EMAGE mouse gene expression spatial database

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EMAGE:19977

Npas3 neuronal PAS domain protein 3 ( MGI:1351610)
TS23 (14.5 dpc)
in situ hybridisation

Data Images


"Pseudo-wholemount" of euxassay_009424. This image has been made by aligning and collapsing the constitutent sections. Information about the method.	euxassay_009424_01	euxassay_009424_02	euxassay_009424_03	euxassay_009424_04

euxassay_009424_05	euxassay_009424_06	euxassay_009424_07	euxassay_009424_08	euxassay_009424_09

euxassay_009424_10	euxassay_009424_11	euxassay_009424_12	euxassay_009424_13	euxassay_009424_14

euxassay_009424_15	euxassay_009424_16	euxassay_009424_17	euxassay_009424_18	euxassay_009424_19

euxassay_009424_20	euxassay_009424_21	euxassay_009424_22	euxassay_009424_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:

19977_wholemount_strong.wlz

19977_wholemount_moderate.wlz

19977_wholemount_weak.wlz

19977_wholemount_possible.wlz

19977_wholemount_not_detected.wlz

(what is wlz format?)

Download all expression domains:

EMAGE:19977_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

hypothalamus mantle layer

weak

regional

weak expression: see section 09

hypothalamus ventricular layer

weak

regional

weak expression: see section 11 12 13

diencephalon lateral wall mantle layer

weak

regional

weak expression: see section 07 08 09 13 14 15 16

diencephalon lateral wall ventricular layer

weak

regional

weak expression: see section 11 12 13

telencephalon mantle layer

moderate

regional

moderate expression: see section 01 02 weak expression: see section 03 04 05 06 07 15

medulla oblongata basal plate mantle layer

moderate

single cell

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

rest of cerebellum mantle layer

moderate

regional

moderate expression: see section 08 09 10 14 15 weak expression: see section 06 07 16

pons mantle layer

moderate

regional

moderate expression: see section 08 09 13 14 15 weak expression: see section 07 16 17 18

pons ventricular layer

moderate

regional

moderate expression: see section 10 12 13

midbrain mantle layer

moderate

regional

moderate expression: see section 08 09 10 13 14 15 16 weak expression: see section 07

midbrain ventricular layer

moderate

regional

moderate expression: see section 12 13

ventral grey horn

moderate

single cell

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

Annotation Validation:

spatial mapping by EMAGE editor, text annotation by author

Detection Reagent

Type:	in situ hybridisation probe
Identifier:	T36838
Entity Detected:	Npas3, neuronal PAS domain protein 3 ( MGI:1351610)
Sequence:	sense strand is shown >T36838 TCCTCTTCTCAGTCAGAGACCCCTGAGCCAGTGGAGACGACCAGCCCTAGTCTGCTAACCACGGACAACA CCCTTGAACGGTCCTTTTTCATCCGAATGAAGTCTACTCTGACCAAACGTGGAGTCCACATCAAGTCATC TGGGTATAAGGTGATTCACATAACAGGCCGGCTTCGCCTCAGAGTGCCGCTGTCCCACGGGAGGACCGTC CCCAGCCAAATCATGGGTCTGGTGGTTGTGGCTCACGCCTTGCCTCCCCCTACGATCAATGAAGTCAGAA TTGACTGCCATATGTTCGTCACTCGAGTAAACATGGATCTCAATATCATTTACTGTGAAAATAGGATTAG TGATTACATGGATCTGACCCCTGTAGACATCGTAGGGAAAAGATGCTACCACTTCATCCATGCCGAAGAT GTAGAAGGCATCAGGCACAGTCACCTGGACTTGCTGAATAAGGGTCAGTGTGTGACCAAGTACTACCGCT GGATGCAGAAGAATGGAGGCTACATCTGGATACAGTCTAGTGCCACCATAGCTATTAATGCGAAGAATGC AAATGAGAAGAACATCATCTGGGTGAATTATCTTCTTAGTAATCCGGAGTACAAGGACACACCCATGGAC ATT
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 74752. Forward Primer - name:074752_F_cDNA_Npas3, sequence:TCCTCTTCTCAGTCAGAGACCC; Reverse Primer - name:074752_N_SP6_cDNA_Npas3, sequence:AATGTCCATGGGTGTGTCCTT. 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:19976 same embryo
	EMAGE:19974 same embryo
	EMAGE:19973 same embryo
	EMAGE:19972 same embryo
	EMAGE:19975 same embryo
	EurExpress:euxassay_009424 same experiment
	MGI:4826759 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