Probe:	UI-M-AI0-aaq-d-01-0-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	Ambiguous		Slit2-Shh E11.5_coronal	Staining is either absent or ubiquitous 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, mam and supramam zones and the TT.
TS19: diencephalon lateral wall ventricular layer	Very strong	Non-Uniform	Slit2-Shh E11.5_coronal	Staining is very strong in the VZ of the ventral POA, AVH & VMH nucleus, strong in prethalamus & either absent or ubiquitous in the dorsal thalamus, dorsal POA, PVH & ARH nuclei, anterior & posterior IDs, premam, mam & supramam zones & TT.
TS19: telencephalon mantle layer	Ambiguous		Slit2-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	Very strong	Non-Uniform	Slit2-Shh E11.5_coronal	There is very strong staining in the ventricular zone of the cerebral cortex. Staining is either absent or ubiquitous in the ventricular zone of the ganglionic eminences.

Structure	Level	Pattern	Image	Note
TS20: cerebral cortex intermediate zone	Ambiguous		Slit2-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	Very strong		Slit2-Shh E12.5_coronal	There is very strong staining in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Slit2-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		Slit2-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	Slit2-Shh E12.5_coronal	There is very strong staining in the ventricular zone of the premam and mam zones. Staining is either absent or ubiquitous in the ventricular zone of the TT and the supramam zone.
TS20: ganglionic eminence	Ambiguous		Slit2-Shh E12.5_coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS20: hypothalamus mantle layer	Moderate	Non-Uniform	Slit2-Shh E12.5_coronal	There is moderate staining in the mantle zone of the ventral POA and the AVH and weak staining in the PVH and VMH nuclei. Staining is either absent or ubiquitous in the mantle zone of the dorsal POA, the ARH nucleus and anterior and posterior IDs.
TS20: hypothalamus ventricular layer	Very strong	Non-Uniform	Slit2-Shh E12.5_coronal	Staining is very strong in the VZ of the ventral POA & AVH, strong in the VMH nucleus, moderate in the dorsal POA & weak in the PVH nucleus. Staining is either absent or ubiquitous in the VZ of anterior & posterior IDs & the ARH nucleus.
TS20: thalamus mantle layer	Moderate	Non-Uniform	Slit2-Shh E12.5_coronal	There is moderate staining in the mantle zone of the dorsal thalamus. Staining is either absent or ubiquitous in the mantle zone of the prethalamus.
TS20: thalamus ventricular layer	Ambiguous		Slit2-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		Slit2-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	Strong		Slit2-Shh E14.5_coronal	There is strong staining in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Slit2-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		Slit2-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	Slit2-Shh E14.5_coronal	There is very strong staining in the ventricular zone of the premam and mam zones. Staining is either absent or ubiquitous in the ventricular zone of the TT and the supramam zone.
TS22: ganglionic eminence	Moderate	Non-Uniform	Slit2-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	Weak	Non-Uniform	Slit2-Shh E14.5_coronal	There is weak staining in the mantle zone of the PVH nucleus. Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the VMH and ARH nuclei, the AVH and anterior and posterior IDs.
TS22: hypothalamus ventricular layer	Very strong	Non-Uniform	Slit2-Shh E14.5_coronal	There is very strong staining in the ventricular zone of the dorsal POA and PVH and VMH nuclei and strong staining in the ventral POA. Staining is either absent or ubiquitous in the ventricular zone of the AVH, anterior and posterior IDs and ARH nucleus.
TS22: thalamus mantle layer	Moderate	Non-Uniform	Slit2-Shh E14.5_coronal	There is moderate staining in the mantle zone of the dorsal thalamus. Staining is either absent or ubiquitous in the mantle zone of the prethalamus.
TS22: thalamus ventricular layer	Moderate	Non-Uniform	Slit2-Shh E14.5_coronal	There is moderate staining in the ventricular zone of the dorsal thalamus and weak staining in the prethalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Ambiguous		Slit2-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		Slit2-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Slit2-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		Slit2-Shh E16.5_coronal	Staining is either absent or ubiquitous in the mantle zone of the premam zone.
TS24: diencephalon ventricular layer	Very strong		Slit2-Shh E16.5_coronal	There is very strong staining in the ventricular zone of the premam zone.
TS24: ganglionic eminence	Weak	Non-Uniform	Slit2-Shh E16.5_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.
TS24: hypothalamus mantle layer	Moderate	Non-Uniform	Slit2-Shh E16.5_coronal	There is moderate staining in the mantle zone of the VMH nucleus and weak staining in the PVH and SCH nuclei. Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the DMH and ARH nuclei, the AVH, the DAH and the PH.
TS24: hypothalamus ventricular layer	Very strong	Non-Uniform	Slit2-Shh E16.5_coronal	There is very strong staining in the ventricular zone of the dorsal and ventral POAs, the PVH, DMH, VMH and ARH nuclei, the AVH, the DAH and the PH and weak staining in the SCH nucleus.
TS24: thalamus mantle layer	Ambiguous		Slit2-Shh E16.5_coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS24: thalamus ventricular layer	Weak	Non-Uniform	Slit2-Shh E16.5_coronal	There is weak staining in the ventricular zone of the dorsal thalamus. Staining is either absent or ubiquitous in the ventricular zone of the prethalamus.