Probe:	UI-M-BH3-awi-h-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	Very strong	Non-Uniform	Ebf3-Shh E11.5-coronal , Ebf3-shh E11.5-sagittal-2 , Ebf3-SHH E11.5-sagittal	Staining is very strong in the MZ of prethalamus, PVH nucleus, TT & mam zone, strong in supramam zone, moderate in dorsal thalamus & either absent or ubiquitous in the dorsal & ventral POAs, AVH, anterior & posterior IDs, VMH & ARH nuclei & premam zone.
TS19: diencephalon lateral wall ventricular layer	Very strong	Non-Uniform	Ebf3-shh E11.5-sagittal-2 , Ebf3-SHH E11.5-sagittal , Ebf3-Shh E11.5-coronal	There is very strong staining in the VZ of the prethalamus & PVH nucleus. Staining is either absent or ubiquitous in the VZ of the dorsal thalamus, dorsal & ventral POAs, VMH & ARH nuclei, AVH, anterior & posterior IDs, premam, mam & supramam zones & TT.
TS19: telencephalon mantle layer	Very strong	Non-Uniform	Ebf3-shh E11.5-sagittal-2 , Ebf3-Shh E11.5-coronal , Ebf3-SHH E11.5-sagittal	There is very 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		Ebf3-Shh E11.5-coronal , Ebf3-shh E11.5-sagittal-2 , Ebf3-SHH E11.5-sagittal	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	Ambiguous		Ebf3-shh E12.5-sagittal-2 , Ebf3-SHH E12.5-sagittal , Ebf3-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	Moderate		Ebf3-shh E12.5-sagittal-2 , Ebf3-SHH E12.5-sagittal , Ebf3-Shh E12.5-coronal	There is moderate staining in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Ebf3-Shh E12.5-coronal , Ebf3-SHH E12.5-sagittal , Ebf3-shh E12.5-sagittal-2	Staining is either absent or ubiquitous in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS20: diencephalon mantle layer	Very strong	Non-Uniform	Ebf3-shh E12.5-sagittal-2 , Ebf3-SHH E12.5-sagittal , Ebf3-Shh E12.5-coronal	There is very strong staining in the mantle zone of the mam and supramam zones. Staining is either absent or ubiquitous in the mantle zone of the premam zone and the TT.
TS20: diencephalon ventricular layer	Very strong	Non-Uniform	Ebf3-shh E12.5-sagittal-2 , Ebf3-Shh E12.5-coronal , Ebf3-SHH E12.5-sagittal	There is very strong staining in the ventricular zone of the mam zone and supramam zones. Staining is either absent or ubiquitous in the ventricular zone of the premam zone and the TT.
TS20: ganglionic eminence	Ambiguous		Ebf3-shh E12.5-sagittal-2 , Ebf3-Shh E12.5-coronal , Ebf3-SHH E12.5-sagittal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS20: hypothalamus mantle layer	Very strong	Non-Uniform	Ebf3-SHH E12.5-sagittal , Ebf3-Shh E12.5-coronal , Ebf3-shh E12.5-sagittal-2	There is very strong staining in the MZ of the PVH nucleus and the AVH and strong staining in the ventral POA. Staining is either absent or ubiquitous in the MZ of the dorsal POA, the anterior and posterior IDs and the VMH and ARH nuclei.
TS20: hypothalamus ventricular layer	Very strong	Non-Uniform	Ebf3-Shh E12.5-coronal , Ebf3-shh E12.5-sagittal-2 , Ebf3-SHH E12.5-sagittal	There is very strong staining in the VZ of the PVH nucleus and the AVH and strong staining in the ventral POA. Staining is either absent or ubiquitous in the VZ of the dorsal POA, the anterior and posterior IDs and the VMH and ARH nuclei.
TS20: thalamus mantle layer	Very strong	Non-Uniform	Ebf3-shh E12.5-sagittal-2 , Ebf3-SHH E12.5-sagittal , Ebf3-Shh E12.5-coronal	There is very strong staining in the mantle zone of the prethalamus. Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus.
TS20: thalamus ventricular layer	Very strong	Non-Uniform	Ebf3-shh E12.5-sagittal-2 , Ebf3-SHH E12.5-sagittal , Ebf3-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	Very strong		Ebf3-shh E14.5-sagittal-2 , Ebf3-SHH E14.5-sagittal , Ebf3-Shh E14.5-coronal	There is very strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Ambiguous		Ebf3-shh E14.5-sagittal-2 , Ebf3-Shh E14.5-coronal , Ebf3-SHH E14.5-sagittal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Very strong		Ebf3-SHH E14.5-sagittal , Ebf3-Shh E14.5-coronal , Ebf3-shh E14.5-sagittal-2	There is very strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Very strong	Non-Uniform	Ebf3-shh E14.5-sagittal-2 , Ebf3-SHH E14.5-sagittal , Ebf3-Shh E14.5-coronal	There is very strong staining in the mantle zone of the mam and supramam zones and the TT. Staining is either absent or ubiquitous in the mantle zone of the premam zone.
TS22: diencephalon ventricular layer	Very strong	Non-Uniform	Ebf3-Shh E14.5-coronal , Ebf3-SHH E14.5-sagittal , Ebf3-shh E14.5-sagittal-2	There is very strong staining in the ventricular zone of the mam and supramam zones and the TT. Staining is either absent or ubiquitous in the ventricular zone of the premam zone.
TS22: ganglionic eminence	Ambiguous		Ebf3-shh E14.5-sagittal-2 , Ebf3-SHH E14.5-sagittal , Ebf3-Shh E14.5-coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS22: hypothalamus mantle layer	Very strong	Non-Uniform	Ebf3-SHH E14.5-sagittal , Ebf3-Shh E14.5-coronal , Ebf3-shh E14.5-sagittal-2	There is very strong staining in the mantle zone of the dorsal POA and strong staining the PVH nucleus and the AVH. Staining is either absent or ubiquitous in the mantle zone of the ventral POA, anterior and posterior IDs and the VMH and ARH nuclei.
TS22: hypothalamus ventricular layer	Very strong	Non-Uniform	Ebf3-shh E14.5-sagittal-2 , Ebf3-SHH E14.5-sagittal , Ebf3-Shh E14.5-coronal	There is very strong staining in the VZ of the dorsal POA and strong staining in the PVH nucleus and the AVH. Staining is either absent or ubiquitous in the VZ of the ventral POA, anterior and posterior IDs and the VMH and ARH nuclei.
TS22: thalamus mantle layer	Very strong	Non-Uniform	Ebf3-shh E14.5-sagittal-2 , Ebf3-Shh E14.5-coronal , Ebf3-SHH E14.5-sagittal	There is very strong staining in the mantle zone of the prethalamus and moderate staining in the dorsal thalamus.
TS22: thalamus ventricular layer	Very strong	Non-Uniform	Ebf3-SHH E14.5-sagittal , Ebf3-Shh E14.5-coronal , Ebf3-shh E14.5-sagittal-2	There is very 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	Very strong		Ebf3-shh E16.5-sagittal-7 , Ebf3-shh E16.5-sagittal-10 , Ebf3-shh E16.5-sagittal-8 , Ebf3-shh E16.5.-sagittal-3 , Ebf3-shh E16.5.-sagittal-2 , Ebf3-shh E16.5-sagittal-11 , Ebf3-shh E16.5-sagittal-9 , Ebf3-shh E16.5-sagittal-5 , Ebf3-shh E16.5-sagittal-2 , Ebf3-shh E16.5-sagittal-4 , Ebf3-SHH E16.5-sagittal , Ebf3-shh E16.5-sagittal-6	There is very strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Ambiguous		Ebf3-shh E16.5-sagittal-10 , Ebf3-shh E16.5-sagittal-9 , Ebf3-shh E16.5-sagittal-4 , Ebf3-shh E16.5.-sagittal-3 , Ebf3-shh E16.5-sagittal-5 , Ebf3-shh E16.5.-sagittal-2 , Ebf3-shh E16.5-sagittal-7 , Ebf3-shh E16.5-sagittal-8 , Ebf3-shh E16.5-sagittal-2 , Ebf3-shh E16.5-sagittal-11 , Ebf3-shh E16.5-sagittal-6 , Ebf3-SHH E16.5-sagittal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Very strong		Ebf3-shh E16.5-sagittal-11 , Ebf3-shh E16.5-sagittal-8 , Ebf3-shh E16.5-sagittal-2 , Ebf3-shh E16.5-sagittal-7 , Ebf3-shh E16.5.-sagittal-2 , Ebf3-shh E16.5-sagittal-10 , Ebf3-SHH E16.5-sagittal , Ebf3-shh E16.5-sagittal-9 , Ebf3-shh E16.5-sagittal-4 , Ebf3-shh E16.5.-sagittal-3 , Ebf3-shh E16.5-sagittal-6 , Ebf3-shh E16.5-sagittal-5	There is very strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Very strong	Non-Uniform	Ebf3-shh E16.5-sagittal-6 , Ebf3-shh E16.5-sagittal-9 , Ebf3-shh E16.5-sagittal-11 , Ebf3-shh E16.5-sagittal-8 , Ebf3-shh E16.5-sagittal-4 , Ebf3-shh E16.5.-sagittal-3 , Ebf3-shh E16.5-sagittal-2 , Ebf3-shh E16.5-sagittal-7 , Ebf3-shh E16.5-sagittal-5 , Ebf3-shh E16.5-sagittal-10 , Ebf3-SHH E16.5-sagittal , Ebf3-shh E16.5.-sagittal-2	There is very strong staining in the mantle zone of the mam and supramam zone. Staining is either absent or ubiquitous in the mantle zone of the premam zone.
TS24: diencephalon ventricular layer	Ambiguous		Ebf3-shh E16.5-sagittal-5 , Ebf3-shh E16.5-sagittal-9 , Ebf3-shh E16.5-sagittal-7 , Ebf3-shh E16.5-sagittal-4 , Ebf3-shh E16.5.-sagittal-2 , Ebf3-shh E16.5-sagittal-10 , Ebf3-shh E16.5-sagittal-6 , Ebf3-SHH E16.5-sagittal , Ebf3-shh E16.5.-sagittal-3 , Ebf3-shh E16.5-sagittal-8 , Ebf3-shh E16.5-sagittal-11 , Ebf3-shh E16.5-sagittal-2	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS24: ganglionic eminence	Ambiguous		Ebf3-shh E16.5.-sagittal-2 , Ebf3-shh E16.5-sagittal-11 , Ebf3-shh E16.5-sagittal-8 , Ebf3-shh E16.5-sagittal-7 , Ebf3-SHH E16.5-sagittal , Ebf3-shh E16.5-sagittal-10 , Ebf3-shh E16.5-sagittal-9 , Ebf3-shh E16.5-sagittal-5 , Ebf3-shh E16.5-sagittal-6 , Ebf3-shh E16.5-sagittal-2 , Ebf3-shh E16.5-sagittal-4 , Ebf3-shh E16.5.-sagittal-3	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS24: hypothalamus mantle layer	Very strong	Non-Uniform	Ebf3-shh E16.5-sagittal-2 , Ebf3-shh E16.5-sagittal-7 , Ebf3-shh E16.5-sagittal-6 , Ebf3-shh E16.5.-sagittal-3 , Ebf3-shh E16.5-sagittal-11 , Ebf3-shh E16.5-sagittal-8 , Ebf3-shh E16.5-sagittal-10 , Ebf3-shh E16.5-sagittal-4 , Ebf3-shh E16.5.-sagittal-2 , Ebf3-shh E16.5-sagittal-5 , Ebf3-shh E16.5-sagittal-9 , Ebf3-SHH E16.5-sagittal	There is very strong staining in the mantle zone of the dorsal and ventral POAs, the PVH nucleus, the AVH and the PH. Staining is either absent or ubiquitous in the mantle zone of the DAH and the SCH, DMH, VMH and ARH nuclei.
TS24: hypothalamus ventricular layer	Ambiguous		Ebf3-shh E16.5-sagittal-6 , Ebf3-SHH E16.5-sagittal , Ebf3-shh E16.5-sagittal-9 , Ebf3-shh E16.5.-sagittal-2 , Ebf3-shh E16.5-sagittal-8 , Ebf3-shh E16.5-sagittal-7 , Ebf3-shh E16.5-sagittal-10 , Ebf3-shh E16.5-sagittal-5 , Ebf3-shh E16.5-sagittal-4 , Ebf3-shh E16.5-sagittal-11 , Ebf3-shh E16.5-sagittal-2 , Ebf3-shh E16.5.-sagittal-3	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	Very strong		Ebf3-shh E16.5.-sagittal-3 , Ebf3-shh E16.5-sagittal-4 , Ebf3-shh E16.5-sagittal-5 , Ebf3-shh E16.5-sagittal-6 , Ebf3-shh E16.5-sagittal-7 , Ebf3-shh E16.5-sagittal-2 , Ebf3-shh E16.5-sagittal-10 , Ebf3-shh E16.5-sagittal-8 , Ebf3-shh E16.5-sagittal-9 , Ebf3-shh E16.5.-sagittal-2 , Ebf3-shh E16.5-sagittal-11 , Ebf3-SHH E16.5-sagittal	There is very strong staining in the mantle zone of the dorsal thalamus and prethalamus.
TS24: thalamus ventricular layer	Ambiguous		Ebf3-shh E16.5-sagittal-11 , Ebf3-shh E16.5-sagittal-4 , Ebf3-shh E16.5-sagittal-2 , Ebf3-shh E16.5.-sagittal-3 , Ebf3-shh E16.5-sagittal-9 , Ebf3-shh E16.5-sagittal-6 , Ebf3-shh E16.5-sagittal-5 , Ebf3-shh E16.5-sagittal-8 , Ebf3-shh E16.5.-sagittal-2 , Ebf3-shh E16.5-sagittal-7 , Ebf3-SHH E16.5-sagittal , Ebf3-shh E16.5-sagittal-10	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.