Probe:	UI-M-BH1-amf-h-02-0-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		Efnb1-Shh E11.5-coronal , Efnb1-Shh E11.5-sagittal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus, the 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	Efnb1-Shh E11.5-coronal , Efnb1-Shh E11.5-sagittal	Staining is strong in the VZ of the dorsal POA, VMH & ARH nuclei, premam zone & TT, moderate in mam & supramam zones, weak in dorsal thalamus, prethalamus, PVH nucleus & anterior & posterior IDs & either absent or ubiquitous in the ventral POA & AVH.
TS19: telencephalon mantle layer	Very strong	Non-Uniform	Efnb1-Shh E11.5-coronal , Efnb1-Shh E11.5-sagittal	There is very strong staining in the postmitotic neurons in the intermediate zone and cortical plate of the cerebral cortex and moderate staining in the mantle zone of the ganglionic eminences.
TS19: telencephalon ventricular layer	Very strong	Non-Uniform	Efnb1-Shh E11.5-sagittal , Efnb1-Shh E11.5-coronal	There is very strong staining in the ventricular zone of the cerebral cortex and strong staining in the ventricular zone of the ganglionic eminences.

Structure	Level	Pattern	Image	Note
TS20: cerebral cortex intermediate zone	Ambiguous		Efnb1-Shh E12.5-sagittal , Efnb1-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	Strong		Efnb1-Shh E12.5-coronal , Efnb1-Shh E12.5-sagittal	There is strong staining in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Efnb1-Shh E12.5-coronal , Efnb1-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		Efnb1-Shh E12.5-coronal , Efnb1-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	Strong	Non-Uniform	Efnb1-Shh E12.5-sagittal , Efnb1-Shh E12.5-coronal	There is strong staining in the ventricular zone of the premam zone and the TT and moderate staining in the mam and supramam zones.
TS20: ganglionic eminence	Strong	Non-Uniform	Efnb1-Shh E12.5-coronal , Efnb1-Shh E12.5-sagittal	There is strong staining in the ventricular zone of the ganglionic eminences and weak, scattered staining in the mantle zone of the ganglionic eminences.
TS20: hypothalamus mantle layer	Ambiguous		Efnb1-Shh E12.5-sagittal , Efnb1-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	Efnb1-Shh E12.5-sagittal , Efnb1-Shh E12.5-coronal	There is strong staining in the VZ of the dorsal and ventral POAs, the posterior ID and the VMH and ARH nuclei and weak staining in the PVH nucleus and the anterior ID. Staining is either absent or ubiquitous in the VZ of the AVH.
TS20: thalamus mantle layer	Ambiguous		Efnb1-Shh E12.5-sagittal , Efnb1-Shh E12.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Strong	Non-Uniform	Efnb1-Shh E12.5-coronal , Efnb1-Shh E12.5-sagittal	There is strong staining in the ventricular zone of the prethalamus and moderate staining the in dorsal thalamus.

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Ambiguous		Efnb1-Shh E14.5-coronal , Efnb1-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		Efnb1-Shh E14.5-sagittal , Efnb1-Shh E14.5-coronal	There is very strong staining in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Efnb1-Shh E14.5-coronal , Efnb1-Shh 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	Moderate	Non-Uniform	Efnb1-Shh E14.5-coronal , Efnb1-Shh E14.5-sagittal	There is moderate, scattered 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.
TS22: diencephalon ventricular layer	Strong	Non-Uniform	Efnb1-Shh E14.5-sagittal , Efnb1-Shh E14.5-coronal	There is strong staining in the ventricular zone of the premam and mam zones and the TT and moderate staining in the supramam zone.
TS22: ganglionic eminence	Very strong	Non-Uniform	Efnb1-Shh E14.5-coronal , Efnb1-Shh E14.5-sagittal	There is very strong staining in the ventricular zone of the ganglionic eminences and weak, scattered staining in the mantle zone of the ganglionic eminences.
TS22: hypothalamus mantle layer	Strong	Non-Uniform	Efnb1-Shh E14.5-sagittal , Efnb1-Shh E14.5-coronal	There is strong staining in the mantle zone of the dorsal and ventral POAs and ARH nucleus and weak staining in the PVH nucleus. Staining is either absent or ubiquitous in the mantle zone of the AVH, anterior and posterior IDs and the VMH nucleus.
TS22: hypothalamus ventricular layer	Strong	Non-Uniform	Efnb1-Shh E14.5-coronal , Efnb1-Shh E14.5-sagittal	There is strong staining in the ventricular zone of the posterior ID and VMH and ARH nuclei. Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH nucleus, the AVH and anterior ID.
TS22: thalamus mantle layer	Strong		Efnb1-Shh E14.5-sagittal , Efnb1-Shh E14.5-coronal	There is strong staining in the mantle zone of the dorsal thalamus and prethalamus.
TS22: thalamus ventricular layer	Ambiguous		Efnb1-Shh E14.5-sagittal , Efnb1-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	Ambiguous		Efnb1-Shh E16.5-sagittal , Efnb1-Shh E16.5-coronal	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		Efnb1-Shh E16.5-sagittal , Efnb1-Shh E16.5-coronal	There is very strong staining in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Efnb1-Shh E16.5-sagittal , Efnb1-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	Moderate	Non-Uniform	Efnb1-Shh E16.5-coronal , Efnb1-Shh E16.5-sagittal	There is moderate staining in the mantle zone of the premam and mam zones. Staining is either absent or ubiquitous in the mantle zone of the supramam zone.
TS24: diencephalon ventricular layer	Very strong	Non-Uniform	Efnb1-Shh E16.5-sagittal , Efnb1-Shh E16.5-coronal	There is very strong staining in the ventricular zone of the premam and mam zones and moderate staining in the supramam zone.
TS24: ganglionic eminence	Very strong	Non-Uniform	Efnb1-Shh E16.5-sagittal , Efnb1-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	Moderate	Non-Uniform	Efnb1-Shh E16.5-coronal , Efnb1-Shh E16.5-sagittal	There is moderate staining in the mantle zone of the VMH and ARH nuclei. Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH, SCH and DMH nuclei, the AVH, the DAH and the PH.
TS24: hypothalamus ventricular layer	Very strong	Non-Uniform	Efnb1-Shh E16.5-sagittal , Efnb1-Shh E16.5-coronal	There is very strong staining in the VZ of the dorsal & ventral POAs, the DMH, VMH & ARH nuclei & the PH, moderate staining in the PVH nucleus & the DAH & weak staining in the AVH. Staining is either absent or ubiquitous in the VZ of the SCH nucleus.
TS24: thalamus mantle layer	Ambiguous		Efnb1-Shh E16.5-coronal , Efnb1-Shh E16.5-sagittal	Staining is either absent or ubiquitous in the mantle zone of the prethalamus.
TS24: thalamus ventricular layer	Very strong		Efnb1-Shh E16.5-coronal , Efnb1-Shh E16.5-sagittal	There is very strong staining in the ventricular zone of the dorsal thalamus and prethalamus.