Probe:	UI-M-CG0p-bfe-e-12-0-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		Prox1-Shh E11.5_coronal , Prox1-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	Strong	Non-Uniform	Prox1-Shh E11.5_sagittal , Prox1-Shh E11.5_coronal	Staining is strong in the VZ of the TT, moderate in prethalamus, dorsal & ventral POAs, PVH nucleus, posterior ID & premam zone & either absent or ubiquitous in the dorsal thalamus, AVH, anterior ID, VMH & ARH nuclei & mam & supramam zones.
TS19: telencephalon mantle layer	Ambiguous		Prox1-Shh E11.5_coronal , Prox1-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	Non-Uniform	Prox1-Shh E11.5_sagittal , Prox1-Shh E11.5_coronal	There is moderate staining in the ventricular zone of the ganglionic eminences. Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.

Structure	Level	Pattern	Image	Note
TS20: cerebral cortex intermediate zone	Ambiguous		Prox1-Shh E12.5_coronal , Prox1-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		Prox1-Shh E12.5_coronal , Prox1-Shh E12.5_sagittal	There is moderate staining in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Prox1-Shh E12.5_sagittal , Prox1-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	Strong	Non-Uniform	Prox1-Shh E12.5_coronal , Prox1-Shh E12.5_sagittal	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 and the TT.
TS20: diencephalon ventricular layer	Strong	Non-Uniform	Prox1-Shh E12.5_sagittal , Prox1-Shh E12.5_coronal	There is strong staining in the ventricular zone of the TT. Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS20: ganglionic eminence	Strong	Non-Uniform	Prox1-Shh E12.5_coronal , Prox1-Shh E12.5_sagittal	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	Strong	Non-Uniform	Prox1-Shh E12.5_coronal , Prox1-Shh E12.5_sagittal	There is strong staining in the mantle zone of the posterior ID. 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 ID.
TS20: hypothalamus ventricular layer	Strong	Non-Uniform	Prox1-Shh E12.5_coronal , Prox1-Shh E12.5_sagittal	There is strong staining in the ventricular zone of the dorsal and ventral POAs. Staining is either absent or ubiquitous in the ventricular zone of the PVH, VMH and ARH nuclei, the AVH and anterior and posterior IDs.
TS20: thalamus mantle layer	Ambiguous		Prox1-Shh E12.5_sagittal , Prox1-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	Non-Uniform	Prox1-Shh E12.5_sagittal , Prox1-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	Ambiguous		Prox1-Shh E14.5_sagittal , Prox1-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	Weak		Prox1-Shh E14.5_sagittal , Prox1-Shh E14.5_coronal	There is weak staining in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Prox1-Shh E14.5_sagittal , Prox1-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	Strong	Non-Uniform	Prox1-Shh E14.5_sagittal , Prox1-Shh E14.5_coronal	There is strong staining in the mantle zone of the premam zone and weak staining in the TT. Staining is either absent or ubiquitous in the mantle zone of the mam and supramam zones.
TS22: diencephalon ventricular layer	Moderate	Non-Uniform	Prox1-Shh E14.5_sagittal , Prox1-Shh E14.5_coronal	There is moderate 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	Moderate	Non-Uniform	Prox1-Shh E14.5_sagittal , Prox1-Shh E14.5_coronal	There is moderate staining in the mantle zone of the ganglionic eminences. Staining is either absent or ubiquitous in the ventricular zone of the ganglionic eminences.
TS22: hypothalamus mantle layer	Weak	Non-Uniform	Prox1-Shh E14.5_sagittal , Prox1-Shh E14.5_coronal	There is weak staining in the mantle zone of the posterior ID and ARH nucleus. Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH and VMH nuclei, the AVH and anterior ID.
TS22: hypothalamus ventricular layer	Moderate	Non-Uniform	Prox1-Shh E14.5_coronal , Prox1-Shh E14.5_sagittal	There is moderate staining in the ventricular zone of the dorsal and ventral POAs and the posterior ID and weak staining in the AVH. Staining is either absent or ubiquitous in the ventricular zone of the PVH, VMH and ARH nuclei and anterior ID.
TS22: thalamus mantle layer	Very strong	Non-Uniform	Prox1-Shh E14.5_sagittal , Prox1-Shh E14.5_coronal	There is very strong 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	Weak	Non-Uniform	Prox1-Shh E14.5_coronal , Prox1-Shh E14.5_sagittal	There is weak 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
TS24: cerebral cortex intermediate zone	Ambiguous		Prox1-Shh E16.5_coronal , Prox1-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	Ambiguous		Prox1-Shh E16.5_coronal , Prox1-Shh E16.5_sagittal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Prox1-Shh E16.5_coronal , Prox1-Shh E16.5_sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Moderate	Non-Uniform	Prox1-Shh E16.5_sagittal , Prox1-Shh E16.5_coronal	There is moderate 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	Moderate	Non-Uniform	Prox1-Shh E16.5_sagittal , Prox1-Shh E16.5_coronal	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.
TS24: ganglionic eminence	Weak	Non-Uniform	Prox1-Shh E16.5_coronal , Prox1-Shh E16.5_sagittal	There is weak 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	Moderate	Non-Uniform	Prox1-Shh E16.5_sagittal , Prox1-Shh E16.5_coronal	There is moderate staining in the mantle zone of the PH. 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 and the DAH.
TS24: hypothalamus ventricular layer	Moderate	Non-Uniform	Prox1-Shh E16.5_coronal , Prox1-Shh E16.5_sagittal	There is moderate staining in the ventricular zone of the dorsal POA and the PH. Staining is either absent or ubiquitous in the ventricular zone of the ventral POA, the PVH, SCH, DMH, VMH and ARH nuclei, the AVH and the DAH.
TS24: thalamus mantle layer	Very strong	Non-Uniform	Prox1-Shh E16.5_sagittal , Prox1-Shh E16.5_coronal	There is very strong staining in the mantle zone of the dorsal thalamus. Staining is either absent or ubiquitous in the mantle zone of the prethalamus.
TS24: thalamus ventricular layer	Weak	Non-Uniform	Prox1-Shh E16.5_sagittal , Prox1-Shh E16.5_coronal	There is weak staining in the ventricular zone of the prethalamus. Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus.