EMAGE mouse gene expression spatial database

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EMAGE:17824

Cntn3 contactin 3 ( MGI:99534)
TS23 (14.5 dpc)
in situ hybridisation

Data Images


"Pseudo-wholemount" of euxassay_009023. This image has been made by aligning and collapsing the constitutent sections. Information about the method.	euxassay_009023_01	euxassay_009023_02	euxassay_009023_03	euxassay_009023_04

euxassay_009023_05	euxassay_009023_06	euxassay_009023_07	euxassay_009023_08	euxassay_009023_09

euxassay_009023_10	euxassay_009023_11	euxassay_009023_12	euxassay_009023_13	euxassay_009023_14

euxassay_009023_15	euxassay_009023_16	euxassay_009023_17	euxassay_009023_18	euxassay_009023_19

euxassay_009023_20	euxassay_009023_21	euxassay_009023_22	euxassay_009023_23	euxassay_009023_24

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:

17824_wholemount_strong.wlz

17824_wholemount_moderate.wlz

17824_wholemount_weak.wlz

17824_wholemount_possible.wlz

17824_wholemount_not_detected.wlz

(what is wlz format?)

Download all expression domains:

EMAGE:17824_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

hypothalamus mantle layer

weak

regional

weak expression: see section 15 16

diencephalon lateral wall mantle layer

weak

regional

weak expression: see section 08 09 10 11 12 13 14 15 16 17

olfactory cortex marginal layer

strong

regional

strong expression: see section 14 15 16 moderate expression: see section 11 12 13 17 18

medulla oblongata basal plate mantle layer

moderate

regional

moderate expression: see section 08 09 10 11 13 14 15 16 17

midbrain mantle layer

moderate

regional

moderate expression: see section 06 07 08 09 10 11 12 13 14 15 16 17 18 19

ventral grey horn

moderate

single cell

moderate expression: see section 09 10 11 13 14 15 16

Annotation Validation:

spatial mapping by EMAGE editor, text annotation by author

Detection Reagent

Type:	in situ hybridisation probe
Identifier:	T36171
Entity Detected:	Cntn3, contactin 3 ( MGI:99534)
Sequence:	sense strand is shown >T36171 CTACACCTGCACAGCAGAAAACCAGTTTGGGAAAGCAAATGGCACAACCCACTTGGTTGTGACAGAACCT ACGAGAATAATTTTGGCACCTTCAAACATGGACGTTGCTGTTGGTGAGAGCGTCATTTTACCCTGCCAGG TTCAACATGATCCCCTATTAGACATAATGTTTGCCTGGTATTTCAATGGAGCCCTTACAGACTTTAAGAA AGATGGATCTCACTTTGAGAAAGTTGGTGGGAGTTCATCTGGTGATTTAATGATCAGAAACATTCAATTG AAACACAGTGGGAAGTACGTATGTATGGTGCAGACAGGGGTGGACAGTGTTTCCTCTGCAGCTGAGCTCA TCGTGAGAGGTTCACCTGGGCCACCGGAAAATGTGAAGGTAGATGAAATTACAGACACAACAGCCCAGCT CTCTTGGACGGAAGGCACGGACAGTCATAGCCCAGTTATATCGTATGCAGTCCAAGCTAGGACGCCTTTC TCTGTGGGCTGGCAAAGTGTCAGAACAGTACCTGAGGTCATTGATGGCAAGACACATACAGCTACTGTCG TGGAGTTAAACCCATGGGTGGAATATGAATTTCGCATTGTAGCCAGTAACAAAATCGGAGGTGGAGAACC CAGTTTACCCTCAGAAAAAGTAAGGACTGAAGAGGCAGCTCCAGAAATCGCACCTTCTGAGGTCAGCGGA GGAGGTGGAAGCCGATCTGAACTAGTGATAACCTGGGATCCAGTCCCTGAAGAACTACAGAATGGAGGAG GTTTTGGGTATGTGGTTGCTTTCCGCCCACTTGGGGTTACCACCTGGATC
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 98274. Forward Primer - name:098274_F_cDNA_Cntn3, sequence:CTACACCTGCACAGCAGAAAAC; Reverse Primer - name:098274_N_SP6_cDNA_Cntn3, sequence:GATCCAGGTGGTAACCCCAAG. 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:17825 same embryo
	EMAGE:17828 same embryo
	EMAGE:17823 same embryo
	EMAGE:17826 same embryo
	EMAGE:17827 same embryo
	EurExpress:euxassay_009023 same experiment
	MGI:4823963 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