Probe:	UI-M-BH1-alw-g-01-0-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	Lmo3-Shh-E11.5-sagittal , Lmo3-Shh E11.5-coronal	There is strong staining in the MZ of the prethalamus, PVH nucleus & the AVH. Staining is either absent or ubiquitous in the MZ of the dorsal thalamus, dorsal & ventral POAs, VMH & ARH nuclei, anterior & posterior IDs, premam, mam & supramam zones & TT.
TS19: diencephalon lateral wall ventricular layer	Strong	Non-Uniform	Lmo3-Shh E11.5-coronal , Lmo3-Shh-E11.5-sagittal	Staining is strong in the VZ of the dorsal thalamus & moderate in the premam zone. Staining is either absent or ubiquitous in the VZ of prethalamus, dorsal & ventral POAs, PVH, VMH & ARH nuclei, AVH, anterior & posterior IDs, mam & supramam zones & TT.
TS19: telencephalon mantle layer	Ambiguous		Lmo3-Shh E11.5-coronal , Lmo3-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	Non-Uniform	Lmo3-Shh-E11.5-sagittal , Lmo3-Shh E11.5-coronal	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		Lmo3-Shh E12.5-coronal , Lmo3-Shh-E12.5-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		Lmo3-Shh E12.5-coronal , Lmo3-Shh-E12.5-sagittal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Lmo3-Shh E12.5-coronal , Lmo3-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	Moderate	Non-Uniform	Lmo3-Shh-E12.5-sagittal , Lmo3-Shh E12.5-coronal	There is moderate staining in the mantle zone of the premam zone and the TT. Staining is either absent or ubiquitous in the mantle zone of the mam and supramam zones.
TS20: diencephalon ventricular layer	Ambiguous		Lmo3-Shh-E12.5-sagittal , Lmo3-Shh E12.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones and the TT.
TS20: ganglionic eminence	Strong		Lmo3-Shh E12.5-coronal , Lmo3-Shh-E12.5-sagittal	There is strong staining in the ventricular and mantle zones of the ganglionic eminences.
TS20: hypothalamus mantle layer	Strong	Non-Uniform	Lmo3-Shh-E12.5-sagittal , Lmo3-Shh E12.5-coronal	There is strong staining in the mantle zone of the dorsal POA and PVH nucleus. Staining is either absent or ubiquitous in the mantle zone of the ventral POA, the VMH and ARH nuclei, the AVH and anterior and posterior IDs.
TS20: hypothalamus ventricular layer	Moderate	Non-Uniform	Lmo3-Shh E12.5-coronal , Lmo3-Shh-E12.5-sagittal	There is moderate staining in the ventricular zone of the PVH nucleus, the AVH and anterior and posterior IDs. Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs and the VMH and ARH nuclei.
TS20: thalamus mantle layer	Strong	Non-Uniform	Lmo3-Shh E12.5-coronal , Lmo3-Shh-E12.5-sagittal	There is 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		Lmo3-Shh E12.5-coronal , Lmo3-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	Strong		Lmo3-Shh E14.5-coronal , Lmo3-Shh-E14.5-sagittal	There is strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Ambiguous		Lmo3-Shh-E14.5-sagittal , Lmo3-Shh E14.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Strong		Lmo3-Shh E14.5-coronal , Lmo3-Shh-E14.5-sagittal	There is strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Strong	Non-Uniform	Lmo3-Shh E14.5-coronal , Lmo3-Shh-E14.5-sagittal	There is 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	Moderate	Non-Uniform	Lmo3-Shh E14.5-coronal , Lmo3-Shh-E14.5-sagittal	There is moderate staining in the ventricular zone of the premam zone. Staining is either absent or ubiquitous in the ventricular zone of the mam and supramam zones and the TT.
TS22: ganglionic eminence	Moderate		Lmo3-Shh E14.5-coronal , Lmo3-Shh-E14.5-sagittal	There is moderate staining in the ventricular and mantle zones of the ganglionic eminences.
TS22: hypothalamus mantle layer	Strong	Non-Uniform	Lmo3-Shh E14.5-coronal , Lmo3-Shh-E14.5-sagittal	There is strong 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, the ARH nucleus and anterior and posterior IDs.
TS22: hypothalamus ventricular layer	Ambiguous		Lmo3-Shh-E14.5-sagittal , Lmo3-Shh E14.5-coronal	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	Strong	Non-Uniform	Lmo3-Shh-E14.5-sagittal , Lmo3-Shh E14.5-coronal	There is strong staining in the mantle zone of the dorsal thalamus and weak staining in the prethalamus.
TS22: thalamus ventricular layer	Ambiguous		Lmo3-Shh E14.5-coronal , Lmo3-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		Lmo3-Shh E16.5-coronal , Lmo3-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	Strong		Lmo3-Shh-E16.5-sagittal , Lmo3-Shh E16.5-coronal	There is strong staining in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Lmo3-Shh-E16.5-sagittal , Lmo3-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	Lmo3-Shh-E16.5-sagittal , Lmo3-Shh E16.5-coronal	There is strong staining in the mantle zone of the mam zone and moderate, scattered staining in the premam and supramam zones.
TS24: diencephalon ventricular layer	Ambiguous		Lmo3-Shh E16.5-coronal , Lmo3-Shh-E16.5-sagittal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS24: ganglionic eminence	Moderate		Lmo3-Shh-E16.5-sagittal , Lmo3-Shh E16.5-coronal	There is moderate staining in the ventricular and mantle zones of the ganglionic eminences.
TS24: hypothalamus mantle layer	Strong	Non-Uniform	Lmo3-Shh-E16.5-sagittal , Lmo3-Shh E16.5-coronal	There is strong staining in the MZ of the VMH nucleus, moderate staining in the PVH nucleus and weak staining in the dorsal POA. Staining is either absent or ubiquitous in the MZ of the ventral POA, the SCH, DMH and ARH nuclei, the AVH, DAH and PH.
TS24: hypothalamus ventricular layer	Ambiguous		Lmo3-Shh-E16.5-sagittal , Lmo3-Shh E16.5-coronal	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	Strong	Non-Uniform	Lmo3-Shh E16.5-coronal , Lmo3-Shh-E16.5-sagittal	There is 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		Lmo3-Shh-E16.5-sagittal , Lmo3-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.