Probe:	UI-M-AM0-adv-f-10-0-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	Slc17a6-Shh E11.5_coronal	Staining is very strong in the MZ of the prethalamus, dorsal & ventral POAs, PVH nucleus, AVH & mam zone, moderate in dorsal thalamus & VMH nucleus & either absent or ubiquitous in anterior & posterior IDs, ARH nucleus, premam & supramam zones & TT.
TS19: diencephalon lateral wall ventricular layer	Ambiguous		Slc17a6-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		Slc17a6-Shh E11.5_coronal	There is strong staining 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		Slc17a6-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	Very strong		Slc17a6-Shh E12.5_coronal	There is very strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS20: cerebral cortex ventricular layer	Ambiguous		Slc17a6-Shh E12.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Very strong		Slc17a6-Shh E12.5_coronal	There is very strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS20: diencephalon mantle layer	Very strong	Non-Uniform	Slc17a6-Shh E12.5_coronal	There is very strong 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 and the TT.
TS20: diencephalon ventricular layer	Ambiguous		Slc17a6-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		Slc17a6-Shh E12.5_coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS20: hypothalamus mantle layer	Very strong	Non-Uniform	Slc17a6-Shh E12.5_coronal	There is very strong staining in the MZ of the PVH nucleus & the AVH, moderate staining in the VMH nucleus & weak staining in the ventral POA. Staining is either absent or ubiquitous in the MZ of the dorsal POA, the ARH nucleus & anterior & posterior IDs.
TS20: hypothalamus ventricular layer	Ambiguous		Slc17a6-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	Very strong		Slc17a6-Shh E12.5_coronal	There is very strong staining in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Ambiguous		Slc17a6-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	Very strong		Slc17a6-Shh E14.5_coronal	There is very strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Ambiguous		Slc17a6-Shh E14.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Very strong		Slc17a6-Shh E14.5_coronal	There is very strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Weak	Scattered	Slc17a6-Shh E14.5_coronal	There is weak, scattered staining in the mantle zone of the premam zone and the TT.
TS22: diencephalon ventricular layer	Ambiguous		Slc17a6-Shh E14.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam zone and the TT.
TS22: ganglionic eminence	Ambiguous		Slc17a6-Shh E14.5_coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS22: hypothalamus mantle layer	Very strong	Non-Uniform	Slc17a6-Shh E14.5_coronal	There is very strong staining in the mantle zone of the PVH and VMH nuclei, the AVH and posterior ID and moderate staining in the ventral POA. Staining is either absent or ubiquitous in the mantle zone of the dorsal POA, anterior ID and ARH nucleus.
TS22: hypothalamus ventricular layer	Ambiguous		Slc17a6-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	Very strong		Slc17a6-Shh E14.5_coronal	There is very strong staining in the mantle zone of the dorsal thalamus and prethalamus.
TS22: thalamus ventricular layer	Ambiguous		Slc17a6-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	Very strong		Slc17a6-Shh E16.5_coronal	There is very strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Ambiguous		Slc17a6-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Very strong		Slc17a6-Shh E16.5_coronal	There is very strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: ganglionic eminence	Ambiguous		Slc17a6-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	Slc17a6-Shh E16.5_coronal	There is very strong staining in the MZ of the VMH nucleus, strong staining in the PVH & DMH nuclei & the DAH & moderate staining in the ventral POA. Staining is either absent or ubiquitous in the MZ of the dorsal POA, the AVH & the SCH & ARH nuclei.
TS24: hypothalamus ventricular layer	Ambiguous		Slc17a6-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 and the DAH.
TS24: thalamus mantle layer	Very strong		Slc17a6-Shh E16.5_coronal	There is very strong staining in the mantle zone of the dorsal thalamus and prethalamus.
TS24: thalamus ventricular layer	Ambiguous		Slc17a6-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.