EMAGE mouse gene expression spatial database

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EMAGE:15408

Shmt1 serine hydroxymethyltransferase 1 (soluble) ( MGI:98299)
TS23 (14.5 dpc)
in situ hybridisation

Data Images


"Pseudo-wholemount" of euxassay_010621. This image has been made by aligning and collapsing the constitutent sections. Information about the method.	euxassay_010621_01	euxassay_010621_02	euxassay_010621_03	euxassay_010621_04

euxassay_010621_05	euxassay_010621_06	euxassay_010621_07	euxassay_010621_08	euxassay_010621_09

euxassay_010621_10	euxassay_010621_11	euxassay_010621_12	euxassay_010621_13	euxassay_010621_14

euxassay_010621_15	euxassay_010621_16	euxassay_010621_17	euxassay_010621_18	euxassay_010621_19

euxassay_010621_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:

15408_wholemount_strong.wlz

15408_wholemount_moderate.wlz

15408_wholemount_weak.wlz

15408_wholemount_possible.wlz

15408_wholemount_not_detected.wlz

(what is wlz format?)

Download all expression domains:

EMAGE:15408_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

thymus primordium

weak

regional

weak expression: see section 07 08 10 11

submandibular gland primordium

moderate

regional

moderate expression: see section 05 06 15 weak expression: see section 07 13 14

pancreas

weak

regional

weak expression: see section 05 06 07 08

vibrissa

weak

regional

weak expression: see section 05 06 07 08 18 20

telencephalon ventricular layer

weak

homogeneous

weak expression: see section 02 03 04 05 06 07 08 09 10 11 13 14 15 16 17 18

midbrain ventricular layer

weak

regional

weak expression: see section 04 05 06 07 08 09 10

hindgut

weak

regional

weak expression: see section 10 11

rectum

weak

regional

weak expression: see section 10

midgut

weak

regional

weak expression: see section 09 10 11 12 13 14 15 16

lower jaw incisor

weak

regional

weak expression: see section 10 11 14 15

lower jaw molar

moderate

regional

moderate expression: see section 16 weak expression: see section 05 06

upper jaw incisor

weak

regional

weak expression: see section 11 12 15

upper jaw molar

moderate

regional

moderate expression: see section 16 17 weak expression: see section 05 06

renal cortex

weak

regional

weak expression: see section 04 05 06 12 13 14 15

Annotation Validation:

spatial mapping by EMAGE editor, text annotation by author

Detection Reagent

Type:	in situ hybridisation probe
Identifier:	T31152
Entity Detected:	Shmt1, serine hydroxymethyltransferase 1 (soluble) ( MGI:98299)
Sequence:	sense strand is shown >T31152 GACCGGAGGAACAGACGTTTACGGCCAGCTCCCGAAACCAAGTGAACTGGAGGCCACCCTGCACCAAGGG TTGGAACCTTTTCACAAAATCCACGCTCCTAATACAAGGCAACTCTGAACCAGTGCAATGGCAGACAGGG ATGCCACCCTGTGGGCTTCTCATGAGAAGATGTTGTCGCAGCCCCTCAAGGACAGTGATGCCGAGGTTTA CAGCATCATTAAAAAGGAGAGCAACCGGCAGAGGGTCGGATTAGAGCTGATTGCCTCGGAGAATTTTGCC AGCCGAGCTGTGTTGGAGGCCCTGGGATCTTGCTTAAATAACAAATACTCTGAGGGATATCCAGGCCAAA GGTATTATGGCGGGACCGAGTTCATCGATGAGCTGGAGATGCTGTGTCAGAAGCGTGCATTACAGGCCTA CCATCTGGATCCTCAGTGCTGGGGTGTCAATGTCCAGCCTTATTCAGGCTCCCCTGCAAACTTTGCTGTG TATACTGCCCTGGTAGAGCCTCATGGGCGAATCATGGGCTTGGACCTGCCAGACGGTGGCCATCTGACCC ATGGCTTCATGACAGACAAGAAGAAAATCTCTGCCACATCTATCTTCTTTGAATCCATGCCTTATAAGGT GTACCCAGAGACTGGGTACATCAACTATGACCAGCTGGAGGAGAATGCCAGCCTCTTCCACCCGAAGCTG ATCATCGCAGGGACCAGCTGCTACTCCCGGAACCTGGACTACGCACGGCTGCGGAAGATTGCGGATGATA ATGGGGCGTATCTCATGGCAGACATGGCACATATCAGTGGGCTCGTGGCAGCTGGGGTGGTGCCCTCCCC CTTTGAACA
Notes:	The probe template was received by the EURExpress consortium as an aliquot of PCR product from the Allen Brain Atlas (originally amplified from the plasmid IMAGE:4160579), and this was re-amplified using the gene-specific Allen Brain Atlas Primer Pair 53393. Forward Primer - name:053393_F_IRAV44_g03_Shmt1, sequence:GACCGGAGGAACAGACGTT; Reverse Primer - name:053393_R_SP6_IRAV44_g03_Shmt1, sequence:GTGTTCAAAGGGGGAGGG. 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:15410 same embryo
	EMAGE:15411 same embryo
	EMAGE:15406 same embryo
	EMAGE:15407 same embryo
	EMAGE:15409 same embryo
	EurExpress:euxassay_010621 same experiment
	MGI:4828061 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