Probe:	UI-M-CD1-azt-f-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	Moderate	Non-Uniform	Ephb2-shh E11.5-coronal	There is moderate staining in the MZ of the dorsal thalamus & prethalamus. Staining is either absent or ubiquitous in the MZ of the dorsal & ventral POAs, the PVH, VMH & ARH nuclei, the AVH, anterior & posterior IDs, premam, mam & supramam zones & the TT.
TS19: diencephalon lateral wall ventricular layer	Very strong	Non-Uniform	Ephb2-shh E11.5-coronal	Staining is very strong in the VZ of the mam & supramam zones, strong in anterior & posterior IDs, ARH nucleus, premam zone & TT, moderate in dorsal thalamus, prethalamus & VMH nucleus & weak in dorsal & ventral POAs, PVH nucleus & the AVH.
TS19: telencephalon mantle layer	Ambiguous		Ephb2-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	Weak	Non-Uniform	Ephb2-shh E11.5-coronal	There is weak 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		Ephb2-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		Ephb2-shh E12.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Ephb2-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	Ambiguous		Ephb2-shh E12.5-coronal	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		Ephb2-shh E12.5-coronal	There is very strong staining in the ventricular zone of the premam, mam and supramam zones and the TT.
TS20: ganglionic eminence	Weak	Non-Uniform	Ephb2-shh E12.5-coronal	There is weak 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		Ephb2-shh E12.5-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.
TS20: hypothalamus ventricular layer	Very strong	Non-Uniform	Ephb2-shh E12.5-coronal	There is very strong staining in the ventricular zone of the anterior and posterior IDs, VMH and ARH nuclei, moderate staining in the dorsal and ventral POAs, the PVH nucleus and the AVH.
TS20: thalamus mantle layer	Strong	Non-Uniform	Ephb2-shh E12.5-coronal	There is strong staining in the mantle zone of the dorsal thalamus and moderate staining in the prethalamus.
TS20: thalamus ventricular layer	Strong	Non-Uniform	Ephb2-shh E12.5-coronal	There is strong staining in the ventricular zone of the prethalamus and weak staining in the dorsal thalamus.

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Ambiguous		Ephb2-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		Ephb2-shh E14.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Ephb2-shh E14.5-coronal	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	Ephb2-shh E14.5-coronal	There is very strong staining in the mantle zone of the premam and mam zones and the TT. Staining is either absent or ubiquitous in the mantle zone of the supramam zone.
TS22: diencephalon ventricular layer	Ambiguous		Ephb2-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	Ambiguous		Ephb2-shh E14.5-coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS22: hypothalamus mantle layer	Very strong	Non-Uniform	Ephb2-shh E14.5-coronal	There is very strong staining in the mantle zone of the ARH nucleus. Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH and VMH nuclei, the AVH and anterior and posterior IDs.
TS22: hypothalamus ventricular layer	Very strong	Non-Uniform	Ephb2-shh E14.5-coronal	There is very strong staining in the VZ of the anterior & posterior IDs & the VMH nucleus, strong staining in the dorsal & ventral POAs & the AVH & weak staining in the PVH nucleus. Staining is either absent or ubiquitous in the VZ of the ARH nucleus.
TS22: thalamus mantle layer	Moderate	Non-Uniform	Ephb2-shh E14.5-coronal	There is moderate staining in the mantle zone of the dorsal thalamus and weak staining in the prethalamus.
TS22: thalamus ventricular layer	Very strong	Non-Uniform	Ephb2-shh E14.5-coronal	There is very strong staining in the ventricular zone of the prethalamus. Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Ambiguous		Ephb2-shh E16.5-coronal	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Ambiguous		Ephb2-shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Ephb2-shh E16.5-coronal	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	Ephb2-shh E16.5-coronal	There is weak staining in the mantle zone of the premam zone. Staining is either absent or ubiquitous in the mantle zone of the mam and supramam zones.
TS24: diencephalon ventricular layer	Very strong	Non-Uniform	Ephb2-shh E16.5-coronal	There is very strong staining in the ventricular zone of the mam zone and weak staining in the supramam zone. Staining is either absent or ubiquitous in the ventricular zone of the premam zone.
TS24: ganglionic eminence	Weak	Non-Uniform	Ephb2-shh E16.5-coronal	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	Ephb2-shh E16.5-coronal	There is moderate staining in the mantle zone of the SCH, DMH and VMH nuclei and weak staining in the dorsal and ventral POAs, the PVH nucleus, the AVH, the DAH and the PH. Staining is either absent or ubiquitous in the mantle zone of the ARH nucleus.
TS24: hypothalamus ventricular layer	Moderate	Non-Uniform	Ephb2-shh E16.5-coronal	There is moderate staining in the ventricular zone of the PH. 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 and the DAH.
TS24: thalamus mantle layer	Very strong	Non-Uniform	Ephb2-shh E16.5-coronal	There is very strong staining in the mantle zone of the prethalamus and moderate staining in the dorsal thalamus.
TS24: thalamus ventricular layer	Ambiguous		Ephb2-shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.