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| Status |
Public on Jul 01, 2017 |
| Title |
Copy number variation of genes (exons) in invasive Cottus compared to the parental species, Cottus rhenanus and Cottus perifretum. |
| Platform organism |
Cottus |
| Sample organisms |
Cottus; Cottus perifretum; Cottus rhenanus |
| Experiment type |
Genome variation profiling by array
|
| Summary |
Hybridization between Cottus rhenanus and C. perifretum has resulted in an evolutionary young hybrid lineage of invasive Cottus that has colonized a new habitat where the parental species are not found (Nolte et al. 2005; Proc. R. Soc. B 272: 2379–2387). This CGH array was designed to screen for copy number variation among Cottus species and to find gene duplicates that are unique to the hybrid lineage (see also Dennenmoser et al. 2017; Copy number increases of transposable elements and protein coding genes in an invasive fish of hybrid origin).
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| Overall design |
SurePrint G3 custom CGH 8x60k microarray with five technical replicates per probe and a 15 bp linker added to each probe as recommended by Agilent. The experimental design was a two-color experiment (Cottus individual vs. common reference) with 24 biological replicates (3 species x 8 individuals). Each Cottus individual was co-hybridized with the same Cottus perifretum individual as a common reference. The normalization procedure included a calibration step to account for probe-specific binding behavior, which was assessed using a custom designed calibration array (see also Dennenmoser et al. 2017; Copy number increases of transposable elements and protein coding genes in an invasive fish of hybrid origin).
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| Contributor(s) |
Dennenmoser S, Nolte AW |
| Citation(s) |
28390096 |
| |
| Submission date |
Jan 03, 2017 |
| Last update date |
Jul 02, 2017 |
| Contact name |
Stefan Dennenmoser |
| E-mail(s) |
[email protected]
|
| Organization name |
Max-Planck Institute for Evolutionary Biology
|
| Department |
Evolutionary Genetics
|
| Street address |
August-Thienemann Str. 2
|
| City |
Ploen |
| ZIP/Postal code |
24306 |
| Country |
Germany |
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| Platforms (1) |
| GPL22811 |
Agilent-070467 Cottus CGH array G4126A |
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| Samples (24)
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| This SubSeries is part of SuperSeries: |
| GSE93065 |
Copy number variation in an invasive fish of hybrid origin |
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| Relations |
| BioProject |
PRJNA359765 |
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