Probe:	UI-M-BH0-aje-c-10-0-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	Strong	Non-Uniform	Fem1b-Shh E11.5-sagittal	There is strong staining in the MZ of the prethalamus, moderate staining in the dorsal thalamus, dorsal & ventral POAs, the PVH, VMH & ARH nuclei, the anterior & posterior IDs, the premam, mam & supramam zones & the TT & weak staining in the AVH.
TS19: diencephalon lateral wall ventricular layer	Moderate		Fem1b-Shh E11.5-sagittal	There is moderate staining in the VZ of the dorsal thalamus, the prethalamus, dorsal and ventral POAs, the PVH, VMH and ARH nuclei, the anterior and posterior IDs, the premam, mam and supramam zones and the TT and weak staining in the AVH.
TS19: telencephalon mantle layer	Moderate		Fem1b-Shh E11.5-sagittal	There is moderate staining 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	Moderate		Fem1b-Shh E11.5-sagittal	There is moderate staining in the ventricular zone of the cerebral cortex and the ganglionic eminences.

Structure	Level	Pattern	Image	Note
TS20: cerebral cortex intermediate zone	Moderate		Fem1b-Shh E12.5-sagittal , Fem1b-Shh E12.5-coronal	There is moderate staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS20: cerebral cortex ventricular layer	Moderate		Fem1b-Shh E12.5-sagittal , Fem1b-Shh E12.5-coronal	There is moderate staining in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Moderate		Fem1b-Shh E12.5-coronal , Fem1b-Shh E12.5-sagittal	There is moderate staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS20: diencephalon mantle layer	Strong	Non-Uniform	Fem1b-Shh E12.5-sagittal , Fem1b-Shh E12.5-coronal	There is strong staining in the mantle zone of the mam zone and moderate staining in the in the mantle zone of the premam and supramam zones and the TT.
TS20: diencephalon ventricular layer	Moderate		Fem1b-Shh E12.5-sagittal , Fem1b-Shh E12.5-coronal	There is moderate staining in the ventricular zone of the premam, mam and supramam zones and the TT.
TS20: ganglionic eminence	Moderate		Fem1b-Shh E12.5-coronal , Fem1b-Shh E12.5-sagittal	There is moderate staining in the ventricular and mantle zones of the ganglionic eminences.
TS20: hypothalamus mantle layer	Moderate		Fem1b-Shh E12.5-coronal , Fem1b-Shh E12.5-sagittal	There is moderate staining 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	Moderate	Non-Uniform	Fem1b-Shh E12.5-coronal , Fem1b-Shh E12.5-sagittal	There is moderate staining in the ventricular zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei and anterior and posterior IDs and weak staining in the AVH.
TS20: thalamus mantle layer	Moderate		Fem1b-Shh E12.5-sagittal , Fem1b-Shh E12.5-coronal	There is moderate staining in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Moderate		Fem1b-Shh E12.5-coronal , Fem1b-Shh E12.5-sagittal	There is moderate staining in the ventricular zone of the dorsal thalamus and prethalamus.

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Moderate		Fem1b-Shh E14.5-sagittal , Fem1b-Shh E14.5-coronal	There is moderate staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer	Moderate		Fem1b-Shh E14.5-coronal , Fem1b-Shh E14.5-sagittal	There is moderate staining in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Moderate		Fem1b-Shh E14.5-sagittal , Fem1b-Shh E14.5-coronal	There is moderate staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Strong	Non-Uniform	Fem1b-Shh E14.5-coronal , Fem1b-Shh E14.5-sagittal	There is strong staining in the mantle zone of the mam zone and moderate staining in the premam zone and the TT and weak staining in the supramam zone.
TS22: diencephalon ventricular layer	Weak		Fem1b-Shh E14.5-coronal , Fem1b-Shh E14.5-sagittal	There is weak staining in the ventricular zone of the premam, mam and supramam zones and the TT.
TS22: ganglionic eminence	Moderate		Fem1b-Shh E14.5-coronal , Fem1b-Shh E14.5-sagittal	There is moderate staining in the ventricular and mantle zones of the ganglionic eminences.
TS22: hypothalamus mantle layer	Strong	Non-Uniform	Fem1b-Shh E14.5-coronal , Fem1b-Shh E14.5-sagittal	There is strong staining in the mantle zone of the AVH and moderate staining in the dorsal and ventral POAs, PVH, VMH and ARH nuclei and weak staining in the anterior and posterior IDs.
TS22: hypothalamus ventricular layer	Weak	Non-Uniform	Fem1b-Shh E14.5-sagittal , Fem1b-Shh E14.5-coronal	There is weak staining in the ventricular zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei and the AVH. Staining is either absent or ubiquitous in the ventricular zone of the anterior and posterior IDs.
TS22: thalamus mantle layer	Weak		Fem1b-Shh E14.5-coronal , Fem1b-Shh E14.5-sagittal	There is weak staining in the mantle zone of the dorsal thalamus and prethalamus.
TS22: thalamus ventricular layer	Strong	Non-Uniform	Fem1b-Shh E14.5-sagittal , Fem1b-Shh E14.5-coronal	There is strong staining in the ventricular zone of the dorsal thalamus and moderate staining in the prethalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Ambiguous		Fem1b-Shh E16.5-coronal , Fem1b-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	Weak		Fem1b-Shh E16.5-coronal , Fem1b-Shh E16.5-sagittal	There is weak staining in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Fem1b-Shh E16.5-sagittal , Fem1b-Shh E16.5-coronal	Staining is either absent or ubiquitous in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Ambiguous		Fem1b-Shh E16.5-sagittal , Fem1b-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	Ambiguous		Fem1b-Shh E16.5-sagittal , Fem1b-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS24: ganglionic eminence	Weak	Non-Uniform	Fem1b-Shh E16.5-coronal , Fem1b-Shh E16.5-sagittal	There is weak 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	Strong	Non-Uniform	Fem1b-Shh E16.5-coronal , Fem1b-Shh E16.5-sagittal	There is strong staining in the MZ of the PVH nucleus & moderate staining in the dorsal & ventral POAs, the DMH, VMH & ARH nuclei, the AVH, the DAH & the PH. Staining is either absent or ubiquitous in the MZ of the SCH nucleus & the PH.
TS24: hypothalamus ventricular layer	Ambiguous		Fem1b-Shh E16.5-sagittal , Fem1b-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	Strong	Non-Uniform	Fem1b-Shh E16.5-coronal , Fem1b-Shh E16.5-sagittal	There is strong staining in the mantle zone of the dorsal thalamus and weak staining in the prethalamus.
TS24: thalamus ventricular layer	Ambiguous		Fem1b-Shh E16.5-sagittal , Fem1b-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.