Probe:	UI-M-AP0-abi-h-08-0-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	Robo1-Shh E11.5_sagittal , Robo1-Shh E11.5_coronal	Staining is strong in the MZ of the dorsal thalamus, prethalamus, dorsal & ventral POAs, PVH nucleus & AVH, moderate in the mam & supramam zones, weak in anterior & posterior IDs & either absent or ubiquitous in the VMH & ARH nuclei, premam zone & TT.
TS19: diencephalon lateral wall ventricular layer	Ambiguous		Robo1-Shh E11.5_sagittal , Robo1-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	Strong	Non-Uniform	Robo1-Shh E11.5_sagittal , Robo1-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		Robo1-Shh E11.5_sagittal , Robo1-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		Robo1-Shh E12.5_coronal , Robo1-Shh E12.5_sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS20: cerebral cortex ventricular layer	Ambiguous		Robo1-Shh E12.5_coronal , Robo1-Shh E12.5_sagittal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Robo1-Shh E12.5_coronal , Robo1-Shh E12.5_sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS20: diencephalon mantle layer	Strong	Non-Uniform	Robo1-Shh E12.5_coronal , Robo1-Shh E12.5_sagittal	There is strong staining in the mantle zone of the TT and mam zone and weak staining in the supramam zone. Staining is either absent or ubiquitous in the mantle zone of the premam zone.
TS20: diencephalon ventricular layer	Ambiguous		Robo1-Shh E12.5_coronal , Robo1-Shh E12.5_sagittal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones and the TT.
TS20: ganglionic eminence	Very strong	Non-Uniform	Robo1-Shh E12.5_coronal , Robo1-Shh E12.5_sagittal	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.
TS20: hypothalamus mantle layer	Strong	Non-Uniform	Robo1-Shh E12.5_sagittal , Robo1-Shh E12.5_coronal	There is strong staining in the mantle zone of the VMH nucleus and weak staining in the dorsal and ventral POAs. Staining is either absent or ubiquitous in the mantle zone of the PVH and ARH nuclei, the AVH and anterior and posterior IDs.
TS20: hypothalamus ventricular layer	Weak	Non-Uniform	Robo1-Shh E12.5_coronal , Robo1-Shh E12.5_sagittal	There is weak staining in the ventricular zone of the anterior and posterior IDs. Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei and the AVH.
TS20: thalamus mantle layer	Very strong		Robo1-Shh E12.5_coronal , Robo1-Shh E12.5_sagittal	There is very strong staining in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Ambiguous		Robo1-Shh E12.5_coronal , Robo1-Shh E12.5_sagittal	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		Robo1-Shh E14.5_sagittal , Robo1-Shh E14.5_coronal	There is moderate staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Ambiguous		Robo1-Shh E14.5_sagittal , Robo1-Shh E14.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Moderate		Robo1-Shh E14.5_sagittal , Robo1-Shh E14.5_coronal	There is moderate staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Strong	Non-Uniform	Robo1-Shh E14.5_sagittal , Robo1-Shh E14.5_coronal	There is strong staining in the mantle zone of the TT and the mam zone and weak staining in the supramam zone. Staining is either absent or ubiquitous in the mantle zone of the premam zone.
TS22: diencephalon ventricular layer	Ambiguous		Robo1-Shh E14.5_coronal , Robo1-Shh E14.5_sagittal	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	Robo1-Shh E14.5_sagittal , Robo1-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	Non-Uniform	Robo1-Shh E14.5_sagittal , Robo1-Shh E14.5_coronal	There is moderate staining in the MZ of the dorsal and ventral POAs and the AVH and weak staining in the PVH nucleus. Staining is either absent or ubiquitous in the MZ of the anterior and posterior IDs, the VMH and ARH nuclei and the AVH.
TS22: hypothalamus ventricular layer	Weak	Non-Uniform	Robo1-Shh E14.5_coronal , Robo1-Shh E14.5_sagittal	There is weak staining in the ventricular zone of the AVH and anterior and posterior IDs. Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs and the PVH, VMH and ARH nuclei.
TS22: thalamus mantle layer	Strong	Non-Uniform	Robo1-Shh E14.5_coronal , Robo1-Shh E14.5_sagittal	There is strong 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	Strong		Robo1-Shh E14.5_coronal , Robo1-Shh E14.5_sagittal	There is strong staining in the ventricular zone of the dorsal thalamus and prethalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Strong		Robo1-Shh E16.5_sagittal , Robo1-Shh E16.5_coronal	There is strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Ambiguous		Robo1-Shh E16.5_sagittal , Robo1-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Strong		Robo1-Shh E16.5_sagittal , Robo1-Shh E16.5_coronal	There is strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Weak	Non-Uniform	Robo1-Shh E16.5_sagittal , Robo1-Shh E16.5_coronal	There is weak staining in the mantle zone of the mam and supramam zones. Staining is either absent or ubiquitous in the mantle zone of the premam zone.
TS24: diencephalon ventricular layer	Strong	Non-Uniform	Robo1-Shh E16.5_coronal , Robo1-Shh E16.5_sagittal	There is strong staining in the ventricular zone of the premam and mam zones. Staining is either absent or ubiquitous in the ventricular zone of the supramam zone.
TS24: ganglionic eminence	Strong	Non-Uniform	Robo1-Shh E16.5_sagittal , Robo1-Shh E16.5_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.
TS24: hypothalamus mantle layer	Moderate	Non-Uniform	Robo1-Shh E16.5_coronal , Robo1-Shh E16.5_sagittal	There is moderate staining in the mantle zone of the dorsal and ventral POAs and weak staining in the AVH and the DAH. Staining is either absent or ubiquitous in the mantle zone of the PVH, SCH, DMH, VMH and ARH nuclei and the PH.
TS24: hypothalamus ventricular layer	Strong	Non-Uniform	Robo1-Shh E16.5_coronal , Robo1-Shh E16.5_sagittal	There is strong staining in the VZ of the VMH nucleus & the PH, moderate staining in the AVH, the DAH & DMH nucleus & weak staining in the PVH nucleus. Staining is either absent or ubiquitous in the VZ of the dorsal & ventral POAs & SCH & ARH nuclei.
TS24: thalamus mantle layer	Ambiguous		Robo1-Shh E16.5_coronal , Robo1-Shh E16.5_sagittal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS24: thalamus ventricular layer	Strong	Non-Uniform	Robo1-Shh E16.5_coronal , Robo1-Shh E16.5_sagittal	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.