EMAGE mouse gene expression spatial database

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EMAGE:19223

Scn8a sodium channel, voltage-gated, type VIII, alpha ( MGI:103169)
TS23 (14.5 dpc)
in situ hybridisation

Data Images


"Pseudo-wholemount" of euxassay_001982. This image has been made by aligning and collapsing the constitutent sections. Information about the method.	euxassay_001982_01	euxassay_001982_02	euxassay_001982_03	euxassay_001982_04

euxassay_001982_05	euxassay_001982_06	euxassay_001982_07	euxassay_001982_08	euxassay_001982_09

euxassay_001982_10	euxassay_001982_11	euxassay_001982_12	euxassay_001982_13	euxassay_001982_14

euxassay_001982_15	euxassay_001982_16	euxassay_001982_17	euxassay_001982_18	euxassay_001982_19

euxassay_001982_20	euxassay_001982_21	euxassay_001982_22

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:

19223_wholemount_strong.wlz

19223_wholemount_moderate.wlz

19223_wholemount_weak.wlz

19223_wholemount_possible.wlz

19223_wholemount_not_detected.wlz

(what is wlz format?)

Download all expression domains:

EMAGE:19223_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

brain

moderate

homogeneous

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

facial vii ganglion

moderate

regional

moderate expression: see section 05 06 07 18

glossopharyngeal ix ganglion

moderate

regional

moderate expression: see section 07 16

trigeminal v ganglion

moderate

regional

moderate expression: see section 04 05 06 07 08 09 16 17 18 19 20

vestibulocochlear viii ganglion

moderate

regional

moderate expression: see section 06 07 08 16 17

spinal cord

moderate

homogeneous

moderate expression: see section 09 10 11 12 13 14

cervico-thoracic ganglion

moderate

regional

moderate expression: see section 09 13

cervical ganglion

moderate

regional

moderate expression: see section 08 15

thoracic ganglion

moderate

regional

moderate expression: see section 11 12 13

dorsal root ganglion

moderate

regional

moderate expression: see section 06 07 08 09 10 13 14 15 16

kidney calyx

moderate

regional

moderate expression: see section 06 07 16

kidney pelvis

moderate

regional

moderate expression: see section 08 09 14 15

nucleus pulposus

moderate

regional

moderate expression: see section 11 12

Annotation Validation:

spatial mapping by EMAGE editor, text annotation by author

Detection Reagent

Type:	in situ hybridisation probe
Identifier:	T2463
Entity Detected:	Scn8a, sodium channel, voltage-gated, type VIII, alpha ( MGI:103169)
Sequence:	sense strand is shown >T2463 TGGCCTCGAGGCAGATTCGGACGAGGGGCGCACGTAACCGAATTCTCCCGTTGACCAGAATCTGCCTATT CATTTCCTGTCTCTTCCCACTTTTCTAGCAAACTTTTACATGGTCCCTGGCATGCTAGAACCCTTGCTCT GCGGGAACAGCTCTGACGCCGGGCAATGCCCAGAGGGGTTCCAGTGCATGAAAGCAGGAAGAAATCCCAA CTACGGCTACACCAGCTTCGACACCTTCAGCTGGGCCTTCCTGGCACTGTTCCGCCTCATGACTCAGGAC TACTGGGAGAACTTATACCAGCTGACCTTACGAGCGGCTGGGAAAACGTACATGATCTTCTTTGTCTTGG TGATCTTCGTGGGTTCTTTCTATTTGGTGAACTTGATCTTGGCTGTGGTGGCCATGGCTTACGAAGAGCA GAACCAGGCAACACTGGAGGAGGCAGAGCAGAAAGAGGCAGAGTTCAAGGCGATGCTGGAGCAGCTCAAG AAGCAGCAGGAGGAGGCGCAGGCTGCTGCAATGGCCACTTCGGCGGGCACCGTCTCAGAAG
Notes:	The probe template was PCR amplified from IMAGE:1248052 using vector specific primers. Forward Primer - name:RZPD M13 forward, sequence:GCTATTACGCCAGCTGGCGAAAGGGGGATGTG; Reverse Primer - name:RZPD M13 reverse, sequence:CCCCAGGCTTTACACTTTATGCTTCCGGCTCG. Anti-sense probe was then transcribed from the PCR amplified template using T3 polymerase. EMAGE Editor's Note: the partial probe sequence indicated here was given by the EURExpress Consortium and has been checked using BLAST comparison against all available partial insert sequences of IMAGE:1248052 from NCBI. In cases where no BLAST hit was found (because the two sequence reads are found at opposing ends of the insert sequence), both end sequences were then checked against the appropriate cDNA RefSeq to ensure validity of the information.
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:19222 same embryo
	EMAGE:19225 same embryo
	EMAGE:19224 same embryo
	EurExpress:euxassay_001982 same experiment
	MGI:4827905 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