Probe:	UI-M-BH3-avf-h-04-0-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		Tcf19-Shh E11.5_sagittal , Tcf19-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	Strong		Tcf19-Shh E11.5_sagittal , Tcf19-Shh E11.5_coronal	There is strong, 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		Tcf19-Shh E11.5_coronal , Tcf19-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	Strong	Scattered	Tcf19-Shh E11.5_sagittal , Tcf19-Shh E11.5_coronal	There is strong, 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		Tcf19-Shh E12.5_sagittal , Tcf19-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	Scattered	Tcf19-Shh E12.5_coronal , Tcf19-Shh E12.5_sagittal	There is strong, scattered staining in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Tcf19-Shh E12.5_coronal , Tcf19-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		Tcf19-Shh E12.5_coronal , Tcf19-Shh E12.5_sagittal	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	Tcf19-Shh E12.5_sagittal , Tcf19-Shh E12.5_coronal	There is strong staining in the ventricular zone of the premam and mam zones and weak, scattered staining in the supramam zone and the TT.
TS20: ganglionic eminence	Strong	Non-Uniform	Tcf19-Shh E12.5_sagittal , Tcf19-Shh E12.5_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.
TS20: hypothalamus mantle layer	Ambiguous		Tcf19-Shh E12.5_sagittal , Tcf19-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	Tcf19-Shh E12.5_sagittal , Tcf19-Shh E12.5_coronal	There is strong staining in the ventricular zone of the ventral POA, the AVH and VMH and ARH nuclei, moderate, scattered staining in the dorsal POA and weak, scattered staining in the PVH nucleus and anterior and posterior IDs.
TS20: thalamus mantle layer	Ambiguous		Tcf19-Shh E12.5_sagittal , Tcf19-Shh E12.5_coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Strong		Tcf19-Shh E12.5_sagittal , Tcf19-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	Scattered	Tcf19-Shh E14.5_sagittal , Tcf19-Shh E14.5_coronal	There is weak, scattered staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Strong	Scattered	Tcf19-Shh E14.5_coronal , Tcf19-Shh E14.5_sagittal	There is strong, scattered staining in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Weak	Scattered	Tcf19-Shh E14.5_sagittal , Tcf19-Shh E14.5_coronal	There is weak, scattered staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Ambiguous		Tcf19-Shh E14.5_sagittal , Tcf19-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	Moderate	Non-Uniform	Tcf19-Shh E14.5_sagittal , Tcf19-Shh E14.5_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 TT and the supramam zone.
TS22: ganglionic eminence	Strong	Non-Uniform	Tcf19-Shh E14.5_sagittal , Tcf19-Shh E14.5_coronal	There is strong, scattered staining in the ventricular zone of the ganglionic eminences and weak, scattered staining in the mantle zone of the ganglionic eminences.
TS22: hypothalamus mantle layer	Ambiguous		Tcf19-Shh E14.5_coronal , Tcf19-Shh E14.5_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.
TS22: hypothalamus ventricular layer	Moderate	Non-Uniform	Tcf19-Shh E14.5_sagittal , Tcf19-Shh E14.5_coronal	There is moderate staining in the ventricular zone of the ventral POA and the AVH. Staining is either absent or ubiquitous in the ventricular zone of the dorsal POA, the PVH, VMH and ARH nuclei and anterior and posterior IDs.
TS22: thalamus mantle layer	Ambiguous		Tcf19-Shh E14.5_sagittal , Tcf19-Shh E14.5_coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS22: thalamus ventricular layer	Weak	Non-Uniform	Tcf19-Shh E14.5_coronal , Tcf19-Shh E14.5_sagittal	There is weak staining in the ventricular zone of the dorsal thalamus. Staining is either absent or ubiquitous in the ventricular zone of the prethalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Moderate	Scattered	Tcf19-Shh E16.5_sagittal , Tcf19-Shh E16.5_coronal	There is moderate, scattered staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Very strong		Tcf19-Shh E16.5_sagittal , Tcf19-Shh E16.5_coronal	There is very strong staining in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Moderate	Scattered	Tcf19-Shh E16.5_coronal , Tcf19-Shh E16.5_sagittal	There is moderate, scattered staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Weak	Non-Uniform	Tcf19-Shh E16.5_coronal , Tcf19-Shh E16.5_sagittal	There is weak 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.
TS24: diencephalon ventricular layer	Weak	Non-Uniform	Tcf19-Shh E16.5_coronal , Tcf19-Shh E16.5_sagittal	There is weak staining in the ventricular zone of the mam zone. Staining is either absent or ubiquitous in the ventricular zone of the premam and supramam zones.
TS24: ganglionic eminence	Very strong	Non-Uniform	Tcf19-Shh E16.5_coronal , Tcf19-Shh E16.5_sagittal	There is very strong staining in the ventricular zone of the ganglionic eminences and moderate, scattered staining in the mantle zone of the ganglionic eminences.
TS24: hypothalamus mantle layer	Ambiguous		Tcf19-Shh E16.5_sagittal , Tcf19-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	Weak	Non-Uniform	Tcf19-Shh E16.5_coronal , Tcf19-Shh E16.5_sagittal	There is weak staining in the ventricular zone of the SCH nucleus. Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH, DMH, VMH and ARH nuclei, the AVH, the DAH and the PH.
TS24: thalamus mantle layer	Ambiguous		Tcf19-Shh E16.5_coronal , Tcf19-Shh E16.5_sagittal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS24: thalamus ventricular layer	Weak	Non-Uniform	Tcf19-Shh E16.5_coronal , Tcf19-Shh E16.5_sagittal	There is weak staining in the ventricular zone of the dorsal thalamus. Staining is either absent or ubiquitous in the ventricular zone of the prethalamus.