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| Status |
Public on May 04, 2019 |
| Title |
Transcriptome sequencing of a keystone aquatic herbivore yields insights on the temperature-dependent metabolism of essential lipids [15°C] |
| Organism |
Daphnia magna |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The availability of polyunsaturated fatty acids (PUFAs) in food items influences the fitness of organisms at higher trophic levels. Omega 3 and omega 6 fatty acids are essential compounds that cannot be synthesised de novo in these animals. Especially the omega 3 PUFA eicosapentaenoic acid (EPA) is an important molecule, as it is a limiting nutritional component for growth and reproduction in numerous marine and freshwater zooplankton species. With our transcriptomic study in Daphnia magna we address the transcriptomic network behind the metabolism and conversion that is connected to physiological EPA-limitation under temperature stress (20°C vs. 15°C).
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| Overall design |
We conducted a feeding experiment in Daphnia magna with strictly controlled diets to address EPA-dependent expression profiles. Two different EPA-free basis food sources were used in the experiment: the green alga (GA) Acutodesmus obliquus and the Cyanobacterium (CY) Synechococcus elongatus. The PUFA EPA was added via liposomes to half of the experimental groups fed with GA or CY to provide a comparable design for monitoring effects of EPA availability. In addition, we also monitored Daphnia magna fed with Cryptomonas ssp. (CRY), serving as a natural positive control (contains naturally EPA). We analysed animals that were exposed to the defined food conditions from hatch until they reached maturity. In total, 5 treatment groups were prepared for sequencing with 3 replicates each. Replicate sample pools consisted of 5 mature specimens to ensure appropriate amounts for RNA extraction and comparability. Using the Illumina HiSeq 4000 platform in paired-end mode we gathered ~ 52.9 million reads per single replicate for transcriptomic analyses.
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| Contributor(s) |
Windisch HS, Fink P |
| Citation(s) |
31752680 |
| BioProject |
PRJNA391248 |
| Submission date |
May 03, 2019 |
| Last update date |
Dec 05, 2019 |
| Contact name |
Heidrun Sigrid Windisch |
| E-mail(s) |
Heidrun.Windisch@hhu.de
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| Phone |
+49 211 81 - 1 35 66
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| Organization name |
Heinrich-Heine-University
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| Department |
Cell Biology and Zoology
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| Street address |
Universitätsstrasse 1
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| City |
Düsseldorf |
| State/province |
NRW |
| ZIP/Postal code |
40225 |
| Country |
Germany |
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| Platforms (1) |
| GPL24325 |
Illumina HiSeq 4000 (Daphnia magna) |
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| Samples (15)
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| This SubSeries is part of SuperSeries: |
| GSE130674 |
Transcriptome sequencing of a keystone aquatic herbivore yields insights on the temperature-dependent metabolism of essential lipids |
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| Relations |
| SRA |
SRP109969 |
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