EMAGE mouse gene expression spatial database

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EMAGE:11824

Clrn3 clarin 3 ( MGI:2142022)
TS23 (14.5 dpc)
in situ hybridisation

Data Images


"Pseudo-wholemount" of euxassay_007101. This image has been made by aligning and collapsing the constitutent sections. Information about the method.	euxassay_007101_01	euxassay_007101_02	euxassay_007101_03	euxassay_007101_04

euxassay_007101_05	euxassay_007101_06	euxassay_007101_07	euxassay_007101_08	euxassay_007101_09

euxassay_007101_10	euxassay_007101_11	euxassay_007101_12	euxassay_007101_13	euxassay_007101_14

euxassay_007101_15	euxassay_007101_16	euxassay_007101_17	euxassay_007101_18	euxassay_007101_19

euxassay_007101_20	euxassay_007101_21	euxassay_007101_22	euxassay_007101_23	euxassay_007101_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:

11824_wholemount_strong.wlz

11824_wholemount_moderate.wlz

11824_wholemount_weak.wlz

11824_wholemount_possible.wlz

11824_wholemount_not_detected.wlz

(what is wlz format?)

Download all expression domains:

EMAGE:11824_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

hindgut

strong

regional

strong expression: see section 13 14

rectum

strong

regional

strong expression: see section 13

midgut

strong

regional

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

kidney calyx

strong

regional

strong expression: see section 07 08 19 20 weak expression: see section 09 18

Annotation Validation:

spatial mapping by EMAGE editor, text annotation by author

Detection Reagent

Type:	in situ hybridisation probe
Identifier:	T4606
Entity Detected:	Clrn3, clarin 3 ( MGI:2142022)
Sequence:	sense strand is shown >T4606 ACTTCCCAGGAAGACGCAGGTTTTACATTTACAACCAAGTGCTAGACGTCCTTTCTAAATACTGGATCCC AAATGATAAGGCCCCCAAATATTCTAAGGTTGCTGTTGTTTTATCGCGGGGAGCTTTCTTCCTGAGAAAA TGCCAACCACACAGAAAACGTTGATGTTCCTGTCTGGCTTTCTCACAAGCCTGGGCTCAGTTGTTGTCAT CTGCTCCATTCTTGCGACTCAGGCATGGATCACCAGCAGGATTTTCTTTACAGATGCTATCTCCAACGGT ACCATTGTTATTACCTATGGGCTCTTCCGTGGTACGAGTGCTCAAGAGTTGAATGAAGGCCTTCAAGATC TGGACAAAAACTTTGAAGTTTTAGGGATATTGGACAATTCTTCCCAGAAGTCTTTGCACCTGGTGGTCAT CCTCCTCCTGATCCTGAGTCTGGCAGCTTCCGTGCTGAGCTCAGTGTTCACCTTCTACAACAGCATCAGC AACCCTTACCAGACGTTCCTGGGACCTATGGGTGTCTATACCTGGAATGGACTCAGCGCATCCTTTGTGT TTCTGGCCATGGTTCTGTTCGTGGGGAATGCCGAGTCCAACCATCTCTCAGACAAGCTCTCCCAGAAGCT TTATCCAGATACCACAAACAAGAGAACAACCCACACTTACGGATACTCGTTTTGGCTCACCCTGCATGTC ATCTTTCTCAATATTGTCACTGCGGTCATCATCATTTTCTATCAGAAGGCCCGATACCGGCAGAAGCAGG AGCAGAGGAAGCCGGTGGAATATGCTCCAAGGGATGGCATTTTATTCTGAGTCCTGTCTCATAGCCCATT TGCACTGTCTCTGCCAAACTGACTCACTCCTCTGAACACTGCATGGCAGAGCAACTGTCAGGTGCCATCG CTTCTGGAACCACGACACCATGTCCTGCCTATAGATGGTGCTTGTATCTTCCTCCATGGACTTCCTCCTG AAAAGAGTTTTCTCCTAAGATCAGGAAAATGATTGGGAAGGGCTGTGGTCTAGAGTAATCCAAAAGAGGG CAGCCTGGGGCCTGCAGGCCTTTCTCATTTGACCCTGCTATCGGCAGTAATATAGGTCTGTGGGGTGTTT TGCCTTTCCTGTGACTAGATAAACAGACTATAGCCCCTATGACCTTGTCCTCTGGATTGATCAGGCATTT CGGTCCATGATAAGTATAAGGATTTTTAAGCAGAGAAGCACTCTGAACTAATTTTTTTCACTCAGAAGTT AGATACAGAAGGATAAAGGATGGGATGACCCTGTGTTCTGGTCCCTTGGTGGCTGTTGTGACTTCCAGGT TTCTTTCCTTCAGTGAGGGCTAGACACTTGCAGAGCTTGGGACTTGGGAAGTCATGCATGAACAGATTGG AGGTAAAATATGGTCTCTTCCAGTAAATAGAAAGTCAGAAAACTAGCAAAGGCACCAAAATGTATTCTGC ATGGTTTTCCAGTGTGACATTTCCTTTTTAAAACATCTGATTGAGAACCCTTCAGCCTGGACTATCCTAT AGGCTGCCACAGTGACAACTGACAGACCTGAAAAGTGACCTCCTTTCATGTGTTGACGGAGTCTTAAAAC AGTAGCTCAATGACAAGTGGTGGATCTTATGAAGCTAGATGACCTTCAACACTCAGAGATGTGAGCTGGG TCGCCAAAGTGTTGGCAGCAGCATGCTGGGTTTATTTACTACCAGGCAGACGAGAAAGACATTTAATAAG CTCTTACTTGACTACTCCAATTAAAACAGTTGCTTAGGGTTGGAGGTCATCCCTCCATTGTAGAACACTA AGGTGCCTAGAGTGTGACAGGCCCTGGGTTCCATCTCTACCTCCGTAAAAACAAAACAAGCAGGTAATGA CAGAATTGTGCTTGTGGTTTGAAAGGATGGATCTCTATCATGCTCTCCCTTGAAGACCTACTAATTCAAG ATTACTTTTACCTAATAAATTATTAAAAGGTTACTATACTATTTTCTTTACTCTTTTCATGAGTGTAAGT GCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
Notes:	The probe template was PCR amplified from IMAGE:4989703 using vector (pCMV-SPORT6) specific primers. Forward Primer - name:RZPD T7, sequence:TAATACGACTCACTATAGGG; Reverse Primer - name:RZPD sp6, sequence:ATTTAGGTGACACTATAG. Anti-sense probe was then transcribed from the PCR amplified template using Sp6 polymerase. EMAGE Editor's Note: the probe sequence indicated here was given by the EURExpress Consortium and has been checked using a computational method whereby a BLAST comparison was made against the full insert sequence of IMAGE:4989703 which was retrieved directly from NCBI.
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:11826 same embryo
	EMAGE:11825 same embryo
	EMAGE:11829 same embryo
	EMAGE:11827 same embryo
	EMAGE:11828 same embryo
	EurExpress:euxassay_007101 same experiment
	MGI:4823937 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