Probe:	UI-M-AJ1-aha-f-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	Pou2f2-Shh E11.5_sagittal , Pou2f2-Shh E11.5_coronal	Staining is strong in the MZ of the prethalamus, dorsal POA & mam zone, moderate in PVH & VMH nuclei, AVH, anterior & posterior IDs, TT & supramam zone, weak in dorsal thalamus & either absent or ubiquitous in ventral POA, ARH nucleus & premam zone.
TS19: diencephalon lateral wall ventricular layer	Ambiguous		Pou2f2-Shh E11.5_sagittal , Pou2f2-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	Weak	Non-Uniform	Pou2f2-Shh E11.5_sagittal , Pou2f2-Shh E11.5_coronal	There is weak 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		Pou2f2-Shh E11.5_sagittal , Pou2f2-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	Ambiguous		Pou2f2-Shh E12.5_sagittal , Pou2f2-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		Pou2f2-Shh E12.5_coronal , Pou2f2-Shh E12.5_sagittal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Pou2f2-Shh E12.5_coronal , Pou2f2-Shh E12.5_sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS20: diencephalon mantle layer	Strong	Non-Uniform	Pou2f2-Shh E12.5_sagittal , Pou2f2-Shh E12.5_coronal	There is strong staining in the mantle zone of the mam zone and weak staining in the TT. Staining is either absent or ubiquitous in the mantle zone of the premam and supramam zones.
TS20: diencephalon ventricular layer	Ambiguous		Pou2f2-Shh E12.5_coronal , Pou2f2-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	Weak	Non-Uniform	Pou2f2-Shh E12.5_sagittal , Pou2f2-Shh E12.5_coronal	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.
TS20: hypothalamus mantle layer	Moderate	Non-Uniform	Pou2f2-Shh E12.5_sagittal , Pou2f2-Shh E12.5_coronal	There is moderate staining in the mantle zone of the PVH and VMH nuclei and the AVH and weak staining in the dorsal and ventral POAs, anterior and posterior IDs and ARH nucleus.
TS20: hypothalamus ventricular layer	Ambiguous		Pou2f2-Shh E12.5_coronal , Pou2f2-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	Pou2f2-Shh E12.5_sagittal , Pou2f2-Shh E12.5_coronal	There is very strong staining in the mantle zone of the dorsal thalamus and strong staining in the prethalamus.
TS20: thalamus ventricular layer	Ambiguous		Pou2f2-Shh E12.5_coronal , Pou2f2-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		Pou2f2-Shh E14.5_sagittal , Pou2f2-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		Pou2f2-Shh E14.5_sagittal , Pou2f2-Shh E14.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Pou2f2-Shh E14.5_coronal , Pou2f2-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	Strong	Non-Uniform	Pou2f2-Shh E14.5_coronal , Pou2f2-Shh E14.5_sagittal	There is strong staining in the mantle zone of the mam zone. Staining is either absent or ubiquitous in the mantle zone of the premam and supramam zones and the TT.
TS22: diencephalon ventricular layer	Ambiguous		Pou2f2-Shh E14.5_sagittal , Pou2f2-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	Weak	Non-Uniform	Pou2f2-Shh E14.5_coronal , Pou2f2-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	Strong	Non-Uniform	Pou2f2-Shh E14.5_sagittal , Pou2f2-Shh E14.5_coronal	There is strong staining in the mantle zone of the PVH, VMH and ARH nucleus, moderate ventral POA and anterior and posterior IDs and weak staining in the dorsal POA and the AVH.
TS22: hypothalamus ventricular layer	Ambiguous		Pou2f2-Shh E14.5_coronal , Pou2f2-Shh E14.5_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	Pou2f2-Shh E14.5_coronal , Pou2f2-Shh E14.5_sagittal	There is very strong staining in the mantle zone of the dorsal thalamus and weak staining in the prethalamus.
TS22: thalamus ventricular layer	Ambiguous		Pou2f2-Shh E14.5_coronal , Pou2f2-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		Pou2f2-Shh E16.5_coronal , Pou2f2-Shh E16.5_sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Ambiguous		Pou2f2-Shh E16.5_coronal , Pou2f2-Shh E16.5_sagittal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Pou2f2-Shh E16.5_sagittal , Pou2f2-Shh E16.5_coronal	Staining is either absent or ubiquitous in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Strong	Non-Uniform	Pou2f2-Shh E16.5_sagittal , Pou2f2-Shh E16.5_coronal	There is strong staining in the mantle zone of the mam zone. Staining is either absent or ubiquitous in the mantle zone of the premam and supramam zones.
TS24: diencephalon ventricular layer	Ambiguous		Pou2f2-Shh E16.5_sagittal , Pou2f2-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS24: ganglionic eminence	Ambiguous		Pou2f2-Shh E16.5_coronal , Pou2f2-Shh E16.5_sagittal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS24: hypothalamus mantle layer	Strong	Non-Uniform	Pou2f2-Shh E16.5_sagittal , Pou2f2-Shh E16.5_coronal	There is strong staining in the mantle zone of the SCH, VMH and ARH nuclei and the PH, moderate staining in the dorsal and ventral POAs, PVH and DMH nuclei and the DAH and weak staining in the AVH.
TS24: hypothalamus ventricular layer	Ambiguous		Pou2f2-Shh E16.5_coronal , Pou2f2-Shh E16.5_sagittal	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	Pou2f2-Shh E16.5_sagittal , Pou2f2-Shh E16.5_coronal	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.
TS24: thalamus ventricular layer	Ambiguous		Pou2f2-Shh E16.5_sagittal , Pou2f2-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.