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Title: Identification and functional impact of genomic copy number variants in zebrafish, an important human disease model (Zebrafish Strain CNVs) (expression array)      
dateReleased:
12-27-2011
description:
Copy number variants (CNVs) represent a substantial source of genomic variation in vertebrates, but the zebrafish reference genome has no annotated CNV information. We developed a zebrafish CNV map using 80 zebrafish genomes from laboratory strains (AB, Tubingen, and WIK) and one native population, identifying 6,080 CNV elements. Overlapping or adjacent CNVs account for 14.6% of the genome, representing four times the CNV levels from other vertebrates including humans. Highest intra-specific CNV levels were observed for Tubingen, a common laboratory strain due to high fecundity. Tubingen variation likely represents higher initial population size and composite population founders initiating the laboratory strain. Extensive zebrafish CNVs, along with associated phenotypic impacts, advocates for increased usage of isogenic strains for genetic studies intended for human disease translation.  7 full sib adult hybrid fish used for expression Quantatitive Trait Loci (eQLT) analysis to support CNV affects on gene expresion in zebrafish.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-28239
refinement:
raw
alternateIdentifiers:
28239
keywords:
functional genomics
dateModified:
05-02-2014
availability:
available
types:
gene expression
name:
Danio rerio
ID:
A-MEXP-1510
name:
Agilent D. rerio (Zebrafish) Oligo Microarray 4x44K 019161 G2519F 85 cols x 532 rows
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-28239/E-GEOD-28239.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-28239/E-GEOD-28239.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28239
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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