Probe:	UI-M-BH3-axc-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	Ambiguous		Bmper-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	Strong	Non-Uniform	Bmper-shh E11.5-coronal	There is strong staining in the VZ of the dorsal POA. Staining is either absent or ubiquitous in the VZ of the dorsal thalamus, the prethalamus, ventral POA, the PVH, VMH & ARH nuclei, the AVH, anterior & posterior IDs, premam, mam & supramam zones & TT.
TS19: telencephalon mantle layer	Ambiguous		Bmper-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	Non-Uniform	Bmper-shh E11.5-coronal	There is strong 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		Bmper-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		Bmper-shh E12.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Bmper-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	Weak	Non-Uniform	Bmper-shh E12.5-coronal	There is weak staining in the mantle zone of the TT. Staining is either absent or ubiquitous in the mantle zone of the premam, mam and supramam zones.
TS20: diencephalon ventricular layer	Ambiguous		Bmper-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	Ambiguous		Bmper-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	Bmper-shh E12.5-coronal	There is strong staining in the mantle zone of the AVH. Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei and anterior and posterior IDs.
TS20: hypothalamus ventricular layer	Very strong	Non-Uniform	Bmper-shh E12.5-coronal	There is very strong staining in the VZ of the dorsal POA and PVH nucleus and weak staining in the anterior ID. Staining is either absent or ubiquitous in the VZ of the ventral POA, the AVH, the posterior ID and the VMH and ARH nuclei.
TS20: thalamus mantle layer	Ambiguous		Bmper-shh E12.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Very strong	Non-Uniform	Bmper-shh E12.5-coronal	There is very strong staining in the ventricular zone of the dorsal thalamus. Staining is either absent or ubiquitous in the ventricular zone of the prethalamus.

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