Probe:	UI-M-BH3-avi-c-03-0-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	Ambiguous		Col22a1-Shh E11.5-coronal	Staining is either absent or ubiquitous in the mantle 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: diencephalon lateral wall ventricular layer	Strong	Non-Uniform	Col22a1-Shh E11.5-coronal	There is strong staining in the VZ of the dorsal POA, PVH nucleus & AVH. Staining is either absent or ubiquitous in the VZ of the dorsal thalamus, prethalamus, ventral DOA, anterior & posterior IDs, VMH & ARH nuclei & premam, mam & supramam zones & TT.
TS19: telencephalon mantle layer	Ambiguous		Col22a1-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	Strong	Non-Uniform	Col22a1-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	Ambiguous		Col22a1-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		Col22a1-Shh E12.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Col22a1-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	Ambiguous		Col22a1-Shh E12.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the premam, mam and supramam zones and the TT.
TS20: diencephalon ventricular layer	Ambiguous		Col22a1-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	Very strong	Non-Uniform	Col22a1-Shh E12.5-coronal	There is very strong staining in the ventricular zone of the ganglionic eminences. Staining is either absent or ubiquitous in the mantle zone of the ganglionic eminences.
TS20: hypothalamus mantle layer	Moderate	Non-Uniform	Col22a1-Shh E12.5-coronal	There is moderate staining in the mantle zone of the AVH. Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei and the anterior and posterior IDs.
TS20: hypothalamus ventricular layer	Strong	Non-Uniform	Col22a1-Shh E12.5-coronal	There is strong staining in the VZ of the dorsal and ventral POAs, the PVH nucleus and the AVH and moderate staining in the anterior and posterior IDs. Staining is either absent or ubiquitous in the VZ of the VMH and ARH nuclei.
TS20: thalamus mantle layer	Ambiguous		Col22a1-Shh E12.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Moderate	Non-Uniform	Col22a1-Shh E12.5-coronal	There is moderate staining in the ventricular zone of the prethalamus. Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus.

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Ambiguous		Col22a1-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	Very strong		Col22a1-Shh E14.5-coronal	There is very strong staining in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Col22a1-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	Ambiguous		Col22a1-Shh E14.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the premam, mam and supramam zones and the TT.
TS22: diencephalon ventricular layer	Very strong	Non-Uniform	Col22a1-Shh E14.5-coronal	There is very strong staining in the ventricular zone of the TT. Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS22: ganglionic eminence	Strong	Non-Uniform	Col22a1-Shh E14.5-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.
TS22: hypothalamus mantle layer	Ambiguous		Col22a1-Shh E14.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei, the AVH and anterior and posterior IDs.
TS22: hypothalamus ventricular layer	Very strong	Non-Uniform	Col22a1-Shh E14.5-coronal	There is very strong staining in the VZ of the PVH nucleus, the AVH and anterior and posterior IDs and moderate staining in the dorsal POA. Staining is either absent or ubiquitous in the VZ of the ventral POA and the VMH and ARH nuclei.
TS22: thalamus mantle layer	Ambiguous		Col22a1-Shh E14.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS22: thalamus ventricular layer	Strong	Non-Uniform	Col22a1-Shh E14.5-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.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Ambiguous		Col22a1-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	Strong		Col22a1-Shh E16.5-coronal	There is strong staining in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Col22a1-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	Ambiguous		Col22a1-Shh E16.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the premam, mam and supramam zones.
TS24: diencephalon ventricular layer	Ambiguous		Col22a1-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS24: ganglionic eminence	Very strong	Non-Uniform	Col22a1-Shh E16.5-coronal	There is very 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	Ambiguous		Col22a1-Shh E16.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH, SCH, DMH, VMH and ARH nuclei, the AVH, the DAH and the PH.
TS24: hypothalamus ventricular layer	Very strong	Non-Uniform	Col22a1-Shh E16.5-coronal	There is very strong staining in the VZ of the PVH nucleus, the AVH & the DAH, strong staining in the DMH nucleus & the PH & moderate staining in the ventral POA. Staining is either absent or ubiquitous in the VZ of the dorsal POA, SCH, VMH & ARH nuclei.
TS24: thalamus mantle layer	Ambiguous		Col22a1-Shh E16.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS24: thalamus ventricular layer	Very strong	Non-Uniform	Col22a1-Shh E16.5-coronal	There is very strong staining in the ventricular zone of the prethalamus. Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus.