EMAGE mouse gene expression spatial database

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EMAGE:15642

Col6a4 collagen, type VI, alpha 4 ( MGI:1915803)
TS23 (14.5 dpc)
in situ hybridisation

Data Images


"Pseudo-wholemount" of euxassay_010834. This image has been made by aligning and collapsing the constitutent sections. Information about the method.	euxassay_010834_01	euxassay_010834_02	euxassay_010834_03	euxassay_010834_04

euxassay_010834_05	euxassay_010834_06	euxassay_010834_07	euxassay_010834_08	euxassay_010834_09

euxassay_010834_10	euxassay_010834_11	euxassay_010834_12	euxassay_010834_13	euxassay_010834_14

euxassay_010834_15	euxassay_010834_16	euxassay_010834_17	euxassay_010834_18	euxassay_010834_19

euxassay_010834_20	euxassay_010834_21	euxassay_010834_22	euxassay_010834_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:

15642_wholemount_strong.wlz

15642_wholemount_moderate.wlz

15642_wholemount_weak.wlz

15642_wholemount_possible.wlz

15642_wholemount_not_detected.wlz

(what is wlz format?)

Download all expression domains:

EMAGE:15642_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

esophagus

strong

regional

strong expression: see section 10

stomach

strong

regional

strong expression: see section 09 10 11 15 moderate expression: see section 03 04 05 06 07 08

hindgut

strong

regional

strong expression: see section 14

midgut

strong

regional

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

Annotation Validation:

spatial mapping by EMAGE editor, text annotation by author

Detection Reagent

Type:	in situ hybridisation probe
Identifier:	T38367
Entity Detected:	Col6a4, collagen, type VI, alpha 4 ( MGI:1915803)
Sequence:	sense strand is shown >T38367 TAGTTGTCCTGGTGACAGATGGGGAGTCCAGTGATGAGGTCCAGGATGTGGCTGACCAGCTGAAAAGAGA CGGGGTCTTTGTGTTTGTGGTAGGGATCAATATTCAAGATGTCCAAGAGTTGCAGAAAATAGCCAACGAG CCGTTTGAGGAGTTTCTCTTCACCACAGAAAACTTCAGCATCTTGCAGGCGCTCTCAGGAACCCTCCTTC AGGCCCTGTGTTCCACGGTGGAGAGGCAGATGAAAAAGTCTACCAAGACCTACGCAGACGTGGTCTTTCT TATTGACACCTCCCAGGGGACATCACAGGCTAGTTTCCAGTGGATGCAGAATTTCATCTCTAGAATTATT GGCATCCTGGAGGTCGGCCAGGACAAATACCAGATTGGGCTGGCTCAGTATAGCGATCAAGGTCACACTG AGTTTTTGTTCAATACCCACAAGACCCGGAATGAGATGGTCGCACACATCCATGAACTCTTGGTGTTCCA AGGTGGCTCCAGGAAGACTGGCCAAGGCCTTCGGTTTCTTCATCGGACTTTCTTCCAGGAGGCAGCAGGA AGCCGGCTCTTACAGGGTGTCCCTCAGTATGTGGTAGTCATTACTTCAGGGAAATCTGAGGACGAGGTCG GAGAGGTCGCACAGATCCTGAGGAAGAGAGGCGTGGACATCGTGTCTGTGGGCTTGCAGGACTTTGACAG GGCAGAACTGGAGGGGATAGGGCCTGTAGTGCTTGTGTCTGACCTGCAGGGAGAAGATAGAATCAGACAG CTAATGCTGGATGTGAATATGTTCATCCAGGGGAGTCCAAAGCCTCCACGGGTCATGACTGATGTTGCGA AGGACGCTGTAG
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 109412. Forward Primer - name:109412_F_cDNA_LOC235580, sequence:TAGTTGTCCTGGTGACAGATGG; Reverse Primer - name:109412_N_SP6_cDNA_LOC235580, sequence:CTACAGCGTCCTTCGCAACAT. 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:15641 same embryo
	EMAGE:15643 same embryo
	EMAGE:15639 same embryo
	EMAGE:15638 same embryo
	EMAGE:15640 same embryo
	EurExpress:euxassay_010834 same experiment
	MGI:4824425 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