Overview of RNAseq datasets in GenoSysFat
An overview of RNA sequencing data generated in GenoSysFat (and a couple of others).
Source: Email from Simen Rød Sandve to Jon Olav Vik and Fabian Grammes 2017-02-10, titled "RNAseq generert i GSF".
This should be turned into separate RNAseq Assays when we can allocate people for it. Currently the following have records already:
Tissue panel for gene expression in ZF, Med, RT https://fairdomhub.org/assays/324
Tissue panel for gene expression in ZF,Med,RT- RNA sequencing https://fairdomhub.org/assays/395
RNA sequencing Feed switch- Liver and Gut https://fairdomhub.org/assays/352
There is also an Investigation for Sally: https://fairdomhub.org/investigations/85
All RNA datasets should get the Technology type set correctly, so we can retrieve an updated overview like this at a later time.
SEEK ID: https://fairdomhub.org/assays/491
Experimental assay
Projects: GenoSysFat
Investigation: Omega-3 metabolism of salmon in relation to diet and genetics
Study: GSF1: Salmon feed-switch experiment vegetable and fish oil 2015-2016
Assay position:
Assay type: Experimental Assay Type
Technology type: Rna-seq
Organisms: Salmo salar
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Created: 31st Mar 2017 at 14:27
Last updated: 20th Aug 2021 at 10:21
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Projects: GenoSysFat, DigiSal
Institutions: Norwegian University of Life Sciences
https://orcid.org/0000-0002-9551-9280
Projects: GenoSysFat, DigiSal
Institutions: Norwegian University of Life Sciences
https://orcid.org/0000-0003-4989-5311
Systems biology for salmon farming is what I do. I lead the DigiSal project (http://tinyurl.com/digisal), whose full title is "Towards the Digital Salmon: From a reactive to a pre-emptive research strategy in aquaculture". DigiSal is part of Digital Life, the first call dedicated to systems biology by the Research Council of Norway. I'm also one of the lead modellers in GenoSysFat (http://tinyurl.com/genosysfat), working to improve the omega-3 content of salmon farmed on sustainable feeds by ...
Salmon farming in the future must navigate conflicting and shifting demands of sustainability, shifting feed prices, disease, and product quality. The industry needs to develop a flexible, integrated basis of knowledge for rapid response to new challenges. The Digital Salmon will be an ensemble of mathematical descriptions of salmon physiology, combining mathematics, high-dimensional data analysis, computer science and measurement technology with genomics and experimental biology into a concerted ...
Projects: GenoSysFat, DigiSal, SEEK tutorial for DigiSal, DigiSal-BT8121
Web page: http://tinyurl.com/digisal
Salmon farmed on modern feeds contains less of the healthy, long-chain fatty acids (EPA and DHA) than before. Up until the turn of the millennium, farmed salmon were fed fish oil as a replacement for their omega-3 rich natural prey. However, fish oil is now a scarce resource, and more than half of the fat in modern feeds comes from plant oils that are inexpensive, but devoid of long-chain omega-3 fatty acids. How can we increase the omega-3 content of salmon on sustainable feeds?
One option is ...
Programme: The Digital Salmon
Public web page: http://tinyurl.com/genosysfat
Atlantic salmon is a main source of essential ω-3 long-chain polyunsaturated fatty acids (LC-PUFA) in many Western diets, especially eicosapentaenoic acid (20:5n-3, EPA) and docosahexaenoic acid (22:6n-3, DHA). However, farmed salmon meat now contains less healthy ω-3 fatty acids (FA) than before, due to the shift from marine to vegetable lipid feed sources. An important future aquaculture challenge is therefore to maintain a healthy and high EPA/DHA content when farmed salmon is fed a vegetable ...
Submitter: Jon Olav Vik
Studies: GSF1: Salmon feed-switch experiment vegetable and fish oil 2015-2016
Assays: Fatty acid contents in feed using Gas chromatography/FAME analysis, Fatty acid contents in tissues using Gas chromatography/FAME analysis, Feed switch 2015-09 Solbergstranda, pilot proteomics, Feed switch 2015-09, 2016-01 Solbergstranda, gross phenotypes, Feed switch 2015-09, 2016-01 Solbergstranda, gut microbiota composition,..., Lipidomics, Metabolomics, Overview of RNAseq datasets in GenoSysFat, RNA sequencing Feed switch- Liver and Gut
This experiment is designed to pinpoint where in the metabolic network there are differences between salmon of different genetic families and on different diets. Analyses of this material will help inform feeding and breeding strategies.
Salmon will be reared on feeds with contrasting levels of very-long-chain polyunsaturated fatty acids. Then some fish will be crossed over to the other diet while others remain as controls. This perturbation of diet should provoke changes in omega-3 metabolism ...
Submitter: Jon Olav Vik
Investigation: Omega-3 metabolism of salmon in relation to die...
Assays: Fatty acid contents in feed using Gas chromatography/FAME analysis, Fatty acid contents in tissues using Gas chromatography/FAME analysis, Feed switch 2015-09 Solbergstranda, pilot proteomics, Feed switch 2015-09, 2016-01 Solbergstranda, gross phenotypes, Feed switch 2015-09, 2016-01 Solbergstranda, gut microbiota composition,..., Lipidomics, Metabolomics, Overview of RNAseq datasets in GenoSysFat, RNA sequencing Feed switch- Liver and Gut
Excel file summarizing:
- Name of the RNAseq study
- Orion path were the .fastq files are stored
- Year the libraries were sequenced
- short description
