Probe:	UI-M-BH3-awu-d-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	Thsd4-Shh E11.5_coronal	Staining is strong in the MZ of posterior ID & VMH nucleus, moderate in dorsal thalamus, weak in ventral POA & either absent or ubiquitous in the prethalamus, dorsal POA, PVH & ARH nuclei, AVH, anterior ID, premam, mam & supramam zones & TT.
TS19: diencephalon lateral wall ventricular layer	Ambiguous		Thsd4-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	Ambiguous		Thsd4-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	Ambiguous		Thsd4-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		Thsd4-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	Ambiguous		Thsd4-Shh E12.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Thsd4-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	Strong	Non-Uniform	Thsd4-Shh E12.5_coronal	There is strong staining in the mantle zone of the premam zone and the TT. Staining is either absent or ubiquitous in the mantle zone of the mam and supramam zones.
TS20: diencephalon ventricular layer	Ambiguous		Thsd4-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		Thsd4-Shh E12.5_coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS20: hypothalamus mantle layer	Strong	Non-Uniform	Thsd4-Shh E12.5_coronal	There is strong staining in the MZ of the VMH nucleus, moderate staining in the ventral POA and weak staining in the posterior ID. Staining is either absent or ubiquitous in the MZ of the dorsal POA, the PVH and ARH nuclei, the AVH and anterior ID.
TS20: hypothalamus ventricular layer	Strong	Non-Uniform	Thsd4-Shh E12.5_coronal	There is strong staining in the ventricular zone of the dorsal POA. Staining is either absent or ubiquitous in the ventricular zone of the ventral POA, the PVH, VMH and ARH nuclei, the AVH and anterior and posterior IDs.
TS20: thalamus mantle layer	Strong	Non-Uniform	Thsd4-Shh E12.5_coronal	There is strong staining in the mantle zone of the prethalamus. Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus.
TS20: thalamus ventricular layer	Ambiguous		Thsd4-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		Thsd4-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	Scattered	Thsd4-Shh E14.5_coronal	There is strong, scattered staining in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Thsd4-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	Strong	Non-Uniform	Thsd4-Shh E14.5_coronal	There is strong, scattered staining in the mantle zone of the premam zone and the TT. Staining is either absent or ubiquitous in the mantle zone of the mam and supramam zones.
TS22: diencephalon ventricular layer	Ambiguous		Thsd4-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	Ambiguous		Thsd4-Shh E14.5_coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS22: hypothalamus mantle layer	Strong	Non-Uniform	Thsd4-Shh E14.5_coronal	There is strong, scattered staining in the mantle zone of the VMH and ARH nuclei and weak staining in the ventral POA. Staining is either absent or ubiquitous in the mantle zone of the dorsal POA, the PVH nucleus, the AVH and anterior and posterior IDs.
TS22: hypothalamus ventricular layer	Ambiguous		Thsd4-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	Weak	Non-Uniform	Thsd4-Shh E14.5_coronal	There is weak staining in the mantle zone of the prethalamus. Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus.
TS22: thalamus ventricular layer	Strong	Non-Uniform	Thsd4-Shh E14.5_coronal	There is strong staining in the ventricular zone of the prethalamus and moderate, scattered staining in the dorsal thalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Ambiguous		Thsd4-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	Moderate		Thsd4-Shh E16.5_coronal	There is moderate staining in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Thsd4-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	Strong	Non-Uniform	Thsd4-Shh E16.5_coronal	There is strong staining in the mantle zone of the premam zone. Staining is either absent or ubiquitous in the mantle zone of the mam and supramam zones.
TS24: diencephalon ventricular layer	Ambiguous		Thsd4-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS24: ganglionic eminence	Ambiguous		Thsd4-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS24: hypothalamus mantle layer	Strong	Non-Uniform	Thsd4-Shh E16.5_coronal	There is strong staining in the mantle zone of the VMH nucleus and the PH. Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH, SCH, DMH and ARH nuclei, the AVH and the DAH.
TS24: hypothalamus ventricular layer	Strong	Non-Uniform	Thsd4-Shh E16.5_coronal	There is strong staining in the ventricular zone of the DMH and VMH nuclei. Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH, SCH and ARH nuclei, the AVH, the DAH and the PH.
TS24: thalamus mantle layer	Weak	Non-Uniform	Thsd4-Shh E16.5_coronal	There is weak staining in the mantle zone of the prethalamus. Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus.
TS24: thalamus ventricular layer	Strong	Non-Uniform	Thsd4-Shh E16.5_coronal	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.