Probe:	UI-M-BH1-anq-f-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	Strong	Non-Uniform	Tmem2-Shh E11.5_coronal	Staining is strong in the MZ of the prethalamus, dorsal POA, PVH nucleus, AVH, anterior & posterior IDs, mam & supramam zones & TT, moderate in the dorsal thalamus & either absent or ubiquitous in the ventral POA, VMH & ARH nuclei & premam zone.
TS19: diencephalon lateral wall ventricular layer	Weak	Non-Uniform	Tmem2-Shh E11.5_coronal	There is weak staining in the VZ of the dorsal thalamus. Staining is either absent or ubiquitous in the VZ of the prethalamus, dorsal & ventral POAs, the PVH, VMH & ARH nuclei, the AVH, anterior & posterior IDs, premam, mam & supramam zones & the TT.
TS19: telencephalon mantle layer	Moderate	Non-Uniform	Tmem2-Shh E11.5_coronal	There is moderate 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		Tmem2-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		Tmem2-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		Tmem2-Shh E12.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Tmem2-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	Tmem2-Shh E12.5_coronal	There is 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 and the TT.
TS20: diencephalon ventricular layer	Ambiguous		Tmem2-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	Moderate	Non-Uniform	Tmem2-Shh E12.5_coronal	There is moderate 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	Tmem2-Shh E12.5_coronal	There is strong staining in the mantle zone of the AVH. Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei and anterior and posterior IDs.
TS20: hypothalamus ventricular layer	Very strong	Non-Uniform	Tmem2-Shh E12.5_coronal	There is very strong staining in the ventricular zone of the PVH nucleus and strong staining in the AVH. Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the VMH and ARH nuclei and anterior and posterior IDs.
TS20: thalamus mantle layer	Very strong	Non-Uniform	Tmem2-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	Weak	Non-Uniform	Tmem2-Shh E12.5_coronal	There is weak staining in the ventricular zone of the dorsal thalamus. Staining is either absent or ubiquitous in the ventricular zone of the prethalamus.

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Ambiguous		Tmem2-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		Tmem2-Shh E14.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Tmem2-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	Moderate	Non-Uniform	Tmem2-Shh E14.5_coronal	There is moderate 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 and the TT.
TS22: diencephalon ventricular layer	Ambiguous		Tmem2-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	Weak	Non-Uniform	Tmem2-Shh E14.5_coronal	There is weak 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	Tmem2-Shh E14.5_coronal	There is strong staining in the mantle zone of the AVH and moderate staining in the PVH nucleus. Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the VMH and ARH nuclei and anterior and posterior IDs.
TS22: hypothalamus ventricular layer	Ambiguous		Tmem2-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	Moderate		Tmem2-Shh E14.5_coronal	There is moderate staining in the mantle zone of the dorsal thalamus and prethalamus.
TS22: thalamus ventricular layer	Very strong	Non-Uniform	Tmem2-Shh E14.5_coronal	There is very strong staining in the ventricular zone of the dorsal thalamus. Staining is either absent or ubiquitous in the ventricular zone of the prethalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Moderate		Tmem2-Shh E16.5_coronal	There is moderate staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Ambiguous		Tmem2-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Moderate		Tmem2-Shh E16.5_coronal	There is moderate staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Ambiguous		Tmem2-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		Tmem2-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS24: ganglionic eminence	Strong	Non-Uniform	Tmem2-Shh E16.5_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.
TS24: hypothalamus mantle layer	Moderate	Non-Uniform	Tmem2-Shh E16.5_coronal	There is moderate staining in the mantle zone of the SCH nucleus and weak staining in the dorsal and ventral POAs. Staining is either absent or ubiquitous in the mantle zone of the PVH, DMH, VMH and ARH nuclei, the AVH, the DAH and the PH.
TS24: hypothalamus ventricular layer	Weak	Non-Uniform	Tmem2-Shh E16.5_coronal	There is weak staining in the ventricular zone of the PH. 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 and the DAH.
TS24: thalamus mantle layer	Strong	Non-Uniform	Tmem2-Shh E16.5_coronal	There is strong staining in the mantle zone of the prethalamus and moderate staining in the dorsal thalamus.
TS24: thalamus ventricular layer	Ambiguous		Tmem2-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.