EMAGE mouse gene expression spatial database

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EMAGE:7167

Sox9 SRY-box containing gene 9 ( MGI:98371)
TS23 (14.5 dpc)
in situ hybridisation

Data Images


"Pseudo-wholemount" of euxassay_002633. This image has been made by aligning and collapsing the constitutent sections. Information about the method.	euxassay_002633_01	euxassay_002633_02	euxassay_002633_03	euxassay_002633_04

euxassay_002633_05	euxassay_002633_06	euxassay_002633_07	euxassay_002633_08	euxassay_002633_09

euxassay_002633_10	euxassay_002633_11	euxassay_002633_12	euxassay_002633_13	euxassay_002633_14

euxassay_002633_15	euxassay_002633_16	euxassay_002633_17	euxassay_002633_18	euxassay_002633_19

euxassay_002633_20	euxassay_002633_21	euxassay_002633_22	euxassay_002633_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:

7167_wholemount_strong.wlz

7167_wholemount_moderate.wlz

7167_wholemount_weak.wlz

7167_wholemount_possible.wlz

7167_wholemount_not_detected.wlz

(what is wlz format?)

Download all expression domains:

EMAGE:7167_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

hindlimb digit 1 mesenchyme

strong

regional

strong expression: see section 04 22 23

hindlimb digit 2 mesenchyme

strong

regional

strong expression: see section 04 06 07 08 10 22 23 weak expression: see section 09

hindlimb digit 3 mesenchyme

strong

regional

strong expression: see section 04 06 07 08 10 22 23 weak expression: see section 09

hindlimb digit 4 mesenchyme

strong

regional

strong expression: see section 06 07 08 10 22 23 weak expression: see section 09

hindlimb digit 5 mesenchyme

strong

regional

strong expression: see section 22 23

femur

moderate

regional

moderate expression: see section 08 09 10 21 22 weak expression: see section 07 19 20

pectoral girdle and thoracic body wall musculature

strong

regional

strong expression: see section 09 10 11 12 moderate expression: see section 13 17 weak expression: see section 08 14 15 16

pancreas

moderate

regional

moderate expression: see section 09 weak expression: see section 08 10 11 13 14 15

vibrissa

moderate

regional

moderate expression: see section 02 03 weak expression: see section 04 18 19 20

hypothalamus ventricular layer

strong

regional

strong expression: see section 11 12 13

diencephalon lateral wall ventricular layer

strong

regional

strong expression: see section 11 12 13

olfactory cortex ventricular layer

strong

homogeneous

strong expression: see section 08 10 14 15

telencephalon ventricular layer

strong

homogeneous

strong expression: see section 01 02 03 04 05 06 07 08 10 11 12 13 14 15 16 20 21 22 23 moderate expression: see section 18 19

medulla oblongata alar plate ventricular layer

moderate

regional

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

medulla oblongata basal plate ventricular layer

moderate

regional

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

rest of cerebellum ventricular layer

strong

regional

strong expression: see section 09 moderate expression: see section 04 05 06 07 08 16 17 18 19 20 weak expression: see section 03

pons ventricular layer

strong

regional

strong expression: see section 09 moderate expression: see section 08 11 12 13 14 15 16 17 weak expression: see section 10

midbrain ventricular layer

strong

regional

strong expression: see section 09 10 11 12 13 14 15 16 moderate expression: see section 08 17

spinal cord ventricular layer

moderate

regional

moderate expression: see section 13 14

pharyngo-tympanic tube

strong

regional

strong expression: see section 01 02 weak expression: see section 23

naris

strong

regional

strong expression: see section 13 14

nasal septum

strong

regional

strong expression: see section 10 11 12 13 14

kidney calyx

moderate

regional

moderate expression: see section 21 weak expression: see section 07 08 09 10 17 18 19 20

lung

moderate

spotted

moderate expression: see section 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 17 18 19 20 21 weak expression: see section 16 22 23

trachea

strong

regional

strong expression: see section 12 13 14

nucleus pulposus

moderate

regional

moderate expression: see section 10 11 12 13 14 15

basisphenoid bone

strong

regional

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

exoccipital bone

strong

regional

strong expression: see section 01 moderate expression: see section 02 03 04 05 06 07 16 18 19 20 21 22 23

orbito-sphenoid

strong

regional

strong expression: see section 01 14 moderate expression: see section 03 04 06 07 08 11 12 16 17 18 19 20 22 23 weak expression: see section 02 05

viscerocranium

strong

regional

Expression in the turbinate bone.

axial skeleton tail region

moderate

regional

moderate expression: see section 14 15 16 17 19 20

Annotation Validation:

spatial mapping by EMAGE editor, text annotation by author

Detection Reagent

Type:	in situ hybridisation probe
Identifier:	T5186
Entity Detected:	Sox9, SRY-box containing gene 9 ( MGI:98371)
Sequence:	sense strand is shown >T5186 CCACGCGTCCGAGCGCTGCTCGGAACTGCCTGGAAACTTCTGTGGGAGCGACAACTTTACCAGTTTCAGT CCAGGAACTTTTCTTTGCAAGAGAGACGAGGTGCAAGTGGCCCCGGTTTCGTTCTCTGTTTTCCCTCCCT CCTCCTCCGCTCCGACTCGCCTTCCCCGGGTTTAGAGCCGGCAGCTGAGACCCGCCACCCAGCGCCTCTG CTAAGTGCCCGCCGCCGCAGCCCGGTGACGCGCCAACCTCCCCGGGAGCCGTTCGCTCGGCGTCCGCGTC CGGGCAGCTGAGGGAAGAGGAGCCCCAGCCGCCGCGGCTTCTCGCCTTTCCCGGCCACCCGCCCCCTGCC CCGGGCTCGCGTATGAATCTCCTGGACCCCTTCATGAAGATGACCGACGAGCAGGAGAAGGGCCTGTCTG GCGCCCCCAGCCCCACCATGTCGGAGGACTCGGCTGGTTCGCCCTGTCCCTCGGGCTCCGGCTCGGACAC GGAGAACACCCGGCCCCAGGAGAACACCTTCCCCAAGGGCGAGCCGGATCTGAAGAAGGAGAGCGAGGAA GATAAGTTCCCCGTGTGCATCCGCGAGGCGGTCAGCCAGGTGCTGAAGGGCTACGACTGGACGCTGGTGC CCATGCCCGTGCGCGTCAACGGCTCCAGCAAGAACAAGCCACACGTCAAGCGACCCATGAACGCCTTCAT GGTGTGGGCGCAGGCTGCGCGCAGGAAGCTGGCAGACCAGTACCCGCATCTGCACAACGCGGAGCTCAGC AAGACTCTGGGCAAGCTCTGGAGGCTGCTGAACGAGAGCGAGAAGAGACCCTTCGTGGAGGAGGCGGAGC GGCTGCGCGTGCAGCACAAGAAAGACCACCCCGATTACAAGTACCAGCCCCGGCGGAGGAAGTCGGTGAA GAACGGACAAGCGGAGGCCGAAGAGGCCACGGAACAGACTCACATCTCTCCTAATGCTATCTTCAAGGCG CTGCAAGCCGACTCCCCACATTCCTCCTCCGGCATGAGTGAGGTGCACTCCCCGGGCGAGCACTCTGGGC AATCTCAGGGTCCGCCGACCCCACCCACCACTCCCAAAACCGACGTGCAAGCTGGCAAAGTTGATCTGAA GCGAGAGGGGCGCCCTCTGGCAGAGGGGGGCAGACAGCCCCCCATCGACTTCCGCGACGTGGACATCGGT GAACTGAGCAGCGACGTCATCTCCAACATTGAGACCTTCGACGTCAATGAGTTTGACCAATACTTGCCAC CCAACGGCCACCCAGGGGTTCCGGCCACCCACGGCCAGGTCACCTACACTGGCAGTTACGGCATCAGCAG CACCGCACCCACCCCTGCGACCGCGGGCCACGTGTGGATGTCGAAGCAGCAGGCGCCGCCCCCTCCTCCG CAGCAGCCTCCGCAGGCCCCGCAAGCCCCACAGGCGCCTCCGCAGCAGCAAGCACCCCCGCAGCAGCCGC AGGCACCCCAGCAGCAGCAGGCACACACGCTCACCACGCTGAGCAGCGAGCCAGGCCAGTCCCAGCGAAC GCACATCAAGACGGAGCAGCTGAGCCCCAGCCACTACAGCGAGCAGCAGCAGCACTCCCCGCAACAGATC TCCTACAGCCCCTTCAACCTTCCTCACTACAGCCCCTCCTACCCGCCCATCACCCGCTCGCAATACGACT ACGCTGACCATCAGAACTCCGGCTCCTACTACAGTCACGCAGCCGGCCAGGGCTCAGGGCTCTACTCCAC CTTCACTTACATGAACCCCGCGCAGCGCCCCATGTACACCCCCATCGCTGACACCTCCGGGGTCCCTTCC ATCCCGCAGACCCACAGCCCGCAGCACTGGGAACAACCAGTCTACACACAGCTCACCAGACCCTGAGAAG AGAAAAGCTATGGTGACAGAGCTGATCTTTTTTTTTTTTTTTTTTAAAGAAGAAAAGAAAGAAACGAAAA GAAAAAGCTGAAGAAATCAAGAACCAATTGAAATTCCTTTGGACACTTTTTTTTTTGTCTATCGTTAATT TTTAAAGACATGTAAAGGAAGGTAACGATTGCTGGGATTCCAGGAGAGAGACTTTAAGACTTTGTCTGAG CTCATGACAACATATTGCAAATGGCCGGGCCACTCGTGGCCAGACGGACAGCACTCCTGGCCAGATGGAC CCACCAGTATCAGCGAGGAGGGGCTTGTCTCCTTCAGAGTTAACATGGAGGACGATTGGAGAATCTCCCT GCCTGTTTGGACTTTGTAATTATTTTTTAGCCGTAATTAAAGAAAAAAAAAGTCCTCTGTGAGGAATATT CTCTATTTTAAATACTTTTAGTATGTACTGTGTATGACTCATTACCATTTTGAGGGGATTTATACATATT TTAGATAAAAAAAGTTAAATGCTCTTATTTTTCCAACAGCTTAACTACTCCTAGTTCAAGAGTGTCCCTT AGCCTTCCTTGCAACCAGAGTATTTTTGTACAGATTTGCTTTCTCCTAAACAAACAAACAAAAACAAAAA CAAAAAAAACAAAAAAAAATGAAAAAAAAAAAAAAAA
Notes:	The probe template was PCR amplified from IMAGE:5351850 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:5351850 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:7170 same embryo
	EMAGE:7168 same embryo
	EMAGE:7172 same embryo
	EMAGE:7169 same embryo
	EMAGE:7171 same embryo
	EurExpress:euxassay_002633 same experiment
	MGI:4828394 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