Probe:	UI-M-BH0-aiz-d-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	Plxna3-Shh E11.5_coronal	Staining is strong in the MZ of the dorsal thalamus, anterior & posterior IDs, the TT & mam & supramam zones, moderate in the VMH nucleus & either absent or ubiquitous in the prethalamus, dorsal & ventral POAs, PVH & ARH nuclei, AVH & premam zone.
TS19: diencephalon lateral wall ventricular layer	Strong	Non-Uniform	Plxna3-Shh E11.5_coronal	There is strong staining in the VZ of the prethalamus, dorsal & ventral POAs & PVH nucleus. Staining is either absent or ubiquitous in the VZ of the dorsal thalamus, VMH & ARH nuclei, the AVH, anterior & posterior IDs, premam, mam & supramam zones & TT.
TS19: telencephalon mantle layer	Strong	Non-Uniform	Plxna3-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		Plxna3-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		Plxna3-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		Plxna3-Shh E12.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Plxna3-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	Moderate	Non-Uniform	Plxna3-Shh E12.5_coronal	There is moderate staining in the mantle zone of the premam and mam zones and the TT and weak staining in the supramam zone.
TS20: diencephalon ventricular layer	Ambiguous		Plxna3-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	Weak	Non-Uniform	Plxna3-Shh E12.5_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.
TS20: hypothalamus mantle layer	Moderate	Non-Uniform	Plxna3-Shh E12.5_coronal	There is moderate staining in the mantle zone of the AVH and VMH nucleus and weak staining in the dorsal and ventral POAs, the PVH and ARH nuclei and anterior and posterior IDs.
TS20: hypothalamus ventricular layer	Ambiguous		Plxna3-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	Weak		Plxna3-Shh E12.5_coronal	There is weak staining in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Ambiguous		Plxna3-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	Moderate	Scattered	Plxna3-Shh E14.5_coronal	There is moderate, scattered staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Ambiguous		Plxna3-Shh E14.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Moderate	Scattered	Plxna3-Shh E14.5_coronal	There is moderate, scattered staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Moderate	Non-Uniform	Plxna3-Shh E14.5_coronal	There is moderate, scattered staining in the mantle zone of the TT and weak staining in the mam zone. Staining is either absent or ubiquitous in the mantle zone of the premam and supramam zone.
TS22: diencephalon ventricular layer	Ambiguous		Plxna3-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	Plxna3-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	Moderate	Non-Uniform	Plxna3-Shh E14.5_coronal	There is moderate, scattered staining in the mantle zone of the dorsal and ventral POAs and anterior and posterior IDs. Staining is either absent or ubiquitous in the mantle zone of the PVH, VMH and ARH nuclei and the AVH.
TS22: hypothalamus ventricular layer	Ambiguous		Plxna3-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	Non-Uniform	Plxna3-Shh E14.5_coronal	There is strong staining in the mantle zone of the prethalamus and moderate, scattered staining in the dorsal thalamus.
TS22: thalamus ventricular layer	Strong	Non-Uniform	Plxna3-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	Scattered	Plxna3-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	Very strong		Plxna3-Shh E16.5_coronal	There is very strong staining in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Very strong	Scattered	Plxna3-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	Ambiguous		Plxna3-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		Plxna3-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS24: ganglionic eminence	Very strong	Non-Uniform	Plxna3-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	Moderate	Non-Uniform	Plxna3-Shh E16.5_coronal	There is moderate, scattered staining in the mantle zone of the dorsal and ventral POAs and the DAH. Staining is either absent or ubiquitous in the mantle zone of the PVH, SCH, DMH, VMH and ARH nuclei, the AVH and the PH.
TS24: hypothalamus ventricular layer	Strong	Non-Uniform	Plxna3-Shh E16.5_coronal	Staining is strong in the VZ of the dorsal & ventral POAs, DAH & PH, strong & scattered in the DMH nucleus & moderate & scattered in the VMH nucleus. Staining is either absent or ubiquitous in the VZ of the PVH, SCH & ARH nuclei & AVH.
TS24: thalamus mantle layer	Very strong	Non-Uniform	Plxna3-Shh E16.5_coronal	There is very strong staining in the mantle zone of the prethalamus and strong, scattered staining in the dorsal thalamus.
TS24: thalamus ventricular layer	Very strong	Non-Uniform	Plxna3-Shh E16.5_coronal	There is very strong staining in the ventricular zone of the prethalamus and strong staining in the dorsal thalamus.