Probe:	UI-M-CD1-bas-c-12-0-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	Ambiguous		Hmgb2-Shh E11.5-sagittal , Hmgb2-Shh E11.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus, 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: diencephalon lateral wall ventricular layer	Strong		Hmgb2-Shh E11.5-sagittal , Hmgb2-Shh E11.5-coronal	There is strong, scattered staining 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	Ambiguous		Hmgb2-Shh E11.5-coronal , Hmgb2-Shh E11.5-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	Scattered	Hmgb2-Shh E11.5-coronal , Hmgb2-Shh E11.5-sagittal	There is strong, scattered staining in the ventricular zone of the cerebral cortex and the ganglionic eminences.

Structure	Level	Pattern	Image	Note
TS20: cerebral cortex intermediate zone	Ambiguous		Hmgb2-Shh E12.5-sagittal , Hmgb2-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	Strong	Scattered	Hmgb2-Shh E12.5-coronal , Hmgb2-Shh E12.5-sagittal	There is strong, scattered staining in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Hmgb2-Shh E12.5-sagittal , Hmgb2-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	Ambiguous		Hmgb2-Shh E12.5-sagittal , Hmgb2-Shh E12.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the premam, mam and supramam zones and the TT.
TS20: diencephalon ventricular layer	Strong	Scattered	Hmgb2-Shh E12.5-sagittal , Hmgb2-Shh E12.5-coronal	There is strong, scattered staining in the ventricular zone of the premam, mam and supramam zones and the TT.
TS20: ganglionic eminence	Strong	Non-Uniform	Hmgb2-Shh E12.5-sagittal , Hmgb2-Shh E12.5-coronal	There is strong, scattered staining in the ventricular zone of the ganglionic eminences and weak, scattered staining in the mantle zone of the ganglionic eminences.
TS20: hypothalamus mantle layer	Ambiguous		Hmgb2-Shh E12.5-coronal , Hmgb2-Shh E12.5-sagittal	Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei, the AVH and anterior and posterior IDs.
TS20: hypothalamus ventricular layer	Strong	Non-Uniform	Hmgb2-Shh E12.5-coronal , Hmgb2-Shh E12.5-sagittal	There is strong, scattered staining in the ventricular zone of the dorsal and ventral POAs, VMH and ARH nuclei, the AVH and anterior and posterior IDs and weak, scattered staining in the PVH nucleus.
TS20: thalamus mantle layer	Ambiguous		Hmgb2-Shh E12.5-sagittal , Hmgb2-Shh E12.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Strong	Non-Uniform	Hmgb2-Shh E12.5-coronal , Hmgb2-Shh E12.5-sagittal	There is strong staining in the ventricular zone of the dorsal thalamus and strong, scattered staining in the prethalamus.

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Ambiguous		Hmgb2-Shh E14.5-sagittal , Hmgb2-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	Very strong		Hmgb2-Shh E14.5-sagittal , Hmgb2-Shh E14.5-coronal	There is very strong staining in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Hmgb2-Shh E14.5-sagittal , Hmgb2-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	Ambiguous		Hmgb2-Shh E14.5-sagittal , Hmgb2-Shh E14.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the premam, mam and supramam zones and the TT.
TS22: diencephalon ventricular layer	Strong	Non-Uniform	Hmgb2-Shh E14.5-coronal , Hmgb2-Shh E14.5-sagittal	There is strong staining in the ventricular zone of the premam and mam zones and weak staining in the TT. Staining is either absent or ubiquitous in the ventricular zone of the supramam zone.
TS22: ganglionic eminence	Very strong	Non-Uniform	Hmgb2-Shh E14.5-sagittal , Hmgb2-Shh E14.5-coronal	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.
TS22: hypothalamus mantle layer	Ambiguous		Hmgb2-Shh E14.5-sagittal , Hmgb2-Shh E14.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei, the AVH and anterior and posterior IDs.
TS22: hypothalamus ventricular layer	Strong	Non-Uniform	Hmgb2-Shh E14.5-coronal , Hmgb2-Shh E14.5-sagittal	There is strong staining in the VZ of the ventral POA, the AVH and the VMH nucleus and weak, scattered staining in the dorsal POA, PVH nucleus and the anterior and posterior IDs. Staining is either absent or ubiquitous in the VZ of the ARH nucleus.
TS22: thalamus mantle layer	Ambiguous		Hmgb2-Shh E14.5-sagittal , Hmgb2-Shh E14.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS22: thalamus ventricular layer	Strong	Non-Uniform	Hmgb2-Shh E14.5-sagittal , Hmgb2-Shh E14.5-coronal	There is strong staining in the ventricular zone of the dorsal thalamus and weak staining in the prethalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Weak	Scattered	Hmgb2-Shh E16.5-sagittal , Hmgb2-Shh E16.5-coronal	There is weak, scattered staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Very strong		Hmgb2-Shh E16.5-sagittal , Hmgb2-Shh E16.5-coronal	There is very strong staining in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Weak	Scattered	Hmgb2-Shh E16.5-sagittal , Hmgb2-Shh E16.5-coronal	There is weak, scattered staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Weak	Scattered	Hmgb2-Shh E16.5-sagittal , Hmgb2-Shh E16.5-coronal	There is weak, scattered staining in the mantle zone of the premam, mam and supramam zones.
TS24: diencephalon ventricular layer	Strong	Non-Uniform	Hmgb2-Shh E16.5-sagittal , Hmgb2-Shh E16.5-coronal	There is strong staining in the ventricular zone of the premam and mam zones. Staining is either absent or ubiquitous in the ventricular zone of the supramam zone.
TS24: ganglionic eminence	Very strong	Non-Uniform	Hmgb2-Shh E16.5-coronal , Hmgb2-Shh E16.5-sagittal	There is very strong staining in the ventricular zone of the ganglionic eminences and weak, scattered staining in the mantle zone of the ganglionic eminences.
TS24: hypothalamus mantle layer	Strong	Non-Uniform	Hmgb2-Shh E16.5-sagittal , Hmgb2-Shh E16.5-coronal	There is strong staining in the MZ of the VMH nucleus and weak, scattered staining in the ventral POA, DMH and ARH nuclei and the PH. Staining is either absent or ubiquitous in the MZ of the dorsal POA, PVH and SCH nuclei, the AVH and the DAH.
TS24: hypothalamus ventricular layer	Strong	Non-Uniform	Hmgb2-Shh E16.5-coronal , Hmgb2-Shh E16.5-sagittal	There is strong staining in the VZ of the dorsal and ventral POAs and weak, scattered staining in the PVH and DMH nuclei, the AVH and the DAH. Staining is either absent or ubiquitous in the VZ of the SCH, VMH and ARH nuclei and the PH.
TS24: thalamus mantle layer	Weak	Non-Uniform	Hmgb2-Shh E16.5-sagittal , Hmgb2-Shh E16.5-coronal	There is weak, scattered 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	Strong	Non-Uniform	Hmgb2-Shh E16.5-coronal , Hmgb2-Shh E16.5-sagittal	There is strong staining in the ventricular zone of the dorsal thalamus. Staining is either absent or ubiquitous in the ventricular zone of the prethalamus.