Probe:	UI-M-BH1-ana-a-06-0-UI.s2
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	Bhlhb9-Shh E11.5-coronal	There is very strong staining in the mantle zone of the PVH nucleus and the AVH. Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus, the prethalamus, dorsal and ventral POAs and the anterior and posterior IDs.
TS19: diencephalon lateral wall ventricular layer	Ambiguous		Bhlhb9-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 nucleus, the AVH and anterior and posterior IDs.
TS19: telencephalon mantle layer	Ambiguous		Bhlhb9-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		Bhlhb9-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		Bhlhb9-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		Bhlhb9-Shh E12.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Bhlhb9-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	Very strong		Bhlhb9-Shh E12.5-coronal	There is very strong staining in the mantle zone of the TT.
TS20: diencephalon ventricular layer	Ambiguous		Bhlhb9-Shh E12.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the TT.
TS20: ganglionic eminence	Strong	Non-Uniform	Bhlhb9-Shh E12.5-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.
TS20: hypothalamus mantle layer	Very strong	Non-Uniform	Bhlhb9-Shh E12.5-coronal	There is very strong staining in the mantle zone of the PVH nucleus and the AVH and strong staining in the dorsal POA and the anterior and posterior IDs. Staining is either absent or ubiquitous in the mantle zone of the ventral POA.
TS20: hypothalamus ventricular layer	Ambiguous		Bhlhb9-Shh E12.5-coronal	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	Weak	Non-Uniform	Bhlhb9-Shh E12.5-coronal	There is weak, scattered staining in the mantle zone of the dorsal thalamus and prethalamus. Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus.
TS20: thalamus ventricular layer	Ambiguous		Bhlhb9-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		Bhlhb9-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	Moderate		Bhlhb9-Shh E14.5-coronal	There is moderate, scattered staining in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Bhlhb9-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	Moderate		Bhlhb9-Shh E14.5-coronal	There is moderate staining in the mantle zone of the premam and mam zones and the TT.
TS22: diencephalon ventricular layer	Ambiguous		Bhlhb9-Shh E14.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam and mam zones and the TT.
TS22: ganglionic eminence	Weak	Non-Uniform	Bhlhb9-Shh E14.5-coronal	There is weak staining in the ventricular zone of the ganglionic eminences. Staining is either absent or ubiquitous in the mantle zone of the ganglionic eminences.
TS22: hypothalamus mantle layer	Very strong	Non-Uniform	Bhlhb9-Shh E14.5-coronal	There is very strong staining in the MZ of the PVH nucleus and the AVH and moderate staining in the dorsal and ventral POAs, the anterior and posterior IDs and the VMH nucleus. Staining is either absent or ubiquitous in the MZ of the ARH nucleus.
TS22: hypothalamus ventricular layer	Ambiguous		Bhlhb9-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	Bhlhb9-Shh E14.5-coronal	There is weak 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	Ambiguous		Bhlhb9-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	Ambiguous		Bhlhb9-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		Bhlhb9-Shh E16.5-coronal	There is moderate staining in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Bhlhb9-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	Weak	Non-Uniform	Bhlhb9-Shh E16.5-coronal	There is weak, scattered 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		Bhlhb9-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS24: ganglionic eminence	Weak	Non-Uniform	Bhlhb9-Shh E16.5-coronal	There is weak 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	Bhlhb9-Shh E16.5-coronal	There is moderate staining in the MZ of the VMH nucleus & weak, scattered staining in the the dorsal & ventral POAs, the PVH & DMH nuclei, the AVH, the DAH & the PH. Staining is either absent or ubiquitous in the MZ of the SCH & ARH nuclei.
TS24: hypothalamus ventricular layer	Moderate	Non-Uniform	Bhlhb9-Shh E16.5-coronal	There is moderate staining in the ventricular zone of the dorsal and ventral POAs, the PVH, DMH and VMH nuclei and the DAH. Staining is either absent or ubiquitous in the ventricular zone of the AVH, the SCH and ARH nuclei and the PH.
TS24: thalamus mantle layer	Weak	Non-Uniform	Bhlhb9-Shh E16.5-coronal	There is weak, scattered staining in the mantle zone of the dorsal thalamus. Staining is either absent or ubiquitous in the mantle zone of the prethalamus.
TS24: thalamus ventricular layer	Moderate		Bhlhb9-Shh E16.5-coronal	There is moderate staining in the ventricular zone of the dorsal thalamus and prethalamus.