Probe:	UI-M-CG0p-bqb-g-07-0-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		Sox11-Shh E11.5_coronal	There is strong 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, mam and supramam zones and the TT.
TS19: diencephalon lateral wall ventricular layer	Strong	Non-Uniform	Sox11-Shh E11.5_coronal	There is strong staining in the VZ of the AVH, anterior & posterior IDs & the TT, moderate staining in the VMH & ARH nuclei & premam, mam & supramam zones & weak staining in the dorsal thalamus, prethalamus, dorsal & ventral POAs & PVH nucleus.
TS19: telencephalon mantle layer	Strong	Non-Uniform	Sox11-Shh E11.5_coronal	There is strong staining in the postmitotic neurons in the intermediate zone and cortical plate of the cerebral cortex and weak staining in the mantle zone of the ganglionic eminences.
TS19: telencephalon ventricular layer	Strong	Non-Uniform	Sox11-Shh E11.5_coronal	There is strong staining in the ventricular zone of the ganglionic eminences. Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.

Structure	Level	Pattern	Image	Note
TS20: cerebral cortex intermediate zone	Strong		Sox11-Shh E12.5_coronal	There is strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS20: cerebral cortex ventricular layer	Ambiguous		Sox11-Shh E12.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Strong		Sox11-Shh E12.5_coronal	There is strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS20: diencephalon mantle layer	Strong		Sox11-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	Weak		Sox11-Shh E12.5_coronal	There is weak staining in the ventricular zone of the premam, mam and supramam zones and the TT.
TS20: ganglionic eminence	Strong	Non-Uniform	Sox11-Shh E12.5_coronal	There is strong staining in the mantle zone and weak staining in the ventricular zone of the ganglionic eminences.
TS20: hypothalamus mantle layer	Strong		Sox11-Shh E12.5_coronal	There is strong 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: hypothalamus ventricular layer	Weak		Sox11-Shh E12.5_coronal	There is weak staining 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		Sox11-Shh E12.5_coronal	There is strong staining in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Weak		Sox11-Shh E12.5_coronal	There is weak staining in the ventricular zone of the dorsal thalamus and prethalamus.

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Strong		Sox11-Shh E14.5_coronal	There is strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Ambiguous		Sox11-Shh E14.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Strong		Sox11-Shh E14.5_coronal	There is strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Strong	Non-Uniform	Sox11-Shh E14.5_coronal	There is strong staining in the mantle zone of the mam zone, moderate staining in the TT 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		Sox11-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	Sox11-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	Moderate	Non-Uniform	Sox11-Shh E14.5_coronal	There is moderate staining in the mantle zone of the AVH, anterior ID and VMH nucleus and weak staining in the dorsal and ventral POAs, posterior ID and ARH nucleus. Staining is either absent or ubiquitous in the mantle zone of the PVH nucleus.
TS22: hypothalamus ventricular layer	Strong	Non-Uniform	Sox11-Shh E14.5_coronal	There is strong staining in the ventricular zone of the VMH nucleus and weak staining in 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 and ARH nuclei.
TS22: thalamus mantle layer	Weak		Sox11-Shh E14.5_coronal	There is weak staining in the mantle zone of the dorsal thalamus and prethalamus.
TS22: thalamus ventricular layer	Ambiguous		Sox11-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	Strong		Sox11-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		Sox11-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Strong		Sox11-Shh E16.5_coronal	There is strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Moderate	Non-Uniform	Sox11-Shh E16.5_coronal	There is moderate staining in the mantle zone of the premam and mam zones. Staining is either absent or ubiquitous in the mantle zone of the supramam zone.
TS24: diencephalon ventricular layer	Ambiguous		Sox11-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS24: ganglionic eminence	Strong	Non-Uniform	Sox11-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	Sox11-Shh E16.5_coronal	There is moderate staining in the mantle zone of the dorsal and ventral POAs, DMH, VMH and ARH nuclei and the PH and weak staining in the AVH, DAH and SCH nucleus. Staining is either absent or ubiquitous in the mantle zone of the PVH nucleus.
TS24: hypothalamus ventricular layer	Moderate	Non-Uniform	Sox11-Shh E16.5_coronal	There is moderate staining in the ventricular zone of the SCH nucleus. Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH, DMH, VMH and ARH nuclei, the AVH, the DAH and the PH.
TS24: thalamus mantle layer	Weak		Sox11-Shh E16.5_coronal	There is weak staining in the mantle zone of the dorsal thalamus and prethalamus.
TS24: thalamus ventricular layer	Ambiguous		Sox11-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.