Probe:	UI-M-AQ1-ady-d-12-0-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	Very strong	Non-Uniform	Pbx1-Shh E11.5_coronal , Pbx1-Shh E11.5_sagittal	Staining is very strong in the mam & supramam zones, strong in prethalamus, dorsal POA, PVH nucleus, AVH, anterior & posterior IDs & TT, moderate in ventral POA & premam zone, weak in VMH & ARH nuclei & either absent or ubiquitous in dorsal thalamus.
TS19: diencephalon lateral wall ventricular layer	Very strong	Non-Uniform	Pbx1-Shh E11.5_coronal , Pbx1-Shh E11.5_sagittal	Staining is very strong in the VZ of the supramam zone, strong in mam zone, weak in prethalamus, dorsal & ventral POAs, PVH, VMH & ARH nuclei, AVH, anterior & posterior IDs, premam zone & TT & either absent or ubiquitous in the dorsal thalamus.
TS19: telencephalon mantle layer	Strong	Non-Uniform	Pbx1-Shh E11.5_coronal , Pbx1-Shh E11.5_sagittal	There is strong staining in the mantle zone of the ganglionic eminences. Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone and cortical plate of the cerebral cortex.
TS19: telencephalon ventricular layer	Weak	Non-Uniform	Pbx1-Shh E11.5_coronal , Pbx1-Shh E11.5_sagittal	There is weak 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		Pbx1-Shh E12.5_coronal , Pbx1-Shh E12.5_sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS20: cerebral cortex ventricular layer	Very strong		Pbx1-Shh E12.5_coronal , Pbx1-Shh E12.5_sagittal	There is very strong staining in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Pbx1-Shh E12.5_sagittal , Pbx1-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	Pbx1-Shh E12.5_coronal , Pbx1-Shh E12.5_sagittal	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 supramam zones and the TT.
TS20: diencephalon ventricular layer	Ambiguous		Pbx1-Shh E12.5_sagittal , Pbx1-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	Strong	Non-Uniform	Pbx1-Shh E12.5_sagittal , Pbx1-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	Strong	Non-Uniform	Pbx1-Shh E12.5_sagittal , Pbx1-Shh E12.5_coronal	There is strong staining in the MZ of the dorsal and ventral POAs, PVH nucleus and the AVH, moderate staining in the anterior ID and weak staining in the posterior ID. Staining is either absent or ubiquitous in the MZ of the VMH and ARH nuclei.
TS20: hypothalamus ventricular layer	Ambiguous		Pbx1-Shh E12.5_sagittal , Pbx1-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	Strong	Non-Uniform	Pbx1-Shh E12.5_sagittal , Pbx1-Shh E12.5_coronal	There is strong staining in the mantle zone of the prethalamus and moderate staining in the dorsal thalamus.
TS20: thalamus ventricular layer	Ambiguous		Pbx1-Shh E12.5_sagittal , Pbx1-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		Pbx1-Shh E14.5_sagittal , Pbx1-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	Very strong		Pbx1-Shh E14.5_coronal , Pbx1-Shh E14.5_sagittal	There is very strong staining in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Very strong		Pbx1-Shh E14.5_coronal , Pbx1-Shh E14.5_sagittal	There is very strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Very strong	Non-Uniform	Pbx1-Shh E14.5_coronal , Pbx1-Shh E14.5_sagittal	There is very strong staining in the mantle zone of the mam zone and weak staining in the TT and supramam zones. Staining is either absent or ubiquitous in the mantle zone of the premam zone.
TS22: diencephalon ventricular layer	Ambiguous		Pbx1-Shh E14.5_coronal , Pbx1-Shh E14.5_sagittal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones and the TT.
TS22: ganglionic eminence	Very strong		Pbx1-Shh E14.5_sagittal , Pbx1-Shh E14.5_coronal	There is very strong staining in the ventricular and mantle zones of the ganglionic eminences.
TS22: hypothalamus mantle layer	Strong	Non-Uniform	Pbx1-Shh E14.5_coronal , Pbx1-Shh E14.5_sagittal	There is strong staining in the mantle zone of the AVH and anterior and posterior IDs and weak staining in the dorsal POA. Staining is either absent or ubiquitous in the mantle zone of the ventral POA and PVH, VMH and ARH nuclei.
TS22: hypothalamus ventricular layer	Strong	Non-Uniform	Pbx1-Shh E14.5_sagittal , Pbx1-Shh E14.5_coronal	There is strong staining in the ventricular zone of the ventral POA and weak staining in the AVH. Staining is either absent or ubiquitous in the ventricular zone of the dorsal POA, the PVH, VMH and ARH nuclei and anterior and posterior IDs.
TS22: thalamus mantle layer	Moderate		Pbx1-Shh E14.5_sagittal , Pbx1-Shh E14.5_coronal	There is moderate staining in the mantle zone of the dorsal thalamus and prethalamus.
TS22: thalamus ventricular layer	Ambiguous		Pbx1-Shh E14.5_sagittal , Pbx1-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	Strong		Pbx1-Shh E16.5_coronal , Pbx1-Shh E16.5_sagittal	There is strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Very strong		Pbx1-Shh E16.5_sagittal , Pbx1-Shh E16.5_coronal	There is very strong staining in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Strong		Pbx1-Shh E16.5_coronal , Pbx1-Shh E16.5_sagittal	There is strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Very strong	Non-Uniform	Pbx1-Shh E16.5_sagittal , Pbx1-Shh E16.5_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.
TS24: diencephalon ventricular layer	Ambiguous		Pbx1-Shh E16.5_coronal , Pbx1-Shh E16.5_sagittal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS24: ganglionic eminence	Very strong	Non-Uniform	Pbx1-Shh E16.5_coronal , Pbx1-Shh E16.5_sagittal	There is very strong staining in the ventricular zone of the ganglionic eminences and moderate, scattered staining in the mantle zone of the ganglionic eminences.
TS24: hypothalamus mantle layer	Very strong	Non-Uniform	Pbx1-Shh E16.5_coronal , Pbx1-Shh E16.5_sagittal	There is very strong staining in the mantle zone of the SCH nucleus and weak staining in the AVH and the DAH. Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH, DMH, VMH and ARH nuclei and the PH.
TS24: hypothalamus ventricular layer	Ambiguous		Pbx1-Shh E16.5_coronal , Pbx1-Shh E16.5_sagittal	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	Very strong		Pbx1-Shh E16.5_coronal , Pbx1-Shh E16.5_sagittal	There is very strong staining in the mantle zone of the dorsal thalamus and prethalamus.
TS24: thalamus ventricular layer	Weak	Non-Uniform	Pbx1-Shh E16.5_sagittal , Pbx1-Shh E16.5_coronal	There is weak staining in the ventricular zone of the dorsal thalamus. Staining is either absent or ubiquitous in the ventricular zone of the prethalamus.