Probe:	UI-M-AH1-agq-h-09-0-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	Weak	Non-Uniform	6430548M08Rik-Shh E11.5-coronal	There is weak staining in the MZ of posterior ID & premam zone. 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 ID, mam & supramam zones & the TT.
TS19: diencephalon lateral wall ventricular layer	Strong	Non-Uniform	6430548M08Rik-Shh E11.5-coronal	There is strong staining in the VZ of the PVH nucleus. Staining is either absent or ubiquitous in the VZ of the dorsal thalamus, prethalamus, dorsal & ventral POAs, the AVH, anterior & posterior IDs, VMH & ARH nuclei, premam, mam & supramam zones & TT.
TS19: telencephalon mantle layer	Ambiguous		6430548M08Rik-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		6430548M08Rik-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		6430548M08Rik-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		6430548M08Rik-Shh E12.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		6430548M08Rik-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	Non-Uniform	6430548M08Rik-Shh E12.5-coronal	There is very strong staining in the mantle zone of the premam and mam zones and the TT and moderate staining in the supramam zone.
TS20: diencephalon ventricular layer	Ambiguous		6430548M08Rik-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	Weak	Non-Uniform	6430548M08Rik-Shh E12.5-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.
TS20: hypothalamus mantle layer	Very strong	Non-Uniform	6430548M08Rik-Shh E12.5-coronal	There is very strong staining in the mantle zone of the AVH and the VMH nucleus, strong staining in the mantle zone of the dorsal and ventral POAs, the PVH nucleus and the anterior and posterior IDs and moderate staining in the ARH nucleus.
TS20: hypothalamus ventricular layer	Ambiguous		6430548M08Rik-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	Very strong	Non-Uniform	6430548M08Rik-Shh E12.5-coronal	There is very strong staining in the mantle zone of the prethalamus and moderate staining in the dorsal thalamus.
TS20: thalamus ventricular layer	Ambiguous		6430548M08Rik-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	Strong		6430548M08Rik-Shh E14.5-coronal	There is strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Ambiguous		6430548M08Rik-Shh E14.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Strong		6430548M08Rik-Shh E14.5-coronal	There is strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Very strong	Non-Uniform	6430548M08Rik-Shh E14.5-coronal	There is very strong staining in the mantle zone of the mam zone, strong staining in the premam zone and the TT and weak staining in the supramam zone.
TS22: diencephalon ventricular layer	Ambiguous		6430548M08Rik-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		6430548M08Rik-Shh E14.5-coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS22: hypothalamus mantle layer	Very strong	Non-Uniform	6430548M08Rik-Shh E14.5-coronal	There is very strong staining in the MZ of the AVH and posterior ID, strong staining in the anterior ID and weak staining in the VMH and ARH nuclei. Staining is either absent or ubiquitous in the MZ of the dorsal and ventral POAs and the PVH nucleus.
TS22: hypothalamus ventricular layer	Strong	Non-Uniform	6430548M08Rik-Shh E14.5-coronal	There is strong staining in the ventricular zone of the dorsal and ventral POAs and the PVH nucleus. Staining is either absent or ubiquitous in the ventricular zone of the AVH, the anterior and posterior IDs and the VMH and ARH nuclei.
TS22: thalamus mantle layer	Ambiguous		6430548M08Rik-Shh E14.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS22: thalamus ventricular layer	Very strong	Non-Uniform	6430548M08Rik-Shh E14.5-coronal	There is very strong staining in the ventricular zone of the dorsal thalamus and strong staining the prethalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Very strong		6430548M08Rik-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		6430548M08Rik-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Very strong		6430548M08Rik-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	Moderate		6430548M08Rik-Shh E16.5-coronal	There is moderate staining in the mantle zone of the premam, mam and supramam zones.
TS24: diencephalon ventricular layer	Ambiguous		6430548M08Rik-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		6430548M08Rik-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	6430548M08Rik-Shh E16.5-coronal	There is strong staining in the mantle zone of the PVH nucleus, moderate staining in the dorsal and ventral POAs, the AVH, the DAH and the SCH, DMH, VMH and ARH nuclei and the PH.
TS24: hypothalamus ventricular layer	Ambiguous		6430548M08Rik-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH, SCH, DMH, VMH and ARH nuclei, the AVH, the DAH and the PH.
TS24: thalamus mantle layer	Moderate		6430548M08Rik-Shh E16.5-coronal	There is moderate staining in the mantle zone of the dorsal thalamus and prethalamus.
TS24: thalamus ventricular layer	Very strong	Non-Uniform	6430548M08Rik-Shh E16.5-coronal	There is very strong staining in the ventricular zone of the dorsal thalamus. Staining is either absent or ubiquitous in the ventricular zone of the prethalamus.