Probe:	UI-M-BH1-anb-e-10-0-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		Trip6-Shh E11.5_sagittal , Trip6-Shh E11.5_coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus, 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	Moderate	Scattered	Trip6-Shh E11.5_coronal , Trip6-Shh E11.5_sagittal	There is moderate, scattered staining 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	Ambiguous		Trip6-Shh E11.5_coronal , Trip6-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	Moderate	Scattered	Trip6-Shh E11.5_sagittal , Trip6-Shh E11.5_coronal	There is moderate, scattered staining in the ventricular zone of the cerebral cortex and the ganglionic eminences.

Structure	Level	Pattern	Image	Note
TS20: cerebral cortex intermediate zone	Ambiguous		Trip6-Shh E12.5_coronal , Trip6-Shh E12.5_sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS20: cerebral cortex ventricular layer	Moderate		Trip6-Shh E12.5_sagittal , Trip6-Shh E12.5_coronal	There is moderate, scattered staining in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Trip6-Shh E12.5_coronal , Trip6-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		Trip6-Shh E12.5_sagittal , Trip6-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	Very strong	Non-Uniform	Trip6-Shh E12.5_sagittal , Trip6-Shh E12.5_coronal	There is very strong staining in the ventricular zone of the premam and mam zones and moderate, scattered staining in the TT and supramam zone.
TS20: ganglionic eminence	Moderate	Non-Uniform	Trip6-Shh E12.5_coronal , Trip6-Shh E12.5_sagittal	There is moderate, scattered staining in the ventricular zone of the ganglionic eminences. Staining is either absent or ubiquitous in the mantle zone of the ganglionic eminences.
TS20: hypothalamus mantle layer	Ambiguous		Trip6-Shh E12.5_coronal , Trip6-Shh E12.5_sagittal	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	Very strong	Non-Uniform	Trip6-Shh E12.5_coronal , Trip6-Shh E12.5_sagittal	There is very strong, scattered staining in the ventricular zone of the ARH nucleus and moderate, scattered staining in the dorsal and ventral POAs, the PVH and VMH nuclei, the AVH and anterior and posterior IDs.
TS20: thalamus mantle layer	Ambiguous		Trip6-Shh E12.5_coronal , Trip6-Shh E12.5_sagittal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Very strong	Non-Uniform	Trip6-Shh E12.5_sagittal , Trip6-Shh E12.5_coronal	There is very strong staining in the ventricular zone of the prethalamus and moderate, scattered staining in the dorsal thalamus.

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Ambiguous		Trip6-Shh E14.5_sagittal , Trip6-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	Strong	Scattered	Trip6-Shh E14.5_sagittal , Trip6-Shh E14.5_coronal	There is strong, scattered staining in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Trip6-Shh E14.5_sagittal , Trip6-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	Ambiguous		Trip6-Shh E14.5_coronal , Trip6-Shh E14.5_sagittal	Staining is either absent or ubiquitous in the mantle zone of the premam, mam and supramam zones and the TT.
TS22: diencephalon ventricular layer	Weak	Scattered	Trip6-Shh E14.5_sagittal , Trip6-Shh E14.5_coronal	There is weak, scattered staining in the ventricular zone of the premam, mam and supramam zones and the TT.
TS22: ganglionic eminence	Strong	Non-Uniform	Trip6-Shh E14.5_sagittal , Trip6-Shh E14.5_coronal	There is strong, scattered 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		Trip6-Shh E14.5_sagittal , Trip6-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	Weak	Scattered	Trip6-Shh E14.5_coronal , Trip6-Shh E14.5_sagittal	There is weak, scattered staining 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	Ambiguous		Trip6-Shh E14.5_sagittal , Trip6-Shh E14.5_coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS22: thalamus ventricular layer	Moderate	Scattered	Trip6-Shh E14.5_coronal , Trip6-Shh E14.5_sagittal	There is moderate, scattered staining in the ventricular zone of the dorsal thalamus and prethalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Ambiguous		Trip6-Shh E16.5_coronal , Trip6-Shh E16.5_sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Strong		Trip6-Shh E16.5_sagittal , Trip6-Shh E16.5_coronal	There is strong staining in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Trip6-Shh E16.5_sagittal , Trip6-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		Trip6-Shh E16.5_sagittal , Trip6-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	Moderate	Non-Uniform	Trip6-Shh E16.5_sagittal , Trip6-Shh E16.5_coronal	There is moderate 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	Trip6-Shh E16.5_sagittal , Trip6-Shh E16.5_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.
TS24: hypothalamus mantle layer	Ambiguous		Trip6-Shh E16.5_sagittal , Trip6-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	Moderate	Non-Uniform	Trip6-Shh E16.5_sagittal , Trip6-Shh E16.5_coronal	There is moderate staining in the ventricular zone of the AVH, the DAH and the VMH and ARH nuclei and weak staining in the dorsal and ventral POAs, the PVH, SCH and DMH nuclei and the PH.
TS24: thalamus mantle layer	Ambiguous		Trip6-Shh E16.5_sagittal , Trip6-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		Trip6-Shh E16.5_sagittal , Trip6-Shh E16.5_coronal	There is strong staining in the ventricular zone of the dorsal thalamus and prethalamus.