EMAGE mouse gene expression spatial database

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EMAGE:15561

Sema6d sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D ( MGI:2387661)
TS23 (14.5 dpc)
in situ hybridisation

Data Images


"Pseudo-wholemount" of euxassay_010735. This image has been made by aligning and collapsing the constitutent sections. Information about the method.	euxassay_010735_01	euxassay_010735_02	euxassay_010735_03	euxassay_010735_04

euxassay_010735_05	euxassay_010735_06	euxassay_010735_07	euxassay_010735_08	euxassay_010735_09

euxassay_010735_10	euxassay_010735_11	euxassay_010735_12	euxassay_010735_13	euxassay_010735_14

euxassay_010735_15	euxassay_010735_16	euxassay_010735_17	euxassay_010735_18	euxassay_010735_19

euxassay_010735_20	euxassay_010735_21	euxassay_010735_22	euxassay_010735_23

View assay images:
Expression pattern clarity:
Find spatially similar wholemount expression patterns:

Expression Pattern Description

Spatial Annotation:

Annotation colour key:

	strong
	moderate
	weak
	possible
	not detected

wholemount mapping

Download individual expression domains:

15561_wholemount_strong.wlz

15561_wholemount_moderate.wlz

15561_wholemount_weak.wlz

15561_wholemount_possible.wlz

15561_wholemount_not_detected.wlz

(what is wlz format?)

Download all expression domains:

EMAGE:15561_all_domains.zip

Find spatially similar wholemount expression patterns:

EMAGE spatially similar wholemount patterns

Morphological match to the template:

Text Annotation:

Structure

Level

Pattern

Notes

embryo

strong

single cell

strong expression: see section 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 20 21 22 23

diencephalon lateral wall mantle layer

strong

single cell

strong expression: see section 05 06 07 08 09 10 11 12 13 14 15 16 17 18

diencephalon lateral wall ventricular layer

strong

regional

strong expression: see section 11 12

cerebral cortex mantle layer

strong

regional

strong expression: see section 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 20 21 22 23

cerebral cortex ventricular layer

strong

regional

strong expression: see section 01 02 03 22 23

telencephalon mantle layer

strong

single cell

strong expression: see section 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 20 21 22 23

telencephalon ventricular layer

strong

regional

strong expression: see section 13 14

medulla oblongata alar plate mantle layer

strong

single cell

strong expression: see section 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 20

medulla oblongata basal plate mantle layer

strong

single cell

strong expression: see section 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 20

rest of cerebellum mantle layer

strong

single cell

strong expression: see section 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 20

rest of cerebellum marginal layer

strong

regional

strong expression: see section 02 03 04 05 06 07 08 09 10 12 13 14 15 16 17 18 19 20 21

pons mantle layer

strong

single cell

strong expression: see section 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 20

midbrain mantle layer

strong

single cell

strong expression: see section 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18

facial vii ganglion

strong

regional

strong expression: see section 07

glossopharyngeal ix ganglion

strong

regional

strong expression: see section 06 18 19

trigeminal v ganglion

strong

regional

strong expression: see section 03 04 05 06 07 08 09 17 18 19 20 21 22

vestibulocochlear viii ganglion

strong

regional

strong expression: see section 04 05 06 08 09 16 17 18 19 20 21

spinal cord mantle layer

strong

single cell

strong expression: see section 09 10 11 12 13 14 15

spinal cord ventricular layer

strong

regional

strong expression: see section 12 13

dorsal root ganglion

strong

regional

strong expression: see section 07 08 09 10 11 12 13 15 16 17 18

Annotation Validation:

spatial mapping by EMAGE editor, text annotation by author

Detection Reagent

Type:	in situ hybridisation probe
Identifier:	T38319
Entity Detected:	Sema6d, sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D ( MGI:2387661)
Sequence:	sense strand is shown >T38319 ATATGGTACCCGGTGTCAGAACATTTAAGCGTTCTAAATAATTTTGTGCTGCTATCCATCAGAACGTCTA TTCCAGCCTTGCCAGCTTAAGAACTTAGAGAAATTAAGAGGTATCTTTGATGTATCTACCAGTATTCAAT AGTAACATTTACCTGTCCACTGTGAATCAAAGCCTGGGGCACGCTACTCAACCTTAGACACACTTACAGG CTTTTATTTTGATTGTGTTATTTTATTTTCCATACAGTAAAAAATGTCCTCTCTTAACTCCTCTCACCCC CAACTCCCAAGGCAAAAGAGAAACCAAAAGTAGGACAAAAGAAAGAGACAGACAGACAGACAGACAGAAC AGGAATTACAGTTGGCTTAGCAGGGAGGATCTGTAGAGCTCTCGATGATCCTTCCTCCATGTGTGTCCTG TGAGGATTTTGCTCATGAGTCATGCAGGCAGTGACAGTGAACTGTAAATACCACATGTGAGTTTACCTGG ATCTGTGCATTTTGTGCCTTATTCACTCGAGTGGTAGAAGTTCCGCGGTATGTTGAGTGTTTCCACTACA GAGCATCATTTCCCATGTGCCACTTGTAAATGTTTTGCAGCCAGCACCTGAGGACTTCTTATACAGTCAT AAAGCCACCTAGAGCGATTTGTTGTTGAGCAACGCCGCCCCTTCCCTCCAGGATCAGAAGCAGCACCCAC CCTTGCCATGATAAACATTCCATCCCCTGCTGTTCTGATAATGTGAAGTCAGATGAGGGTTCCCAGGTTA TGTGGCACCTGCGGAAACCATGTCTAGAGTCGTTTCTATGTAGCTTGGCAGAGCCCACTGATGGCTGCAG GTGTGTAGCCTACTGACAGCTTTGGTTAACCCACTG
Notes:	The probe template was received by the EURExpress consortium as an aliquot of PCR product from the Allen Brain Atlas (originally amplified from wild type C57BL/6J mouse whole brain cDNA), and this was re-amplified using the gene-specific Allen Brain Atlas Primer Pair 146726. Forward Primer - name:146726_F_cDNA_Sema6d, sequence:ATATGGTACCCGGTGTCAGAAC; Reverse Primer - name:146726_N_SP6_cDNA_Sema6d, sequence:CAGTGGGTTAACCAAAGCTGTC. The reverse primer contains a 5' extension containing an Sp6 RNA polymerase binding site (this extension is not shown in the primer sequence listed here). Anti-sense probe was transcribed from the PCR amplified template using Sp6 polymerase.
Chemistry:	RNA
Strand:	antisense
Label:	digoxigenin

Specimen

Organism:	mouse
Strain:	C57BL/6
Age:	14.5 dpc
Theiler Stage:	TS23
Mutations:	none (wild-type)
Preparation:	section

Procedures

Fixation:	none
Embedding:	cryosection (OCT)
Staining procedure:	alkaline phosphatase + NBT/BCIP

General Information

Authors:	Dr. Graciana Diez-Roux, Prof. Gregor Eichele, Prof. Richard Baldock, Dr. Duncan Davidson, Prof. Stylianos Antonarakis, Dr. Marie Laure Yaspo, Prof. Salvador Martinez Perez, Dr. Pascal Dolle, Dr. David Tannahill, Prof. Pier Paolo Di Fiore, Mr. Stefan Kruse, Mr. Paolo Sarmientos, Dr. Uwe Radelof, Prof. Andrea Ballabio.
Principal investigator:	Professor Andrea Ballabio, Fondazione Telethon, TIGEM Instituto di Genetica e Medicina, Via Pietro Castellino 111 80131, Napoli, Italy 80131
Submitted by:	EMAGE EDITOR, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, UK EH4 2XU
Experiment type:	screen
References:	[ doi:10.1371/journal.pbio.1000582] [ PMID:21267068] Diez-Roux G, Banfi S, Sultan M, Geffers L, Anand S, Rozado D, et al 2011 A High-Resolution Anatomical Atlas of the Transcriptome in the Mouse Embryo PLoS Biol (9)
Links:	EMAGE:15560 same embryo
	EMAGE:15559 same embryo
	EMAGE:15562 same embryo
	EMAGE:15558 same embryo
	EMAGE:15563 same embryo
	EurExpress:euxassay_010735 same experiment
	MGI:4827950 same experiment
	Ensembl same gene
	Allen Brain Atlas same gene
	BioGPS same gene
	International Mouse Knockout Project Status same gene
	GEISHA Chicken ISH Database same gene
	EMBL-EBI Gene Expression Atlas same gene
	BrainStars same gene
	ViBrism same gene
Data Source