Probe:	UI-M-BG1-aif-f-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		epdr2-shh e11.5-coronal	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	Moderate	Non-Uniform	epdr2-shh e11.5-coronal	Staining is moderate and scattered in the VZ of dorsal thalamus, prethalamus, dorsal POA, PVH nucleus, anterior & posterior IDs, premam & supramam zones & TT, moderate in mam zone & either absent or ubiquitous in ventral POA, AVH & VMH & ARH nuclei.
TS19: telencephalon mantle layer	Ambiguous		epdr2-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	Moderate	Scattered	epdr2-shh e11.5-coronal	There is moderate, scattered staining in the ventricular zone of the cerebral cortex and the ganglionic eminences.

Structure	Level	Pattern	Image	Note
TS20: cerebral cortex intermediate zone	Ambiguous		Epdr2-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	Moderate		Epdr2-Shh E12.5-coronal	There is moderate staining in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Epdr2-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		Epdr2-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	Moderate	Non-Uniform	Epdr2-Shh E12.5-coronal	There is moderate staining in the ventricular zone of the mam zone and moderate, scattered staining in the premam and supramam zones and the TT.
TS20: ganglionic eminence	Moderate	Non-Uniform	Epdr2-Shh E12.5-coronal	There is moderate, scattered 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		Epdr2-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	Moderate	Non-Uniform	Epdr2-Shh E12.5-coronal	There is moderate, scattered staining in the VZ of the anterior and posterior IDs and weak, scattered staining in the dorsal POA and the PVH nucleus. Staining is either absent or ubiquitous in the VZ of the ventral POA, AVH and VMH and ARH nuclei.
TS20: thalamus mantle layer	Ambiguous		Epdr2-Shh E12.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Moderate		Epdr2-Shh E12.5-coronal	There is moderate staining in the ventricular zone of the dorsal thalamus and prethalamus.

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Ambiguous		Epdr2-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	Moderate		Epdr2-Shh E14.5-coronal	There is moderate, scattered staining in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Epdr2-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	Ambiguous		Epdr2-Shh E14.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the premam, mam and supramam zones and the TT.
TS22: diencephalon ventricular layer	Moderate		Epdr2-Shh E14.5-coronal	There is moderate staining in the ventricular zone of the premam, mam and supramam zones and the TT.
TS22: ganglionic eminence	Moderate	Non-Uniform	Epdr2-Shh E14.5-coronal	There is moderate, scattered staining in the ventricular zone of the ganglionic eminences. Staining is either absent or ubiquitous in the mantle zone of the ganglionic eminences.
TS22: hypothalamus mantle layer	Ambiguous		Epdr2-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	Strong	Non-Uniform	Epdr2-Shh E14.5-coronal	There is strong staining in the VZ of the dorsal POA, moderate staining in the anterior and posterior IDs and the VMH nucleus and weak staining in the PVH and ARH nuclei and the AVH. Staining is either absent or ubiquitous in the VZ of the ventral POA.
TS22: thalamus mantle layer	Ambiguous		Epdr2-Shh E14.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS22: thalamus ventricular layer	Strong	Non-Uniform	Epdr2-Shh E14.5-coronal	There is strong staining in the ventricular zone of the prethalamus and moderate staining in the dorsal thalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Ambiguous		Epdr2-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	Weak	Scattered	Epdr2-Shh E16.5-coronal	There is weak, scattered staining in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Epdr2-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	Ambiguous		Epdr2-Shh E16.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the premam, mam and supramam zones.
TS24: diencephalon ventricular layer	Strong		Epdr2-Shh E16.5-coronal	There is strong staining in the ventricular zone of the premam, mam and supramam zones.
TS24: ganglionic eminence	Ambiguous		Epdr2-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS24: hypothalamus mantle layer	Ambiguous		Epdr2-Shh E16.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH, SCH, DMH, VMH and ARH nuclei, the AVH, the DAH and the PH.
TS24: hypothalamus ventricular layer	Strong	Non-Uniform	Epdr2-Shh E16.5-coronal	There is strong staining in the ventricular zone of the dorsal and ventral POAs, the DMH, VMH and ARH nuclei and the PH and weak staining in the PVH and SCH nuclei, the AVH and the DAH.
TS24: thalamus mantle layer	Weak	Non-Uniform	Epdr2-Shh E16.5-coronal	There is weak, scattered staining in the mantle zone of the dorsal thalamus. Staining is either absent or ubiquitous in the mantle zone of the prethalamus.
TS24: thalamus ventricular layer	Strong		Epdr2-Shh E16.5-coronal	There is strong staining in the ventricular zone of the dorsal thalamus and prethalamus.