EMAGE mouse gene expression spatial database

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EMAGE:18954

Pcdh9 protocadherin 9 ( MGI:1306801)
TS23 (14.5 dpc)
in situ hybridisation

Data Images


"Pseudo-wholemount" of euxassay_014258. This image has been made by aligning and collapsing the constitutent sections. Information about the method.	euxassay_014258_01	euxassay_014258_02	euxassay_014258_03	euxassay_014258_04

euxassay_014258_05	euxassay_014258_06	euxassay_014258_07	euxassay_014258_08	euxassay_014258_09

euxassay_014258_10	euxassay_014258_11	euxassay_014258_12	euxassay_014258_13	euxassay_014258_14

euxassay_014258_15	euxassay_014258_16	euxassay_014258_17	euxassay_014258_18	euxassay_014258_19

euxassay_014258_20	euxassay_014258_21	euxassay_014258_22	euxassay_014258_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:

18954_wholemount_strong.wlz

18954_wholemount_moderate.wlz

18954_wholemount_weak.wlz

18954_wholemount_possible.wlz

18954_wholemount_not_detected.wlz

(what is wlz format?)

Download all expression domains:

EMAGE:18954_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

vertebral axis musculature

moderate

single cell

moderate expression: see section 02 03 weak expression: see section 04 05 06 07 08

diencephalon lateral wall mantle layer

weak

regional

weak expression: see section 09 11

medulla oblongata basal plate mantle layer

weak

regional

weak expression: see section 07 08 10 13 14 15 16 17

not examined

regional

not examined expression: see section 07 08 09

pons mantle layer

weak

regional

weak expression: see section 06 16 17

midbrain mantle layer

weak

regional

weak expression: see section 09 10 11

facial vii ganglion

moderate

regional

moderate expression: see section 03 04 19

vestibulocochlear viii ganglion

weak

regional

weak expression: see section 05 18

Annotation Validation:

spatial mapping by EMAGE editor, text annotation by author

Detection Reagent

Type:	in situ hybridisation probe
Identifier:	T38699
Entity Detected:	Pcdh9, protocadherin 9 ( MGI:1306801)
Sequence:	sense strand is shown >T38699 CTTTGATTTATGCTGGGACCTCTATACTTGACATTATACTTCAAACAAAACTTTAAAAGATAAGCATTAA ACCTATTGTGCTGTTAACACCGTTAGTGGACACTTGTAAGTCAATCAGTGTTAAAGTATTTGTAAATAGA AGCAAGCTATTATTAACAATTTTGTGTACTTATAGCACTCACCTACAAATGTTATAGCATAATTCTGTGT TGATGGTTGCTCCTTTCCTTTTCTCTATTGCCCTCTTTCTTCTTATTTTTGTTGTTTCTTTCAGTGAGGT GTTTCCGCGTTAGTAGTCTGTCTTGGCACACGTTGTTCAAAGAATCTTAAATATTTGTGTTTTAAAATGG TTCTGAAATTTTGCTTCTTCTATGATAACTTAGAATGTTAGAACTCTGTAAAAATATAAAGACAAAAGAA AATATGAAAACTTCAAACAACAATAGCAGCAGACAAATGCTTCTGCACACTCTTGGAAATTCAGAACCTC TTTTTGACATCCTTATTTTCAAAGTAGGCAAAATTAAAAATGACGTAATTAGTACCATTAAGTGAGAAAG TGATGGGAAGTGTTATCCATCAAGTGTGATATAATATTCTGTACTTGTTACTCTTTCAAAACTAACGTAT TAAAATCAGTATATATTGAAGAAAAAATCATTACTCAAAAAATAGTTTCAATTGGGCAAATGTGTGTCTC CAACTTTGTTGAAATGACAGAGTTTGTGTTGATCCTCATATACAATACTGTTGTTGTAACACAAGTGTTA TTAGACCATAGCCACAAAATATTTAATGTGTTGTGCCTTCATGATGTAACAGAACATTCTCCAGG
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 159447. Forward Primer - name:159447_F_cDNA_Mm.211229, sequence:CTTTGATTTATGCTGGGACCTC; Reverse Primer - name:159447_N_SP6_cDNA_Mm.211229, sequence:CCTGGAGAATGTTCTGTTACATC. 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:18955 same embryo
	EMAGE:18951 same embryo
	EMAGE:18953 same embryo
	EMAGE:18952 same embryo
	EurExpress:euxassay_014258 same experiment
	MGI:4827081 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