Probe:	UI-M-AH1-agr-a-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	Strong	Non-Uniform	Nhlh2-Shh E11.5_sagittal , Nhlh2-Shh E11.5_coronal	Staining is strong in the MZ of the prethalamus, dorsal & ventral POAs, PVH nucleus & mam & supramam zones, moderate in dorsal thalamus, weak in anterior ID & either absent or ubiquitous in the AVH, posterior ID, VMH & ARH nuclei, premam zone & TT.
TS19: diencephalon lateral wall ventricular layer	Strong	Non-Uniform	Nhlh2-Shh E11.5_coronal , Nhlh2-Shh E11.5_sagittal	There is strong staining in the VZ of the dorsal POA, PVH nucleus & mam & supramam zones. Staining is either absent or ubiquitous in the VZ of dorsal thalamus, prethalamus, ventral POA, VMH & ARH nuclei, AVH, anterior & posterior IDs, premam zone & TT.
TS19: telencephalon mantle layer	Moderate	Non-Uniform	Nhlh2-Shh E11.5_coronal , Nhlh2-Shh E11.5_sagittal	There is moderate 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	Ambiguous		Nhlh2-Shh E11.5_sagittal , Nhlh2-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	Moderate		Nhlh2-Shh E12.5_sagittal , Nhlh2-Shh E12.5_coronal	There is moderate staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS20: cerebral cortex ventricular layer	Ambiguous		Nhlh2-Shh E12.5_coronal , Nhlh2-Shh E12.5_sagittal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Moderate		Nhlh2-Shh E12.5_sagittal , Nhlh2-Shh E12.5_coronal	There is moderate staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS20: diencephalon mantle layer	Weak	Non-Uniform	Nhlh2-Shh E12.5_sagittal , Nhlh2-Shh E12.5_coronal	There is weak, scattered 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	Nhlh2-Shh E12.5_coronal , Nhlh2-Shh E12.5_sagittal	There is very strong staining in the ventricular zone of the mam and supramam zones. Staining is either absent or ubiquitous in the ventricular zone of the premam zone and the TT.
TS20: ganglionic eminence	Ambiguous		Nhlh2-Shh E12.5_coronal , Nhlh2-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	Nhlh2-Shh E12.5_sagittal , Nhlh2-Shh E12.5_coronal	There is very strong staining in the MZ of the PVH nucleus and moderate staining in the anterior ID and VMH nucleus. Staining is either absent or ubiquitous in the MZ of the dorsal and ventral POAs, the ARH nucleus, the AVH and posterior ID.
TS20: hypothalamus ventricular layer	Very strong	Non-Uniform	Nhlh2-Shh E12.5_sagittal , Nhlh2-Shh E12.5_coronal	There is very strong staining in the ventricular zone of the AVH. Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei and anterior and posterior IDs.
TS20: thalamus mantle layer	Very strong		Nhlh2-Shh E12.5_coronal , Nhlh2-Shh E12.5_sagittal	There is very strong staining in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Very strong		Nhlh2-Shh E12.5_coronal , Nhlh2-Shh E12.5_sagittal	There is very strong staining in the ventricular zone of the dorsal thalamus and prethalamus.

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Strong		Nhlh2-Shh E14.5_sagittal , Nhlh2-Shh E14.5_coronal	There is strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Ambiguous		Nhlh2-Shh E14.5_sagittal , Nhlh2-Shh E14.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Strong		Nhlh2-Shh E14.5_sagittal , Nhlh2-Shh E14.5_coronal	There is strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Very strong	Non-Uniform	Nhlh2-Shh E14.5_coronal , Nhlh2-Shh E14.5_sagittal	There is very strong staining in the mantle zone of the supramam zone and moderate staining in the mam zone. Staining is either absent or ubiquitous in the mantle zone of the premam zone and the TT.
TS22: diencephalon ventricular layer	Ambiguous		Nhlh2-Shh E14.5_coronal , Nhlh2-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	Weak	Non-Uniform	Nhlh2-Shh E14.5_coronal , Nhlh2-Shh E14.5_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.
TS22: hypothalamus mantle layer	Moderate	Non-Uniform	Nhlh2-Shh E14.5_sagittal , Nhlh2-Shh E14.5_coronal	There is moderate staining in the mantle zone of the PVH and VMH nuclei and the AVH. Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, anterior and posterior IDs and ARH nucleus.
TS22: hypothalamus ventricular layer	Strong	Non-Uniform	Nhlh2-Shh E14.5_sagittal , Nhlh2-Shh E14.5_coronal	There is strong staining in the VZ of the PVH nucleus and moderate staining in the AVH and VMH nucleus. Staining is either absent or ubiquitous in the VZ of the dorsal and ventral POAs, the ARH nucleus and anterior and posterior IDs.
TS22: thalamus mantle layer	Very strong	Non-Uniform	Nhlh2-Shh E14.5_sagittal , Nhlh2-Shh E14.5_coronal	There is very strong staining in the mantle zone of the prethalamus and strong staining in the dorsal thalamus.
TS22: thalamus ventricular layer	Very strong	Non-Uniform	Nhlh2-Shh E14.5_coronal , Nhlh2-Shh E14.5_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		Nhlh2-Shh E16.5_coronal , Nhlh2-Shh E16.5_sagittal	There is very strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Ambiguous		Nhlh2-Shh E16.5_sagittal , Nhlh2-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Very strong		Nhlh2-Shh E16.5_sagittal , Nhlh2-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	Weak	Non-Uniform	Nhlh2-Shh E16.5_coronal , Nhlh2-Shh E16.5_sagittal	There is weak, scattered 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.
TS24: diencephalon ventricular layer	Strong	Non-Uniform	Nhlh2-Shh E16.5_coronal , Nhlh2-Shh E16.5_sagittal	There is strong staining in the ventricular zone of the mam zone and moderate, scattered staining in the supramam zone. Staining is either absent or ubiquitous in the ventricular zone of the premam zone.
TS24: ganglionic eminence	Ambiguous		Nhlh2-Shh E16.5_sagittal , Nhlh2-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS24: hypothalamus mantle layer	Moderate	Non-Uniform	Nhlh2-Shh E16.5_sagittal , Nhlh2-Shh E16.5_coronal	There is moderate staining in the mantle zone of the PVH nucleus and the DAH and weak staining in the VMH nucleus. Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the SCH, DMH and ARH nuclei, the AVH and the PH.
TS24: hypothalamus ventricular layer	Moderate	Non-Uniform	Nhlh2-Shh E16.5_coronal , Nhlh2-Shh E16.5_sagittal	There is moderate staining in the VZ of the PVH and SCH nuclei and weak, scattered staining in the PH. Staining is either absent or ubiquitous in the VZ of the dorsal and ventral POAs, the DMH, VMH and ARH nuclei, the AVH and the DAH.
TS24: thalamus mantle layer	Very strong	Non-Uniform	Nhlh2-Shh E16.5_coronal , Nhlh2-Shh E16.5_sagittal	There is very strong staining in the mantle zone of the dorsal thalamus and strong staining in the prethalamus.
TS24: thalamus ventricular layer	Ambiguous		Nhlh2-Shh E16.5_sagittal , Nhlh2-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.