Probe:	UI-M-BH2.1-ape-h-07-0-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	Acvr1-Shh E11.5-coronal-2 , Acvr1-Shh E11.5-coronal , Acvr1-Shh E11.5-sagittal	There is weak staining in the MZ of anterior ID. Staining is either absent or ubiquitous in the MZ of the dorsal thalamus, prethalamus, dorsal & ventral POAs, the PVH, VMH & ARH nuclei, the AVH, posterior ID, the premam, mam & supramam zones & the TT.
TS19: diencephalon lateral wall ventricular layer	Moderate	Non-Uniform	Acvr1-Shh E11.5-sagittal , Acvr1-Shh E11.5-coronal , Acvr1-Shh E11.5-coronal-2	Staining is moderate in the VZ of the VMH nucleus, premam zone & ARH nucleus. Staining is either absent or ubiquitous in the VZ of dorsal thalamus, prethalamus, dorsal & ventral POAs, PVH nucleus, AVH, anterior & posterior IDs, mam & supramam zones & TT.
TS19: telencephalon mantle layer	Ambiguous		Acvr1-Shh E11.5-coronal-2 , Acvr1-Shh E11.5-coronal , Acvr1-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	Ambiguous		Acvr1-Shh E11.5-coronal-2 , Acvr1-Shh E11.5-sagittal , Acvr1-Shh E11.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex and the ganglionic eminences.

Structure	Level	Pattern	Image	Note
TS20: cerebral cortex intermediate zone	Weak		Acvr1-Shh E12.5-sagittal , Acvr1-Shh E12.5-coronal-2 , Acvr1-Shh E12.5-coronal	There is weak staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS20: cerebral cortex ventricular layer	Ambiguous		Acvr1-Shh E12.5-coronal-2 , Acvr1-Shh E12.5-sagittal , Acvr1-Shh E12.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Weak		Acvr1-Shh E12.5-coronal-2 , Acvr1-Shh E12.5-coronal , Acvr1-Shh E12.5-sagittal	There is weak staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS20: diencephalon mantle layer	Moderate	Non-Uniform	Acvr1-Shh E12.5-coronal-2 , Acvr1-Shh E12.5-sagittal , Acvr1-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	Ambiguous		Acvr1-Shh E12.5-coronal , Acvr1-Shh E12.5-coronal-2 , Acvr1-Shh E12.5-sagittal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones and the TT.
TS20: ganglionic eminence	Ambiguous		Acvr1-Shh E12.5-coronal , Acvr1-Shh E12.5-coronal-2 , Acvr1-Shh E12.5-sagittal	Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS20: hypothalamus mantle layer	Moderate	Non-Uniform	Acvr1-Shh E12.5-coronal , Acvr1-Shh E12.5-sagittal , Acvr1-Shh E12.5-coronal-2	There is moderate staining in the mantle zone of the VMH and ARH nuclei and weak staining in the anterior ID. Staining is either absent or ubiquitous in the mantle zone of the dorsal and ventral POAs, the PVH nucleus, the AVH and posterior ID.
TS20: hypothalamus ventricular layer	Ambiguous		Acvr1-Shh E12.5-coronal-2 , Acvr1-Shh E12.5-coronal , Acvr1-Shh E12.5-sagittal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei, the AVH and anterior and posterior IDs.
TS20: thalamus mantle layer	Ambiguous		Acvr1-Shh E12.5-coronal , Acvr1-Shh E12.5-sagittal , Acvr1-Shh E12.5-coronal-2	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Ambiguous		Acvr1-Shh E12.5-coronal , Acvr1-Shh E12.5-sagittal , Acvr1-Shh E12.5-coronal-2	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Moderate		Acvr1-Shh E14.5-sagittal , Acvr1-Shh E14.5-coronal-2 , Acvr1-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	Ambiguous		Acvr1-Shh E14.5-coronal-2 , Acvr1-Shh E14.5-sagittal , Acvr1-Shh E14.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Moderate		Acvr1-Shh E14.5-coronal-2 , Acvr1-Shh E14.5-coronal , Acvr1-Shh E14.5-sagittal	There is moderate staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer	Moderate	Non-Uniform	Acvr1-Shh E14.5-sagittal , Acvr1-Shh E14.5-coronal-2 , Acvr1-Shh E14.5-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.
TS22: diencephalon ventricular layer	Ambiguous		Acvr1-Shh E14.5-sagittal , Acvr1-Shh E14.5-coronal , Acvr1-Shh E14.5-coronal-2	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones and the TT.
TS22: ganglionic eminence	Strong	Non-Uniform	Acvr1-Shh E14.5-coronal-2 , Acvr1-Shh E14.5-sagittal , Acvr1-Shh E14.5-coronal	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	Moderate	Non-Uniform	Acvr1-Shh E14.5-coronal-2 , Acvr1-Shh E14.5-coronal , Acvr1-Shh E14.5-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 nucleus, the AVH and anterior and posterior IDs.
TS22: hypothalamus ventricular layer	Ambiguous		Acvr1-Shh E14.5-coronal-2 , Acvr1-Shh E14.5-coronal , Acvr1-Shh E14.5-sagittal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH, VMH and ARH nuclei, the AVH and anterior and posterior IDs.
TS22: thalamus mantle layer	Strong	Non-Uniform	Acvr1-Shh E14.5-sagittal , Acvr1-Shh E14.5-coronal-2 , Acvr1-Shh E14.5-coronal	There is strong staining in the mantle zone of the dorsal thalamus. Staining is either absent or ubiquitous in the mantle zone of the prethalamus.
TS22: thalamus ventricular layer	Ambiguous		Acvr1-Shh E14.5-coronal , Acvr1-Shh E14.5-coronal-2 , Acvr1-Shh E14.5-sagittal	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		Acvr1-Shh E16.5-coronal-2 , Acvr1-Shh E16.5-sagittal , Acvr1-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	Ambiguous		Acvr1-Shh E16.5-coronal-2 , Acvr1-Shh E16.5-sagittal , Acvr1-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Acvr1-Shh E16.5-sagittal , Acvr1-Shh E16.5-coronal-2 , Acvr1-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	Acvr1-Shh E16.5-coronal-2 , Acvr1-Shh E16.5-coronal , Acvr1-Shh E16.5-sagittal	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.
TS24: diencephalon ventricular layer	Ambiguous		Acvr1-Shh E16.5-sagittal , Acvr1-Shh E16.5-coronal-2 , Acvr1-Shh E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS24: ganglionic eminence	Strong	Non-Uniform	Acvr1-Shh E16.5-sagittal , Acvr1-Shh E16.5-coronal-2 , Acvr1-Shh E16.5-coronal	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	Moderate	Non-Uniform	Acvr1-Shh E16.5-sagittal , Acvr1-Shh E16.5-coronal-2 , Acvr1-Shh E16.5-coronal	There is moderate staining in the mantle zone of the ARH nucleus and weak in the VMH nucleus. 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	Ambiguous		Acvr1-Shh E16.5-coronal-2 , Acvr1-Shh E16.5-coronal , Acvr1-Shh E16.5-sagittal	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	Acvr1-Shh E16.5-coronal , Acvr1-Shh E16.5-coronal-2 , Acvr1-Shh E16.5-sagittal	There is strong staining in the mantle zone of the dorsal thalamus. Staining is either absent or ubiquitous in the mantle zone of the prethalamus.
TS24: thalamus ventricular layer	Ambiguous		Acvr1-Shh E16.5-coronal , Acvr1-Shh E16.5-coronal-2 , Acvr1-Shh E16.5-sagittal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.