EMAGE mouse gene expression spatial database

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EMAGE:10380

Col9a2 collagen, type IX, alpha 2 ( MGI:88466)
TS23 (14.5 dpc)
in situ hybridisation

Data Images


"Pseudo-wholemount" of euxassay_000512. This image has been made by aligning and collapsing the constitutent sections. Information about the method.	euxassay_000512_01	euxassay_000512_02	euxassay_000512_03	euxassay_000512_04

euxassay_000512_05	euxassay_000512_06	euxassay_000512_07	euxassay_000512_08	euxassay_000512_09

euxassay_000512_10	euxassay_000512_11	euxassay_000512_12	euxassay_000512_13	euxassay_000512_14

euxassay_000512_15	euxassay_000512_16	euxassay_000512_17	euxassay_000512_18	euxassay_000512_19

euxassay_000512_20	euxassay_000512_21	euxassay_000512_22	euxassay_000512_23	euxassay_000512_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:

10380_wholemount_strong.wlz

10380_wholemount_moderate.wlz

10380_wholemount_weak.wlz

10380_wholemount_possible.wlz

10380_wholemount_not_detected.wlz

(what is wlz format?)

Download all expression domains:

EMAGE:10380_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

rib

strong

regional

strong expression: see section 01 02 03 04 08 24

hand mesenchyme

moderate

regional

moderate expression: see section 01 02 03 04 24

hindlimb digit 1 mesenchyme

moderate

regional

moderate expression: see section 06

hindlimb digit 2 mesenchyme

moderate

regional

moderate expression: see section 06 24

hindlimb digit 3 mesenchyme

moderate

regional

moderate expression: see section 06 07 24

hindlimb digit 4 mesenchyme

moderate

regional

moderate expression: see section 07 23 24

hindlimb digit 5 mesenchyme

moderate

regional

moderate expression: see section 07 24

hip mesenchyme

moderate

regional

moderate expression: see section 01 02 03 04

otic capsule

moderate

regional

moderate expression: see section 01 02 03 04 05 06 07 08 09 15 16 17 18 19 20 21 22 23 24

viscerocranium

strong

regional

Expression in the turbinate bone.

axial skeleton cervical region

strong

regional

strong expression: see section 08 15 16 moderate expression: see section 10 11 12 weak expression: see section 13

axial skeleton lumbar region

strong

regional

strong expression: see section 13 15 16 moderate expression: see section 12 14

axial skeleton sacral region

strong

regional

strong expression: see section 13 15 16 moderate expression: see section 14

axial skeleton thoracic region

strong

regional

strong expression: see section 12 15 16 moderate expression: see section 10 11 14 weak expression: see section 13

cranium

strong

regional

strong expression: see section 01 02 03 04 05 06 07 08 19 20 21 22 23 24

pectoral girdle and thoracic body wall skeleton

strong

regional

strong expression: see section 01 02 03 04 06 07 08 10 11 12 15 16 19 20 21 22 23 24 moderate expression: see section 14 18

axial skeleton tail region

strong

regional

strong expression: see section 15 16

Annotation Validation:

spatial mapping by EMAGE editor, text annotation by author

Detection Reagent

Type:	in situ hybridisation probe
Identifier:	T1730
Entity Detected:	Col9a2, collagen, type IX, alpha 2 ( MGI:88466)
Sequence:	sense strand is shown >T1730 TGGCCTCGAGCCAGATTCGGCACGAGGAGGGGTTGGGGGAGGGAGAGCACGGGAGTAAAGGTGAGGCCAA CAGAGCCAAGTATTGGAGAGCCACCCCTCCCAAGGGAAGAGGGTAGCTTCTCTTCCTGGAGTACCAACTA CCCCTCACCCATGCCTTTCAGCACTGGGCCATCCCACCCTCGGGGCAGGGGGGACTGAGGCTTCTGGTGG TCCTTACCCTATTCTTATTCTCTGGACTTATTTTTATTGGGTATCTTTTGGGGGAGAATACCTTGAGGTG GCAGTTCTTAGGCCAGCCCTGCTATTGCCTGTCTCCCATCCCAGTATTTAAACATCCATCTTNCCCTGGT CCCCCAGTCTCTTTTGGCCA
Notes:	The probe template was PCR amplified from IMAGE:480602 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:480602 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:10379 same embryo
	EMAGE:10382 same embryo
	EMAGE:10383 same embryo
	EMAGE:10381 same embryo
	EurExpress:euxassay_000512 same experiment
	MGI:4823996 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