Probe:	UI-M-BH0-aja-c-03-0-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		Zfp312-Shh E11.5_coronal , Zfp312-Shh 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	Zfp312-Shh E11.5_coronal , Zfp312-Shh E11.5_sagittal	There is strong staining in the VZ of the prethalamus, dorsal & ventral POAs, PVH nucleus, AVH & premam & mam zones. Staining is either absent or ubiquitous in the VZ of the dorsal thalamus, anterior & posterior IDs, VMH & ARH nuclei, TT & supramam zone.
TS19: telencephalon mantle layer	Ambiguous		Zfp312-Shh E11.5_coronal , Zfp312-Shh E11.5_sagittal	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	Zfp312-Shh E11.5_coronal , Zfp312-Shh E11.5_sagittal	There is strong staining in the ventricular zone of the cerebral cortex. Staining is either absent or ubiquitous in the ventricular zone of the ganglionic eminences.

Structure	Level	Pattern	Image	Note
TS20: cerebral cortex intermediate zone	Ambiguous		Zfp312-Shh E12.5_coronal , Zfp312-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		Zfp312-Shh E12.5_sagittal , Zfp312-Shh E12.5_coronal	There is very strong staining in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Zfp312-Shh E12.5_coronal , Zfp312-Shh 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	Ambiguous		Zfp312-Shh E12.5_coronal , Zfp312-Shh E12.5_sagittal	Staining is either absent or ubiquitous in the mantle zone of the premam, mam and supramam zones and the TT.
TS20: diencephalon ventricular layer	Very strong	Non-Uniform	Zfp312-Shh E12.5_sagittal , Zfp312-Shh E12.5_coronal	There is very strong staining in the ventricular zone of the premam and mam zones and the TT. Staining is either absent or ubiquitous in the ventricular zone of the supramam zone.
TS20: ganglionic eminence	Ambiguous		Zfp312-Shh E12.5_sagittal , Zfp312-Shh E12.5_coronal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS20: hypothalamus mantle layer	Ambiguous		Zfp312-Shh E12.5_sagittal , Zfp312-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	Very strong	Non-Uniform	Zfp312-Shh E12.5_coronal , Zfp312-Shh E12.5_sagittal	Staining is very strong in the VZ of the dorsal & ventral POAs, strong in the PVH nucleus & AVH, moderate in the VMH nucleus & weak in anterior & posterior IDs. Staining is either absent or ubiquitous in the VZ of the ARH nucleus.
TS20: thalamus mantle layer	Ambiguous		Zfp312-Shh E12.5_sagittal , Zfp312-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	Non-Uniform	Zfp312-Shh E12.5_coronal , Zfp312-Shh E12.5_sagittal	There is very strong staining in the ventricular zone of the prethalamus. Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus.

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Very strong		Zfp312-Shh E14.5_sagittal , Zfp312-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	Strong		Zfp312-Shh E14.5_coronal , Zfp312-Shh E14.5_sagittal	There is strong staining in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Very strong		Zfp312-Shh E14.5_sagittal , Zfp312-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		Zfp312-Shh E14.5_sagittal , Zfp312-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	Zfp312-Shh E14.5_sagittal , Zfp312-Shh E14.5_coronal	There is very strong staining in the ventricular zone of the premam and mam zones and the TT. Staining is either absent or ubiquitous in the ventricular zone of the supramam zone.
TS22: ganglionic eminence	Strong	Non-Uniform	Zfp312-Shh E14.5_coronal , Zfp312-Shh E14.5_sagittal	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.
TS22: hypothalamus mantle layer	Very strong	Non-Uniform	Zfp312-Shh E14.5_sagittal , Zfp312-Shh E14.5_coronal	There is very strong staining in the MZ of the PVH nucleus, strong staining in the dorsal POA and moderate staining in the AVH. Staining is either absent or ubiquitous in the MZ of the ventral POA, the VMH and ARH nuclei and anterior and posterior IDs.
TS22: hypothalamus ventricular layer	Very strong	Non-Uniform	Zfp312-Shh E14.5_sagittal , Zfp312-Shh E14.5_coronal	There is very strong staining in the VZ of the PVH nucleus, moderate staining in the dorsal & ventral POAs & weak staining in the anterior & posterior IDs & the VMH nucleus. Staining is either absent or ubiquitous in the VZ of the AVH & the ARH nucleus.
TS22: thalamus mantle layer	Strong	Non-Uniform	Zfp312-Shh E14.5_coronal , Zfp312-Shh E14.5_sagittal	There is strong 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	Very strong	Non-Uniform	Zfp312-Shh E14.5_coronal , Zfp312-Shh E14.5_sagittal	There is very strong staining in the ventricular zone of the prethalamus. Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Very strong		Zfp312-Shh E16.5_coronal , Zfp312-Shh E16.5_sagittal	There is very strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Moderate		Zfp312-Shh E16.5_coronal , Zfp312-Shh E16.5_sagittal	There is moderate staining in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Very strong		Zfp312-Shh E16.5_coronal , Zfp312-Shh E16.5_sagittal	There is very strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Ambiguous		Zfp312-Shh E16.5_coronal , Zfp312-Shh E16.5_sagittal	Staining is either absent or ubiquitous in the mantle zone of the premam, mam and supramam zones.
TS24: diencephalon ventricular layer	Strong	Non-Uniform	Zfp312-Shh E16.5_sagittal , Zfp312-Shh E16.5_coronal	There is strong staining in the ventricular zone of the mam zone and weak staining in the premam zone. Staining is either absent or ubiquitous in the ventricular zone of the supramam zone.
TS24: ganglionic eminence	Strong	Non-Uniform	Zfp312-Shh E16.5_coronal , Zfp312-Shh E16.5_sagittal	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.
TS24: hypothalamus mantle layer	Very strong	Non-Uniform	Zfp312-Shh E16.5_coronal , Zfp312-Shh E16.5_sagittal	There is very 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, SCH, DMH, VMH and ARH nuclei, the AVH, the DAH and the PH.
TS24: hypothalamus ventricular layer	Strong	Non-Uniform	Zfp312-Shh E16.5_sagittal , Zfp312-Shh E16.5_coronal	There is strong staining in the ventricular zone of the PVH nucleus and weak staining in the dorsal and ventral POAs, the DAH and the PH. Staining is either absent or ubiquitous in the ventricular zone of the AVH and the SCH, DMH, VMH and ARH nuclei.
TS24: thalamus mantle layer	Ambiguous		Zfp312-Shh E16.5_coronal , Zfp312-Shh E16.5_sagittal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS24: thalamus ventricular layer	Very strong	Non-Uniform	Zfp312-Shh E16.5_coronal , Zfp312-Shh E16.5_sagittal	There is very strong staining in the ventricular zone of the prethalamus. Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus.