Probe:	UI-M-CG0p-bqb-f-06-0-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	Ltbp3-Shh E11.5-sagittal , Ltbp3-Shh E11.5-coronal	There is weak staining in the MZ of the dorsal thalamus. Staining is either absent or ubiquitous in the MZ of the prethalamus, dorsal & ventral POAs, PVH, VMH & ARH nuclei, the AVH, the anterior & posterior IDs, the premam, mam & supramam zones & the TT.
TS19: diencephalon lateral wall ventricular layer	Weak	Non-Uniform	Ltbp3-Shh E11.5-sagittal , Ltbp3-Shh E11.5-coronal	There is weak staining in the VZ of the dorsal & ventral POAs. Staining is either absent or ubiquitous in the VZ of the dorsal thalamus, the prethalamus, the PVH, VMH & ARH nuclei, the AVH, anterior & posterior IDs, premam, mam & supramam zones & the TT.
TS19: telencephalon mantle layer	Ambiguous		Ltbp3-Shh E11.5-coronal , Ltbp3-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	Ltbp3-Shh E11.5-sagittal , Ltbp3-Shh E11.5-coronal	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		Ltbp3-Shh E12.5-coronal , Ltbp3-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	Strong		Ltbp3-Shh E12.5-sagittal , Ltbp3-Shh E12.5-coronal	There is strong staining in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Ltbp3-Shh E12.5-sagittal , Ltbp3-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	Ambiguous		Ltbp3-Shh E12.5-sagittal , Ltbp3-Shh E12.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the premam, mam and supramam zones and the TT.
TS20: diencephalon ventricular layer	Strong	Non-Uniform	Ltbp3-Shh E12.5-sagittal , Ltbp3-Shh E12.5-coronal	There is 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 and the TT.
TS20: ganglionic eminence	Weak	Non-Uniform	Ltbp3-Shh E12.5-coronal , Ltbp3-Shh E12.5-sagittal	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	Ambiguous		Ltbp3-Shh E12.5-sagittal , Ltbp3-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	Strong	Non-Uniform	Ltbp3-Shh E12.5-sagittal , Ltbp3-Shh E12.5-coronal	There is strong staining in the ventricular zone of the dorsal and ventral POAs, the AVH and VMH nucleus. Staining is either absent or ubiquitous in the ventricular zone of the PVH and ARH nuclei and anterior and posterior IDs.
TS20: thalamus mantle layer	Ambiguous		Ltbp3-Shh E12.5-sagittal , Ltbp3-Shh E12.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Weak	Non-Uniform	Ltbp3-Shh E12.5-coronal , Ltbp3-Shh E12.5-sagittal	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

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Ambiguous		Ltbp3-Shh E14.5-coronal , Ltbp3-Shh 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	Very strong		Ltbp3-Shh E14.5-sagittal , Ltbp3-Shh E14.5-coronal	There is very strong staining in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Ltbp3-Shh E14.5-sagittal , Ltbp3-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	Ambiguous		Ltbp3-Shh E14.5-sagittal , Ltbp3-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	Strong	Non-Uniform	Ltbp3-Shh E14.5-coronal , Ltbp3-Shh E14.5-sagittal	There is strong staining in the ventricular zone of the premam, mam and supramam zones and weak staining in the TT.
TS22: ganglionic eminence	Weak	Non-Uniform	Ltbp3-Shh E14.5-coronal , Ltbp3-Shh E14.5-sagittal	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.
TS22: hypothalamus mantle layer	Ambiguous		Ltbp3-Shh E14.5-sagittal , Ltbp3-Shh E14.5-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.
TS22: hypothalamus ventricular layer	Strong	Non-Uniform	Ltbp3-Shh E14.5-sagittal , Ltbp3-Shh E14.5-coronal	There is strong staining in the ventricular zone of the dorsal and ventral POAs, the AVH and VMH nucleus and weak staining in the anterior and posterior IDs. Staining is either absent or ubiquitous in the ventricular zone of the PVH and ARH nuclei.
TS22: thalamus mantle layer	Ambiguous		Ltbp3-Shh E14.5-sagittal , Ltbp3-Shh E14.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS22: thalamus ventricular layer	Moderate		Ltbp3-Shh E14.5-sagittal , Ltbp3-Shh E14.5-coronal	There is moderate staining in the ventricular zone of the dorsal thalamus and prethalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Ambiguous		Ltbp3-Shh E16.5-coronal , Ltbp3-Shh E16.5-sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Very strong		Ltbp3-Shh E16.5-coronal , Ltbp3-Shh E16.5-sagittal	There is very strong staining in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Ltbp3-Shh E16.5-coronal , Ltbp3-Shh E16.5-sagittal	Staining is either absent or ubiquitous in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Ambiguous		Ltbp3-Shh E16.5-sagittal , Ltbp3-Shh E16.5-coronal	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	Ltbp3-Shh E16.5-coronal , Ltbp3-Shh E16.5-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.
TS24: ganglionic eminence	Very strong	Non-Uniform	Ltbp3-Shh E16.5-sagittal , Ltbp3-Shh E16.5-coronal	There is very strong 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	Ambiguous		Ltbp3-Shh E16.5-coronal , Ltbp3-Shh E16.5-sagittal	Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH, SCH, DMH, VMH and ARH nuclei, the AVH, the DAH and the PH.
TS24: hypothalamus ventricular layer	Very strong	Non-Uniform	Ltbp3-Shh E16.5-sagittal , Ltbp3-Shh E16.5-coronal	There is very strong staining in the VZ of the dorsal & ventral POAs & the SCH nucleus, strong staining in the AVH & weak staining in the DMH nucleus & the PH. Staining is either absent or ubiquitous in the VZ of the PVH, VMH & ARH nuclei & the DAH.
TS24: thalamus mantle layer	Ambiguous		Ltbp3-Shh E16.5-sagittal , Ltbp3-Shh E16.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS24: thalamus ventricular layer	Very strong	Non-Uniform	Ltbp3-Shh E16.5-sagittal , Ltbp3-Shh E16.5-coronal	There is very strong staining in the ventricular zone of the dorsal thalamus and strong staining in the prethalamus.