shh E12.5-sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS20: diencephalon mantle layer	Ambiguous		Epha3-Shh E12.5-coronal , Epha3-Shh E12.5-sagittal	Staining is either absent or ubiquitous in the mantle zone of the premam, mam and supramam zones and the TT.
TS20: diencephalon ventricular layer	Very strong	Non-Uniform	Epha3-Shh E12.5-sagittal , Epha3-Shh E12.5-coronal	There is very strong staining in the ventricular zone of the mam and supramam zones and moderate staining in the premam zone and the TT.
TS20: ganglionic eminence	Very strong	Non-Uniform	Epha3-Shh E12.5-sagittal , Epha3-Shh E12.5-coronal	There is very strong 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	Ambiguous		Epha3-Shh E12.5-coronal , Epha3-Shh E12.5-sagittal	Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei, the AVH and anterior and posterior IDs.
TS20: hypothalamus ventricular layer	Very strong	Non-Uniform	Epha3-Shh E12.5-sagittal , Epha3-Shh E12.5-coronal	There is very strong staining in the VZ of the PVH nucleus and the AVH and moderate staining in the posterior ID. Staining is either absent or ubiquitous in the VZ of the dorsal and ventral POAs, anterior ID and VMH and ARH nuclei.
TS20: thalamus mantle layer	Strong	Non-Uniform	Epha3-Shh E12.5-coronal , Epha3-Shh E12.5-sagittal	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.
TS20: thalamus ventricular layer	Very strong		Epha3-Shh E12.5-coronal , Epha3-Shh E12.5-sagittal	There is very strong staining in the ventricular zone of the prethalamus.

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Very strong		Epha3-Shh E14.5-sagittal , Epha3-Shh E14.5-coronal	There is very strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Ambiguous		Epha3-Shh E14.5-sagittal , Epha3-Shh E14.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Very strong		Epha3-Shh E14.5-sagittal , Epha3-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	Very strong	Non-Uniform	Epha3-Shh E14.5-sagittal , Epha3-Shh E14.5-coronal	There is very strong staining in the mantle zone of the mam and supramam zone. Staining is either absent or ubiquitous in the mantle zone of the premam zone and the TT.
TS22: diencephalon ventricular layer	Ambiguous		Epha3-Shh E14.5-sagittal , Epha3-Shh E14.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones and the TT.
TS22: ganglionic eminence	Very strong	Non-Uniform	Epha3-Shh E14.5-coronal , Epha3-Shh E14.5-sagittal	There is very strong 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	Ambiguous		Epha3-Shh E14.5-sagittal , Epha3-Shh E14.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei, the AVH and anterior and posterior IDs.
TS22: hypothalamus ventricular layer	Ambiguous		Epha3-Shh E14.5-coronal , Epha3-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	Very strong		Epha3-Shh E14.5-coronal , Epha3-Shh E14.5-sagittal	There is very strong staining in the mantle zone of the dorsal thalamus and prethalamus.
TS22: thalamus ventricular layer	Ambiguous		Epha3-Shh E14.5-coronal , Epha3-Shh E14.5-sagittal	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		Epha3-Shh E16.5-coronal , Epha3-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		Epha3-Shh E16.5-sagittal , Epha3-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Very strong		Epha3-Shh E16.5-coronal , Epha3-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	Moderate	Non-Uniform	Epha3-Shh E16.5-sagittal , Epha3-Shh E16.5-coronal	There is moderate staining in the mantle zone of the mam zone. Staining is either absent or ubiquitous in the mantle zone of the premam and supramam zones.
TS24: diencephalon ventricular layer	Very strong	Non-Uniform	Epha3-Shh E16.5-coronal , Epha3-Shh E16.5-sagittal	There is very strong staining in the ventricular zone of the mam and supramam zones. Staining is either absent or ubiquitous in the ventricular zone of the premam zone.
TS24: ganglionic eminence	Very strong	Non-Uniform	Epha3-Shh E16.5-coronal , Epha3-Shh E16.5-sagittal	There is very strong staining in the ventricular zone of the ganglionic eminences and moderate, scattered staining in the mantle zone of the ganglionic eminences.
TS24: hypothalamus mantle layer	Strong	Non-Uniform	Epha3-Shh E16.5-coronal , Epha3-Shh E16.5-sagittal	There is strong staining in the mantle zone of the ventral POA. Staining is either absent or ubiquitous in the mantle zone of the dorsal POA, the PVH, SCH, DMH, VMH and ARH nuclei, the AVH, the DAH and the PH.
TS24: hypothalamus ventricular layer	Ambiguous		Epha3-Shh E16.5-sagittal , Epha3-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		Epha3-Shh E16.5-coronal , Epha3-Shh E16.5-sagittal	There is very strong staining in the mantle zone of the dorsal thalamus and prethalamus.
TS24: thalamus ventricular layer	Ambiguous		Epha3-Shh E16.5-coronal , Epha3-Shh E16.5-sagittal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.