Probe:	UI-M-BH0-akj-c-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	Ambiguous		Punc-Shh E11.5_coronal , PUNC(D)+Shh(F)-E11.5_sagittal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus, 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	Punc-Shh E11.5_coronal , PUNC(D)+Shh(F)-E11.5_sagittal	Staining is strong in the VZ of the dorsal thalamus, prethalamus, dorsal & ventral POAs & mam zone & weak in premam zone. Staining is either absent or ubiquitous in the VZ of the PVH, VMH & ARH nuclei, AVH, anterior & posterior IDs, TT & supramam zone.
TS19: telencephalon mantle layer	Ambiguous		PUNC(D)+Shh(F)-E11.5_sagittal , Punc-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	PUNC(D)+Shh(F)-E11.5_sagittal , Punc-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		PUNC(D)+shh(F)-E12.5_sagittal , Punc-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		PUNC(D)+shh(F)-E12.5_sagittal , Punc-Shh E12.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Punc-Shh E12.5_coronal , PUNC(D)+shh(F)-E12.5_sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS20: diencephalon mantle layer	Moderate	Non-Uniform	PUNC(D)+shh(F)-E12.5_sagittal , Punc-Shh E12.5_coronal	There is moderate staining in the mantle zone of the premam zone. Staining is either absent or ubiquitous in the mantle zone of the mam and supramam zones and the TT.
TS20: diencephalon ventricular layer	Very strong	Non-Uniform	Punc-Shh E12.5_coronal , PUNC(D)+shh(F)-E12.5_sagittal	There is very strong staining in the ventricular zone of the mam zone. Staining is either absent or ubiquitous in the ventricular zone of the premam and supramam zones and the TT.
TS20: ganglionic eminence	Moderate	Non-Uniform	Punc-Shh E12.5_coronal , PUNC(D)+shh(F)-E12.5_sagittal	There is moderate 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	Ambiguous		Punc-Shh E12.5_coronal , PUNC(D)+shh(F)-E12.5_sagittal	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	Strong	Non-Uniform	Punc-Shh E12.5_coronal , PUNC(D)+shh(F)-E12.5_sagittal	There is strong staining in the ventricular zone of the dorsal POA. Staining is either absent or ubiquitous in the ventricular zone of the ventral POA, the PVH, VMH and ARH nuclei, the AVH and anterior and posterior IDs.
TS20: thalamus mantle layer	Ambiguous		PUNC(D)+shh(F)-E12.5_sagittal , Punc-Shh E12.5_coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Very strong		Punc-Shh E12.5_coronal , PUNC(D)+shh(F)-E12.5_sagittal	There is very strong staining in the ventricular zone of the dorsal thalamus and prethalamus.

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Ambiguous		Punc-Shh E14.5_coronal , PUNC(D)+Shh(F)-E14.5_sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Ambiguous		PUNC(D)+Shh(F)-E14.5_sagittal , Punc-Shh E14.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Punc-Shh E14.5_coronal , PUNC(D)+Shh(F)-E14.5_sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Ambiguous		PUNC(D)+Shh(F)-E14.5_sagittal , Punc-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	PUNC(D)+Shh(F)-E14.5_sagittal , Punc-Shh E14.5_coronal	There is very strong staining in the ventricular zone of the premam and mam zones. Staining is either absent or ubiquitous in the ventricular zone of the TT and supramam zone.
TS22: ganglionic eminence	Very strong	Non-Uniform	Punc-Shh E14.5_coronal , PUNC(D)+Shh(F)-E14.5_sagittal	There is very strong staining in the ventricular zone of the ganglionic eminences and moderate staining in the mantle zone of the ganglionic eminences.
TS22: hypothalamus mantle layer	Ambiguous		Punc-Shh E14.5_coronal , PUNC(D)+Shh(F)-E14.5_sagittal	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	Punc-Shh E14.5_coronal , PUNC(D)+Shh(F)-E14.5_sagittal	There is very strong staining in the ventricular zone of the dorsal POA. Staining is either absent or ubiquitous in the ventricular zone of the ventral POA, the PVH, VMH and ARH nuclei, the AVH and anterior and posterior IDs.
TS22: thalamus mantle layer	Ambiguous		PUNC(D)+Shh(F)-E14.5_sagittal , Punc-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		PUNC(D)+Shh(F)-E14.5_sagittal , Punc-Shh E14.5_coronal	There is very strong staining in the ventricular zone of the dorsal thalamus and prethalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Moderate	Scattered	Punc-Shh E16.5_coronal , PUNC(D)+Shh(F)-E16.5_sagittal	There is moderate, scattered staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Strong		Punc-Shh E16.5_coronal , PUNC(D)+Shh(F)-E16.5_sagittal	There is strong staining in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Moderate	Scattered	PUNC(D)+Shh(F)-E16.5_sagittal , Punc-Shh E16.5_coronal	There is moderate, scattered staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Ambiguous		Punc-Shh E16.5_coronal , PUNC(D)+Shh(F)-E16.5_sagittal	Staining is either absent or ubiquitous in the mantle zone of the premam, mam and supramam zones.
TS24: diencephalon ventricular layer	Very strong	Non-Uniform	PUNC(D)+Shh(F)-E16.5_sagittal , Punc-Shh E16.5_coronal	There is very strong staining in the ventricular zone of the mam and supramam zones. Staining is either absent or ubiquitous in the ventricular zone of the premam zone.
TS24: ganglionic eminence	Moderate	Non-Uniform	Punc-Shh E16.5_coronal , PUNC(D)+Shh(F)-E16.5_sagittal	There is moderate 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	Weak	Non-Uniform	PUNC(D)+Shh(F)-E16.5_sagittal , Punc-Shh E16.5_coronal	There is weak staining in the mantle zone of the PVH nucleus. Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the SCH, DMH, VMH and ARH nuclei, the AVH, the DAH and the PH.
TS24: hypothalamus ventricular layer	Strong	Non-Uniform	Punc-Shh E16.5_coronal , PUNC(D)+Shh(F)-E16.5_sagittal	There is strong staining in the ventricular zone of the dorsal POA. Staining is either absent or ubiquitous in the ventricular zone of the ventral POA, the PVH, SCH, DMH, VMH and ARH nuclei, the AVH, the DAH and the PH.
TS24: thalamus mantle layer	Ambiguous		Punc-Shh E16.5_coronal , PUNC(D)+Shh(F)-E16.5_sagittal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS24: thalamus ventricular layer	Strong		Punc-Shh E16.5_coronal , PUNC(D)+Shh(F)-E16.5_sagittal	There is strong staining in the ventricular zone of the dorsal thalamus and prethalamus.