Probe:	UI-M-AP0-abe-b-05-0-UI.s2
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	Bcor-shh E11.5-coronal	Staining is moderate in the MZ of the dorsal thalamus, dorsal & ventral POAs, PVH nucleus & anterior & posterior IDs & weak in prethalamus. Staining is either absent or ubiquitous in the MZ of the AVH, VMH & ARH nuclei, premam, mam & supramam zones & TT.
TS19: diencephalon lateral wall ventricular layer	Ambiguous		Bcor-shh E11.5-coronal	Staining is either absent or ubiquitous in the ventricular 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: telencephalon mantle layer	Weak	Non-Uniform	Bcor-shh E11.5-coronal	There is weak, scattered staining in the mantle zone of the ganglionic eminences. Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone and cortical plate of the cerebral cortex.
TS19: telencephalon ventricular layer	Ambiguous		Bcor-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		Bcor-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		Bcor-shh E12.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Bcor-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	Bcor-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 zone, mam and supramam zones.
TS20: diencephalon ventricular layer	Ambiguous		Bcor-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	Weak	Non-Uniform	Bcor-shh E12.5-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.
TS20: hypothalamus mantle layer	Strong	Non-Uniform	Bcor-shh E12.5-coronal	There is strong staining in the mantle zone of the posterior ID and the VMH nucleus and moderate staining in the AVH and anterior ID. Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs and the PVH and ARH nuclei.
TS20: hypothalamus ventricular layer	Weak	Non-Uniform	Bcor-shh E12.5-coronal	There is weak staining in the ventricular zone of the VMH nucleus. Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH and ARH nuclei, the AVH and anterior and posterior IDs.
TS20: thalamus mantle layer	Weak	Non-Uniform	Bcor-shh E12.5-coronal	There is weak 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	Ambiguous		Bcor-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	Weak		Bcor-shh E14.5-coronal	There is weak staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Ambiguous		Bcor-shh E14.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Weak		Bcor-shh E14.5-coronal	There is weak staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Moderate	Non-Uniform	Bcor-shh E14.5-coronal	There is moderate 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 and the TT.
TS22: diencephalon ventricular layer	Ambiguous		Bcor-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		Bcor-shh E14.5-coronal	There is moderate staining in the ventricular and mantle zones of the ganglionic eminences.
TS22: hypothalamus mantle layer	Strong	Non-Uniform	Bcor-shh E14.5-coronal	There is strong staining in the MZ of the ventral POA and the AVH, moderate staining in the posterior ID and the VMH and ARH nuclei. Staining is either absent or ubiquitous in the MZ of the dorsal POA, the PVH nucleus and the anterior ID.
TS22: hypothalamus ventricular layer	Ambiguous		Bcor-shh E14.5-coronal	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	Weak	Non-Uniform	Bcor-shh E14.5-coronal	There is weak staining in the mantle zone of the dorsal thalamus. Staining is either absent or ubiquitous in the mantle zone of the prethalamus.
TS22: thalamus ventricular layer	Ambiguous		Bcor-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		Bcor-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		Bcor-shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Bcor-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		Bcor-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	Ambiguous		Bcor-shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS24: ganglionic eminence	Ambiguous		Bcor-shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS24: hypothalamus mantle layer	Strong	Non-Uniform	Bcor-shh E16.5-coronal	There is strong staining in the mantle zone of the AVH and weak staining in the dorsal and ventral POAs and the VMH nucleus. Staining is either absent or ubiquitous in the mantle zone of the PVH, SCH, DMH and ARH nuclei, the DAH and the PH.
TS24: hypothalamus ventricular layer	Ambiguous		Bcor-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	Ambiguous		Bcor-shh E16.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS24: thalamus ventricular layer	Ambiguous		Bcor-shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.