Probe:	UI-M-BH3-awd-f-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	Very strong	Non-Uniform	Lhx5-Shh E11.5-coronal , Lhx5-Shh 11.5-sagittal	Staining is very strong in the MZ of the mam zone, strong in prethalamus, dorsal & ventral POAs, PVH nucleus & AVH & either absent or ubiquitous in the dorsal thalamus, anterior & posterior IDs, VMH & ARH nuclei, premam & supramam zones & TT.
TS19: diencephalon lateral wall ventricular layer	Very strong	Non-Uniform	Lhx5-Shh 11.5-sagittal , Lhx5-Shh E11.5-coronal	Staining is very strong in the VZ of the mam zone, strong in prethalamus, dorsal & ventral POAs, PVH nucleus & AVH & either absent or ubiquitous in the dorsal thalamus, anterior & posterior IDs, VMH & ARH nuclei, premam & supramam zones & TT.
TS19: telencephalon mantle layer	Ambiguous		Lhx5-Shh E11.5-coronal , Lhx5-Shh 11.5-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	Lhx5-Shh E11.5-coronal , Lhx5-Shh 11.5-sagittal	There is strong 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		Lhx5-Shh E12.5-coronal , Lhx5-Shh 12.5-sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS20: cerebral cortex ventricular layer	Ambiguous		Lhx5-Shh E12.5-coronal , Lhx5-Shh 12.5-sagittal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Lhx5-Shh 12.5-sagittal , Lhx5-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	Very strong	Non-Uniform	Lhx5-Shh 12.5-sagittal , Lhx5-Shh E12.5-coronal	There is very strong staining in the mantle zone of the mam zone and moderate, scattered staining in the premam and supramam zones. Staining is either absent or ubiquitous in the mantle zone of the TT.
TS20: diencephalon ventricular layer	Very strong	Non-Uniform	Lhx5-Shh 12.5-sagittal , Lhx5-Shh E12.5-coronal	There is very strong staining in the ventricular zone of the mam zone and moderate, scattered staining in the premam zone. Staining is either absent or ubiquitous in the ventricular zone of the supramam zone and the TT.
TS20: ganglionic eminence	Strong	Non-Uniform	Lhx5-Shh E12.5-coronal , Lhx5-Shh 12.5-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	Very strong	Non-Uniform	Lhx5-Shh 12.5-sagittal , Lhx5-Shh E12.5-coronal	There is very strong staining in the mantle zone of the dorsal and ventral POAs, PVH nucleus and the AVH. Staining is either absent or ubiquitous in the mantle zone of the anterior and posterior IDs and VMH and ARH nuclei.
TS20: hypothalamus ventricular layer	Very strong	Non-Uniform	Lhx5-Shh 12.5-sagittal , Lhx5-Shh E12.5-coronal	There is very strong staining in the ventricular zone of the dorsal and ventral POAs, the PVH nucleus and the AVH. Staining is either absent or ubiquitous in the ventricular zone of the anterior and posterior IDs and VMH and ARH nuclei.
TS20: thalamus mantle layer	Very strong	Non-Uniform	Lhx5-Shh E12.5-coronal , Lhx5-Shh 12.5-sagittal	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	Ambiguous		Lhx5-Shh 12.5-sagittal , Lhx5-Shh E12.5-coronal	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		Lhx5-Shh E14.5-coronal , Lhx5-Shh 14.5-sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Ambiguous		Lhx5-Shh 14.5-sagittal , Lhx5-Shh E14.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Lhx5-Shh 14.5-sagittal , Lhx5-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	Very strong	Non-Uniform	Lhx5-Shh 14.5-sagittal , Lhx5-Shh E14.5-coronal	There is very strong staining in the mantle zone of the mam zone and strong, scattered staining in the premam and supramam zones and the TT.
TS22: diencephalon ventricular layer	Very strong	Non-Uniform	Lhx5-Shh E14.5-coronal , Lhx5-Shh 14.5-sagittal	There is very strong staining in the ventricular zone of the mam zone. Staining is either absent or ubiquitous in the ventricular zone of the premam and supramam zones and the TT.
TS22: ganglionic eminence	Strong	Non-Uniform	Lhx5-Shh E14.5-coronal , Lhx5-Shh 14.5-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.
TS22: hypothalamus mantle layer	Very strong	Non-Uniform	Lhx5-Shh E14.5-coronal , Lhx5-Shh 14.5-sagittal	There is very strong staining in the MZ of the dorsal & ventral POAs, the PVH nucleus & the AVH, moderate staining in the ARH nucleus & weak staining in the VMH nucleus. Staining is either absent or ubiquitous in the MZ of the anterior & posterior IDs.
TS22: hypothalamus ventricular layer	Ambiguous		Lhx5-Shh E14.5-coronal , Lhx5-Shh 14.5-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	Very strong	Non-Uniform	Lhx5-Shh E14.5-coronal , Lhx5-Shh 14.5-sagittal	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.
TS22: thalamus ventricular layer	Very strong	Non-Uniform	Lhx5-Shh E14.5-coronal , Lhx5-Shh 14.5-sagittal	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
TS24: cerebral cortex intermediate zone	Very strong		Lhx5-Shh 16.5-sagittal-10 , Lhx5-Shh 16.5-sagittal-6 , Lhx5-Shh 16.5-sagittal-9 , Lhx5-Shh 16.5-sagittal-2 , Lhx5-Shh 16.5-sagittal-7 , Lhx5-Shh 16.5-sagittal , Lhx5-Shh 16.5-sagittal-3 , Lhx5-Shh 16.5-sagittal-11 , Lhx5-Shh 16.5-sagittal-4 , Lhx5-Shh 16.5-sagittal-5 , Lhx5-Shh E16.5-coronal , Lhx5-Shh 16.5-sagittal-8	There is very strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Ambiguous		Lhx5-Shh 16.5-sagittal , Lhx5-Shh 16.5-sagittal-9 , Lhx5-Shh E16.5-coronal , Lhx5-Shh 16.5-sagittal-8 , Lhx5-Shh 16.5-sagittal-11 , Lhx5-Shh 16.5-sagittal-3 , Lhx5-Shh 16.5-sagittal-4 , Lhx5-Shh 16.5-sagittal-5 , Lhx5-Shh 16.5-sagittal-6 , Lhx5-Shh 16.5-sagittal-10 , Lhx5-Shh 16.5-sagittal-7 , Lhx5-Shh 16.5-sagittal-2	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Very strong		Lhx5-Shh 16.5-sagittal-11 , Lhx5-Shh 16.5-sagittal-10 , Lhx5-Shh 16.5-sagittal , Lhx5-Shh 16.5-sagittal-9 , Lhx5-Shh 16.5-sagittal-5 , Lhx5-Shh 16.5-sagittal-3 , Lhx5-Shh 16.5-sagittal-6 , Lhx5-Shh 16.5-sagittal-2 , Lhx5-Shh 16.5-sagittal-4 , Lhx5-Shh 16.5-sagittal-7 , Lhx5-Shh 16.5-sagittal-8 , Lhx5-Shh E16.5-coronal	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	Lhx5-Shh 16.5-sagittal-7 , Lhx5-Shh 16.5-sagittal-11 , Lhx5-Shh 16.5-sagittal-10 , Lhx5-Shh 16.5-sagittal-9 , Lhx5-Shh 16.5-sagittal-6 , Lhx5-Shh 16.5-sagittal-2 , Lhx5-Shh 16.5-sagittal , Lhx5-Shh 16.5-sagittal-4 , Lhx5-Shh 16.5-sagittal-8 , Lhx5-Shh 16.5-sagittal-3 , Lhx5-Shh E16.5-coronal , Lhx5-Shh 16.5-sagittal-5	There is very strong staining in the mantle zone of the mam zone, strong, scattered staining in the premam zone and moderate staining in the supramam zone.
TS24: diencephalon ventricular layer	Very strong	Non-Uniform	Lhx5-Shh 16.5-sagittal-5 , Lhx5-Shh 16.5-sagittal , Lhx5-Shh 16.5-sagittal-2 , Lhx5-Shh 16.5-sagittal-9 , Lhx5-Shh 16.5-sagittal-3 , Lhx5-Shh 16.5-sagittal-6 , Lhx5-Shh 16.5-sagittal-10 , Lhx5-Shh 16.5-sagittal-11 , Lhx5-Shh 16.5-sagittal-7 , Lhx5-Shh 16.5-sagittal-8 , Lhx5-Shh E16.5-coronal , Lhx5-Shh 16.5-sagittal-4	There is very strong staining in the ventricular zone of the mam zone. Staining is either absent or ubiquitous in the ventricular zone of the premam and supramam zones.
TS24: ganglionic eminence	Moderate	Non-Uniform	Lhx5-Shh 16.5-sagittal-11 , Lhx5-Shh 16.5-sagittal , Lhx5-Shh 16.5-sagittal-4 , Lhx5-Shh 16.5-sagittal-5 , Lhx5-Shh 16.5-sagittal-2 , Lhx5-Shh 16.5-sagittal-6 , Lhx5-Shh 16.5-sagittal-9 , Lhx5-Shh 16.5-sagittal-10 , Lhx5-Shh E16.5-coronal , Lhx5-Shh 16.5-sagittal-8 , Lhx5-Shh 16.5-sagittal-7 , Lhx5-Shh 16.5-sagittal-3	There is moderate staining in the ventricular zone of the ganglionic eminences. Staining is either absent or ubiquitous in the mantle zone of the ganglionic eminences.
TS24: hypothalamus mantle layer	Strong	Non-Uniform	Lhx5-Shh 16.5-sagittal-7 , Lhx5-Shh 16.5-sagittal-10 , Lhx5-Shh 16.5-sagittal-8 , Lhx5-Shh 16.5-sagittal-11 , Lhx5-Shh 16.5-sagittal-4 , Lhx5-Shh 16.5-sagittal , Lhx5-Shh 16.5-sagittal-9 , Lhx5-Shh 16.5-sagittal-3 , Lhx5-Shh E16.5-coronal , Lhx5-Shh 16.5-sagittal-6 , Lhx5-Shh 16.5-sagittal-5 , Lhx5-Shh 16.5-sagittal-2	Staining is strong in the MZ of the dorsal & ventral POAs, strong & scattered in the PH, moderate in the PVH, DMH & ARH nuclei, AVH & DAH & moderate & scattered in the SCH nucleus. Staining is either absent or ubiquitous in the MZ of the VMH nucleus.
TS24: hypothalamus ventricular layer	Ambiguous		Lhx5-Shh 16.5-sagittal-8 , Lhx5-Shh 16.5-sagittal-6 , Lhx5-Shh 16.5-sagittal-2 , Lhx5-Shh 16.5-sagittal-9 , Lhx5-Shh 16.5-sagittal-11 , Lhx5-Shh E16.5-coronal , Lhx5-Shh 16.5-sagittal-10 , Lhx5-Shh 16.5-sagittal-4 , Lhx5-Shh 16.5-sagittal-7 , Lhx5-Shh 16.5-sagittal-3 , Lhx5-Shh 16.5-sagittal , Lhx5-Shh 16.5-sagittal-5	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	Non-Uniform	Lhx5-Shh 16.5-sagittal-5 , Lhx5-Shh 16.5-sagittal-10 , Lhx5-Shh 16.5-sagittal-11 , Lhx5-Shh 16.5-sagittal-3 , Lhx5-Shh 16.5-sagittal-4 , Lhx5-Shh E16.5-coronal , Lhx5-Shh 16.5-sagittal-2 , Lhx5-Shh 16.5-sagittal-8 , Lhx5-Shh 16.5-sagittal , Lhx5-Shh 16.5-sagittal-9 , Lhx5-Shh 16.5-sagittal-7 , Lhx5-Shh 16.5-sagittal-6	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.
TS24: thalamus ventricular layer	Very strong	Non-Uniform	Lhx5-Shh 16.5-sagittal , Lhx5-Shh 16.5-sagittal-8 , Lhx5-Shh 16.5-sagittal-4 , Lhx5-Shh 16.5-sagittal-2 , Lhx5-Shh 16.5-sagittal-10 , Lhx5-Shh 16.5-sagittal-3 , Lhx5-Shh 16.5-sagittal-5 , Lhx5-Shh 16.5-sagittal-7 , Lhx5-Shh 16.5-sagittal-9 , Lhx5-Shh 16.5-sagittal-11 , Lhx5-Shh 16.5-sagittal-6 , Lhx5-Shh E16.5-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.