Probe:	UI-M-AK1-aew-c-12-0-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	Pvrl3-Shh E11.5_coronal	Staining is very strong in the MZ of the prethalamus & moderate in dorsal thalamus & dorsal POA. Staining is either absent or ubiquitous in the MZ of the ventral POA, PVH, VMH & ARH nuclei, AVH, anterior & posterior IDs, premam, mam & supramam zones & TT.
TS19: diencephalon lateral wall ventricular layer	Very strong	Non-Uniform	Pvrl3-Shh E11.5_coronal	Staining is very strong in the VZ of the prethalamus, moderate in PVH nucleus & mam zone, weak in posterior ID, premam & supramam zones & TT & either absent or ubiquitous in dorsal thalamus, dorsal & ventral POAs, AVH, anterior ID & VMH & ARH nuclei.
TS19: telencephalon mantle layer	Ambiguous		Pvrl3-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	Weak	Non-Uniform	Pvrl3-Shh E11.5_coronal	There is weak staining in the ventricular zone of the ganglionic eminences. Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.

Structure	Level	Pattern	Image	Note
TS20: cerebral cortex intermediate zone	Ambiguous		Pvrl3-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	Moderate		Pvrl3-Shh E12.5_coronal	There is moderate, scattered staining in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Pvrl3-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		Pvrl3-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	Very strong	Non-Uniform	Pvrl3-Shh E12.5_coronal	There is very strong staining in the ventricular zone of the supramam zone and moderate staining in the mam zone. Staining is either absent or ubiquitous in the ventricular zone of the premam zone and the TT.
TS20: ganglionic eminence	Weak	Non-Uniform	Pvrl3-Shh E12.5_coronal	There is weak, scattered staining in the ventricular zone of the ganglionic eminences. Staining is either absent or ubiquitous in the mantle zone of the ganglionic eminences.
TS20: hypothalamus mantle layer	Ambiguous		Pvrl3-Shh E12.5_coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei, the AVH and anterior and posterior IDs.
TS20: hypothalamus ventricular layer	Very strong	Non-Uniform	Pvrl3-Shh E12.5_coronal	There is very strong staining in the VZ of the AVH and weak staining in the PVH nucleus and anterior and posterior IDs. Staining is either absent or ubiquitous in the VZ of the dorsal and ventral POAs and the VMH and ARH nuclei.
TS20: thalamus mantle layer	Ambiguous		Pvrl3-Shh E12.5_coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Very strong	Non-Uniform	Pvrl3-Shh E12.5_coronal	There is very strong staining in the ventricular zone of the prethalamus and moderate, scattered staining in the dorsal thalamus.

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Ambiguous		Pvrl3-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	Moderate		Pvrl3-Shh E14.5_coronal	There is moderate staining in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Pvrl3-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		Pvrl3-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	Very strong	Non-Uniform	Pvrl3-Shh E14.5_coronal	There is very strong staining in the ventricular zone of the mam zone, moderate staining in the premam and supramam zones and weak staining in the TT.
TS22: ganglionic eminence	Moderate	Non-Uniform	Pvrl3-Shh E14.5_coronal	There is moderate staining in the ventricular zone of the ganglionic eminences. Staining is either absent or ubiquitous in the mantle zone of the ganglionic eminences.
TS22: hypothalamus mantle layer	Ambiguous		Pvrl3-Shh E14.5_coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei, the AVH and anterior and posterior IDs.
TS22: hypothalamus ventricular layer	Moderate	Non-Uniform	Pvrl3-Shh E14.5_coronal	There is moderate staining in the ventricular zone of the PVH nucleus and anterior and posterior IDs and weak staining in the AVH and the VMH and ARH nuclei. Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs.
TS22: thalamus mantle layer	Ambiguous		Pvrl3-Shh E14.5_coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS22: thalamus ventricular layer	Very strong	Non-Uniform	Pvrl3-Shh E14.5_coronal	There is very strong staining in the ventricular zone of the dorsal thalamus and moderate staining in the prethalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Ambiguous		Pvrl3-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	Weak		Pvrl3-Shh E16.5_coronal	There is weak staining in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Pvrl3-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		Pvrl3-Shh E16.5_coronal	Staining is either absent or ubiquitous in the mantle zone of the premam zone.
TS24: diencephalon ventricular layer	Moderate		Pvrl3-Shh E16.5_coronal	There is moderate staining in the ventricular zone of the premam zone.
TS24: ganglionic eminence	Ambiguous		Pvrl3-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS24: hypothalamus mantle layer	Ambiguous		Pvrl3-Shh E16.5_coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH, SCH, DMH, VMH and ARH nuclei, the AVH, the DAH and the PH.
TS24: hypothalamus ventricular layer	Strong	Non-Uniform	Pvrl3-Shh E16.5_coronal	There is strong staining in the VZ of the dorsal & ventral POAs & the PVH nucleus, moderate staining in the AVH, DAH & PH & the DMH nucleus & weak staining in the SCH & VMH nuclei. Staining is either absent or ubiquitous in the VZ of the ARH nucleus.
TS24: thalamus mantle layer	Ambiguous		Pvrl3-Shh E16.5_coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS24: thalamus ventricular layer	Very strong		Pvrl3-Shh E16.5_coronal	There is very strong staining in the ventricular zone of the dorsal thalamus and prethalamus.