Probe:	UI-M-BH3-aup-b-11-0-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	Strong	Non-Uniform	Rbig1-Shh E11.5_sagittal , Rbig1-Shh E11.5_coronal	There is strong staining in the MZ of the dorsal & ventral POAs, PVH nucleus, AVH, posterior ID & TT. Staining is either absent or ubiquitous in the MZ of the dorsal thalamus, prethalamus, VMH & ARH nuclei, anterior ID & premam, mam & supramam zones.
TS19: diencephalon lateral wall ventricular layer	Ambiguous		Rbig1-Shh E11.5_sagittal , Rbig1-Shh E11.5_coronal	Staining is either absent or ubiquitous 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	Strong		Rbig1-Shh E11.5_sagittal , Rbig1-Shh E11.5_coronal	There is strong staining 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	Ambiguous		Rbig1-Shh E11.5_sagittal , Rbig1-Shh E11.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex and the ganglionic eminences.

Structure	Level	Pattern	Image	Note
TS20: cerebral cortex intermediate zone	Strong		Rbig1-Shh E12.5_coronal , Rbig1-Shh E12.5_sagittal	There is strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS20: cerebral cortex ventricular layer	Ambiguous		Rbig1-Shh E12.5_sagittal , Rbig1-Shh E12.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Strong		Rbig1-Shh E12.5_sagittal , Rbig1-Shh E12.5_coronal	There is strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS20: diencephalon mantle layer	Strong	Non-Uniform	Rbig1-Shh E12.5_sagittal , Rbig1-Shh E12.5_coronal	There is strong staining in the mantle zone of the premam zone and the TT. Staining is either absent or ubiquitous in the mantle zone of the mam and supramam zones.
TS20: diencephalon ventricular layer	Ambiguous		Rbig1-Shh E12.5_coronal , Rbig1-Shh E12.5_sagittal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones and the TT.
TS20: ganglionic eminence	Strong	Non-Uniform	Rbig1-Shh E12.5_coronal , Rbig1-Shh E12.5_sagittal	There is strong staining in the mantle zone of the ganglionic eminences. Staining is either absent or ubiquitous in the ventricular zone of the ganglionic eminences.
TS20: hypothalamus mantle layer	Strong	Non-Uniform	Rbig1-Shh E12.5_coronal , Rbig1-Shh E12.5_sagittal	There is strong staining in the mantle zone of the ventral POA, PVH nucleus, the AVH and posterior ID. Staining is either absent or ubiquitous in the mantle zone of the dorsal POA, anterior ID and VMH and ARH nuclei.
TS20: hypothalamus ventricular layer	Ambiguous		Rbig1-Shh E12.5_coronal , Rbig1-Shh E12.5_sagittal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei, the AVH and anterior and posterior IDs.
TS20: thalamus mantle layer	Strong		Rbig1-Shh E12.5_sagittal , Rbig1-Shh E12.5_coronal	There is strong staining in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Ambiguous		Rbig1-Shh E12.5_coronal , Rbig1-Shh E12.5_sagittal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Ambiguous		Rbig1-Shh E14.5_sagittal , Rbig1-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	Ambiguous		Rbig1-Shh E14.5_coronal , Rbig1-Shh E14.5_sagittal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Rbig1-Shh E14.5_sagittal , Rbig1-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	Rbig1-Shh E14.5_coronal , Rbig1-Shh E14.5_sagittal	There is strong staining in the mantle zone of the premam zone and the TT. Staining is either absent or ubiquitous in the mantle zone of the mam and supramam zones.
TS22: diencephalon ventricular layer	Ambiguous		Rbig1-Shh E14.5_coronal , Rbig1-Shh E14.5_sagittal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones and the TT.
TS22: ganglionic eminence	Moderate	Non-Uniform	Rbig1-Shh E14.5_sagittal , Rbig1-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	Moderate	Non-Uniform	Rbig1-Shh E14.5_coronal , Rbig1-Shh E14.5_sagittal	There is moderate staining in the mantle zone of the ventral POA and weak staining in the PVH nucleus and the posterior ID. Staining is either absent or ubiquitous in the mantle zone of the dorsal POA, the VMH and ARH nuclei, the AVH and anterior ID.
TS22: hypothalamus ventricular layer	Ambiguous		Rbig1-Shh E14.5_coronal , Rbig1-Shh E14.5_sagittal	Staining is either absent or ubiquitous 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	Strong	Non-Uniform	Rbig1-Shh E14.5_sagittal , Rbig1-Shh E14.5_coronal	There is strong staining in the mantle zone of the dorsal thalamus and weak staining in the prethalamus.
TS22: thalamus ventricular layer	Ambiguous		Rbig1-Shh E14.5_coronal , Rbig1-Shh E14.5_sagittal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Ambiguous		Rbig1-Shh E16.5_sagittal , Rbig1-Shh E16.5_coronal	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Ambiguous		Rbig1-Shh E16.5_sagittal , Rbig1-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Rbig1-Shh E16.5_sagittal , Rbig1-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		Rbig1-Shh E16.5_coronal , Rbig1-Shh E16.5_sagittal	Staining is either absent or ubiquitous in the mantle zone of the premam, mam and supramam zones.
TS24: diencephalon ventricular layer	Ambiguous		Rbig1-Shh E16.5_sagittal , Rbig1-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS24: ganglionic eminence	Weak	Non-Uniform	Rbig1-Shh E16.5_coronal , Rbig1-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	Strong	Non-Uniform	Rbig1-Shh E16.5_sagittal , Rbig1-Shh E16.5_coronal	There is strong staining in the mantle zone of the dorsal POA and the PH. Staining is either absent or ubiquitous in the mantle zone of the ventral POA, the PVH, SCH, DMH, VMH and ARH nuclei, the AVH and the DAH.
TS24: hypothalamus ventricular layer	Ambiguous		Rbig1-Shh E16.5_sagittal , Rbig1-Shh E16.5_coronal	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 AVH, the DAH and the PH.
TS24: thalamus mantle layer	Ambiguous		Rbig1-Shh E16.5_coronal , Rbig1-Shh E16.5_sagittal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS24: thalamus ventricular layer	Ambiguous		Rbig1-Shh E16.5_sagittal , Rbig1-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.