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 to breed salmon that are well adapted to the feeds of the future. There is heritable variation in salmon’s ability to build EPA and DHA from shorter omega-3 fatty acids. The DNA sequence of salmon is now well known, allowing rapid characterization of heritable differences in nutrient utilization. A salmon family that appears promising on one feed, may not be the best on another. Therefore, we need to understand the salmon’s body as a system: a functional whole made up of parts that mutually affect, but also depend on, each other. A systems understanding of the interplay between feed and genetic factors will allow a tailoring of fish to feed and vice versa, which is robust to fluctuations in feedstuff availability and pricing.
As a first step towards such a systems understanding, the GenoSysFat project involves two biological experiments. 1) A traditional feeding experiment using high- vs low-omega-3 diets and salmon families that differ in feed utilization. 2) A novel study with pieces of liver kept alive and “fed” in laboratory dishes, studying for each fish how different feeds affect metabolism and gene activity. This allows faster and more detailed exploration of the interplay between genetics and feeds. Results will be interpreted with the help of mathematical models for the biochemical reaction networks, which are well established for other species and will be adapted to salmon based on the newly sequenced salmon genome.
Programme: The Digital Salmon
SEEK ID: https://fairdomhub.org/projects/34
Public web page: http://tinyurl.com/genosysfat
Organisms: Danio rerio, Salmo salar, Oncorhynchus mykiss
FAIRDOM PALs: No PALs for this Project
Project created: 16th Oct 2015
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- People (40)
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- Institutions (7)
- Investigations (1+4)
- Studies (1+9)
- Assays (9+26)
- Data files (54+34)
- Models (0+2)
- SOPs (7+5)
- Publications (8)
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- Documents (2)
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Projects: GenoSysFat, DigiSal
Institutions: Norwegian University of Life Sciences
https://orcid.org/0000-0002-4056-0606Projects: GenoSysFat, DigiSal
Institutions: Norwegian University of Life Sciences
https://orcid.org/0000-0001-9533-3227Expertise: Bioinformatics
Projects: GenoSysFat, DigiSal
Institutions: Norwegian University of Life Sciences
Projects: GenoSysFat, DigiSal
Institutions: Norwegian University of Life Sciences
https://orcid.org/0000-0002-9551-9280Projects: GenoSysFat, DigiSal
Institutions: Norwegian University of Life Sciences
https://orcid.org/0000-0002-5322-0192Projects: GenoSysFat, DigiSal
Institutions: Norwegian University of Life Sciences
https://orcid.org/0000-0003-4882-2188Projects: DigiSal, GenoSysFat, SEEK tutorial for DigiSal, FAIRDOM Community Workers
Institutions: Norwegian University of Life Sciences
https://orcid.org/0000-0002-3980-8782I am the data and model manager for the Digital Salmon
Projects: DigiSal, GenoSysFat
Institutions: Norwegian University of Life Sciences
https://orcid.org/0000-0001-6097-2539Expertise: Transcriptomics, Comparative Genomics
Projects: GenoSysFat, DigiSal, SEEK tutorial for DigiSal
Institutions: Norwegian University of Life Sciences
https://orcid.org/0000-0001-5597-8397Projects: DigiSal, GenoSysFat
Institutions: Norwegian University of Life Sciences
https://orcid.org/0000-0001-7828-2309Expertise: Bioinformatics
Tools: Bioinformatics, Genetics, Transcriptomics, Molecular Biology
Projects: DigiSal, GenoSysFat, SAFE-Aqua, Unlock
Institutions: Wageningen University & Research
https://orcid.org/0000-0001-8172-8981Expertise: semantics, Software Engineering, R, Python, Java, Data Management, Databases, Genetics, Genomics, Microbiology
Projects: DigiSal, GenoSysFat
Institutions: Cargill
Projects: PSYSMO, DigiSal, GenoSysFat, HUMET Startup, EmPowerPutida, MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine, SAFE-Aqua, INDIE - Biotechnological production of sustainable indole
Institutions: Helmholtz Centre for Infection Research Braunschweig, Wageningen University & Research
Expertise: Microbiology, Mathematical modelling of biosystems and bioprocesses, Optimal experimental design, Systems Biology, Biotechnology
Tools: Bioinformatics, Genetic modification, Proteomics, Fermentation, Microarray analysis, Computational Systems Biology, Metabolic Engineering, microbiology techniques, reverse engineering, computational platform development, metabolic netwlrk visualization
My research activities has been to use mathematical models and Computational Biology to answer biological questions, intertwining in silico and experimental methods at all stages. I have a strong interest in exploring the interfaces between Fundamental Biology and bona fide Engineering, specifically in the realm of environmental and industrial problems. The research goals of my group are to contribute to the elucidation of mechanisms underlying basic cellular processes, evolution and ecological ...
Projects: DigiSal, GenoSysFat, SEEK tutorial for DigiSal
Institutions: Norwegian University of Life Sciences
Projects: DigiSal, GenoSysFat
Institutions: Norwegian University of Life Sciences
https://orcid.org/0000-0003-0719-1308Projects: DigiSal, GenoSysFat, SEEK tutorial for DigiSal
Institutions: Norwegian University of Life Sciences
Projects: DigiSal, GenoSysFat
Institutions: Norwegian University of Life Sciences
https://orcid.org/0000-0003-1659-132XTools: Bioinformatics
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
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
Snapshots: No snapshots
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
Snapshots: Snapshot 1
16S rRNA amplicon sequencing (Illumina MiSeq, V3-V4 region) to assess community structure.
Submitter: Jon Olav Vik
Assay type: Experimental Assay Type
Technology type: Next generation sequencing
Investigation: Omega-3 metabolism of salmon in relation to die...
Organisms: Salmo salar
SOPs: 16S metagenomic sequencing library preparations, DNA extraction from intestinal samples
Data files: Combined taxonomy table from freshwater and sal..., Feed switch 2015-09 Solbergstranda FASTA for gu..., Feed switch 2015-09 Solbergstranda gut microbio..., Feed switch 2016-01 Solbergstranda FASTA for gu..., Feed switch 2016-01 Solbergstranda gut microbio...
Snapshots: No snapshots
Targeted proteomics for peptides related to fatty acid metabolism. Aim: Check which of these proteins we are able to detect in this experiment.
Submitter: Jon Olav Vik
Assay type: Proteomics
Technology type: Technology Type
Investigation: Omega-3 metabolism of salmon in relation to die...
Organisms: Salmo salar
SOPs: No SOPs
Data files: Feed switch 2015-09 Solbergstranda proteomics o..., Feed switch 2015-09 Solbergstranda target prote...
Snapshots: No snapshots
From the "data accessibility" section of Life-stage associated remodeling of lipid metabolism regulation in Atlantic salmon. (Publication):
Supplementary files have been deposited to datadryad.org under the accession: https://doi.org/10.5061/dryad.j4h65. Raw RNA-Seq data have been deposited into European Nucleotide Archive (ENA) under the project Accession no. PRJEB24480.
Dead links 2022-06-29 (the Shiny ...
Submitter: Graceline Tina Kirubakaran
Assay type: RNA-seq
Technology type: Next generation sequencing
Investigation: Omega-3 metabolism of salmon in relation to die...
Organisms: Salmo salar
SOPs: Liver Slice protocol, RNASeq Template
Data files: Gene_information, Gut- CPM, Gut- Counts, Gut- FPKM, Lipid_Gene_List, Liver- CPM, Liver- Counts, Liver- FPKM, Metadata, Sample metadata
Snapshots: No snapshots
Record of weight, length and sex of fish sampled after feed switch between vegetable and marine oil, in September 2015 (freshwater) and January 2016 (seawater). Young fry arrived at Solbergstranda 2015-02-05 17:20.
Submitter: Thomas Harvey
Assay type: Experimental Assay Type
Technology type: Next generation sequencing
Investigation: Omega-3 metabolism of salmon in relation to die...
Organisms: Salmo salar
SOPs: Schedule for transition to seawater in GSF1, Ge...
Data files: Description of feeds for crossover feeding tria..., Feed switch 2015-09, 2016-01 Solbergstranda gro..., Metabolomics sampleID Old to New
Snapshots: No snapshots
Fatty acids are extracted from samples and converted to fatty acid methyl esters (FAMEs) followed by separation by gas chromatography. This yields fatty acid profiles for each sample as percent of total FAME or milligram FAME per gram of biomass.
Source:
Hei Magny,
Takk!
Et par ting:
- vi trenger å få orden på data... Lurer derfor på om du kan du lage ett dokument som inneholder alle resultat fra GCen? Uten ...
Submitter: Graceline Tina Kirubakaran
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Omega-3 metabolism of salmon in relation to die...
Organisms: No organisms
SOPs: No SOPs
Data files: Fatty acid content in feeds used in GenoSysFat ...
Snapshots: No snapshots
Fatty acids are extracted from samples and converted to fatty acid methyl esters (FAMEs) followed by separation by gas chromatography. This yields fatty acid profiles for each sample as percent of total FAME or milligram FAME per gram of biomass.
Source:
Hei Magny,
Takk!
Et par ting:
- vi trenger å få orden på data... Lurer derfor på om du kan du lage ett dokument som inneholder alle resultat fra GCen? Uten ...
Submitter: Graceline Tina Kirubakaran
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Omega-3 metabolism of salmon in relation to die...
Organisms: No organisms
SOPs: No SOPs
Data files: Fatty acid profile of Muscle, Liver and Gut_Fre..., Fatty acid profile of Muscle, Liver, and Gut -s..., GSF1_Freshwater_FAME, GSF1_Seawater_FAME, Muscle fatty acid analysis GenoSysFat feed-swit...
Snapshots: No snapshots
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 ...
Submitter: Jon Olav Vik
Assay type: Experimental Assay Type
Technology type: Rna-seq
Investigation: Omega-3 metabolism of salmon in relation to die...
NB! The files here are the old version for the files in Lipidomics (Experimental Assay)
Lipidomic analysis by LC-MS of tissue samples from the GSF1 feed-switch experiment. Samples were analyzed at NTNU by Zdenka Bartosova and Per Bruheim.
There are two separate data files of lipid analysis in muscle and liver samples. Excel sheets contains both raw and normalised data of compounds abundance. Normalization to all compounds was used as a normalization method.
We have also performed a "normalization ...
Submitter: Jon Olav Vik
Assay type: Experimental Assay Type
Technology type: Liquid Chromatography Mass Spectrometry
Investigation: Omega-3 metabolism of salmon in relation to die...
Organisms: Salmo salar
SOPs: SOP_Lipid analysis
Data files: NEG FW_Liver_Tentative Compounds Identification, NEG FW_Muscle_Tentative Compounds Identification, NEG Fresh Water Liver, NEG Fresh Water Muscle, NEG SW_Liver_Tentative Compounds Identification, NEG SW_Muscle_Tentative Compounds Identification, NEG_Salt Water Liver, NEG_Salt Water Muscle, POS FW_Liver_Tentative Compounds Identification, POS FW_Muscle_Tentative Compounds Identification, POS_ Fresh Water Liver, POS_ Fresh water Muscle, POS_Normalization_experiment, POS_Salt Water Liver, POS_Salt Water Muscle, Preliminary principal component analysis, SW_Liver_Tentative Compounds Identification- Po..., SW_Muscle_Tentative Compounds Identification- P...
Snapshots: No snapshots
Lipidomic analysis by UPC2-MS of tissue samples from the GSF1 feed-switch experiment. Samples were analyzed at NTNU by Zdenka Bartosova and Per Bruheim.
There are three separate data files of lipid analysis in muscle, liver and gut tissue samples. Excel sheets contains both raw and normalised data of compounds abundance. Normalization to all compounds was used as a normalization method.
Columns: Compound 0.93_858.7669n Anova (p) 0,044998264 q Value 0,009417222 Max Fold Change 1,644961431 Maximum ...
Submitter: Zdenka Bartosova
Assay type: Experimental Assay Type
Technology type: Supercritical fluid chromatography - Mass spectrometry
Investigation: Omega-3 metabolism of salmon in relation to die...
Organisms: Salmo salar
SOPs: No SOPs
Data files: Lipid Class Quantitation- POS Gut SW+FW, Lipid Class Quantitation- POS Liver SW+FW, Lipid Class Quantitation- POS Muscle SW+FW, Lipid identification- POS Gut, Lipid identification- POS Liver, Lipid identification- POS Muscle, POS Gut tissue FW+SW, POS Liver tissue FW+SW, POS Muscle tissue FW+SW
Snapshots: No snapshots
Spreadsheet of weight, length and sex of fish sampled after feed switch between vegetable and marine oil, in September 2015 (freshwater) and January 2016 (seawater).
Spreadsheet columns are:
- Date (YYYY-MM-DD)
- Day (day zero is the day before first feeding with new feed)
- Inputter (person entering data into Excel)
- Tank (1, 2, 4, 5 with Atlantic salmon, 3 and 6 with rainbow trout)
- Section (tanks were divided in half using perforated walls)
- Treatment (explained in sheet "treatments")
...
Creators: Jon Olav Vik, Jacob Seilø Torgersen, Arne Gjuvsland, Sandve Simen, Yang Jin, Tom Harvey
Submitter: Jon Olav Vik
CPM is a descriptive measures for the expression level of a gene.
Creator: Graceline Tina Kirubakaran
Submitters: Jon Olav Vik, Graceline Tina Kirubakaran
Salmon feed switch experiment: Lipid class quantitation for liver tissue samples (POS mode).
Lipid class abbreviations used: CE, cholesterol esters FC, free cholesterol Cer, ceramides HexCer, hexosyl ceramides (ie. galactosyl and glucosyl ceramides) MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols SM, sphingomyelins.
Creators: Zdenka Bartosova, Per Bruheim, Sahar Hassani
Submitter: Zdenka Bartosova
Investigations: Omega-3 metabolism of salmon in relation to die...
Studies: GSF1: Salmon feed-switch experiment vegetable a...
Assays: Lipidomics
Salmon feed switch experiment: Lipid class quantitation for muscle tissue samples (POS mode).
Lipid class abbreviations used: CE, cholesterol esters FC, free cholesterol Cer, ceramides HexCer, hexosyl ceramides (ie. galactosyl and glucosyl ceramides) MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols SM, sphingomyelins.
Creators: Zdenka Bartosova, Per Bruheim, Sahar Hassani
Submitter: Zdenka Bartosova
Investigations: Omega-3 metabolism of salmon in relation to die...
Studies: GSF1: Salmon feed-switch experiment vegetable a...
Assays: Lipidomics
Salmon feed switch experiment: Lipidomic data (POS mode) of gut tissue samples.
Creators: Zdenka Bartosova, Per Bruheim, Sahar Hassani
Submitter: Zdenka Bartosova
Investigations: Omega-3 metabolism of salmon in relation to die...
Studies: GSF1: Salmon feed-switch experiment vegetable a...
Assays: Lipidomics
Salmon feed switch experiment: Lipidomic data (POS mode) of muscle tissue samples.
Creators: Zdenka Bartosova, Per Bruheim, Sahar Hassani
Submitter: Zdenka Bartosova
Investigations: Omega-3 metabolism of salmon in relation to die...
Studies: GSF1: Salmon feed-switch experiment vegetable a...
Assays: Lipidomics
Salmon feed switch experiment: Lipid identification for muscle tissue samples (POS mode).
Lipid abbreviations used: CE, cholesterol esters Cer, ceramides GalCer, galactosyl ceramides GluCer, glucosyl ceramides MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols PI, phosphatidylinositols PS, phosphatidylserines SM, sphingomyelins.
The 'O-' ...
Creators: Zdenka Bartosova, Per Bruheim, Sahar Hassani
Submitter: Zdenka Bartosova
Investigations: Omega-3 metabolism of salmon in relation to die...
Studies: GSF1: Salmon feed-switch experiment vegetable a...
Assays: Lipidomics
Salmon feed switch experiment: Lipid identification for liver tissue samples (POS mode).
Lipid abbreviations used: CE, cholesterol esters Cer, ceramides GalCer, galactosyl ceramides GluCer, glucosyl ceramides MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols PI, phosphatidylinositols PS, phosphatidylserines SM, sphingomyelins.
The 'O-' ...
Creators: Zdenka Bartosova, Per Bruheim, Sahar Hassani
Submitter: Zdenka Bartosova
Investigations: Omega-3 metabolism of salmon in relation to die...
Studies: GSF1: Salmon feed-switch experiment vegetable a...
Assays: Lipidomics
Salmon feed switch experiment: Lipid identification for gut tissue samples (POS mode).
Lipid abbreviations used: CE, cholesterol esters Cer, ceramides GalCer, galactosyl ceramides GluCer, glucosyl ceramides MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols PI, phosphatidylinositols PS, phosphatidylserines SM, sphingomyelins.
The 'O-' prefix ...
Creators: Zdenka Bartosova, Per Bruheim, Sahar Hassani
Submitter: Zdenka Bartosova
Investigations: Omega-3 metabolism of salmon in relation to die...
Studies: GSF1: Salmon feed-switch experiment vegetable a...
Assays: Lipidomics
Salmon feed switch experiment: Lipid class quantitation for gut tissue samples (POS mode).
Lipid class abbreviations used: CE, cholesterol esters FC, free cholesterol Cer, ceramides HexCer, hexosyl ceramides (ie. galactosyl and glucosyl ceramides) MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols SM, sphingomyelins.
Creators: Zdenka Bartosova, Per Bruheim, Sahar Hassani
Submitter: Zdenka Bartosova
Investigations: Omega-3 metabolism of salmon in relation to die...
Studies: GSF1: Salmon feed-switch experiment vegetable a...
Assays: Lipidomics
Salmon feed switch experiment: Lipidomics data (POS mode) of liver samples.
Creators: Zdenka Bartosova, Per Bruheim, Sahar Hassani
Submitter: Zdenka Bartosova
Investigations: Omega-3 metabolism of salmon in relation to die...
Studies: GSF1: Salmon feed-switch experiment vegetable a...
Assays: Lipidomics
Muscle samples (fresh water sampling) - Identification of compounds based on the LipidBlast database.
Creators: Zdenka Bartosova, Per Bruheim, Jon Olav Vik, Thomas Harvey
Submitter: Zdenka Bartosova
Investigations: Omega-3 metabolism of salmon in relation to die...
Studies: GSF1: Salmon feed-switch experiment vegetable a...
Assays: Metabolomics
Negative mode lipidomics of muscle samples from saltwater sampling.
Creators: Zdenka Bartosova, Per Bruheim, Jon Olav Vik, Thomas Harvey
Submitter: Zdenka Bartosova
Investigations: Omega-3 metabolism of salmon in relation to die...
Studies: GSF1: Salmon feed-switch experiment vegetable a...
Assays: Metabolomics
Muscle samples (salt water sampling) - Identification of compounds based on the LipidBlast database.
Creators: Zdenka Bartosova, Per Bruheim, Jon Olav Vik, Thomas Harvey
Submitter: Zdenka Bartosova
Investigations: Omega-3 metabolism of salmon in relation to die...
Studies: GSF1: Salmon feed-switch experiment vegetable a...
Assays: Metabolomics
Liver samples (salt water sampling) - Identification of compounds based on the LipidBlast database.
Creators: Zdenka Bartosova, Per Bruheim, Jon Olav Vik, Thomas Harvey, Sahar Hassani
Submitter: Zdenka Bartosova
Investigations: Omega-3 metabolism of salmon in relation to die...
Studies: GSF1: Salmon feed-switch experiment vegetable a...
Assays: Metabolomics
Liver samples (fresh water sampling) - Identification of compounds based on the LipidBlast database.
Creators: Zdenka Bartosova, Per Bruheim, Jon Olav Vik, Thomas Harvey
Submitter: Zdenka Bartosova
Investigations: Omega-3 metabolism of salmon in relation to die...
Studies: GSF1: Salmon feed-switch experiment vegetable a...
Assays: Metabolomics
Liver samples (fresh water sampling) - Identification of compounds based on the LipidBlast database.
Creators: Zdenka Bartosova, Per Bruheim, Jon Olav Vik, Thomas Harvey
Submitter: Zdenka Bartosova
Investigations: Omega-3 metabolism of salmon in relation to die...
Studies: GSF1: Salmon feed-switch experiment vegetable a...
Assays: Metabolomics
Muscle samples (fresh water sampling) - Identification of compounds based on the LipidBlast database.
Creators: Zdenka Bartosova, Per Bruheim, Jon Olav Vik, Thomas Harvey
Submitter: Zdenka Bartosova
Investigations: Omega-3 metabolism of salmon in relation to die...
Studies: GSF1: Salmon feed-switch experiment vegetable a...
Assays: Metabolomics
Salmon feed experiment: Lipidomic data (NEG mode) of muscle samples from fresh water sampling.
Creators: Zdenka Bartosova, Per Bruheim, Jon Olav Vik, Thomas Harvey
Submitter: Zdenka Bartosova
Investigations: Omega-3 metabolism of salmon in relation to die...
Studies: GSF1: Salmon feed-switch experiment vegetable a...
Assays: Metabolomics
Salmon feed experiment: Lipidomic data (NEG mode) of liver samples from fresh water sampling.
Creators: Zdenka Bartosova, Per Bruheim, Jon Olav Vik, Thomas Harvey, Sahar Hassani
Submitter: Zdenka Bartosova
Investigations: Omega-3 metabolism of salmon in relation to die...
Studies: GSF1: Salmon feed-switch experiment vegetable a...
Assays: Metabolomics
Extraction procedure and lipid analysis.
Creators: Zdenka Bartosova, Jon Olav Vik, Per Bruheim, Thomas Harvey
Submitter: Zdenka Bartosova
Investigations: Omega-3 metabolism of salmon in relation to die...
Studies: GSF1: Salmon feed-switch experiment vegetable a...
Assays: Metabolomics
Winter conditions for 5 weeks (6th october – 10th November):
- Light on 12 hours per day
- Turn off water heating
- Feeding probably needs to be adjusted according to lower metabolism and feed intake in cold water
Spring condition (10th of November – 15th of December):
- Water heating on
- constant light (24hrs/day)
Vaccination (when and by whom?)
Transfer to sea-water (15th of December)
Last sampling for GenoSysFat in sea water (5th January – 25th of January).
Source: email with subject ...
Creators: Jon Olav Vik, Sandve Simen
Submitter: Jon Olav Vik
Source: Tom Harvey [E- mail from Jon Olav 19 May 2016]
Creators: Graceline Tina Kirubakaran, Thomas Harvey, Jacob Seilø Torgersen
Submitter: Graceline Tina Kirubakaran
Investigations: Omega-3 metabolism of salmon in relation to die...
Studies: GSF1: Salmon feed-switch experiment vegetable a... and 5 hidden items
Assays: RNA sequencing Feed switch- Liver and Gut and 17 hidden items
Use this template when you upload RNA sequencing data. Email : 31 May 2016 More columns need to be added PE/SE etc?
Creators: Graceline Tina Kirubakaran, Jon Olav Vik, Thomas Harvey, Sandve Simen, Hanne Hellerud Hansen
Submitter: Graceline Tina Kirubakaran
Investigations: Omega-3 metabolism of salmon in relation to die... and 2 hidden items
Studies: GSF1: Salmon feed-switch experiment vegetable a... and 7 hidden items
Assays: RNA sequencing Feed switch- Liver and Gut and 8 hidden items
Describes the workflow used for preparation of a 16S rRNA gene amplicon (V3-V4 region) Library for sequencing on a MiSeq platform (Illumina) using V3 sequencing chemistry with 300 base pairs paired-end reads.
Creators: Inga Leena Angell, Jon Olav Vik, Graceline Tina Kirubakaran, Sahar Hassani
Submitter: Inga Leena Angell
Investigations: Omega-3 metabolism of salmon in relation to die... and 1 hidden item
Studies: GSF1: Salmon feed-switch experiment vegetable a... and 1 hidden item
Assays: Feed switch 2015-09, 2016-01 Solbergstranda, gu... and 1 hidden item
All creators
Describes how the DNA was isolated from salmon intestinal samples before preparations of 16S rRNA gene amplicons for the Illumina MiSeq system.
Creators: Stuart Owen, Sahar Hassani, RAGNHILD ÅNESTAD, Jesse van Dam, Dagmar Waltemath, Kristina Vagonyte-Hallan, Kristil Sundsaasen, Natalie Stanford, Lars Snipen, Sandve Simen, Jacob Seilø Torgersen, Inga Leena Angell, Dominic Nanton, Vitor Martins dos Santos, Torgeir R. Hvidsten, Thomas Harvey, Hanne Hellerud Hansen, Fabian Grammes, Arne Gjuvsland, Gareth Gillard, Graceline Tina Kirubakaran, Jon Olav Vik
Submitter: Inga Leena Angell
We have adapted the definitions of terms in [ISA best practice][1] and [programmes and projects][2]:
Programme = Overarching research theme (The Digital Salmon) Project = Research grant (DigiSal, GenoSysFat) Investigation = a particular biological process, phenomenon or thing (typically corresponds to [plans for] one or more closely related papers) Study = experiment whose design reflects a specific biological research question Assay = standardized measurement or diagnostic experiment using a ...
Creators: Jon Olav Vik, Natalie Stanford
Submitter: Jon Olav Vik
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Abstract (Expand)
Authors: Y Jin, IL Angell, SR Sandve, LG Snipen, Y Olsen, K Rudi
Date Published: 24th Jan 2019
Publication Type: Not specified
DOI: 10.3354/aei00297
Citation: Aquacult. Environ. Interact. 11 : 31
Abstract (Expand)
Authors: Knut Rudi, Inga Leena Angell, Phillip B. Pope, Jon Olav Vik, Simen Rød Sandve, Lars-Gustav Snipen
Date Published: 15th Jan 2018
Publication Type: Not specified
DOI: 10.1128/AEM.01974-17
Citation: Appl Environ Microbiol 84(2) : e01974-17
Abstract (Expand)
Author: R. C. Edgar
Date Published: 18th Aug 2013
Publication Type: Not specified
PubMed ID: 23955772
Citation: Nat Methods. 2013 Oct;10(10):996-8. doi: 10.1038/nmeth.2604. Epub 2013 Aug 18.
Abstract (Expand)
Author: M. Bekaert
Date Published: 14th Nov 2012
Publication Type: Not specified
PubMed ID: 23166792
Citation: PLoS One. 2012;7(11):e49903. doi: 10.1371/journal.pone.0049903. Epub 2012 Nov 14.
Abstract (Expand)
Author: R. C. Edgar
Date Published: 12th Aug 2010
Publication Type: Not specified
PubMed ID: 20709691
Citation: Bioinformatics. 2010 Oct 1;26(19):2460-1. doi: 10.1093/bioinformatics/btq461. Epub 2010 Aug 12.
Abstract
Authors: J. G. Caporaso, J. Kuczynski, J. Stombaugh, K. Bittinger, F. D. Bushman, E. K. Costello, N. Fierer, A. G. Pena, J. K. Goodrich, J. I. Gordon, G. A. Huttley, S. T. Kelley, D. Knights, J. E. Koenig, R. E. Ley, C. A. Lozupone, D. McDonald, B. D. Muegge, M. Pirrung, J. Reeder, J. R. Sevinsky, P. J. Turnbaugh, W. A. Walters, J. Widmann, T. Yatsunenko, J. Zaneveld, R. Knight
Date Published: 11th Apr 2010
Publication Type: Not specified
PubMed ID: 20383131
Citation: Nat Methods. 2010 May;7(5):335-6. doi: 10.1038/nmeth.f.303. Epub 2010 Apr 11.
Abstract (Expand)
Authors: A. Brazma, P. Hingamp, J. Quackenbush, G. Sherlock, P. Spellman, C. Stoeckert, J. Aach, W. Ansorge, C. A. Ball, H. C. Causton, T. Gaasterland, P. Glenisson, F. C. Holstege, I. F. Kim, V. Markowitz, J. C. Matese, H. Parkinson, A. Robinson, U. Sarkans, S. Schulze-Kremer, J. Stewart, R. Taylor, J. Vilo, M. Vingron
Date Published: 1st Dec 2001
Publication Type: Not specified
PubMed ID: 11726920
Citation: Nat Genet. 2001 Dec;29(4):365-71.
Abstract (Expand)
Authors: G. Gillard, T. N. Harvey, A. Gjuvsland, Y. Jin, M. Thomassen, S. Lien, M. Leaver, J. S. Torgersen, T. R. Hvidsten, J. O. Vik, S. R. Sandve
Date Published: No date defined
Publication Type: Not specified
PubMed ID: 29431879
Citation: Mol Ecol. 2018 Feb 12. doi: 10.1111/mec.14533.
DigiSal Metabolomics and Lipidomics Update
Conclusion:
- Organic acid test ok
- Next
- Analyze all samples for OA (or selection? – include days and feed variation)
- Then aminoacids?
- Evaluate results – choose some samples for CapIC?
Creator: Per Bruheim
Submitter: Per Bruheim
Investigations: Omega-3 metabolism of salmon in relation to die...
Studies: GSF1: Salmon feed-switch experiment vegetable a...
Assays: Lipidomics, Metabolomics
Data modelling methods that are capable of maintaining block structure, as for example the block structure of the blocks of lipid classes, are called multi-block methods e.g. Consensus Principal Component Analysis (CPCA) and Multi-block Partial Least Squares Regression (MBPLSR). CPCA and MBPLR are two large families of MB methods. The developed methods can still be transferred to other data analysis methods. CPCA and MBPLSR which are extensions of PCA and PLSR to multi-block data sets can be ...
Creator: Sahar Hassani
Submitter: Sahar Hassani
Investigations: Omega-3 metabolism of salmon in relation to die...
Studies: GSF1: Salmon feed-switch experiment vegetable a...
Assays: Lipidomics, Metabolomics