Probe:	MGC clone 13899
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		Mfng-Shh E11.5_coronal , Mfng-Shh E11.5_sagittal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus, prethalamus, dorsal and ventral POAs, PVH nucleus, the AVH and anterior and posterior IDs.
TS19: diencephalon lateral wall ventricular layer	Strong		Mfng-Shh E11.5_sagittal , Mfng-Shh E11.5_coronal	There is strong staining in the ventricular zone of the dorsal thalamus, prethalamus, dorsal and ventral POAs, PVH nucleus, the AVH and anterior and posterior IDs.
TS19: telencephalon mantle layer	Ambiguous		Mfng-Shh E11.5_coronal , Mfng-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	Non-Uniform	Mfng-Shh E11.5_coronal , Mfng-Shh E11.5_sagittal	There is strong staining in the ventricular zone of the ganglionic eminences and weak staining in the cerebral cortex.

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

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Ambiguous		Mfng-Shh E14.5_coronal , Mfng-Shh E14.5_sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Very strong		Mfng-Shh E14.5_coronal , Mfng-Shh E14.5_sagittal	There is very strong staining in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Mfng-Shh E14.5_coronal , Mfng-Shh E14.5_sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Ambiguous		Mfng-Shh E14.5_coronal , Mfng-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	Strong	Non-Uniform	Mfng-Shh E14.5_sagittal , Mfng-Shh E14.5_coronal	There is strong staining in the ventricular zone of the premam zone and the TT. Staining is either absent or ubiquitous in the ventricular zone of the mam and supramam zones.
TS22: ganglionic eminence	Very strong	Non-Uniform	Mfng-Shh E14.5_sagittal , Mfng-Shh E14.5_coronal	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.
TS22: hypothalamus mantle layer	Ambiguous		Mfng-Shh E14.5_coronal , Mfng-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	Mfng-Shh E14.5_sagittal , Mfng-Shh E14.5_coronal	There is strong staining in the ventricular zone of the dorsal and ventral POAs and the AVH and weak staining in the PVH nucleus. Staining is either absent or ubiquitous in the ventricular zone of the anterior and posterior IDs and VMH and ARH nuclei.
TS22: thalamus mantle layer	Ambiguous		Mfng-Shh E14.5_sagittal , Mfng-Shh E14.5_coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS22: thalamus ventricular layer	Very strong	Non-Uniform	Mfng-Shh E14.5_sagittal , Mfng-Shh E14.5_coronal	There is very strong staining in the ventricular zone of the dorsal thalamus and weak staining in the prethalamus.

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