Probe:	UI-M-BH2.1-apr-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	Strong	Non-Uniform	Sox4-Shh E11.5_coronal-2 , Sox4-Shh E11.5_coronal	Staining is strong in the MZ of the dorsal thalamus & prethalamus, moderate & scattered in dorsal & ventral POAs, PVH nucleus & AVH, weak in anterior & posterior ID & weak & scattered in the VMH & ARH nuclei, premam, mam & supramam zones & TT.
TS19: diencephalon lateral wall ventricular layer	Moderate	Non-Uniform	Sox4-Shh E11.5_coronal , Sox4-Shh E11.5_coronal-2	There is moderate, scattered staining in the VZ of the dorsal & ventral POAs, the PVH, VMH & ARH nuclei, the AVH, the anterior & posterior IDs, the premam, mam & supramam zones & the TT & weak, scattered staining in the dorsal thalamus & prethalamus.
TS19: telencephalon mantle layer	Strong	Non-Uniform	Sox4-Shh E11.5_coronal-2 , Sox4-Shh E11.5_coronal	There is strong staining in the postmitotic neurons in the intermediate zone and cortical plate of the cerebral cortex and strong, scattered staining in the mantle zone of the ganglionic eminences.
TS19: telencephalon ventricular layer	Weak	Non-Uniform	Sox4-Shh E11.5_coronal , Sox4-Shh E11.5_coronal-2	There is weak staining in the ventricular zone of the cerebral cortex and weak, scattered staining in the ganglionic eminences.

Structure	Level	Pattern	Image	Note
TS20: cerebral cortex intermediate zone	Ambiguous		Sox4-Shh E12.5_coronal , Sox4-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		Sox4-Shh E12.5_coronal-2 , Sox4-Shh E12.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Sox4-Shh E12.5_coronal , Sox4-Shh E12.5_coronal-2	Staining is either absent or ubiquitous in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS20: ganglionic eminence	Moderate	Non-Uniform	Sox4-Shh E12.5_coronal-2 , Sox4-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	Non-Uniform	Sox4-Shh E12.5_coronal , Sox4-Shh E12.5_coronal-2	There is moderate staining in the mantle zone of the PVH nucleus and the AVH and weak staining in the dorsal and ventral POAs and anterior and posterior IDs.
TS20: hypothalamus ventricular layer	Ambiguous		Sox4-Shh E12.5_coronal , Sox4-Shh E12.5_coronal-2	Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH nucleus, the AVH and anterior and posterior IDs.
TS20: thalamus mantle layer	Moderate		Sox4-Shh E12.5_coronal-2 , Sox4-Shh E12.5_coronal	There is moderate staining in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Ambiguous		Sox4-Shh E12.5_coronal-2 , Sox4-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	Strong		Sox4-Shh E14.5_coronal , Sox4-Shh E14.5_coronal-2	There is strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Ambiguous		Sox4-Shh E14.5_coronal , Sox4-Shh E14.5_coronal-2	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Strong		Sox4-Shh E14.5_coronal , Sox4-Shh E14.5_coronal-2	There is strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Weak		Sox4-Shh E14.5_coronal-2 , Sox4-Shh E14.5_coronal	There is weak staining in the mantle zone of the premam, mam and supramam zones and the TT.
TS22: diencephalon ventricular layer	Ambiguous		Sox4-Shh E14.5_coronal , Sox4-Shh E14.5_coronal-2	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	Sox4-Shh E14.5_coronal , Sox4-Shh E14.5_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.
TS22: hypothalamus mantle layer	Moderate	Non-Uniform	Sox4-Shh E14.5_coronal , Sox4-Shh E14.5_coronal-2	There is moderate staining in the MZ of the VMH nucleus, weak staining in the anterior and posterior IDs and weak, scattered staining in the AVH. Staining is either absent or ubiquitous in the MZ of the dorsal and ventral POAs and the PVH and ARH nuclei.
TS22: hypothalamus ventricular layer	Moderate	Non-Uniform	Sox4-Shh E14.5_coronal-2 , Sox4-Shh E14.5_coronal	There is moderate staining in the ventricular zone of the AVH. Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei and anterior and posterior IDs.
TS22: thalamus mantle layer	Moderate		Sox4-Shh E14.5_coronal , Sox4-Shh E14.5_coronal-2	There is moderate staining in the mantle zone of the dorsal thalamus and prethalamus.
TS22: thalamus ventricular layer	Ambiguous		Sox4-Shh E14.5_coronal-2 , Sox4-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		Sox4-Shh E16.5_coronal-2 , Sox4-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		Sox4-Shh E16.5_coronal , Sox4-Shh E16.5_coronal-2	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Very strong		Sox4-Shh E16.5_coronal , Sox4-Shh E16.5_coronal-2	There is very strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Weak		Sox4-Shh E16.5_coronal , Sox4-Shh E16.5_coronal-2	There is weak staining in the mantle zone of the premam, mam and supramam zones.
TS24: diencephalon ventricular layer	Ambiguous		Sox4-Shh E16.5_coronal , Sox4-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	Strong	Non-Uniform	Sox4-Shh E16.5_coronal-2 , Sox4-Shh E16.5_coronal	There is strong 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	Sox4-Shh E16.5_coronal-2 , Sox4-Shh E16.5_coronal	There is moderate staining in the mantle zone of the PVH and VMH nucleus and weak staining in the dorsal and ventral POAs, DMH and ARH nuclei and the PH. Staining is either absent or ubiquitous in the mantle zone of the AVH, the DAH and the SCH nucleus.
TS24: hypothalamus ventricular layer	Weak	Non-Uniform	Sox4-Shh E16.5_coronal , Sox4-Shh E16.5_coronal-2	There is weak staining in the ventricular zone of the DAH. 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 PH.
TS24: thalamus mantle layer	Strong		Sox4-Shh E16.5_coronal-2 , Sox4-Shh E16.5_coronal	There is strong staining in the mantle zone of the dorsal thalamus and prethalamus.
TS24: thalamus ventricular layer	Ambiguous		Sox4-Shh E16.5_coronal-2 , Sox4-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.