Probe:	UI-M-BH1-aky-d-08-0-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	Gad65-Shh-E11.5-coronal	Staining is very strong in the MZ of the dorsal & ventral POAs & anterior & posterior IDs & strong in the TT. Staining is either absent or ubiquitous in the MZ of the dorsal thalamus, prethalamus, PVH, VMH & ARH nuclei, AVH & premam, mam & supramam zones.
TS19: diencephalon lateral wall ventricular layer	Very strong	Non-Uniform	Gad65-Shh-E11.5-coronal	There is very strong staining in the VZ of the prethalamus. Staining is either absent or ubiquitous in the VZ of the dorsal thalamus, dorsal & ventral POAs, the PVH, VMH & ARH nuclei, the AVH, anterior & posterior IDs, premam, mam & supramam zones & TT.
TS19: telencephalon mantle layer	Very strong	Non-Uniform	Gad65-Shh-E11.5-coronal	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		Gad65-Shh-E11.5-coronal	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		Gad65-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		Gad65-Shh-E12.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Gad65-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	Gad65-Shh-E12.5-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 zones.
TS20: diencephalon ventricular layer	Ambiguous		Gad65-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	Very strong	Non-Uniform	Gad65-Shh-E12.5-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.
TS20: hypothalamus mantle layer	Strong	Non-Uniform	Gad65-Shh-E12.5-coronal	There is strong staining in the mantle zone of the anterior and posterior IDs. Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei and the AVH.
TS20: hypothalamus ventricular layer	Ambiguous		Gad65-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	Very strong	Non-Uniform	Gad65-Shh-E12.5-coronal	There is very strong staining in the mantle zone of the dorsal thalamus and strong staining in the prethalamus.
TS20: thalamus ventricular layer	Ambiguous		Gad65-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		Gad65-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	Ambiguous		Gad65-Shh-E14.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Gad65-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	Gad65-Shh-E14.5-coronal	There is strong, scattered staining in the mantle zone of the premam zone and the TT and moderate staining in the mam zone. Staining is either absent or ubiquitous in the mantle zone of the supramam zone.
TS22: diencephalon ventricular layer	Ambiguous		Gad65-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	Very strong	Non-Uniform	Gad65-Shh-E14.5-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.
TS22: hypothalamus mantle layer	Strong	Non-Uniform	Gad65-Shh-E14.5-coronal	There is strong staining in the mantle zone of the dorsal and ventral POAs and anterior and posterior IDs and moderate staining in the AVH. Staining is either absent or ubiquitous in the mantle zone of the PVH,VMH and ARH nuclei.
TS22: hypothalamus ventricular layer	Ambiguous		Gad65-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	Very strong	Non-Uniform	Gad65-Shh-E14.5-coronal	There is very strong staining in the mantle zone of the prethalamus and moderate staining in the dorsal thalamus.
TS22: thalamus ventricular layer	Very strong	Non-Uniform	Gad65-Shh-E14.5-coronal	There is very 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	Scattered	Gad65-Shh-E16.5-coronal	There is very strong, scattered staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Ambiguous		Gad65-Shh-E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Very strong	Scattered	Gad65-Shh-E16.5-coronal	There is very strong, scattered staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Very strong	Non-Uniform	Gad65-Shh-E16.5-coronal	There is very strong, scattered 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	Very strong	Non-Uniform	Gad65-Shh-E16.5-coronal	There is very strong 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.
TS24: ganglionic eminence	Very strong	Non-Uniform	Gad65-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	Gad65-Shh-E16.5-coronal	There is very strong, scattered staining in the MZ of the dorsal and ventral POAs, the DMH nucleus and the PH and strong, scattered staining in the AVH and DAH. Staining is either absent or ubiquitous in the MZ of the PVH, SCH, VMH and ARH nuclei.
TS24: hypothalamus ventricular layer	Very strong	Non-Uniform	Gad65-Shh-E16.5-coronal	There is very strong staining in the ventricular zone of the dorsal and ventral POAs and the DMH nucleus. Staining is either absent or ubiquitous in the ventricular zone of the PVH, SCH, VMH and ARH nuclei, the AVH, the DAH and the PH.
TS24: thalamus mantle layer	Very strong	Non-Uniform	Gad65-Shh-E16.5-coronal	There is very strong staining in the mantle zone of the prethalamus and strong staining in the dorsal thalamus.
TS24: thalamus ventricular layer	Very strong	Non-Uniform	Gad65-Shh-E16.5-coronal	There is very strong staining in the ventricular zone of the prethalamus. Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus