Probe:	UI-M-BH1-alp-a-02-0-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	Moderate	Non-Uniform	Ypel2-Shh E11.5_sagittal , Ypel2-Shh E11.5_coronal	Staining is moderate in the MZ of the PVH nucleus & premam zone, weak in dorsal thalamus & either absent or ubiquitous in the prethalamus, dorsal & ventral POAs, VMH & ARH nuclei, AVH, anterior & posterior IDs, mam & supramam zones & TT.
TS19: diencephalon lateral wall ventricular layer	Ambiguous		Ypel2-Shh E11.5_sagittal , Ypel2-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	Non-Uniform	Ypel2-Shh E11.5_coronal , Ypel2-Shh E11.5_sagittal	There is strong staining in the postmitotic neurons in the intermediate zone and cortical plate of the cerebral cortex. Staining is either absent or ubiquitous in the mantle zone of the ganglionic eminences.
TS19: telencephalon ventricular layer	Ambiguous		Ypel2-Shh E11.5_sagittal , Ypel2-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	Weak		Ypel2-Shh E12.5_sagittal , Ypel2-Shh E12.5_coronal	There is weak staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS20: cerebral cortex ventricular layer	Ambiguous		Ypel2-Shh E12.5_sagittal , Ypel2-Shh E12.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Weak		Ypel2-Shh E12.5_sagittal , Ypel2-Shh E12.5_coronal	There is weak staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS20: diencephalon mantle layer	Ambiguous		Ypel2-Shh E12.5_sagittal , Ypel2-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	Ambiguous		Ypel2-Shh E12.5_coronal , Ypel2-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	Ambiguous		Ypel2-Shh E12.5_sagittal , Ypel2-Shh E12.5_coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS20: hypothalamus mantle layer	Weak	Non-Uniform	Ypel2-Shh E12.5_sagittal , Ypel2-Shh E12.5_coronal	There is weak staining in the mantle zone of the ventral POA and the AVH. Staining is either absent or ubiquitous in the mantle zone of the dorsal POA, the PVH, VMH and ARH nuclei and anterior and posterior IDs.
TS20: hypothalamus ventricular layer	Ambiguous		Ypel2-Shh E12.5_coronal , Ypel2-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	Very strong	Non-Uniform	Ypel2-Shh E12.5_coronal , Ypel2-Shh E12.5_sagittal	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.
TS20: thalamus ventricular layer	Ambiguous		Ypel2-Shh E12.5_coronal , Ypel2-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		Ypel2-Shh E14.5_coronal , Ypel2-Shh E14.5_sagittal , Ypel2-Shh E14.5_sagittal-2	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Ambiguous		Ypel2-Shh E14.5_sagittal-2 , Ypel2-Shh E14.5_coronal , Ypel2-Shh E14.5_sagittal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Ypel2-Shh E14.5_coronal , Ypel2-Shh E14.5_sagittal-2 , Ypel2-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		Ypel2-Shh E14.5_sagittal , Ypel2-Shh E14.5_sagittal-2 , Ypel2-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	Ambiguous		Ypel2-Shh E14.5_sagittal-2 , Ypel2-Shh E14.5_sagittal , Ypel2-Shh E14.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones and the TT.
TS22: ganglionic eminence	Ambiguous		Ypel2-Shh E14.5_coronal , Ypel2-Shh E14.5_sagittal-2 , Ypel2-Shh E14.5_sagittal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS22: hypothalamus mantle layer	Ambiguous		Ypel2-Shh E14.5_sagittal , Ypel2-Shh E14.5_coronal , Ypel2-Shh E14.5_sagittal-2	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	Ambiguous		Ypel2-Shh E14.5_sagittal-2 , Ypel2-Shh E14.5_sagittal , Ypel2-Shh E14.5_coronal	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	Very strong	Non-Uniform	Ypel2-Shh E14.5_sagittal , Ypel2-Shh E14.5_coronal , Ypel2-Shh E14.5_sagittal-2	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	Ambiguous		Ypel2-Shh E14.5_coronal , Ypel2-Shh E14.5_sagittal-2 , Ypel2-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		Ypel2-Shh E16.5_sagittal , Ypel2-Shh E16.5_coronal , Ypel2-Shh E16.5_sagittal-2	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Ambiguous		Ypel2-Shh E16.5_sagittal , Ypel2-Shh E16.5_coronal , Ypel2-Shh E16.5_sagittal-2	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Ypel2-Shh E16.5_coronal , Ypel2-Shh E16.5_sagittal-2 , Ypel2-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	Ambiguous		Ypel2-Shh E16.5_coronal , Ypel2-Shh E16.5_sagittal-2 , Ypel2-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		Ypel2-Shh E16.5_coronal , Ypel2-Shh E16.5_sagittal-2 , Ypel2-Shh E16.5_sagittal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS24: ganglionic eminence	Ambiguous		Ypel2-Shh E16.5_sagittal-2 , Ypel2-Shh E16.5_coronal , Ypel2-Shh E16.5_sagittal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS24: hypothalamus mantle layer	Ambiguous		Ypel2-Shh E16.5_sagittal , Ypel2-Shh E16.5_coronal , Ypel2-Shh E16.5_sagittal-2	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	Ambiguous		Ypel2-Shh E16.5_coronal , Ypel2-Shh E16.5_sagittal , Ypel2-Shh E16.5_sagittal-2	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	Weak		Ypel2-Shh E16.5_sagittal-2 , Ypel2-Shh E16.5_coronal , Ypel2-Shh E16.5_sagittal	There is weak staining in the mantle zone of the dorsal thalamus and prethalamus.
TS24: thalamus ventricular layer	Ambiguous		Ypel2-Shh E16.5_sagittal , Ypel2-Shh E16.5_sagittal-2 , Ypel2-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.