Probe:	UI-M-BH2.1-apo-e-04-0-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	Very strong	Non-Uniform	CYCLIND2(D)+SHH(F)-E11.5-CORONAL	There is very strong staining in the MZ of the dorsal thalamus, prethalamus, dorsal & ventral POAs & VMH nucleus. Staining is either absent or ubiquitous in the MZ of the PVH & ARH nuclei, AVH, anterior & posterior IDs, premam, mam & supramam zones & TT.
TS19: diencephalon lateral wall ventricular layer	Very strong	Non-Uniform	CYCLIND2(D)+SHH(F)-E11.5-CORONAL	Staining is very strong in premam & mam zones, strong in anterior & posterior IDs & TT, moderate in dorsal thalamus & VMH nuc, weak in ventral POA, PVH nuc & supramam zone & absent or ubiquitous in prethalamus, dorsal POA, ARH nuc & AVH. Some scattered.
TS19: telencephalon mantle layer	Very strong	Non-Uniform	CYCLIND2(D)+SHH(F)-E11.5-CORONAL	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	CYCLIND2(D)+SHH(F)-E11.5-CORONAL	There is very strong staining in the ventricular zone of the cerebral cortex and strong staining in the ganglionic eminences.

Structure	Level	Pattern	Image	Note
TS20: cerebral cortex intermediate zone	Ambiguous		CYCLIND2(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		CYCLIND2(D)+SHH(F)-E12.5-CORONAL	There is very strong staining in the ventricular zone of the cerebral cortex.
TS20: cortical plate	Ambiguous		CYCLIND2(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		CYCLIND2(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	Non-Uniform	CYCLIND2(D)+SHH(F)-E12.5-CORONAL	There is very strong staining in the ventricular zone of the premam and mam zones, moderate, scattered staining in the TT and weak, scattered staining in the supramam zone.
TS20: ganglionic eminence	Very strong	Non-Uniform	CYCLIND2(D)+SHH(F)-E12.5-CORONAL	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.
TS20: hypothalamus mantle layer	Ambiguous		CYCLIND2(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	CYCLIND2(D)+SHH(F)-E12.5-CORONAL	Staining is very strong in the VZ of the dorsal POA & ARH nucleus, moderate in the VMH nucleus, moderate & scattered in posterior ID, weak & scattered staining in the AVH & either absent or ubiquitous in ventral POA, the PVH nucleus & anterior ID.
TS20: thalamus mantle layer	Very strong	Non-Uniform	CYCLIND2(D)+SHH(F)-E12.5-CORONAL	There is very strong staining in the mantle zone of the dorsal thalamus. Staining is either absent or ubiquitous in the mantle zone of the prethalamus.
TS20: thalamus ventricular layer	Strong	Non-Uniform	CYCLIND2(D)+SHH(F)-E12.5-CORONAL	There is strong staining in the ventricular zone of the dorsal thalamus. Staining is either absent or ubiquitous in the ventricular zone of the prethalamus.

Structure	Level	Pattern	Image	Note
TS22: cerebral cortex intermediate zone	Ambiguous		CYCLIND2(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		CYCLIND2(D)+SHH(F)-E14.5-CORONAL	There is very strong staining in the ventricular zone of the cerebral cortex.
TS22: cortical plate	Ambiguous		CYCLIND2(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		CYCLIND2(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	CYCLIND2(D)+SHH(F)-E14.5-CORONAL	There is very strong staining in the ventricular zone of the premam and mam zones. Staining is either absent or ubiquitous in the ventricular zone of the supramam zone and the TT.
TS22: ganglionic eminence	Very strong	Non-Uniform	CYCLIND2(D)+SHH(F)-E14.5-CORONAL	There is very strong staining in the ventricular zone of the ganglionic eminences and moderate staining in the mantle zone of the ganglionic eminences.
TS22: hypothalamus mantle layer	Ambiguous		CYCLIND2(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	CYCLIND2(D)+SHH(F)-E14.5-CORONAL	There is very strong staining in the VZ of the ARH nucleus and moderate staining in the posterior ID. Staining is either absent or ubiquitous in the VZ of the dorsal and ventral POAs, the PVH and VMH nuclei, the AVH and anterior ID.
TS22: thalamus mantle layer	Ambiguous		CYCLIND2(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	Moderate	Non-Uniform	CYCLIND2(D)+SHH(F)-E14.5-CORONAL	There is moderate staining in the ventricular zone of the dorsal thalamus. Staining is either absent or ubiquitous in the ventricular zone of the prethalamus.

Structure	Level	Pattern	Image	Note
TS24: cerebral cortex intermediate zone	Very strong		CYCLIND2(D)+SHH(F)-E16.5-CORONAL	There is very strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer	Weak		CYCLIND2(D)+SHH(F)-E16.5-CORONAL	There is weak staining in the ventricular zone of the cerebral cortex.
TS24: cortical plate	Very strong		CYCLIND2(D)+SHH(F)-E16.5-CORONAL	There is very strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer	Ambiguous		CYCLIND2(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		CYCLIND2(D)+SHH(F)-E16.5-CORONAL	There is strong staining in the ventricular zone of the premam and mam zones.
TS24: ganglionic eminence	Strong	Non-Uniform	CYCLIND2(D)+SHH(F)-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	Ambiguous		CYCLIND2(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	CYCLIND2(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	Ambiguous		CYCLIND2(D)+SHH(F)-E16.5-CORONAL	Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS24: thalamus ventricular layer	Ambiguous		CYCLIND2(D)+SHH(F)-E16.5-CORONAL	Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.