Probe:	UI-M-BH1-amv-d-11-0-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	D9300A07Rik-Shh E11.5_coronal	There is moderate staining in the MZ of the dorsal thalamus, prethalamus & anterior & posterior IDs & weak staining in the dorsal & ventral POAs, PVH & VMH nuclei, premam & supramam zones & TT. Staining is either absent or ubiquitous in the MZ of the AVH.
TS19: diencephalon lateral wall ventricular layer	Strong	Non-Uniform	D9300A07Rik-Shh E11.5_coronal	Staining is strong in the VZ of anterior & posterior IDs, premam & supramam zones & TT, moderate in the dorsal thalamus, prethalamus & VMH nucleus, weak in the dorsal POA & either absent or ubiquitous in the ventral POA, the PVH nucleus & the AVH.
TS19: telencephalon mantle layer	Weak	Non-Uniform	D9300A07Rik-Shh E11.5_coronal	There is weak 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		D9300A07Rik-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		D9300A07Rik-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	Strong		D9300A07Rik-Shh E12.5_coronal	There is strong staining in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		D9300A07Rik-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		D9300A07Rik-Shh E12.5_coronal	There is weak staining in the mantle zone of the premam and supramam zones and the TT.
TS20: diencephalon ventricular layer	Strong	Non-Uniform	D9300A07Rik-Shh E12.5_coronal	There is strong staining in the ventricular zone of the premam zone and the TT and weak staining in the supramam zone.
TS20: ganglionic eminence	Ambiguous		D9300A07Rik-Shh E12.5_coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS20: hypothalamus mantle layer	Weak	Non-Uniform	D9300A07Rik-Shh E12.5_coronal	There is weak staining in the mantle zone of the ventral POAs, the VMH and ARH nuclei, the AVH and anterior and posterior IDs. Staining is either absent or ubiquitous in the mantle zone of the dorsal POA and the PVH nucleus.
TS20: hypothalamus ventricular layer	Strong	Non-Uniform	D9300A07Rik-Shh E12.5_coronal	There is strong staining in the ventricular zone of the ventral POAs, the VMH and ARH nuclei, the AVH and anterior and posterior IDs. Staining is either absent or ubiquitous in the ventricular zone of the dorsal POA and the PVH nucleus.
TS20: thalamus mantle layer	Weak		D9300A07Rik-Shh E12.5_coronal	There is weak staining in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Strong		D9300A07Rik-Shh E12.5_coronal	There is strong staining in the ventricular zone of the dorsal thalamus and prethalamus.

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Weak		D9300A07Rik-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	Moderate		D9300A07Rik-Shh E14.5-coronal	There is moderate staining in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Weak		D9300A07Rik-Shh E14.5-coronal	There is weak staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Ambiguous		D9300A07Rik-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	Strong	Non-Uniform	D9300A07Rik-Shh E14.5-coronal	There is strong staining in the ventricular zone of the TT and supramam zone. Staining is either absent or ubiquitous in the ventricular zone of the premam and mam zones.
TS22: ganglionic eminence	Moderate	Non-Uniform	D9300A07Rik-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	Weak	Non-Uniform	D9300A07Rik-Shh E14.5-coronal	There is weak staining in the mantle zone of the VMH nucleus. Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH and ARH nuclei, the AVH and anterior and posterior IDs.
TS22: hypothalamus ventricular layer	Strong	Non-Uniform	D9300A07Rik-Shh E14.5-coronal	There is strong staining in the ventricular zone of the dorsal and ventral POAs, the PVH and VMH nuclei, the AVH and anterior and posterior IDs. Staining is either absent or ubiquitous in the ventricular zone of the ARH nucleus.
TS22: thalamus mantle layer	Ambiguous		D9300A07Rik-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		D9300A07Rik-Shh E14.5-coronal	There is strong staining in the ventricular zone of the dorsal thalamus and prethalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Ambiguous		D9300A07Rik-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		D9300A07Rik-Shh E16.5-coronal	There is weak staining in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		D9300A07Rik-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		D9300A07Rik-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	D9300A07Rik-Shh E16.5-coronal	There is strong staining in the ventricular zone of the supramam zone. Staining is either absent or ubiquitous in the ventricular zone of the premam and mam zones.
TS24: ganglionic eminence	Ambiguous		D9300A07Rik-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		D9300A07Rik-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	D9300A07Rik-Shh E16.5-coronal	There is strong staining in the ventricular zone of the ventral POAs, the PVH, SCH, DMH and VMH nuclei, the AVH and the DAH and weak staining in the dorsal POA. Staining is either absent or ubiquitous in the ventricular zone of the ARH nucleus and the PH.
TS24: thalamus mantle layer	Ambiguous		D9300A07Rik-Shh E16.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS24: thalamus ventricular layer	Strong	Non-Uniform	D9300A07Rik-Shh E16.5-coronal	There is strong staining in the ventricular zone of the prethalamus and moderate staining in the dorsal thalamus.