Probe:	UI-M-AL1-ahm-f-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	Strong	Non-Uniform	Pak3-Shh E11.5_coronal , Pak3-Shh E11.5_sagittal	Staining is strong in the MZ of the PVH & VMH nuclei & AVH, moderate in the ARH nucleus & premam & mam zones & either absent or ubiquitous in the dorsal thalamus, prethalamus, dorsal & ventral POAs, anterior & posterior IDs, the TT & supramam zone.
TS19: diencephalon lateral wall ventricular layer	Strong	Non-Uniform	Pak3-Shh E11.5_sagittal , Pak3-Shh E11.5_coronal	There is strong staining in the VZ of the prethalamus, dorsal & ventral POAs, PVH nucleus & the AVH. Staining is either absent or ubiquitous in the VZ of the dorsal thalamus, VMH & ARH nuclei, anterior & posterior IDs, premam, mam & supramam zones & TT.
TS19: telencephalon mantle layer	Ambiguous		Pak3-Shh E11.5_coronal , Pak3-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	Pak3-Shh E11.5_coronal , Pak3-Shh E11.5_sagittal	There is strong staining in the ventricular zone of the ganglionic eminences. Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.

Structure	Level	Pattern	Image	Note
TS20: cerebral cortex intermediate zone	Ambiguous		Pak3-Shh E12.5_coronal , Pak3-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	Ambiguous		Pak3-Shh E12.5_sagittal , Pak3-Shh E12.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Pak3-Shh E12.5_sagittal , Pak3-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	Strong	Non-Uniform	Pak3-Shh E12.5_sagittal , Pak3-Shh E12.5_coronal	There is strong staining in the mantle zone of the TT, moderate staining in the premam and mam zones and weak staining in the supramam zone.
TS20: diencephalon ventricular layer	Ambiguous		Pak3-Shh E12.5_coronal , Pak3-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	Strong		Pak3-Shh E12.5_coronal , Pak3-Shh E12.5_sagittal	There is strong staining in the ventricular and mantle zones of the ganglionic eminences.
TS20: hypothalamus mantle layer	Strong	Non-Uniform	Pak3-Shh E12.5_coronal , Pak3-Shh E12.5_sagittal	There is strong staining in the mantle zone of the dorsal and ventral POAs, anterior and posterior IDs and VMH nucleus and weak staining in the PVH and ARH nuclei and the AVH.
TS20: hypothalamus ventricular layer	Strong	Non-Uniform	Pak3-Shh E12.5_sagittal , Pak3-Shh E12.5_coronal	There is strong staining in the ventricular zone of the PVH nucleus and the AVH. Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the VMH and ARH nuclei and anterior and posterior IDs.
TS20: thalamus mantle layer	Strong	Non-Uniform	Pak3-Shh E12.5_sagittal , Pak3-Shh E12.5_coronal	There is strong staining in the mantle zone of the dorsal thalamus and moderate staining in the prethalamus.
TS20: thalamus ventricular layer	Moderate	Non-Uniform	Pak3-Shh E12.5_coronal , Pak3-Shh E12.5_sagittal	There is moderate 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	Ambiguous		Pak3-Shh E14.5_coronal , Pak3-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	Ambiguous		Pak3-Shh E14.5_sagittal , Pak3-Shh E14.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Pak3-Shh E14.5_sagittal , Pak3-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	Weak		Pak3-Shh E14.5_sagittal , Pak3-Shh E14.5_coronal	There is weak staining in the mantle zone of the premam, mam and supramam zones and the TT.
TS22: diencephalon ventricular layer	Weak	Non-Uniform	Pak3-Shh E14.5_sagittal , Pak3-Shh E14.5_coronal	There is weak staining in the ventricular zone of the premam zone. Staining is either absent or ubiquitous in the ventricular zone of the mam and supramam zones and the TT.
TS22: ganglionic eminence	Strong		Pak3-Shh E14.5_sagittal , Pak3-Shh E14.5_coronal	There is strong staining in the ventricular and mantle zones of the ganglionic eminences.
TS22: hypothalamus mantle layer	Strong	Non-Uniform	Pak3-Shh E14.5_coronal , Pak3-Shh E14.5_sagittal	There is strong staining in the mantle zone of the ventral POA, moderate staining in the AVH and weak staining in the PVH, VMH and ARH nuclei and anterior and posterior IDs. Staining is either absent or ubiquitous in the mantle zone of the dorsal POA.
TS22: hypothalamus ventricular layer	Strong	Non-Uniform	Pak3-Shh E14.5_sagittal , Pak3-Shh E14.5_coronal	There is strong staining in the ventricular zone of the ventral POA, PVH and VMH nuclei and the AVH and weak staining in the anterior and posterior IDs and ARH nucleus. Staining is either absent or ubiquitous in the ventricular zone of the dorsal POA.
TS22: thalamus mantle layer	Strong	Non-Uniform	Pak3-Shh E14.5_coronal , Pak3-Shh E14.5_sagittal	There is strong staining in the mantle zone of the prethalamus and weak staining in the dorsal thalamus.
TS22: thalamus ventricular layer	Strong	Non-Uniform	Pak3-Shh E14.5_sagittal , Pak3-Shh E14.5_coronal	There is 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	Moderate		Pak3-Shh E16.5_sagittal , Pak3-Shh E16.5_coronal	There is moderate staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Ambiguous		Pak3-Shh E16.5_sagittal , Pak3-Shh E16.5_coronal	Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Moderate		Pak3-Shh E16.5_sagittal , Pak3-Shh E16.5_coronal	There is moderate staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Weak		Pak3-Shh E16.5_sagittal , Pak3-Shh E16.5_coronal	There is weak staining in the mantle zone of the premam, mam and supramam zones.
TS24: diencephalon ventricular layer	Ambiguous		Pak3-Shh E16.5_sagittal , Pak3-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	Pak3-Shh E16.5_sagittal , Pak3-Shh E16.5_coronal	There is strong staining in the ventricular zone of the ganglionic eminences and weak staining in the mantle zone of the ganglionic eminences.
TS24: hypothalamus mantle layer	Weak	Non-Uniform	Pak3-Shh E16.5_coronal , Pak3-Shh E16.5_sagittal	There is weak staining in the mantle zone of the dorsal and ventral POAs, the PVH, DMH and VMH nuclei, the AVH, the DAH and the PH. Staining is either absent or ubiquitous in the mantle zone of the SCH and ARH nuclei.
TS24: hypothalamus ventricular layer	Moderate	Non-Uniform	Pak3-Shh E16.5_coronal , Pak3-Shh E16.5_sagittal	There is moderate staining in the ventricular zone of the dorsal and ventral POAs and the PVH nucleus. Staining is either absent or ubiquitous in the ventricular zone of the SCH, DMH, VMH and ARH nuclei, the AVH, the DAH and the PH.
TS24: thalamus mantle layer	Strong	Non-Uniform	Pak3-Shh E16.5_coronal , Pak3-Shh E16.5_sagittal	There is strong staining in the mantle zone of the prethalamus and moderate staining in the dorsal thalamus.
TS24: thalamus ventricular layer	Ambiguous		Pak3-Shh E16.5_coronal , Pak3-Shh E16.5_sagittal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.