Probe:	UI-M-CG0p-bep-f-09-0-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		Thbs1-Shh E11.5_coronal , Thbs1-Shh E11.5_sagittal	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	Very strong	Non-Uniform	Thbs1-Shh E11.5_coronal , Thbs1-Shh E11.5_sagittal	Staining is very strong in prethalamus, strong in dorsal & ventral POAs, VMH and ARH nuclei & premam & mam zones, moderate in PVH nucleus & AVH & absent or ubiquitous in the dorsal thalamus, anterior & posterior IDs, TT & supramam zone; some is scattered.
TS19: telencephalon mantle layer	Ambiguous		Thbs1-Shh E11.5_coronal , Thbs1-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		Thbs1-Shh E11.5_sagittal , Thbs1-Shh E11.5_coronal	There is moderate staining in the ventricular zone of the cerebral cortex and the ganglionic eminences.

Structure	Level	Pattern	Image	Note
TS20: cerebral cortex intermediate zone	Ambiguous		Thbs1-Shh E12.5_sagittal , Thbs1-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		Thbs1-shh E12.5_coronal , Thbs1-Shh E12.5_sagittal	There is strong staining in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Thbs1-Shh E12.5_sagittal , Thbs1-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	Ambiguous		Thbs1-Shh E12.5_sagittal , Thbs1-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	Moderate	Non-Uniform	Thbs1-shh E12.5_coronal , Thbs1-Shh E12.5_sagittal	There is moderate 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	Moderate	Non-Uniform	Thbs1-Shh E12.5_sagittal , Thbs1-shh E12.5_coronal	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		Thbs1-Shh E12.5_sagittal , Thbs1-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	Moderate	Non-Uniform	Thbs1-Shh E12.5_sagittal , Thbs1-shh E12.5_coronal	There is moderate staining in the VZ of the dorsal and ventral POAs, the AVH and the VMH nucleus and moderate, scattered staining in the PVH and ARH nuclei. Staining is either absent or ubiquitous in the VZ of the anterior and posterior IDs.
TS20: thalamus mantle layer	Ambiguous		Thbs1-shh E12.5_coronal , Thbs1-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	Thbs1-Shh E12.5_sagittal , Thbs1-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	Weak	Scattered	Thbs1-Shh E14.5_sagittal , Thbs1-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		Thbs1-Shh E14.5_coronal , Thbs1-Shh E14.5_sagittal	There is strong staining in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Weak	Scattered	Thbs1-Shh E14.5_sagittal , Thbs1-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		Thbs1-Shh E14.5_sagittal , Thbs1-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	Thbs1-Shh E14.5_coronal , Thbs1-Shh E14.5_sagittal	There is strong staining in the ventricular zone of the premam zone and weak, scattered staining in the mam zone. Staining is either absent or ubiquitous in the ventricular zone of the TT and the supramam zone.
TS22: ganglionic eminence	Strong	Non-Uniform	Thbs1-Shh E14.5_coronal , Thbs1-Shh E14.5_sagittal	There is strong staining in the ventricular zone of the ganglionic eminences and weak staining in the mantle zone.
TS22: hypothalamus mantle layer	Ambiguous		Thbs1-Shh E14.5_coronal , Thbs1-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	Strong	Non-Uniform	Thbs1-Shh E14.5_sagittal , Thbs1-Shh E14.5_coronal	There is strong staining in the ventricular zone of the dorsal and ventral POAs and moderate staining in the posterior ID and ARH nucleus. Staining is either absent or ubiquitous in the ventricular zone of the PVH and VMH nuclei, the AVH and anterior ID.
TS22: thalamus mantle layer	Strong	Non-Uniform	Thbs1-Shh E14.5_coronal , Thbs1-Shh E14.5_sagittal	There is strong staining in the mantle zone of the prethalamus and weak staining in the dorsal thalamus.
TS22: thalamus ventricular layer	Strong	Non-Uniform	Thbs1-Shh E14.5_coronal , Thbs1-Shh E14.5_sagittal	There is strong staining in the ventricular zone of the prethalamus and moderate staining in the dorsal thalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Moderate	Scattered	Thbs1-Shh E16.5_sagittal , Thbs1-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		Thbs1-Shh E16.5_sagittal , Thbs1-Shh E16.5_coronal	There is very strong staining in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Moderate	Scattered	Thbs1-Shh E16.5_sagittal , Thbs1-Shh E16.5_coronal	There is moderate, scattered staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Strong	Non-Uniform	Thbs1-Shh E16.5_sagittal , Thbs1-Shh E16.5_coronal	There is strong 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	Ambiguous		Thbs1-Shh E16.5_sagittal , Thbs1-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS24: ganglionic eminence	Very strong	Non-Uniform	Thbs1-Shh E16.5_coronal , Thbs1-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		Thbs1-Shh E16.5_sagittal , Thbs1-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	Thbs1-Shh E16.5_sagittal , Thbs1-Shh E16.5_coronal	There is strong staining in the ventricular zone of the ARH nucleus and the PH. Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH, SCH, DMH and VMH nuclei, the AVH and the DAH.
TS24: thalamus mantle layer	Weak		Thbs1-Shh E16.5_sagittal , Thbs1-Shh E16.5_coronal	There is weak staining in the mantle zone of the dorsal thalamus and prethalamus.
TS24: thalamus ventricular layer	Ambiguous		Thbs1-Shh E16.5_coronal , Thbs1-Shh E16.5_sagittal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.