Probe:	UI-M-BH1-akv-d-09-0-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	Dlx5-Shh E11.5-coronal , Dlx5-Shh E11.5-sagittal-2 , Dlx5-Shh E11.5-sagittal	Staining is very strong in the MZ of the prethalamus, dorsal & ventral POAs, AVH, anterior & posterior IDs & TT, moderate & scattered in the premam zone & either absent or ubiquitous the dorsal thalamus, PVH, VMH & ARH nuclei & mam & supramam zones.
TS19: diencephalon lateral wall ventricular layer	Very strong	Non-Uniform	Dlx5-Shh E11.5-sagittal-2 , Dlx5-Shh E11.5-coronal , Dlx5-Shh E11.5-sagittal	There is very strong staining in the MZ of the prethalamus, dorsal & ventral POAs, anterior & posterior IDs & TT. Staining is either absent or ubiquitous in the VZ of the dorsal thalamus, the PVH, VMH & ARH nuclei, the AVH & premam, mam & supramam zones.
TS19: telencephalon mantle layer	Very strong	Non-Uniform	Dlx5-Shh E11.5-sagittal-2 , Dlx5-Shh E11.5-sagittal , Dlx5-Shh E11.5-coronal	There is very strong staining in the mantle zone of the ganglionic eminences. Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone and cortical plate of the cerebral cortex.
TS19: telencephalon ventricular layer	Very strong	Non-Uniform	Dlx5-Shh E11.5-sagittal-2 , Dlx5-Shh E11.5-sagittal , Dlx5-Shh E11.5-coronal	There is very strong staining in the ventricular zone of the ganglionic eminences. Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone and cortical plate of the cerebral cortex.

Structure	Level	Pattern	Image	Note
TS20: cerebral cortex intermediate zone	Ambiguous		Dlx5-Shh E12.5-sagittal-2 , Dlx5-Shh E12.5-sagittal , Dlx5-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	Ambiguous		Dlx5-Shh E12.5-sagittal-2 , Dlx5-Shh E12.5-sagittal , Dlx5-Shh E12.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Dlx5-Shh E12.5-sagittal-2 , Dlx5-Shh E12.5-sagittal , Dlx5-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	Dlx5-Shh E12.5-sagittal-2 , Dlx5-Shh E12.5-sagittal , Dlx5-Shh E12.5-coronal	There is very strong staining in the mantle zone of the TT and moderate, scattered staining in the premam zone. Staining is either absent or ubiquitous in the mantle zone of the mam and supramam zone.
TS20: diencephalon ventricular layer	Very strong	Non-Uniform	Dlx5-Shh E12.5-coronal , Dlx5-Shh E12.5-sagittal , Dlx5-Shh E12.5-sagittal-2	There is very 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	Very strong	Non-Uniform	Dlx5-Shh E12.5-coronal , Dlx5-Shh E12.5-sagittal-2 , Dlx5-Shh E12.5-sagittal	There is very strong staining in the ventricular zone of the ganglionic eminences and moderate, scattered staining in the mantle zone of the ganglionic eminences.
TS20: hypothalamus mantle layer	Very strong	Non-Uniform	Dlx5-Shh E12.5-sagittal-2 , Dlx5-Shh E12.5-sagittal , Dlx5-Shh E12.5-coronal	There is very strong staining in the mantle zone of the AVH and anterior and posterior IDs and moderate, scattered staining the dorsal and ventral POAs. Staining is either absent or ubiquitous in the mantle zone of the PVH, VMH and ARH nuclei.
TS20: hypothalamus ventricular layer	Very strong	Non-Uniform	Dlx5-Shh E12.5-coronal , Dlx5-Shh E12.5-sagittal-2 , Dlx5-Shh E12.5-sagittal	There is very strong staining in the ventricular zone of the dorsal and ventral POAs, the AVH and anterior and posterior IDs. Staining is either absent or ubiquitous in the ventricular zone of the PVH, VMH and ARH nuclei.
TS20: thalamus mantle layer	Very strong	Non-Uniform	Dlx5-Shh E12.5-sagittal , Dlx5-Shh E12.5-coronal , Dlx5-Shh E12.5-sagittal-2	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	Dlx5-Shh E12.5-sagittal-2 , Dlx5-Shh E12.5-coronal , Dlx5-Shh E12.5-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
TS22: cerebral cortex intermediate zone	Ambiguous		Dlx5-Shh E14.5-sagittal-2 , Dlx5-Shh E14.5-sagittal , Dlx5-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		Dlx5-Shh E14.5-coronal , Dlx5-Shh E14.5-sagittal-2 , Dlx5-Shh E14.5-sagittal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Dlx5-Shh E14.5-coronal , Dlx5-Shh E14.5-sagittal-2 , Dlx5-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	Very strong	Non-Uniform	Dlx5-Shh E14.5-sagittal , Dlx5-Shh E14.5-sagittal-2 , Dlx5-Shh E14.5-coronal	There is very strong staining in the mantle zone of the TT and moderate, scattered staining in the premam zone. Staining is either absent or ubiquitous in the mantle zone of the mam and supramam zone.
TS22: diencephalon ventricular layer	Very strong	Non-Uniform	Dlx5-Shh E14.5-sagittal-2 , Dlx5-Shh E14.5-sagittal , Dlx5-Shh E14.5-coronal	There is very strong staining in the ventricular zone of the TT and moderate staining in the premam zone. Staining is either absent or ubiquitous in the ventricular zone of the mam and supramam.
TS22: ganglionic eminence	Very strong		Dlx5-Shh E14.5-coronal , Dlx5-Shh E14.5-sagittal , Dlx5-Shh E14.5-sagittal-2	There is very strong staining in the ventricular and mantle zones of the ganglionic eminences.
TS22: hypothalamus mantle layer	Very strong	Non-Uniform	Dlx5-Shh E14.5-sagittal , Dlx5-Shh E14.5-coronal , Dlx5-Shh E14.5-sagittal-2	There is very strong staining in the MZ of the AVH and anterior and posterior IDs and moderate, scattered staining the dorsal and ventral ventral POAs and ARH nucleus. Staining is either absent or ubiquitous in the MZ of the PVH and VMH nuclei.
TS22: hypothalamus ventricular layer	Very strong	Non-Uniform	Dlx5-Shh E14.5-coronal , Dlx5-Shh E14.5-sagittal , Dlx5-Shh E14.5-sagittal-2	There is very strong staining in the VZ of the dorsal and ventral POAs, the AVH and anterior and posterior IDs and moderate staining in the ARH nucleus. Staining is either absent or ubiquitous in the VZ of the PVH and VMH nuclei.
TS22: thalamus mantle layer	Moderate	Non-Uniform	Dlx5-Shh E14.5-sagittal-2 , Dlx5-Shh E14.5-coronal , Dlx5-Shh E14.5-sagittal	There is moderate 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	Dlx5-Shh E14.5-sagittal , Dlx5-Shh E14.5-coronal , Dlx5-Shh E14.5-sagittal-2	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	Moderate		Dlx5-Shh E16.5-coronal , Dlx5-Shh E16.5-sagittal-2 , Dlx5-Shh E16.5-sagittal	There is moderate staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Ambiguous		Dlx5-Shh E16.5-sagittal , Dlx5-Shh E16.5-sagittal-2 , Dlx5-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Moderate		Dlx5-Shh E16.5-coronal , Dlx5-Shh E16.5-sagittal-2 , Dlx5-Shh E16.5-sagittal	There is moderate staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Strong	Non-Uniform	Dlx5-Shh E16.5-sagittal , Dlx5-Shh E16.5-sagittal-2 , Dlx5-Shh E16.5-coronal	There is strong, scattered 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	Ambiguous		Dlx5-Shh E16.5-sagittal , Dlx5-Shh E16.5-coronal , Dlx5-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	Very strong		Dlx5-Shh E16.5-sagittal , Dlx5-Shh E16.5-sagittal-2 , Dlx5-Shh E16.5-coronal	There is very strong staining in the ventricular and mantle zones of the ganglionic eminences.
TS24: hypothalamus mantle layer	Very strong	Non-Uniform	Dlx5-Shh E16.5-coronal , Dlx5-Shh E16.5-sagittal , Dlx5-Shh E16.5-sagittal-2	There is very strong staining in the mantle zone of the dorsal and ventral POAs, the AVH, the DAH, the DMH and ARH nuclei and the PH. Staining is either absent or ubiquitous in the mantle zone of the PVH, SCH and VMH nuclei.
TS24: hypothalamus ventricular layer	Very strong	Non-Uniform	Dlx5-Shh E16.5-coronal , Dlx5-Shh E16.5-sagittal , Dlx5-Shh E16.5-sagittal-2	There is very strong staining in the ventricular zone of the dorsal and ventral POAs, the AVH, the DAH, the DMH and ARH nuclei and the PH. Staining is either absent or ubiquitous in the ventricular zone of the PVH, SCH and VMH nuclei.
TS24: thalamus mantle layer	Very strong	Non-Uniform	Dlx5-Shh E16.5-sagittal-2 , Dlx5-Shh E16.5-sagittal , Dlx5-Shh E16.5-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.
TS24: thalamus ventricular layer	Very strong	Non-Uniform	Dlx5-Shh E16.5-coronal , Dlx5-Shh E16.5-sagittal-2 , Dlx5-Shh E16.5-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.