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Gene Expression Data
Assay Details
Assay
Reference: J:157819 Shimogori T, et al., A genomic atlas of mouse hypothalamic development. Nat Neurosci. 2010;13(6):767-75
Assay type: RNA in situ
MGI Accession ID: MGI:4450824
Gene symbol: Sema6d
Gene name: sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D
Probe: UI-M-AJ1-ahg-b-05-0-UI.s1
Probe preparation: Antisense labelled with digoxigenin RNA
Visualized with: Alkaline phosphatase
Results
Specimen S7u: embryonic day 11.5 (more )
Note: Double labeled: blue - Sema6d; brown - Shh (assay MGI:4452154).
Structure Level Pattern Image Note
TS19: diencephalon Absent S7_u This annotation was inferred from the data presented in Supp. Table 4.
Specimen S7v: embryonic day 12.5 (more )
Note: Double labeled: blue - Sema6d; brown - Shh (assay MGI:4452154).
Structure Level Pattern Image Note
TS20: hypothalamus Absent S7_v There is no expression in the suprachiasmatic nucleus.
Specimen S7w: embryonic day 14.5 (more )
Note: Double labeled: blue - Sema6d; brown - Shh (assay MGI:4452154).
Structure Level Pattern Image Note
TS22: diencephalon Present S7_w There is no expression in the suprachiasmatic nucleus.
Specimen S7x: embryonic day 16.5 (more )
Note: Double labeled: blue - Sema6d; brown - Shh (assay MGI:4452154).
Structure Level Pattern Image Note
TS24: hypothalamus Present Regionally restricted S7_x Expression is present in the medial portion of the suprachiasmatic nucleus.
Specimen Sema6d - E11.5: embryonic day 11.5 (more )
Note: Specimen was 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 Sema6d-Shh E11.5_sagittal , Sema6d-Shh 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 Ambiguous Sema6d-Shh E11.5_coronal , Sema6d-Shh E11.5_sagittal Staining is either absent or ubiquitous 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 Sema6d-Shh E11.5_sagittal , Sema6d-Shh 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 Ambiguous Sema6d-Shh E11.5_sagittal , Sema6d-Shh E11.5_coronal Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex and the ganglionic eminences.
Specimen Sema6d - E12.5: embryonic day 12.5 (more )
Note: Specimen was 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
TS20: cerebral cortex intermediate zone Moderate Sema6d-Shh E12.5_sagittal , Sema6d-Shh E12.5_coronal There is moderate staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS20: cerebral cortex ventricular layer Ambiguous Sema6d-Shh E12.5_sagittal , Sema6d-Shh E12.5_coronal Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS20: cortical plate Moderate Sema6d-Shh E12.5_sagittal , Sema6d-Shh E12.5_coronal There is moderate staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS20: diencephalon mantle layer Ambiguous Sema6d-Shh E12.5_coronal , Sema6d-Shh E12.5_sagittal Staining is either absent or ubiquitous in the mantle zone of the premam, mam and supramam zones and the TT.
TS20: diencephalon ventricular layer Ambiguous Sema6d-Shh E12.5_sagittal , Sema6d-Shh E12.5_coronal Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones and the TT.
TS20: ganglionic eminence Moderate Non-Uniform Sema6d-Shh E12.5_coronal , Sema6d-Shh E12.5_sagittal There is moderate staining in the mantle zone of the ganglionic eminences. Staining is either absent or ubiquitous in the ventricular zone of the ganglionic eminences.
TS20: hypothalamus mantle layer Ambiguous Sema6d-Shh E12.5_sagittal , Sema6d-Shh 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 Ambiguous Sema6d-Shh E12.5_sagittal , Sema6d-Shh E12.5_coronal 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 Weak Non-Uniform Sema6d-Shh E12.5_sagittal , Sema6d-Shh E12.5_coronal There is weak 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 Ambiguous Sema6d-Shh E12.5_coronal , Sema6d-Shh E12.5_sagittal Staining is either absent or ubiquitous in the ventricular zone of the dorsal thalamus and prethalamus.
Specimen Sema6d - E14.5: embryonic day 14.5 (more )
Note: Specimen was 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
TS22: cerebral cortex intermediate zone Very strong Sema6d-Shh E14.5_sagittal , Sema6d-Shh E14.5_coronal There is very strong staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS22: cerebral cortex ventricular layer Strong Sema6d-Shh E14.5_sagittal , Sema6d-Shh E14.5_coronal There is strong staining in the ventricular zone of the cerebral cortex.
TS22: cortical plate Very strong Sema6d-Shh E14.5_coronal , Sema6d-Shh E14.5_sagittal There is very strong staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS22: diencephalon mantle layer Ambiguous Sema6d-Shh E14.5_sagittal , Sema6d-Shh 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 Weak Non-Uniform Sema6d-Shh E14.5_sagittal , Sema6d-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 Ambiguous Sema6d-Shh E14.5_sagittal , Sema6d-Shh E14.5_coronal Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS22: hypothalamus mantle layer Ambiguous Sema6d-Shh E14.5_sagittal , Sema6d-Shh 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 Moderate Non-Uniform Sema6d-Shh E14.5_coronal , Sema6d-Shh E14.5_sagittal There is moderate staining in the ventricular zone of the ventral POA and the AVH. 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 Ambiguous Sema6d-Shh E14.5_coronal , Sema6d-Shh E14.5_sagittal Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS22: thalamus ventricular layer Moderate Non-Uniform Sema6d-Shh E14.5_coronal , Sema6d-Shh E14.5_sagittal There is moderate staining in the ventricular zone of the prethalamus and weak staining in the dorsal thalamus.
Specimen Sema6d - E16.5: embryonic day 16.5 (more )
Note: Specimen was 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
TS24: cerebral cortex intermediate zone Weak Sema6d-Shh E16.5_sagittal , Sema6d-Shh E16.5_coronal There is weak staining in the postmitotic neurons in the intermediate zone of the cerebral cortex.
TS24: cerebral cortex ventricular layer Ambiguous Sema6d-Shh E16.5_coronal , Sema6d-Shh E16.5_sagittal Staining is either absent or ubiquitous in the ventricular zone of the cerebral cortex.
TS24: cortical plate Weak Sema6d-Shh E16.5_coronal , Sema6d-Shh E16.5_sagittal There is weak staining in the postmitotic neurons in the cortical plate of the cerebral cortex.
TS24: diencephalon mantle layer Ambiguous Sema6d-Shh E16.5_coronal , Sema6d-Shh E16.5_sagittal Staining is either absent or ubiquitous in the mantle zone of the premam, mam and supramam zones.
TS24: diencephalon ventricular layer Ambiguous Sema6d-Shh E16.5_sagittal , Sema6d-Shh E16.5_coronal Staining is either absent or ubiquitous in the ventricular zone of the premam, mam and supramam zones.
TS24: ganglionic eminence Ambiguous Sema6d-Shh E16.5_coronal , Sema6d-Shh E16.5_sagittal Staining is either absent or ubiquitous in the ventricular and mantle zones of the ganglionic eminences.
TS24: hypothalamus mantle layer Ambiguous Sema6d-Shh E16.5_coronal , Sema6d-Shh E16.5_sagittal 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 Sema6d-Shh E16.5_sagittal , Sema6d-Shh E16.5_coronal There is strong staining in the VZ of the SCH nucleus, moderate staining in the PVH nucleus, the AVH and the DAH and weak staining in the dorsal and ventral POAs. Staining is either absent or ubiquitous in the VZ of the DMH, VMH and ARH nuclei and the PH.
TS24: thalamus mantle layer Ambiguous Sema6d-Shh E16.5_sagittal , Sema6d-Shh E16.5_coronal Staining is either absent or ubiquitous in the mantle zone of the dorsal thalamus and prethalamus.
TS24: thalamus ventricular layer Moderate Sema6d-Shh E16.5_sagittal , Sema6d-Shh E16.5_coronal There is moderate staining in the ventricular zone of the dorsal thalamus and prethalamus.
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Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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