Probe:	IMAGE clone 931627
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	Crym-Shh E11.5-coronal	There is strong staining in the MZ of the TT. Staining is either absent or ubiquitous in the MZ of the dorsal thalamus, prethalamus, dorsal & ventral POAs, the PVH, VMH & ARH nuclei, the AVH, anterior & posterior IDs & premam, mam & supramam zones.
TS19: diencephalon lateral wall ventricular layer	Ambiguous		Crym-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		Crym-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		Crym-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		Crym-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		Crym-Shh E12.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Crym-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		Crym-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		Crym-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		Crym-Shh E12.5-coronal	Staining is either absent or ubiquitous in the venticular and mantle zones of the ganglionic eminences.
TS20: hypothalamus mantle layer	Ambiguous		Crym-Shh E12.5-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.
TS20: hypothalamus ventricular layer	Ambiguous		Crym-Shh E12.5-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.
TS20: thalamus mantle layer	Ambiguous		Crym-Shh E12.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Ambiguous		Crym-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	Very strong		Crym-Shh E14.5-coronal	There is very strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Ambiguous		Crym-Shh E14.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Very strong		Crym-Shh E14.5-coronal	There is very strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Ambiguous		Crym-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	Moderate	Non-Uniform	Crym-Shh E14.5-coronal	There is moderate 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	Ambiguous		Crym-Shh E14.5-coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS22: hypothalamus mantle layer	Ambiguous		Crym-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	Crym-Shh E14.5-coronal	There is very strong staining in the VZ of the PVH and ARH nuclei and the AVH and strong staining in the dorsal POA. Staining is either absent or ubiquitous in the VZ of the ventral POA, the anterior and posterior IDs and VMH nucleus.
TS22: thalamus mantle layer	Ambiguous		Crym-Shh E14.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS22: thalamus ventricular layer	Ambiguous		Crym-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		Crym-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		Crym-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Very strong		Crym-Shh E16.5-coronal	There is very strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Ambiguous		Crym-Shh E16.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the premam zone.
TS24: diencephalon ventricular layer	Very strong		Crym-Shh E16.5-coronal	There is very strong staining in the ventricular zone of the premam zone.
TS24: ganglionic eminence	Ambiguous		Crym-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS24: hypothalamus mantle layer	Ambiguous		Crym-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	Crym-Shh E16.5-coronal	There is very strong staining in the VZ of the dorsal POA, the PVH, DMH, VMH and ARH nuclei, the AVH, the DAH and the PH and weak staining in the ventral POA. Staining is either absent or ubiquitous in the VZ of the SCH nucleus.
TS24: thalamus mantle layer	Ambiguous		Crym-Shh E16.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS24: thalamus ventricular layer	Ambiguous		Crym-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.