Probe:	IMAGE clone 30657664
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	Mlr2-Shh E11.5_coronal	There is strong staining in the mantle zone of the prethalamus, dorsal and ventral POAs, PVH and VMH nuclei, anterior and posterior IDs and the TT. Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and the AVH.
TS19: diencephalon lateral wall ventricular layer	Ambiguous		Mlr2-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 and VMH nuclei, the AVH, the anterior and posterior IDs and the TT.
TS19: telencephalon mantle layer	Strong	Non-Uniform	Mlr2-Shh E11.5_coronal	There is 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		Mlr2-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		Mlr2-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		Mlr2-Shh E12.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Mlr2-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		Mlr2-Shh E12.5_coronal	There is strong staining in the mantle zone of the premam zone and the TT.
TS20: diencephalon ventricular layer	Ambiguous		Mlr2-Shh E12.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam zone and the TT.
TS20: ganglionic eminence	Strong	Non-Uniform	Mlr2-Shh E12.5_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.
TS20: hypothalamus mantle layer	Strong		Mlr2-Shh E12.5_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.
TS20: hypothalamus ventricular layer	Ambiguous		Mlr2-Shh E12.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH and VMH nuclei, the AVH and anterior and posterior IDs.
TS20: thalamus mantle layer	Strong		Mlr2-Shh E12.5_coronal	There is strong staining in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Ambiguous		Mlr2-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		Mlr2-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		Mlr2-Shh E14.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Mlr2-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	Mlr2-Shh E14.5_coronal	There is strong staining in the mantle zone of the premam zone, moderate staining in the mam zone and weak staining in the TT. Staining is either absent or ubiquitous in the mantle zone of the supramam zone.
TS22: diencephalon ventricular layer	Ambiguous		Mlr2-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	Mlr2-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	Mlr2-Shh E14.5_coronal	There is strong staining in the MZ of the VMH nucleus, moderate staining in the AVH and weak staining in the dorsal and ventral POAs and anterior and posterior IDs. Staining is either absent or ubiquitous in the MZ of the PVH and ARH nuclei.
TS22: hypothalamus ventricular layer	Moderate	Non-Uniform	Mlr2-Shh E14.5_coronal	There is moderate 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	Moderate		Mlr2-Shh E14.5_coronal	There is moderate staining in the mantle zone of the dorsal thalamus and prethalamus.
TS22: thalamus ventricular layer	Moderate		Mlr2-Shh E14.5_coronal	There is moderate staining in the ventricular zone of the dorsal thalamus and prethalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Ambiguous		Mlr2-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		Mlr2-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Mlr2-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	Strong	Non-Uniform	Mlr2-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 zone.
TS24: diencephalon ventricular layer	Ambiguous		Mlr2-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS24: ganglionic eminence	Weak	Non-Uniform	Mlr2-Shh E16.5_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.
TS24: hypothalamus mantle layer	Strong	Non-Uniform	Mlr2-Shh E16.5_coronal	There is strong staining in the mantle zone of the VMH and ARH nuclei and moderate staining in the SCH nucleus. Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH and DMH nuclei, the AVH, the DAH and the PH.
TS24: hypothalamus ventricular layer	Moderate	Non-Uniform	Mlr2-Shh E16.5_coronal	There is moderate staining in the ventricular zone of the VMH nucleus. Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH, SCH, DMH and ARH nuclei, the AVH, the DAH and the PH.
TS24: thalamus mantle layer	Weak	Non-Uniform	Mlr2-Shh E16.5_coronal	There is weak staining in the mantle zone of the dorsal thalamus. Staining is either absent or ubiquitous in the mantle zone of the prethalamus.
TS24: thalamus ventricular layer	Ambiguous		Mlr2-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.