Probe:	UI-M-BH1-ali-g-03-0-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	Moderate	Non-Uniform	C130071C03Rik-Shh E11.5-coronal , C130071C03Rik-Shh E11.5-sagittal , C130071C03Rik-Shh E11.5-coronal-2	There is moderate staining in the MZ of the PVH nucleus, AVH & supramam zone. Staining is either absent or ubiquitous in the MZ of dorsal thalamus, prethalamus, dorsal & ventral POAs, anterior & posterior IDs, VMH & ARH nuclei, premam & mam zones & TT.
TS19: diencephalon lateral wall ventricular layer	Strong	Non-Uniform	C130071C03Rik-Shh E11.5-sagittal , C130071C03Rik-Shh E11.5-coronal-2 , C130071C03Rik-Shh E11.5-coronal	Staining is strong in dorsal thalamus & anterior & posterior IDs, moderate in VMH nucleus, premam zone & TT, moderate & scattered in dorsal & ventral POAs, weak in prethalamus & absent or ubiquitous in PVH nucleus, AVH, ARH nucleus & mam & supramam zones.
TS19: telencephalon mantle layer	Weak	Non-Uniform	C130071C03Rik-Shh E11.5-coronal-2 , C130071C03Rik-Shh E11.5-sagittal , C130071C03Rik-Shh E11.5-coronal	There is weak, scattered 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	Strong		C130071C03Rik-Shh E11.5-coronal , C130071C03Rik-Shh E11.5-coronal-2 , C130071C03Rik-Shh E11.5-sagittal	There is strong staining in the ventricular zone of the cerebral cortex and the ganglionic eminences.

Structure	Level	Pattern	Image	Note
TS20: cerebral cortex intermediate zone	Ambiguous		C130071C03Rik-Shh E12.5-sagittal , C130071C03Rik-Shh E12.5-coronal , C130071C03Rik-Shh E12.5-coronal-2	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS20: cerebral cortex ventricular layer	Ambiguous		C130071C03Rik-Shh E12.5-sagittal , C130071C03Rik-Shh E12.5-coronal-2 , C130071C03Rik-Shh E12.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		C130071C03Rik-Shh E12.5-sagittal , C130071C03Rik-Shh E12.5-coronal-2 , C130071C03Rik-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		C130071C03Rik-Shh E12.5-sagittal , C130071C03Rik-Shh E12.5-coronal , C130071C03Rik-Shh E12.5-coronal-2	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	Non-Uniform	C130071C03Rik-Shh E12.5-sagittal , C130071C03Rik-Shh E12.5-coronal-2 , C130071C03Rik-Shh E12.5-coronal	There is strong staining in the ventricular zone of the premam, mam and supramam zones. Staining is either absent or ubiquitous in the ventricular zone of the TT.
TS20: ganglionic eminence	Strong	Non-Uniform	C130071C03Rik-Shh E12.5-sagittal , C130071C03Rik-Shh E12.5-coronal , C130071C03Rik-Shh E12.5-coronal-2	There is strong staining in the ventricular zone of the ganglionic eminences. Staining is either absent or ubiquitous in the mantle zone of the ganglionic eminences.
TS20: hypothalamus mantle layer	Ambiguous		C130071C03Rik-Shh E12.5-sagittal , C130071C03Rik-Shh E12.5-coronal-2 , C130071C03Rik-Shh E12.5-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.
TS20: hypothalamus ventricular layer	Strong	Non-Uniform	C130071C03Rik-Shh E12.5-coronal , C130071C03Rik-Shh E12.5-coronal-2 , C130071C03Rik-Shh E12.5-sagittal	There is strong staining in the ventricular zone of the dorsal and ventral POAs, the PVH and VMH nuclei, the AVH and anterior and posterior IDs. Staining is either absent or ubiquitous in the ventricular zone of the ARH nucleus.
TS20: thalamus mantle layer	Ambiguous		C130071C03Rik-Shh E12.5-sagittal , C130071C03Rik-Shh E12.5-coronal-2 , C130071C03Rik-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	C130071C03Rik-Shh E12.5-coronal , C130071C03Rik-Shh E12.5-coronal-2 , C130071C03Rik-Shh E12.5-sagittal	There is strong staining in the ventricular zone of the prethalamus and moderate staining in the dorsal thalamus.

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Ambiguous		C130071C03Rik-Shh E14.5-sagittal , C130071C03Rik-Shh E14.5-coronal-2 , C130071C03Rik-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	Strong		C130071C03Rik-Shh E14.5-coronal-2 , C130071C03Rik-Shh E14.5-coronal , C130071C03Rik-Shh E14.5-sagittal	There is strong staining in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		C130071C03Rik-Shh E14.5-sagittal , C130071C03Rik-Shh E14.5-coronal-2 , C130071C03Rik-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		C130071C03Rik-Shh E14.5-coronal , C130071C03Rik-Shh E14.5-sagittal , C130071C03Rik-Shh E14.5-coronal-2	Staining is either absent or ubiquitous in the mantle zone of the premam, mam and supramam zones and the TT.
TS22: diencephalon ventricular layer	Moderate	Non-Uniform	C130071C03Rik-Shh E14.5-coronal-2 , C130071C03Rik-Shh E14.5-coronal , C130071C03Rik-Shh E14.5-sagittal	There is moderate staining in the ventricular zone of the premam, mam and supramam zones. Staining is either absent or ubiquitous in the ventricular zone of the TT.
TS22: ganglionic eminence	Strong	Non-Uniform	C130071C03Rik-Shh E14.5-sagittal , C130071C03Rik-Shh E14.5-coronal-2 , C130071C03Rik-Shh E14.5-coronal	There is strong staining in the ventricular zone of the ganglionic eminences. Staining is either absent or ubiquitous in the mantle zone of the ganglionic eminences.
TS22: hypothalamus mantle layer	Ambiguous		C130071C03Rik-Shh E14.5-coronal-2 , C130071C03Rik-Shh E14.5-sagittal , C130071C03Rik-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	C130071C03Rik-Shh E14.5-sagittal , C130071C03Rik-Shh E14.5-coronal , C130071C03Rik-Shh E14.5-coronal-2	There is strong staining in the VZ of the VMH nucleus, moderate staining in the dorsal and ventral POAs, the AVH and anterior and posterior IDs and weak staining in the PVH nucleus. Staining is either absent or ubiquitous in the VZ of the ARH nucleus.
TS22: thalamus mantle layer	Ambiguous		C130071C03Rik-Shh E14.5-coronal-2 , C130071C03Rik-Shh E14.5-coronal , C130071C03Rik-Shh E14.5-sagittal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS22: thalamus ventricular layer	Moderate		C130071C03Rik-Shh E14.5-sagittal , C130071C03Rik-Shh E14.5-coronal , C130071C03Rik-Shh E14.5-coronal-2	There is moderate staining in the ventricular zone of the dorsal thalamus and prethalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Moderate	Scattered	C130071C03Rik-Shh E16.5-coronal-2 , C130071C03Rik-Shh E16.5-sagittal , C130071C03Rik-Shh E16.5-coronal	There is moderate, scattered staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Moderate		C130071C03Rik-Shh E16.5-coronal-2 , C130071C03Rik-Shh E16.5-sagittal , C130071C03Rik-Shh E16.5-coronal	There is moderate staining in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Moderate	Scattered	C130071C03Rik-Shh E16.5-coronal , C130071C03Rik-Shh E16.5-coronal-2 , C130071C03Rik-Shh E16.5-sagittal	There is moderate, scattered staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Ambiguous		C130071C03Rik-Shh E16.5-sagittal , C130071C03Rik-Shh E16.5-coronal , C130071C03Rik-Shh E16.5-coronal-2	Staining is either absent or ubiquitous in the mantle zone of the premam, mam and supramam zones.
TS24: diencephalon ventricular layer	Moderate	Non-Uniform	C130071C03Rik-Shh E16.5-coronal , C130071C03Rik-Shh E16.5-coronal-2 , C130071C03Rik-Shh E16.5-sagittal	There is moderate staining in the ventricular zone of the premam zone and weak staining in the mam and supramam zones.
TS24: ganglionic eminence	Moderate	Non-Uniform	C130071C03Rik-Shh E16.5-coronal-2 , C130071C03Rik-Shh E16.5-coronal , C130071C03Rik-Shh E16.5-sagittal	There is moderate 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	Ambiguous		C130071C03Rik-Shh E16.5-coronal-2 , C130071C03Rik-Shh E16.5-sagittal , C130071C03Rik-Shh E16.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH, SCH, DMH, VMH and ARH nuclei, the AVH, the DAH and the PH.
TS24: hypothalamus ventricular layer	Strong	Non-Uniform	C130071C03Rik-Shh E16.5-sagittal , C130071C03Rik-Shh E16.5-coronal , C130071C03Rik-Shh E16.5-coronal-2	There is strong staining in the VZ of the dorsal POA, moderate staining in the PVH, SCH & DMH nuclei, the DAH & the PH & weak staining in the ventral POA, the AVH & the VMH nucleus. Staining is either absent or ubiquitous in the VZ of the ARH nucleus.
TS24: thalamus mantle layer	Ambiguous		C130071C03Rik-Shh E16.5-coronal , C130071C03Rik-Shh E16.5-sagittal , C130071C03Rik-Shh E16.5-coronal-2	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS24: thalamus ventricular layer	Strong		C130071C03Rik-Shh E16.5-coronal-2 , C130071C03Rik-Shh E16.5-sagittal , C130071C03Rik-Shh E16.5-coronal	There is strong staining in the ventricular zone of the dorsal thalamus and prethalamus.