Probe:	UI-M-BH1-amx-c-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	Strong	Non-Uniform	Ntrk3-Shh E11.5 coronal	There is strong staining in the MZ of the PVH nucleus & AVH, moderate staining in the prethalamus & weak staining in anterior & posterior IDs. Staining is either absent or ubiquitous in the MZ of the dorsal thalamus, dorsal & ventral POAs & VMH nucleus.
TS19: diencephalon lateral wall ventricular layer	Ambiguous		Ntrk3-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 and VMH nuclei, the AVH and anterior and posterior IDs.
TS19: telencephalon mantle layer	Strong	Non-Uniform	Ntrk3-Shh E11.5 coronal	There is strong 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		Ntrk3-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		Ntrk3-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		Ntrk3-Shh E12.5 coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Ntrk3-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	Strong	Non-Uniform	Ntrk3-Shh E12.5 coronal	There is strong staining in the mantle zone of the supramam zone and moderate staining in the mam zone. Staining is either absent or ubiquitous in the mantle zone of the premam zone and the TT.
TS20: diencephalon ventricular layer	Weak	Non-Uniform	Ntrk3-Shh E12.5 coronal	There is weak 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 and the TT.
TS20: ganglionic eminence	Very strong	Non-Uniform	Ntrk3-Shh E12.5 coronal	There is very strong 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	Ntrk3-Shh E12.5 coronal	There is strong staining in the mantle zone of the dorsal and ventral POAs, PVH nucleus and the AVH and weak staining in the anterior and posterior IDs and VMH nucleus. Staining is either absent or ubiquitous in the mantle zone of the ARH nucleus.
TS20: hypothalamus ventricular layer	Ambiguous		Ntrk3-Shh E12.5 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.
TS20: thalamus mantle layer	Ambiguous		Ntrk3-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	Ntrk3-Shh E12.5 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
TS22: cerebral cortex intermediate zone	Very strong		Ntrk3-Shh E14.5 coronal	There is very strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Ambiguous		Ntrk3-Shh E14.5 coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Very strong		Ntrk3-Shh E14.5 coronal	There is very strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Strong		Ntrk3-Shh E14.5 coronal	There is strong staining in the mantle zone of the premam, mam and supramam zones and the TT.
TS22: diencephalon ventricular layer	Ambiguous		Ntrk3-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	Very strong	Non-Uniform	Ntrk3-Shh E14.5 coronal	There is very strong staining in the mantle zone of the ganglionic eminences. Staining is either absent or ubiquitous in the ventricular zone of the ganglionic eminences.
TS22: hypothalamus mantle layer	Very strong	Non-Uniform	Ntrk3-Shh E14.5 coronal	There is very strong staining in the mantle zone of the AVH, strong staining in the anterior and posterior IDs and VMH nucleus, moderate staining in the dorsal and ventral POAs and weak staining in the PVH and ARH nuclei.
TS22: hypothalamus ventricular layer	Ambiguous		Ntrk3-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	Moderate	Non-Uniform	Ntrk3-Shh E14.5 coronal	There is moderate staining in the mantle zone of the prethalamus and weak staining in the dorsal thalamus.
TS22: thalamus ventricular layer	Ambiguous		Ntrk3-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	Very strong		Ntrk3-Shh E16.5 coronal	There is very strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Ambiguous		Ntrk3-Shh E16.5 coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Very strong		Ntrk3-Shh E16.5 coronal	There is very strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Weak		Ntrk3-Shh E16.5 coronal	There is weak staining in the mantle zone of the premam zone.
TS24: diencephalon ventricular layer	Ambiguous		Ntrk3-Shh E16.5 coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam zone.
TS24: ganglionic eminence	Strong	Non-Uniform	Ntrk3-Shh E16.5 coronal	There is strong 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	Strong	Non-Uniform	Ntrk3-Shh E16.5 coronal	There is strong staining in the MZ of the dorsal POA & VMH nucleus, moderate staining in the AVH, DAH & PH, & the SCH nucleus & weak staining in the PVH nucleus. Staining is either absent or ubiquitous in the MZ of the ventral POA & DMH & ARH nuclei.
TS24: hypothalamus ventricular layer	Moderate	Non-Uniform	Ntrk3-Shh E16.5 coronal	There is moderate staining in the ventricular zone of the ventral POA. Staining is either absent or ubiquitous in the ventricular zone of the dorsal POA, the PVH, SCH, DMH, VMH and ARH nuclei, the AVH, the DAH and the PH.
TS24: thalamus mantle layer	Very strong	Non-Uniform	Ntrk3-Shh E16.5 coronal	There is very strong staining in the mantle zone of the dorsal thalamus and strong staining in the prethalamus.
TS24: thalamus ventricular layer	Ambiguous		Ntrk3-Shh E16.5 coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.