Probe:	UI-M-BH2.1-apx-e-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	Very strong	Non-Uniform	Isl1-Shh E11.5-sagittal	Staining is very strong in the MZ of the prethalamus & dorsal & ventral POAs, strong in anterior & posterior IDs, VMH & ARH nuclei, premam zone & TT & either absent or ubiquitous in the dorsal thalamus, PVH nucleus, AVH & mam & supramam zones.
TS19: diencephalon lateral wall ventricular layer	Ambiguous		Isl1-Shh E11.5-sagittal	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	Very strong	Non-Uniform	Isl1-Shh E11.5-sagittal	There is very strong 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		Isl1-Shh E11.5-sagittal	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		Isl1-Shh E12.5-sagittal , Isl1-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		Isl1-Shh E12.5-coronal , Isl1-Shh E12.5-sagittal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Isl1-Shh E12.5-sagittal , Isl1-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	Strong	Non-Uniform	Isl1-Shh E12.5-coronal , Isl1-Shh E12.5-sagittal	There is strong 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 zone.
TS20: diencephalon ventricular layer	Ambiguous		Isl1-Shh E12.5-sagittal , Isl1-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	Non-Uniform	Isl1-Shh E12.5-coronal , Isl1-Shh E12.5-sagittal	There is strong 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	Strong	Non-Uniform	Isl1-Shh E12.5-sagittal , Isl1-Shh E12.5-coronal	There is strong staining in the mantle zone of the dorsal and ventral POAs, the VMH and ARH nuclei and anterior and posterior IDs. Staining is either absent or ubiquitous in the mantle zone of the PVH nucleus and the AVH.
TS20: hypothalamus ventricular layer	Ambiguous		Isl1-Shh E12.5-coronal , Isl1-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	Isl1-Shh E12.5-coronal , Isl1-Shh E12.5-sagittal	There is very 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		Isl1-Shh E12.5-sagittal , Isl1-Shh E12.5-coronal	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		Isl1-Shh E14.5-coronal , Isl1-Shh E14.5-sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Ambiguous		Isl1-Shh E14.5-coronal , Isl1-Shh E14.5-sagittal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Isl1-Shh E14.5-sagittal , Isl1-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	Strong	Non-Uniform	Isl1-Shh E14.5-sagittal , Isl1-Shh E14.5-coronal	There is strong 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 zone.
TS22: diencephalon ventricular layer	Ambiguous		Isl1-Shh E14.5-coronal , Isl1-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	Very strong	Non-Uniform	Isl1-Shh E14.5-coronal , Isl1-Shh E14.5-sagittal	There is very strong 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	Isl1-Shh E14.5-sagittal , Isl1-Shh E14.5-coronal	There is strong staining in the mantle zone of the AVH and VMH and ARH nuclei and moderate staining in the dorsal and ventral POAs. Staining is either absent or ubiquitous in the mantle zone of the PVH nucleus and anterior and posterior IDs.
TS22: hypothalamus ventricular layer	Strong	Non-Uniform	Isl1-Shh E14.5-sagittal , Isl1-Shh E14.5-coronal	There is strong staining in the ventricular zone of the anterior and posterior IDs. Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei and the AVH.
TS22: thalamus mantle layer	Very strong	Non-Uniform	Isl1-Shh E14.5-sagittal , Isl1-Shh E14.5-coronal	There is very strong staining in the mantle zone of the prethalamus. Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus.
TS22: thalamus ventricular layer	Ambiguous		Isl1-Shh E14.5-coronal , Isl1-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		Isl1-Shh E16.5-coronal , Isl1-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		Isl1-Shh E16.5-sagittal , Isl1-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Isl1-Shh E16.5-coronal , Isl1-Shh E16.5-sagittal	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	Isl1-Shh E16.5-sagittal , Isl1-Shh E16.5-coronal	There is strong staining in the mantle zone of the premam zone. Staining is either absent or ubiquitous in the mantle zone of the mam and supramam zones.
TS24: diencephalon ventricular layer	Ambiguous		Isl1-Shh E16.5-sagittal , Isl1-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS24: ganglionic eminence	Very strong	Non-Uniform	Isl1-Shh E16.5-coronal , Isl1-Shh E16.5-sagittal	There is very strong staining in the mantle zone of the ganglionic eminences. Staining is either absent or ubiquitous in the ventricular zone of the ganglionic eminences.
TS24: hypothalamus mantle layer	Strong	Non-Uniform	Isl1-Shh E16.5-coronal , Isl1-Shh E16.5-sagittal	Staining is strong in the MZ of the AVH, DAH & PH, strong & scattered in the DMH, VMH & ARH nuclei, moderate in the dorsal POA & weak & scattered in the ventral POA. Staining is either absent or ubiquitous in the MZ of the PVH & SCH nuclei.
TS24: hypothalamus ventricular layer	Ambiguous		Isl1-Shh E16.5-coronal , Isl1-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	Isl1-Shh E16.5-coronal , Isl1-Shh E16.5-sagittal	There is very strong staining in the mantle zone of the prethalamus. Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus.
TS24: thalamus ventricular layer	Ambiguous		Isl1-Shh E16.5-coronal , Isl1-Shh E16.5-sagittal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.