Probe:	UI-M-AQ1-adz-g-09-0-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		Hist3h2a(D)+SHH(F)-E11.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus, 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	Very strong	Scattered	Hist3h2a(D)+SHH(F)-E11.5-coronal	There is very strong, scattered staining in the ventricular 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: telencephalon mantle layer	Ambiguous		Hist3h2a(D)+SHH(F)-E11.5-coronal	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	Very strong	Scattered	Hist3h2a(D)+SHH(F)-E11.5-coronal	There is very strong, scattered staining in the ventricular zone of the cerebral cortex and the ganglionic eminences.

Structure	Level	Pattern	Image	Note
TS20: cerebral cortex intermediate zone	Ambiguous		Hist3h2a(D)+SHH(F)-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	Very strong	Scattered	Hist3h2a(D)+SHH(F)-E12.5-coronal	There is very strong, scattered staining in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		Hist3h2a(D)+SHH(F)-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		Hist3h2a(D)+SHH(F)-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	Very strong	Scattered	Hist3h2a(D)+SHH(F)-E12.5-coronal	There is very strong, scattered staining in the ventricular zone of the premam, mam and supramam zones and the TT.
TS20: ganglionic eminence	Very strong	Non-Uniform	Hist3h2a(D)+SHH(F)-E12.5-coronal	There is very strong, scattered staining in the ventricular zone of the ganglionic eminences and moderate, scattered staining in the mantle zone of the ganglionic eminences.
TS20: hypothalamus mantle layer	Ambiguous		Hist3h2a(D)+SHH(F)-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	Very strong	Non-Uniform	Hist3h2a(D)+SHH(F)-E12.5-coronal	Staining is very strong in the VZ of the AVH, very strong & scattered in dorsal & ventral POAs, strong in anterior ID, strong & scattered in the VMH & ARH nuclei, moderate in posterior ID & moderate & scattered in the PVH nucleus.
TS20: thalamus mantle layer	Ambiguous		Hist3h2a(D)+SHH(F)-E12.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS20: thalamus ventricular layer	Very strong	Scattered	Hist3h2a(D)+SHH(F)-E12.5-coronal	There is very strong, scattered staining in the ventricular zone of the dorsal thalamus and prethalamus.

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Ambiguous		Hist3h2a(D)+SHH(F)-E14.5-coronal	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	Scattered	Hist3h2a(D)+SHH(F)-E14.5-coronal	There is very strong, scattered staining in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		Hist3h2a(D)+SHH(F)-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		Hist3h2a(D)+SHH(F)-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	Very strong	Non-Uniform	Hist3h2a(D)+SHH(F)-E14.5-coronal	There is very strong staining in the ventricular zone of the premam zone and very strong, scattered staining in the mam zone. Staining is either absent or ubiquitous in the ventricular zone of the supramam zone and the TT.
TS22: ganglionic eminence	Very strong	Non-Uniform	Hist3h2a(D)+SHH(F)-E14.5-coronal	There is very strong, scattered staining in the ventricular zone of the ganglionic eminences and strong staining in the mantle zone of the ganglionic eminences.
TS22: hypothalamus mantle layer	Ambiguous		Hist3h2a(D)+SHH(F)-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	Very strong	Non-Uniform	Hist3h2a(D)+SHH(F)-E14.5-coronal	Staining is very strong and scattered in the VZ of the ARH nucleus, moderate in anterior ID, moderate & scattered in dorsal & ventral POAs, VMH nucleus & AVH, weak & scattered in the PVH nucleus & either absent or ubiquitous in the posterior ID.
TS22: thalamus mantle layer	Ambiguous		Hist3h2a(D)+SHH(F)-E14.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS22: thalamus ventricular layer	Very strong	Non-Uniform	Hist3h2a(D)+SHH(F)-E14.5-coronal	There is very strong, scattered staining in the ventricular zone of the dorsal thalamus and weak, scattered staining in the prethalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Ambiguous		Hist3h2a(D)+SHH(F)-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	Moderate		Hist3h2a(D)+SHH(F)-E16.5-coronal	There is moderate, scattered staining in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Ambiguous		Hist3h2a(D)+SHH(F)-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		Hist3h2a(D)+SHH(F)-E16.5-coronal	Staining is either absent or ubiquitous in the mantle zone of the premam, mam and supramam zones.
TS24: diencephalon ventricular layer	Strong	Non-Uniform	Hist3h2a(D)+SHH(F)-E16.5-coronal	There is strong staining in the ventricular zone of the premam and mam zone. Staining is either absent or ubiquitous in the ventricular zone of the supramam zone.
TS24: ganglionic eminence	Moderate	Non-Uniform	Hist3h2a(D)+SHH(F)-E16.5-coronal	There is moderate, scattered staining in the ventricular zone of the ganglionic eminences and weak, scattered staining in the mantle zone of the ganglionic eminences.
TS24: hypothalamus mantle layer	Ambiguous		Hist3h2a(D)+SHH(F)-E16.5-coronal	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	Strong	Non-Uniform	Hist3h2a(D)+SHH(F)-E16.5-coronal	There is strong staining in the ventricular zone of the ARH nucleus. Staining is either absent or ubiquitous in the ventricular zone of the dorsal and ventral POAs, the PVH, SCH, DMH and VMH nuclei, the AVH, the DAH and the PH.
TS24: thalamus mantle layer	Moderate	Non-Uniform	Hist3h2a(D)+SHH(F)-E16.5-coronal	There is moderate 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		Hist3h2a(D)+SHH(F)-E16.5-coronal	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.