Probe:	UI-M-BH4-bau-h-05-0-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	Nkx6.1-Shh E11.5_coronal	There is strong staining in the MZ of the AVH & posterior ID. Staining is either absent or ubiquitous in the MZ of the dorsal thalamus, prethalamus, dorsal & ventral POAs, the PVH, VMH & ARH nuclei, anterior ID, the premam, mam & supramam zones & the TT.
TS19: diencephalon lateral wall ventricular layer	Strong	Non-Uniform	Nkx6.1-Shh E11.5_coronal	There is strong staining in the VZ of the AVH. Staining is either absent or ubiquitous in the VZ of the dorsal thalamus, prethalamus, dorsal & ventral POAs, the PVH, VMH & ARH nuclei, anterior & posterior IDs, premam, mam & supramam zones & the TT.
TS19: telencephalon mantle layer	Ambiguous		Nkx6.1-Shh E11.5_coronal	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	Ambiguous		Nkx6.1-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		Nkx6.1-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		Nkx6.1-Shh E12.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Nkx6.1-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		Nkx6.1-Shh E12.5_coronal	Staining is either absent or ubiquitous in the mantle zone of the premam, mam and supramam zones and the TT.
TS20: diencephalon ventricular layer	Ambiguous		Nkx6.1-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	Ambiguous		Nkx6.1-Shh E12.5_coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS20: hypothalamus mantle layer	Strong	Non-Uniform	Nkx6.1-Shh E12.5_coronal	There is strong staining in the mantle zone of the AVH and posterior ID. Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei and anterior ID.
TS20: hypothalamus ventricular layer	Strong	Non-Uniform	Nkx6.1-Shh E12.5_coronal	There is strong staining in the ventricular zone of the AVH and anterior ID. Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei and posterior ID.
TS20: thalamus mantle layer	Strong	Non-Uniform	Nkx6.1-Shh E12.5_coronal	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		Nkx6.1-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		Nkx6.1-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		Nkx6.1-Shh E14.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Nkx6.1-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		Nkx6.1-Shh E14.5_coronal	Staining is either absent or ubiquitous in the mantle zone of the premam, mam and supramam zones and the TT.
TS22: diencephalon ventricular layer	Ambiguous		Nkx6.1-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	Ambiguous		Nkx6.1-Shh E14.5_coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS22: hypothalamus mantle layer	Strong	Non-Uniform	Nkx6.1-Shh E14.5_coronal	There is strong staining in the mantle zone of the AVH and posterior ID. Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei and anterior ID.
TS22: hypothalamus ventricular layer	Strong	Non-Uniform	Nkx6.1-Shh E14.5_coronal	There is strong staining in the ventricular zone of the AVH. Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei and anterior and posterior IDs.
TS22: thalamus mantle layer	Very strong	Non-Uniform	Nkx6.1-Shh E14.5_coronal	There is very strong staining in the mantle zone of the dorsal thalamus and strong staining in the prethalamus.
TS22: thalamus ventricular layer	Ambiguous		Nkx6.1-Shh E14.5_coronal	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		Nkx6.1-Shh E16.5_coronal	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Ambiguous		Nkx6.1-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Nkx6.1-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	Ambiguous		Nkx6.1-Shh E16.5_coronal	Staining is either absent or ubiquitous in the mantle zone of the premam, mam and supramam zones.
TS24: diencephalon ventricular layer	Ambiguous		Nkx6.1-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS24: ganglionic eminence	Ambiguous		Nkx6.1-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS24: hypothalamus mantle layer	Very strong	Non-Uniform	Nkx6.1-Shh E16.5_coronal	There is very strong staining in the mantle zone of the SCH nucleus. Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH, DMH, VMH and ARH nuclei, the AVH, the DAH and the PH.
TS24: hypothalamus ventricular layer	Very strong	Non-Uniform	Nkx6.1-Shh E16.5_coronal	There is very strong staining in the VZ of the SCH nucleus, strong staining in the AVH & moderate staining in the VMH nucleus. Staining is either absent or ubiquitous in the VZ of the dorsal & ventral POAs, the PVH, DMH & ARH nuclei, the DAH & the PH.
TS24: thalamus mantle layer	Very strong	Non-Uniform	Nkx6.1-Shh E16.5_coronal	There is very strong staining in the mantle zone of the dorsal thalamus and moderate staining in the prethalamus.
TS24: thalamus ventricular layer	Ambiguous		Nkx6.1-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.