Probe:	UI-M-AH1-ags-h-04-0-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	1500016L03Rik-Shh E11.5-coronal	Staining is strong in the MZ of the prethalamus, moderate in the anterior & posterior IDs & mam zone & either absent or ubiquitous in the dorsal thalamus, dorsal & ventral POAs, PVH, VMH & ARH nuclei, AVH & premam & supramammilary zones & TT.
TS19: diencephalon lateral wall ventricular layer	Ambiguous		1500016L03Rik-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		1500016L03Rik-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		1500016L03Rik-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		1500016L03Rik-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		1500016L03Rik-Shh E12.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		1500016L03Rik-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	1500016L03Rik-Shh E12.5-coronal	There is strong staining in the mantle zone of the mam zone. Staining is either absent or ubiquitous in the mantle zone of the premam and supramammilary zone and the TT.
TS20: diencephalon ventricular layer	Ambiguous		1500016L03Rik-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		1500016L03Rik-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	1500016L03Rik-Shh E12.5-coronal	There is strong staining in the MZ of the posterior ID and moderate staining the AVH and anterior ID. Staining is either absent or ubiquitous in the MZ of the dorsal and ventral POAs and the PVH, VMH and ARH nuclei.
TS20: hypothalamus ventricular layer	Ambiguous		1500016L03Rik-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	Moderate	Non-Uniform	1500016L03Rik-Shh E12.5-coronal	There is moderate 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		1500016L03Rik-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		1500016L03Rik-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	Ambiguous		1500016L03Rik-Shh E14.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		1500016L03Rik-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	Very strong	Non-Uniform	1500016L03Rik-Shh E14.5-coronal	There is very strong staining in the mantle zone of the mam zone. Staining is either absent or ubiquitous in the mantle zone of the premam and supramam zones and the TT.
TS22: diencephalon ventricular layer	Ambiguous		1500016L03Rik-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		1500016L03Rik-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	1500016L03Rik-Shh E14.5-coronal	There is strong staining in the mantle zone of the ventral POA. Staining is either absent or ubiquitous in the mantle zone of the dorsal POA, the PVH, VMH and ARH nuclei, the AVH,and the anterior and posterior IDs.
TS22: hypothalamus ventricular layer	Ambiguous		1500016L03Rik-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	Moderate	Non-Uniform	1500016L03Rik-Shh E14.5-coronal	There is moderate 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	Ambiguous		1500016L03Rik-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		1500016L03Rik-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	Ambiguous		1500016L03Rik-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		1500016L03Rik-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		1500016L03Rik-Shh E16.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the premam zone.
TS24: diencephalon ventricular layer	Ambiguous		1500016L03Rik-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam zone.
TS24: ganglionic eminence	Ambiguous		1500016L03Rik-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS24: hypothalamus mantle layer	Very strong	Non-Uniform	1500016L03Rik-Shh E16.5-coronal	There is very strong staining in the mantle zone of the SCH nucleus. Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH, DMH, VMH and ARH nuclei, the AVH, the DAH and the PH.
TS24: hypothalamus ventricular layer	Moderate	Non-Uniform	1500016L03Rik-Shh E16.5-coronal	There is moderate staining in the ventricular zone of the AVH and the SCH nucleus. Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH, DMH, VMH and ARH nuclei and the DAH and PH.
TS24: thalamus mantle layer	Moderate	Non-Uniform	1500016L03Rik-Shh E16.5-coronal	There is moderate 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	Ambiguous		1500016L03Rik-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.