EMAGE mouse gene expression spatial database

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EMAGE:21196

Hoxd3 homeobox D3 ( MGI:96207)
TS23 (14.5 dpc)
in situ hybridisation

Data Images


euxassay_008983_01	euxassay_008983_02	euxassay_008983_03	euxassay_008983_04	euxassay_008983_05

euxassay_008983_06	euxassay_008983_07	euxassay_008983_08	euxassay_008983_09	euxassay_008983_10

euxassay_008983_11	euxassay_008983_12	euxassay_008983_13	euxassay_008983_14	euxassay_008983_15

euxassay_008983_16	euxassay_008983_17	euxassay_008983_18	euxassay_008983_19	euxassay_008983_20

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:

21196_wholemount_strong.wlz

21196_wholemount_moderate.wlz

21196_wholemount_weak.wlz

21196_wholemount_possible.wlz

21196_wholemount_not_detected.wlz

(what is wlz format?)

Download all expression domains:

EMAGE:21196_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

medulla oblongata alar plate mantle layer

moderate

regional

moderate expression: see section 4 5 6 7 8 9 0 1 2 3 4 5 6

medulla oblongata basal plate mantle layer

moderate

regional

moderate expression: see section 4 5 6 7 8 9 0 1 2 3 4 5 6

spinal cord mantle layer

moderate

regional

moderate expression: see section 5 6 7 8 9 0 1 2 3

stomach

strong

regional

strong expression: see section 4 5 6 7 8 9

rectum

strong

regional

strong expression: see section 3

midgut

strong

regional

strong expression: see section 8 9 0 1 2 3 4 5 6

kidney calyx

moderate

regional

moderate expression: see section 6 7 8 4 5 6

kidney pelvis

moderate

regional

moderate expression: see section 7

collecting duct

moderate

regional

moderate expression: see section 5

ureter

moderate

regional

moderate expression: see section 9 2 3

Annotation Validation:

spatial mapping by EMAGE editor, text annotation by author

Detection Reagent

Type:	in situ hybridisation probe
Identifier:	T35465
Entity Detected:	Hoxd3, homeobox D3 ( MGI:96207)
Sequence:	sense strand is shown >T35465 CAAATCGCAGCCCAATATGTACGGCCTGGCCGCCTACACGGCGCCGCTCAGCAGCTGCCTGCCTCAGCAG AAGCGGTACCCGGCGCCCGAGTTCGAGCCTCACCCCATGGCGAGCAACGGCGGCGGCTTCGCCAGCGCCA ACCTGCAGGGCAGCCCGGTGTACGTGGGCGGCAACTTCGTCGACTCCATGGCGCCCACGTCCGGGCCGGT CTTCAATCTGGGCCACCTCTCGCACCCGTCTTCGGCCAGCGTGGACTACAGTTGCGCCGCGCAAATCCCT GGCAACCATCACCACGGACCCTGCGACCCTCATCCCACCTACACAGATCTCTCGGCTCACCACTCGTCTC AGGGACGCCTGCCCGAGGCCCCCAAACTGACACATCTGTAGCTGTTGCCGCCGGCCAGGCGCAATTACCT CTCTGGTTTTGGTGGCAGAGGTGGTGGTGGGGCGGGGCGGGGCCCGAGGGGCAGTTTAGGGGATCCCCCT CCCTGATCTGGCCTGGCGGATGCCTCACGAGTGGCTTCCAGCGGCCAGGGCTGACGCGACTGGGCCTCCC TCCAGGCGCGTCCTCCTTTGGGTGACTCGCCATAAATCAGCCGCAAGGATCCTCCCCAGTAAACCTGACA GTGCCATAAACTGCGGACCGAGGGACTCTAATCTGGTAATGGTGTCCCTAAGGTAAGTCCTCGACCCATC CGTGGCGAGTCCTGAAGAGGGACTAGGGCCTG
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 64110. Forward Primer - name:064110_F_cDNA_Hoxd3, sequence:CAAATCGCAGCCCAATATGTA; Reverse Primer - name:064110_N_SP6_cDNA_Hoxd3, sequence:CAGGCCCTAGTCCCTCTTCAG. 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:	EurExpress:euxassay_008983 same experiment
	EMAGE:21193 same embryo
	EMAGE:21194 same embryo
	EMAGE:21195 same embryo
	EMAGE:21197 same embryo
	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