Probe:	UI-M-AJ1-agz-h-11-0-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	Moderate	Non-Uniform	Nap1l5-Shh E11.5_coronal	Staining is moderate in the MZ of anterior & posterior IDs & weak in the AVH. Staining is either absent or ubiquitous in the MZ of the dorsal thalamus, prethalamus, dorsal & ventral POAs, PVH, VMH & ARH nuclei, premam, mam & supramam zones & TT.
TS19: diencephalon lateral wall ventricular layer	Ambiguous		Nap1l5-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, VMH and ARH nuclei, the AVH, the anterior and posterior IDs, the premam, mam and supramam zones and the TT.
TS19: telencephalon mantle layer	Ambiguous		Nap1l5-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		Nap1l5-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		Nap1l5-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		Nap1l5-Shh E12.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Nap1l5-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		Nap1l5-Shh E12.5_coronal	There is strong staining in the mantle zone of the premam, mam and supramam zones and the TT.
TS20: diencephalon ventricular layer	Ambiguous		Nap1l5-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		Nap1l5-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	Nap1l5-Shh E12.5_coronal	There is strong staining in the mantle zone of the ventral POA, the PVH, VMH and ARH nuclei, the AVH and anterior and posterior IDs. Staining is either absent or ubiquitous in the mantle zone of the dorsal POA.
TS20: hypothalamus ventricular layer	Ambiguous		Nap1l5-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	Moderate	Non-Uniform	Nap1l5-Shh E12.5_coronal	There is moderate 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	Moderate		Nap1l5-Shh E12.5_coronal	There is moderate staining in the ventricular zone of the dorsal thalamus and prethalamus.

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Ambiguous		Nap1l5-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		Nap1l5-Shh E14.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Nap1l5-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	Very strong	Non-Uniform	Nap1l5-Shh E14.5_coronal	There is very strong staining in the mantle zone of the premam and mam zones and the TT and strong staining in the supramam zone.
TS22: diencephalon ventricular layer	Ambiguous		Nap1l5-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	Nap1l5-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	Very strong	Non-Uniform	Nap1l5-Shh E14.5_coronal	There is very strong staining in the MZ of the dorsal & ventral POAs & the AVH, strong staining in the anterior & posterior IDs & ARH nucleus & weak staining in the VMH nucleus. Staining is either absent or ubiquitous in the MZ of the PVH nucleus.
TS22: hypothalamus ventricular layer	Ambiguous		Nap1l5-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	Non-Uniform	Nap1l5-Shh E14.5_coronal	There is moderate staining in the mantle zone of the prethalamus. Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus.
TS22: thalamus ventricular layer	Ambiguous		Nap1l5-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		Nap1l5-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		Nap1l5-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Nap1l5-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	Very strong		Nap1l5-Shh E16.5_coronal	There is very strong staining in the mantle zone of the premam, mam and supramam zones.
TS24: diencephalon ventricular layer	Ambiguous		Nap1l5-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		Nap1l5-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	Nap1l5-Shh E16.5_coronal	There is very strong staining in the mantle zone of the dorsal and ventral POAs, the PVH, SCH, DMH and ARH nuclei and the PH, strong staining in the AVH and DAH and weak staining in the VMH nucleus.
TS24: hypothalamus ventricular layer	Ambiguous		Nap1l5-Shh E16.5_coronal	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, the DAH and the PH.
TS24: thalamus mantle layer	Strong	Non-Uniform	Nap1l5-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		Nap1l5-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.