Probe:	UI-M-AQ0-aah-f-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	Strong	Non-Uniform	Islr2-Shh E11.5-coronal , Islr2-Shh E11.5-sagittal	There is strong staining in the MZ of the dorsal thalamus, prethalamus, dorsal & ventral POAs, PVH & VMH nuclei, the AVH, anterior & posterior IDs, premam, mam & supramam zones & TT. Staining is either absent or ubiquitous in the MZ of the ARH nucleus.
TS19: diencephalon lateral wall ventricular layer	Ambiguous		Islr2-Shh E11.5-sagittal , Islr2-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	Strong		Islr2-Shh E11.5-coronal , Islr2-Shh E11.5-sagittal	There is strong staining 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	Ambiguous		Islr2-Shh E11.5-coronal , Islr2-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	Strong		Islr2-Shh E12.5-coronal , Islr2-SHH E12.5-sagittal	There is strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS20: cerebral cortex ventricular layer	Ambiguous		Islr2-SHH E12.5-sagittal , Islr2-Shh E12.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Strong		Islr2-SHH E12.5-sagittal , Islr2-Shh E12.5-coronal	There is strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS20: diencephalon mantle layer	Strong	Non-Uniform	Islr2-SHH E12.5-sagittal , Islr2-Shh E12.5-coronal	There is strong staining in the mantle zone of the mam zone and the TT. Staining is either absent or ubiquitous in the mantle zone of the premam and supramam zones.
TS20: diencephalon ventricular layer	Ambiguous		Islr2-Shh E12.5-coronal , Islr2-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	Strong	Non-Uniform	Islr2-Shh E12.5-coronal , Islr2-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	Islr2-SHH E12.5-sagittal , Islr2-Shh E12.5-coronal	There is strong staining in the MZ of the dorsal and ventral POAs and anterior and posterior IDs, moderate staining in the PVH nucleus and the AVH and weak staining in the VMH nucleus. Staining is either absent or ubiquitous in the MZ of the ARH nucleus.
TS20: hypothalamus ventricular layer	Ambiguous		Islr2-SHH E12.5-sagittal , Islr2-Shh E12.5-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.
TS20: thalamus mantle layer	Strong		Islr2-SHH E12.5-sagittal , Islr2-Shh E12.5-coronal	There is strong staining in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Ambiguous		Islr2-Shh E12.5-coronal , Islr2-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		Islr2-Shh E14.5-sagittal , Islr2-Shh E14.5-coronal	There is strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Ambiguous		Islr2-Shh E14.5-coronal , Islr2-Shh E14.5-sagittal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Strong		Islr2-Shh E14.5-sagittal , Islr2-Shh E14.5-coronal	There is strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Strong	Non-Uniform	Islr2-Shh E14.5-coronal , Islr2-Shh E14.5-sagittal	There is strong staining in the mantle zone of the TT and mam zone. Staining is either absent or ubiquitous in the mantle zone of the premam and supramam zones.
TS22: diencephalon ventricular layer	Ambiguous		Islr2-Shh E14.5-sagittal , Islr2-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	Strong	Non-Uniform	Islr2-Shh E14.5-sagittal , Islr2-Shh E14.5-coronal	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.
TS22: hypothalamus mantle layer	Strong	Non-Uniform	Islr2-Shh E14.5-sagittal , Islr2-Shh E14.5-coronal	There is strong staining in the mantle 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 mantle zone of the ARH nucleus.
TS22: hypothalamus ventricular layer	Ambiguous		Islr2-Shh E14.5-sagittal , Islr2-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		Islr2-Shh E14.5-coronal , Islr2-Shh E14.5-sagittal	There is strong staining in the mantle zone of the dorsal thalamus and prethalamus.
TS22: thalamus ventricular layer	Strong	Non-Uniform	Islr2-Shh E14.5-sagittal , Islr2-Shh E14.5-coronal	There is strong staining in the ventricular zone of the prethalamus. Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Very strong		Islr2-Shh E16.5-coronal , Islr2-Shh E16.5-sagittal	There is very strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Ambiguous		Islr2-Shh E16.5-coronal , Islr2-Shh E16.5-sagittal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Very strong		Islr2-Shh E16.5-coronal , Islr2-Shh E16.5-sagittal	There is very strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Very strong	Non-Uniform	Islr2-Shh E16.5-coronal , Islr2-Shh E16.5-sagittal	There is very 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		Islr2-Shh E16.5-coronal , Islr2-Shh E16.5-sagittal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS24: ganglionic eminence	Very strong	Non-Uniform	Islr2-Shh E16.5-sagittal , Islr2-Shh E16.5-coronal	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	Very strong	Non-Uniform	Islr2-Shh E16.5-sagittal , Islr2-Shh E16.5-coronal	There is very strong staining in the MZ of the PVH nucleus & the PH, strong staining in the dorsal POA & DAH & moderate staining in the ventral POA, AVH & VMH nucleus. Staining is either absent or ubiquitous in the MZ of the SCH, DMH & ARH nuclei.
TS24: hypothalamus ventricular layer	Ambiguous		Islr2-Shh E16.5-sagittal , Islr2-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	Very strong	Non-Uniform	Islr2-Shh E16.5-coronal , Islr2-Shh E16.5-sagittal	There is very strong staining in the mantle zone of the prethalamus and strong staining in the thalamus.
TS24: thalamus ventricular layer	Ambiguous		Islr2-Shh E16.5-coronal , Islr2-Shh E16.5-sagittal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.