Probe:	UI-M-BH2.1-apw-c-01-0-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	Ntrk1-Shh E11.5 coronal , Ntrk1-Shh E11.5 sagittal	There is moderate staining in the MZ of the prethalamus. Staining is either absent or ubiquitous in the MZ of the dorsal thalamus, dorsal & ventral POAs, the PVH, VMH & ARH nuclei, the AVH, anterior & posterior IDs, premam, mam & supramam zones & the TT.
TS19: diencephalon lateral wall ventricular layer	Strong	Non-Uniform	Ntrk1-Shh E11.5 sagittal , Ntrk1-Shh E11.5 coronal	There is strong staining in the VZ of the ventral POA, VMH & ARH nuclei, AVH, anterior & posterior IDs, premam & mam zones & TT. Staining is either absent or ubiquitous in the VZ of dorsal thalamus, prethalamus, dorsal POA, PVH nucleus & supramam zone.
TS19: telencephalon mantle layer	Ambiguous		Ntrk1-Shh E11.5 coronal , Ntrk1-Shh E11.5 sagittal	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	Ambiguous		Ntrk1-Shh E11.5 sagittal , Ntrk1-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		Ntrk1-Shh E12.5 sagittal , Ntrk1-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		Ntrk1-Shh E12.5 coronal , Ntrk1-Shh E12.5 sagittal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Ntrk1-Shh E12.5 coronal , Ntrk1-Shh E12.5 sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS20: diencephalon mantle layer	Ambiguous		Ntrk1-Shh E12.5 sagittal , Ntrk1-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	Strong	Non-Uniform	Ntrk1-Shh E12.5 sagittal , Ntrk1-Shh E12.5 coronal	There is strong staining in the ventricular zone of the premam and mam zones and weak, scattered staining in the TT and supramam zone.
TS20: ganglionic eminence	Ambiguous		Ntrk1-Shh E12.5 sagittal , Ntrk1-Shh E12.5 coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS20: hypothalamus mantle layer	Ambiguous		Ntrk1-Shh E12.5 sagittal , Ntrk1-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	Strong	Non-Uniform	Ntrk1-Shh E12.5 coronal , Ntrk1-Shh E12.5 sagittal	There is strong staining in the ventricular zone of the ventral POA, PVH, VMH and ARH nuclei and the AVH and weak, scattered staining in the anterior and posterior IDs. Staining is either absent or ubiquitous in the ventricular zone of the dorsal POA.
TS20: thalamus mantle layer	Moderate	Non-Uniform	Ntrk1-Shh E12.5 sagittal , Ntrk1-Shh E12.5 coronal	There is moderate staining in the mantle zone of the prethalamus and weak staining in the dorsal thalamus.
TS20: thalamus ventricular layer	Strong	Non-Uniform	Ntrk1-Shh E12.5 sagittal , Ntrk1-Shh E12.5 coronal	There is 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	Weak	Scattered	Ntrk1-Shh E14.5 coronal , Ntrk1-Shh E14.5 sagittal	There is weak, scattered staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Ambiguous		Ntrk1-Shh E14.5 coronal , Ntrk1-Shh E14.5 sagittal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Weak	Scattered	Ntrk1-Shh E14.5 coronal , Ntrk1-Shh E14.5 sagittal	There is weak, scattered staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Weak	Non-Uniform	Ntrk1-Shh E14.5 coronal , Ntrk1-Shh E14.5 sagittal	There is weak, scattered staining in the mantle zone of the mam zone. Staining is either absent or ubiquitous in the mantle zone of the premam and supramam zones and the TT.
TS22: diencephalon ventricular layer	Very strong	Non-Uniform	Ntrk1-Shh E14.5 coronal , Ntrk1-Shh E14.5 sagittal	There is very strong staining in the ventricular zone of the premam and mam zones and weak, scattered staining in the TT and supramam zone.
TS22: ganglionic eminence	Strong	Non-Uniform	Ntrk1-Shh E14.5 sagittal , Ntrk1-Shh E14.5 coronal	There is strong 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		Ntrk1-Shh E14.5 sagittal , Ntrk1-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	Very strong	Non-Uniform	Ntrk1-Shh E14.5 sagittal , Ntrk1-Shh E14.5 coronal	There is very strong staining in the VZ of the VMH & ARH nuclei, strong staining in the ventral POA, PVH nucleus & the AVH & weak, scattered staining in the anterior & posterior IDs. Staining is either absent or ubiquitous in the VZ of the dorsal POA.
TS22: thalamus mantle layer	Weak	Non-Uniform	Ntrk1-Shh E14.5 coronal , Ntrk1-Shh E14.5 sagittal	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.
TS22: thalamus ventricular layer	Moderate	Non-Uniform	Ntrk1-Shh E14.5 coronal , Ntrk1-Shh E14.5 sagittal	There is moderate staining in the ventricular zone of the prethalamus and moderate, scattered staining in the dorsal thalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Moderate		Ntrk1-Shh E16.5 sagittal , Ntrk1-Shh E16.5 coronal	There is moderate staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Ambiguous		Ntrk1-Shh E16.5 coronal , Ntrk1-Shh E16.5 sagittal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Moderate		Ntrk1-Shh E16.5 sagittal , Ntrk1-Shh E16.5 coronal	There is moderate staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Strong	Non-Uniform	Ntrk1-Shh E16.5 sagittal , Ntrk1-Shh E16.5 coronal	There is strong staining in the mantle zone of the premam zone and moderate staining in the mam and supramam zone.
TS24: diencephalon ventricular layer	Very strong	Non-Uniform	Ntrk1-Shh E16.5 coronal , Ntrk1-Shh E16.5 sagittal	There is very strong staining in the ventricular zone of the premam and mam zones. Staining is either absent or ubiquitous in the ventricular zone of the supramam zone.
TS24: ganglionic eminence	Strong	Non-Uniform	Ntrk1-Shh E16.5 sagittal , Ntrk1-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	Ntrk1-Shh E16.5 coronal , Ntrk1-Shh E16.5 sagittal	There is strong staining in the mantle zone of the dorsal POA, DMH, VMH and ARH nuclei and the PH. Staining is either absent or ubiquitous in the mantle zone of the ventral POA, PVH and SCH nuclei, the AVH and the DAH.
TS24: hypothalamus ventricular layer	Very strong	Non-Uniform	Ntrk1-Shh E16.5 sagittal , Ntrk1-Shh E16.5 coronal	There is very strong staining in the ventricular zone of the VMH and ARH nuclei and strong staining in the AVH and DAH. Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH, SCH and DMH nuclei and the PH.
TS24: thalamus mantle layer	Moderate	Non-Uniform	Ntrk1-Shh E16.5 sagittal , Ntrk1-Shh E16.5 coronal	There is moderate staining in the mantle zone of the dorsal thalamus and weak staining in the prethalamus.
TS24: thalamus ventricular layer	Strong	Non-Uniform	Ntrk1-Shh E16.5 sagittal , Ntrk1-Shh E16.5 coronal	There is strong staining in the ventricular zone of the prethalamus. Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus.