Probe:	UI-M-AQ1-aec-f-02-0-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		Rufy3-Shh E11.5_coronal-2 , Rufy3-Shh E11.5_coronal	There is moderate staining in the mantle zone of the dorsal thalamus, prethalamus, dorsal and ventral POAs, the PVH, VMH and ARH nuclei, the AVH, the anterior and posterior IDs, the premam zone and the TT.
TS19: diencephalon lateral wall ventricular layer	Ambiguous		Rufy3-Shh E11.5_coronal , Rufy3-Shh E11.5_coronal-2	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 zone and the TT.
TS19: telencephalon mantle layer	Strong	Non-Uniform	Rufy3-Shh E11.5_coronal , Rufy3-Shh E11.5_coronal-2	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.
TS19: telencephalon ventricular layer	Ambiguous		Rufy3-Shh E11.5_coronal , Rufy3-Shh E11.5_coronal-2	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		Rufy3-Shh E12.5_coronal , Rufy3-Shh E12.5_coronal-2	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS20: cerebral cortex ventricular layer	Ambiguous		Rufy3-Shh E12.5_coronal-2 , Rufy3-Shh E12.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Rufy3-Shh E12.5_coronal , Rufy3-Shh E12.5_coronal-2	Staining is either absent or ubiquitous in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS20: diencephalon mantle layer	Moderate		Rufy3-Shh E12.5_coronal-2 , Rufy3-Shh E12.5_coronal	There is moderate staining in the mantle zone of the premam, mam and supramam zones and the TT.
TS20: diencephalon ventricular layer	Ambiguous		Rufy3-Shh E12.5_coronal , Rufy3-Shh E12.5_coronal-2	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	Rufy3-Shh E12.5_coronal-2 , Rufy3-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	Moderate		Rufy3-Shh E12.5_coronal-2 , Rufy3-Shh E12.5_coronal	There is moderate staining in the mantle 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		Rufy3-Shh E12.5_coronal-2 , Rufy3-Shh E12.5_coronal	There is moderate staining in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Ambiguous		Rufy3-Shh E12.5_coronal , Rufy3-Shh E12.5_coronal-2	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.
TS20: hypothalamus ventricular layer	Ambiguous		Rufy3-Shh E12.5_coronal , Rufy3-Shh E12.5_coronal-2	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.

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Moderate		Rufy3-Shh E14.5_coronal-2 , Rufy3-Shh E14.5_coronal	There is moderate staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cortical plate	Moderate		Rufy3-Shh E14.5_coronal-2 , Rufy3-Shh E14.5_coronal	There is moderate staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Moderate		Rufy3-Shh E14.5_coronal , Rufy3-Shh E14.5_coronal-2	There is moderate staining in the mantle zone of the premam, mam and supramam zones and the TT.
TS22: ganglionic eminence	Moderate	Non-Uniform	Rufy3-Shh E14.5_coronal-2 , Rufy3-Shh E14.5_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.
TS22: hypothalamus mantle layer	Moderate		Rufy3-Shh E14.5_coronal , Rufy3-Shh E14.5_coronal-2	There is moderate staining in the mantle 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	Rufy3-Shh E14.5_coronal , Rufy3-Shh E14.5_coronal-2	There is strong staining in the mantle zone of the dorsal thalamus and moderate staining in the prethalamus.
TS22: thalamus ventricular layer	Ambiguous		Rufy3-Shh E14.5_coronal-2 , Rufy3-Shh E14.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.
TS22: cerebral cortex ventricular layer	Ambiguous		Rufy3-Shh E14.5_coronal , Rufy3-Shh E14.5_coronal-2	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: diencephalon ventricular layer	Ambiguous		Rufy3-Shh E14.5_coronal-2 , Rufy3-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: hypothalamus ventricular layer	Ambiguous		Rufy3-Shh E14.5_coronal , Rufy3-Shh E14.5_coronal-2	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.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Strong		Rufy3-Shh E16.5_coronal-2 , Rufy3-Shh E16.5_coronal	There is strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cortical plate	Strong		Rufy3-Shh E16.5_coronal , Rufy3-Shh E16.5_coronal-2	There is strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: hypothalamus mantle layer	Strong	Non-Uniform	Rufy3-Shh E16.5_coronal , Rufy3-Shh E16.5_coronal-2	There is strong staining in the mantle zone of the dorsal and ventral POAs, the PVH, SCH, DMH, VMH and ARH nuclei, the AVH and the PH and weak staining in the DAH.
TS24: thalamus mantle layer	Very strong	Non-Uniform	Rufy3-Shh E16.5_coronal-2 , Rufy3-Shh E16.5_coronal	There is very strong staining in the mantle zone of the dorsal thalamus and strong staining in the prethalamus.
TS24: thalamus ventricular layer	Ambiguous		Rufy3-Shh E16.5_coronal-2 , Rufy3-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.
TS24: cerebral cortex ventricular layer	Ambiguous		Rufy3-Shh E16.5_coronal , Rufy3-Shh E16.5_coronal-2	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: diencephalon mantle layer	Strong		Rufy3-Shh E16.5_coronal-2 , Rufy3-Shh E16.5_coronal	There is strong staining in the mantle zone of the premam, mam and supramam zones.
TS24: hypothalamus ventricular layer	Ambiguous		Rufy3-Shh E16.5_coronal , Rufy3-Shh E16.5_coronal-2	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: diencephalon ventricular layer	Ambiguous		Rufy3-Shh E16.5_coronal , Rufy3-Shh E16.5_coronal-2	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS24: ganglionic eminence	Moderate	Non-Uniform	Rufy3-Shh E16.5_coronal , Rufy3-Shh E16.5_coronal-2	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.

Structure	Level	Pattern	Image	Note
TS19: diencephalon lateral wall mantle layer	Strong	Non-Uniform	Rufy3-Shh E11.5_coronal , Rufy3-Shh E11.5_coronal-2	Staining is strong in the MZ of the prethalamus, dorsal POA, PVH nucleus & TT, moderate in the dorsal thalamus, anterior & posterior IDs, premam, mam & supramam zones, weak in the VMH nucleus & either absent or ubiquitous in the ventral POA & the AVH.
TS19: diencephalon lateral wall ventricular layer	Ambiguous		Rufy3-Shh E11.5_coronal , Rufy3-Shh E11.5_coronal-2	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, the premam, mam and supramam zones and the TT.
TS19: telencephalon mantle layer	Strong	Non-Uniform	Rufy3-Shh E11.5_coronal-2 , Rufy3-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		Rufy3-Shh E11.5_coronal , Rufy3-Shh E11.5_coronal-2	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		Rufy3-Shh E12.5_coronal , Rufy3-Shh E12.5_coronal-2	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS20: cerebral cortex ventricular layer	Ambiguous		Rufy3-Shh E12.5_coronal-2 , Rufy3-Shh E12.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Rufy3-Shh E12.5_coronal , Rufy3-Shh E12.5_coronal-2	Staining is either absent or ubiquitous in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS20: diencephalon mantle layer	Strong		Rufy3-Shh E12.5_coronal-2 , Rufy3-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		Rufy3-Shh E12.5_coronal , Rufy3-Shh E12.5_coronal-2	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones and the TT.
TS20: ganglionic eminence	Strong	Non-Uniform	Rufy3-Shh E12.5_coronal-2 , Rufy3-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 ventricular layer	Ambiguous		Rufy3-Shh E12.5_coronal , Rufy3-Shh E12.5_coronal-2	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	Strong		Rufy3-Shh E12.5_coronal , Rufy3-Shh E12.5_coronal-2	There is strong staining in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Ambiguous		Rufy3-Shh E12.5_coronal-2 , Rufy3-Shh E12.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.
TS20: hypothalamus mantle layer	Strong	Non-Uniform	Rufy3-Shh E12.5_coronal-2 , Rufy3-Shh E12.5_coronal	There is strong staining in the mantle zone of the dorsal and ventral POAs, the PVH nucleus, the AVH and anterior and posterior IDs. Staining is either absent or ubiquitous in the mantle zone of the VMH and ARH nuclei.

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Ambiguous		Rufy3-Shh E14.5_coronal-2 , Rufy3-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		Rufy3-Shh E14.5_coronal , Rufy3-Shh E14.5_coronal-2	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: diencephalon mantle layer	Strong	Non-Uniform	Rufy3-Shh E14.5_coronal , Rufy3-Shh E14.5_coronal-2	There is strong staining in the mantle zone of the premam and mam zones and the TT and weak staining in the supramam zone.
TS22: diencephalon ventricular layer	Ambiguous		Rufy3-Shh E14.5_coronal-2 , Rufy3-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	Moderate	Non-Uniform	Rufy3-Shh E14.5_coronal-2 , Rufy3-Shh E14.5_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.
TS22: hypothalamus ventricular layer	Ambiguous		Rufy3-Shh E14.5_coronal-2 , Rufy3-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		Rufy3-Shh E14.5_coronal-2 , Rufy3-Shh E14.5_coronal	There is strong staining in the mantle zone of the dorsal thalamus and prethalamus.
TS22: thalamus ventricular layer	Ambiguous		Rufy3-Shh E14.5_coronal-2 , Rufy3-Shh E14.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.
TS22: cortical plate	Ambiguous		Rufy3-Shh E14.5_coronal , Rufy3-Shh E14.5_coronal-2	Staining is either absent or ubiquitous in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: hypothalamus mantle layer	Strong	Non-Uniform	Rufy3-Shh E14.5_coronal-2 , Rufy3-Shh E14.5_coronal	There is strong staining in the mantle zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei and anterior and posterior IDs. Staining is either absent or ubiquitous in the mantle zone of the AVH.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Moderate		Rufy3-Shh E16.5_coronal-2 , Rufy3-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		Rufy3-Shh E16.5_coronal-2 , Rufy3-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: ganglionic eminence	Weak	Non-Uniform	Rufy3-Shh E16.5_coronal-2 , Rufy3-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 ventricular layer	Ambiguous		Rufy3-Shh E16.5_coronal , Rufy3-Shh E16.5_coronal-2	Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH and DMH nuclei and the PH.
TS24: thalamus mantle layer	Strong	Non-Uniform	Rufy3-Shh E16.5_coronal-2 , Rufy3-Shh E16.5_coronal	There is strong staining in the mantle zone of the dorsal thalamus and moderate staining in the prethalamus.
TS24: thalamus ventricular layer	Ambiguous		Rufy3-Shh E16.5_coronal , Rufy3-Shh E16.5_coronal-2	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.
TS24: cortical plate	Moderate		Rufy3-Shh E16.5_coronal , Rufy3-Shh E16.5_coronal-2	There is moderate staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: hypothalamus mantle layer	Strong	Non-Uniform	Rufy3-Shh E16.5_coronal-2 , Rufy3-Shh E16.5_coronal	There is strong staining in the mantle zone of the dorsal POA and PVH nucleus and weak staining in the DMH nucleus and the PH. Staining is either absent or ubiquitous in the mantle zone of the ventral POA.