Probe:	Clone 1A/1
Probe preparation:	Antisense labelled with digoxigenin RNA
Visualized with:	Alkaline phosphatase
Assay notes:	The probe used in this assay recognizes multiple message isoforms.

Structure	Level	Pattern	Image	Note
TS17: nervous system	Present	Regionally restricted	2b , 2a	Expression is localized to spatially restricted domains with well-defined boundaries. Signals are predominantly confined to the differentiating zone. It is rare for labeled cells to be seen in the ventricular neuroepithelium.
TS17: midbrain	Strong	Regionally restricted	2b , 2a	There is strong expression in the lateral part of the anterior and posterior tegmental differentiating zone, whereas it is free of signal ventrally. The signal is stronger at the border with the ventricular zone than in outer differentiating cells.
TS17: diencephalon	Present	Regionally restricted	2b , 2a	Although there is expression elswhere in the diencephalon, no expression is detected in the dorsal thalamus, epithalamus or in the posterior preoptic area.
TS17: hindbrain	Present	Regionally restricted	2a , 2b	Although there is expression elswhere in the hindbrain, no expression is detected in the future cerebellum.
TS17: telencephalon	Present	Regionally restricted	2a , 2b	Although there is expression elswhere in the telencephalon, no expression is detected in the future neocortex, hippocampus, rhinencephalon, amygdala, or septal area.

Structure	Level	Pattern	Image	Note
TS17: diencephalon	Strong	Regionally restricted	2c	A strong signal is detected in the lateral part of the ventral diencephalon. No expression is detected in the dorsal thalamus, epithalamus or in the posterior preoptic area.
TS17: hindbrain	Strong	Regionally restricted	2c	There is strong expression in the differentiating zone abutting the pontine and medullary ventricular neuroepithelium of the basal plate. No expression is detected in the future cerebellum.
TS17: midbrain	Present	Regionally restricted	2c	Although there is expression elswhere in the diencephalon, no expression is detected in the future interior and superior colliculi.
TS17: telencephalon	Present	Regionally restricted	2c	Although there is expression elswhere in the telencephalon, no expression is detected in the future neocortex, hippocampus, rhinencephalon, amygdala, or septal area.

Structure	Level	Pattern	Image	Note
TS17: telencephalon	Strong	Regionally restricted	2d	Expression is strong in the medial ganglionic eminence of the ventral telencephalon. These cells form a multilayer structure corresponding to the pallidal differentiating zone. Labeled cells are found in the striatal differentiating zone as well.
TS17: diencephalon	Strong	Regionally restricted	2d	A strong signal is detected in the lateral part of the ventral diencephalon. No expression is detected in the dorsal thalamus, epithalamus or in the posterior preoptic area.
TS17: hindbrain	Strong	Regionally restricted	2d	There is strong expression in the differentiating zone abutting the pontine and medullary ventricular neuroepithelium of the basal plate. No expression is detected in the future cerebellum.
TS17: midbrain	Present	Regionally restricted	2d	Although there is expression elswhere in the midbrain, no expression is detected in the future interior and superior colliculi.

Structure	Level	Pattern	Image	Note
TS17: telencephalon	Strong	Regionally restricted	2e	Expression is strong in the medial ganglionic eminence of the ventral telencephalon. These cells form a multilayer structure corresponding to the pallidal differentiating zone.
TS17: diencephalon	Present	Single cells	2e	A few labeled cells are seen in the region of the anterior preoptic differentiating zone. No expression is detected in the dorsal thalamus, epithalamus or in the posterior preoptic area.
TS17: hindbrain	Present	Regionally restricted	2e	There is strong expression in the differentiating zone abutting the pontine and medullary ventricular neuroepithelium of the basal plate. The cells are segregated into smaller domains. No expression is detected in the future cerebellum.
TS17: midbrain	Present	Regionally restricted	2e	Although there is expression elswhere in the midbrain, no expression is detected in the future interior and superior colliculi.

Structure	Level	Pattern	Image	Note
TS19: telencephalon	Present	Regionally restricted	4a	Expression is present in the medial ganglionic eminence and ventral telencephalon. The strongest signal roughly corresponds to the region of the secondary proliferative population. Moderate expression is seen in the pallidal differentiating zone.
TS19: future spinal cord	Strong		4a
TS19: myelencephalon	Strong		4a
TS19: hindbrain	Present	Graded	4a	A dorsoventral gradient is observed in the structures of the brain alar plate.
TS19: midbrain	Strong	Regionally restricted	4a	Expression is strong in the posterior tegmental region and the perioculomotor nuclei in the anterior tegmental differentiating zone, medium-high in pretectal and tegmental differentiating zones, and not present in the oculomotor nucleus.
TS19: olfactory epithelium	Strong	Regionally restricted	4a	There is strong expression in the olfactory epithelium of the ventral aspect of the olfactory pit.
TS19: diencephalon	Present	Regionally restricted	4a	There are labeled cells in the anterior hypothalamic differentiating zone, subthalamic sulcus, and preoptic area. There is no signal in the hypothalamic anterodorsal nucleus or in the mammillary or supraoptic-paraventricular area.

Structure	Level	Pattern	Image	Note
TS19: telencephalon	Present	Regionally restricted	4b	Expression is present in the posterior septal ventricular neuroepithelium, medial ganglionic eminence, and at the ventral midline. The area of strongest signal roughly corresponds to the region of the secondary proliferative population.
TS19: future spinal cord	Strong	Regionally restricted	4b	There is no expression in rhombomere 6 at its boundaries with rhombomeres 5 and 7.
TS19: myelencephalon	Strong	Regionally restricted	4b	There is no expression in rhombomere 6 at its boundaries with rhombomeres 5 and 7.
TS19: hindbrain	Present	Graded	4b	A dorsoventral gradient is observed in the structures of the brain alar plate. There is expression in the small group of cells in the differentiating zone of the isthmic alar plate. Patches of nonexpression are seen at interrhombomeric boundaries.
TS19: midbrain	Strong	Regionally restricted	4b	Strong expression is present in the posterior tegmental region, including the ventricular neuroepithelium. Moderate to strong expression is seen in the tegmental differentiating zone. No expression is seen in the oculomotor nucleus.
TS19: diencephalon	Present	Regionally restricted	4b	Expression is in the medial part of the ventral hypothalamus, in the area of the future retrochiasmatic and arcuate nuclei, as well as in cells in the diencephalic roof located close to the midline. None is in the ventral tegmental area.
TS19: olfactory epithelium	Present		4b

Structure	Level	Pattern	Image	Note
TS19: telencephalon	Present	Regionally restricted	4c	Expression is present in the medial ganglionic eminence and ventral telencephalon. The strongest signal roughly corresponds to the region of the secondary proliferative population. Moderate expression is seen in the pallidal differentiating zone.
TS19: myelencephalon	Strong	Regionally restricted	4c	Although there is expression elsewhere in the myelencephalon, there is no expression in part of rhombomere 6.
TS19: future spinal cord	Strong		4c
TS19: hindbrain	Present	Graded	4c	A dorsoventral gradient is observed in the structures of the brain alar plate. There is a patch of nonexpression in rhombomere 6.
TS19: midbrain	Present	Regionally restricted	4c	Strong expression is present in the posterior tegmental region, including the ventricular neuroepithelium. There is medium to high expression in pretectal and tegmental differentiating zones.
TS19: olfactory epithelium	Strong	Regionally restricted	4c	There is strong expression in the olfactory epithelium of the ventral aspect of the olfactory pit.
TS19: diencephalon	Present	Regionally restricted	4c	Expression is present in the anterior hypothalamic and thalamic differentiating zone, in the preoptic area, & hypothalamic cell cord. There is no signal in the hypothalamic anterodorsal nucleus or in the mammillary or supraoptic-paraventricular area.

Structure	Level	Pattern	Image	Note
TS19: telencephalon	Present	Regionally restricted	4d	Expression is present in the medial ganglionic eminence, ventral telencephalon, and entopeduncular area. The strongest signal is in the region of the secondary proliferative population. Moderate expression is seen in the pallidal differentiating zone.
TS19: myelencephalon	Strong	Regionally restricted	4d	There is strong expression in rhombomere 4. It exhibits alternate expressing and non-expressing columns.
TS19: future spinal cord	Strong		4d
TS19: hindbrain	Present	Graded	4d	A dorsoventral gradient is observed in the structures of the brain alar plate. There is a patch of nonexpression in rhombomeres 1 and 2.
TS19: olfactory epithelium	Strong	Regionally restricted	4d	There is strong expression in the olfactory epithelium of the ventral aspect of the olfactory pit.
TS19: diencephalon	Present	Regionally restricted	4d	There is expression in the ventral thalamic differentiating zone and preoptic area. There is no expression in the principal thalamic nuclei in the dorsal thalamus.
TS19: cerebellum primordium	Present	Single cells	4d	Expression is present in a row of cells in the differentiating zone of the lateral cerebellar primordium.

Structure	Level	Pattern	Image	Note
TS19: telencephalon	Present	Regionally restricted	4e	Expression is present in the medial ganglionic eminence, ventral telencephalon, and entopeduncular area. The strongest signal is in the region of the secondary proliferative population. Moderate expression is seen in the pallidal differentiating zone.
TS19: myelencephalon	Strong	Regionally restricted	4e	There is strong expression in rhombomere 4. It exhibits alternate expressing and non-expressing columns.
TS19: future spinal cord	Strong		4e
TS19: hindbrain	Present	Graded	4e	A dorsoventral gradient is observed in the structures of the brain alar plate.
TS19: olfactory epithelium	Strong	Regionally restricted	4e	There is strong expression in the olfactory epithelium of the ventral aspect of the olfactory pit.
TS19: diencephalon	Present	Regionally restricted	4e	There is expression in the ventral thalamic differentiating zone, including the pars ventralis thalami. There is no expression in the principal thalamic nuclei in the dorsal thalamus.
TS19: cerebellum primordium	Present	Single cells	4e	Expression is present in a row of cells in the differentiating zone of the lateral cerebellar primordium.

Structure	Level	Pattern	Image	Note
TS19: olfactory epithelium	Strong	Regionally restricted	4f	There is strong expression in the olfactory epithelium of the ventral aspect of the olfactory pit.
TS19: oral epithelium	Weak		4f	There is faint expression in the oral epithelium in both the mandibular and maxillary parts.
TS19: telencephalon	Present	Regionally restricted	4f	Expression is present in the medial ganglionic eminence and ventral telencephalon. The strongest signal is in the region of the secondary proliferative population. Moderate expression is seen in the pallidal differentiating zone and abutting the striatum.
TS19: cerebellum primordium	Present	Single cells	4f	Expression is present in a row of cells in the differentiating zone of the lateral cerebellar primordium.
TS19: myelencephalon	Strong	Regionally restricted	4f	There is strong expression in rhombomere 4. It exhibits alternate expressing and non-expressing columns.
TS19: mandible primordium	Present	Single cells	4f	There is a cluster of expressing cells in the mandible that probably corresponds to a condensation during initial stages of tooth development.

Structure	Level	Pattern	Image	Note
TS19: telencephalon	Strong	Regionally restricted	4g , 4h	Expression is present in the pallidal differenting zone of the medial ganglionic eminence (MGE), in the amygdaloid differentiating zone, and abutting the striatum. In the MGE it includes the region of the secondary proliferative population.
TS19: future spinal cord	Strong		4g , 4h
TS19: myelencephalon	Strong		4g , 4h

Structure	Level	Pattern	Image	Note
TS19: hindbrain	Strong	Regionally restricted		Strong expression is seen in the basal rhombencephalon, including the isthmus.

Structure	Level	Pattern	Image	Note
TS19: midbrain	Present	Regionally restricted	5a	Expression is present in the mesencephalon in columns. There is medium to high expression in the tegmental differentiating zone.

Structure	Level	Pattern	Image	Note
TS19: metencephalon	Strong	Regionally restricted	5b	There is strong expression in the pontine small cell group.
TS19: hindbrain	Present	Regionally restricted	5b	Although expression can be seen elsewhere in the hindbrain, there was a patch of non expression on rhombomeres 1 and 2.
TS19: myelencephalon	Strong	Regionally restricted	5b	There is strong expression in rhombomere 4. It exhibits alternate expressing and non-expressing columns. A weaker, more diffuse signal is seen at approximtely the level of rhombomere 5.
TS19: metencephalon basal plate	Present	Regionally restricted	5b	Three expressing bands are seen that are continuous through the entire length of the pons.
TS19: future spinal cord	Present	Regionally restricted	5b	Expression is present in the dorsal horn of the spinal cord.

Structure	Level	Pattern	Image	Note
TS19: future spinal cord	Present	Regionally restricted	5c	Expression is present in the dorsal and ventral aspects of the differentiating neuroepithelium. It was highest in the intermediate zone and dorsal horn differentiating zone.

Structure	Level	Pattern	Image	Note
TS20: forebrain	Present	Graded	6c	There is an inside-out expression gradient.
TS20: medial ganglionic eminence	Moderate	Regionally restricted	6c	There is medium-high expression in the pallidal differentiating zone, with the strongest signal in the presumptive secondary proliferative population. Other expression was in the entopeduncular area.
TS20: lateral ganglionic eminence	Present	Regionally restricted	6c	Expression is present in the striatal differentiating zone.
TS20: pons	Present		6c
TS20: hypothalamus	Present	Regionally restricted	6c	Expression is seen in the anterior and posterior preoptic area and suprachiasmatic nuclei. Weak expression is in the retrochiasmatic and tuberal area. No expression is in the anterior dorsal nucleus, mammillary area, or supraoptic-paraventricular area.
TS20: thalamus	Present	Regionally restricted	6c	Expression is present in the ventral thalamus, including in the subthalamic sulcus. There is no expression in the principal thalamic nuclei.
TS20: midbrain	Present	Regionally restricted	6c	Medium-high expression is present in the pretectal area & dorsal tegmentum, belonging to perioculomotor nuclei, the mesencephalic reticular formation, the substantia nigra, & the ventral tegmental area. Weak expression is in the superior colliculus.
TS20: cerebellum primordium	Moderate	Regionally restricted	6c	Expression is present in a group of cells in the cerebellar differentiating zone.
TS20: medulla oblongata	Present	Regionally restricted	6c	Expression is present in the differentiating zone. There is no expression in domains in rhombomere 6.

Structure	Level	Pattern	Image	Note
TS20: olfactory epithelium	Present		6d
TS20: forebrain	Present	Graded	6d	There is an inside-out expression gradient.
TS20: medial ganglionic eminence	Moderate	Regionally restricted	6d	There is medium-high expression in the pallidal differentiating zone, with the strongest signal in the presumptive secondary proliferative population.
TS20: cerebral cortex	Present	Single cells	6d	Expression is present in the septal differentiating zone.
TS20: hypothalamus	Present	Regionally restricted	6d	Expression is present in the anterior and posterior preoptic area and suprachiasmatic nuclei. A few weakly stained cells could be seen around the ventral hypothalamus midline. There is weak expression in the retrochiasmatic and tuberal area.
TS20: medulla oblongata	Present	Regionally restricted	6d	Expression is present in the differentiating zone.
TS20: spinal cord	Present		6d	Expression is present in both dorsal and ventral aspects of the neural tube.
TS20: sympathetic ganglion	Weak	Regionally restricted	6d	There is weak expression in the prevertebral ganglia.

Structure	Level	Pattern	Image	Note
TS20: cerebellum primordium	Present		7a
TS20: midbrain	Weak	Regionally restricted	7a	Expression is present in the superior colliculus.

Structure	Level	Pattern	Image	Note
TS20: midbrain	Present	Regionally restricted	7b	There is high-medium expression in the tegmental area, including the perioculomotor nuclei, the mesencephalic reticular formation, the substantia nigra, and the ventra tegmental area. There is no expression in the inferior colliculus.

Structure	Level	Pattern	Image	Note
TS20: thalamus	Present	Regionally restricted	7c	Expression is present in the ventral thalamus, including in the subthalamic sulcus, and in the dorsal thalamic mantle zone. There is no expression in the principal thalamic nuclei.
TS20: epithalamus	Absent		7c	There is no expression in the epithalamic differentiating zone and ventricular neuroepithelium.
TS20: medulla oblongata	Present	Regionally restricted	7c	Although there is expression elsewhere in the myelencephalon, there is no expression in domains in rhombomeres 1 and 2.

Structure	Level	Pattern	Image	Note
TS20: medial ganglionic eminence	Moderate	Regionally restricted	7d	There is medium-high expression in the pallidal differentiating zone, with the strongest signal in the presumptive secondary proliferative population. Low numbers of cells also express in the amygdaloid area.
TS20: lateral ganglionic eminence	Present	Regionally restricted	7d	Expression is present in the striatal differentiating zone.
TS20: hypothalamus	Present	Regionally restricted	7d	Weak expression is present in the retrochiasmatic and tuberal area. No expression is present in the anterior dorsal nucleus, mammillary area, or supraoptic-paraventricular area. Strong expression is present in the hypothalamic cell cord.
TS20: pons	Present		7d

Structure	Level	Pattern	Image	Note
TS20: medial ganglionic eminence	Present	Regionally restricted	7e	There is medium-high expression in the pallidal differentiating zone, with the strongest signal in the presumptive secondary proliferative population. There is also expression in the entopeduncular area.
TS20: lateral ganglionic eminence	Present	Regionally restricted	7e	Expression is present in the striatal differentiating zone.
TS20: hypothalamus	Present	Regionally restricted	7e	Weak expression is present in the retrochiasmatic and tuberal area. No expression is in the anterior dorsal nucleus, mammillary area, or supraoptic-paraventricular area. Strong expression is present in the hypothalamic cell cord.
TS20: medulla oblongata	Present		7e
TS20: pons	Present		7e
TS20: spinal cord	Present		7e

Structure	Level	Pattern	Image	Note
TS20: medial ganglionic eminence	Present	Regionally restricted	7f	There is medium-high expression in the pallidal differentiating zone, with the strongest signal in the presumptive secondary proliferative population. There is also expression in the entopeduncular area.
TS20: lateral ganglionic eminence	Present	Regionally restricted	7f	Expression is present in the striatal differentiating zone.
TS20: pons	Present		7f
TS20: cerebral cortex	Present	Single cells	7f	Expression is present in the septal differentiating zone.
TS20: hypothalamus	Present	Regionally restricted	7f	Expression is seen in the anterior and posterior preoptic area and suprachiasmatic nuclei. Weak expression is present in the retrochiasmatic and tuberal area.
TS20: spinal cord	Present		7f

Structure	Level	Pattern	Image	Note
TS20: medulla oblongata	Present		7g
TS20: pons	Present		7g
TS20: spinal cord	Present		7g

Structure	Level	Pattern	Image	Note
TS20: spinal cord	Present		7i	Expression is present in both dorsal and ventral aspects of the neural tube.

Structure	Level	Pattern	Image	Note
TS20: lens vesicle	Weak	Regionally restricted	7j	Expression is present in the anterior lens epithelium and the posterior lens fibers.
TS20: retina	Present	Regionally restricted	7j	Expression is present in the central (but not peripheral) region, at the base of the optic nerve.