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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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: 1) vi trenger å få orden på data... Lurer derfor på om du kan du lage ett dokument som inneholder alle resultat fra GCen? Uten ...

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: 1) vi trenger å få orden på data... Lurer derfor på om du kan du lage ett dokument som inneholder alle resultat fra GCen? Uten ...

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.

Source: Gareth Gillard. (24 June 2016)

TO DO : Library preparation- Tom and Gareth

File types: Raw counts from HTSeq-count - .counts.txt CPM - .CPM.txt log2 scaled CPM - .log2CPM.txt FPKM - .FPKM.txt log2 scaled FPKM - log2FPKM.txt The scaled counts (CPM, FPKM) are derived from the raw counts, and used TMM normalised effective library sizes (using edgeR functions).

For feed switch experiment:

Count tables, separated for liver and gut tissue (can alter sample separation at any point) ...

Targeted proteomics for peptides related to fatty acid metabolism. Aim: Check which of these proteins we are able to detect in this experiment.

16S rRNA amplicon sequencing (Illumina MiSeq, V3-V4 region) to assess community structure.

CPM is a descriptive measures for the expression level of a gene.

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.

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.

Salmon feed switch experiment: Lipidomic data (POS mode) of gut tissue samples.

Salmon feed switch experiment: Lipidomic data (POS mode) of muscle tissue samples.

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-' ...

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-' ...

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 ...

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.

Salmon feed switch experiment: Lipidomics data (POS mode) of liver samples.

Muscle samples (fresh water sampling) - Identification of compounds based on the LipidBlast database.

Negative mode lipidomics of muscle samples from saltwater sampling.

Muscle samples (salt water sampling) - Identification of compounds based on the LipidBlast database.

Liver samples (salt water sampling) - Identification of compounds based on the LipidBlast database.

Liver samples (fresh water sampling) - Identification of compounds based on the LipidBlast database.

Liver samples (fresh water sampling) - Identification of compounds based on the LipidBlast database.

Muscle samples (fresh water sampling) - Identification of compounds based on the LipidBlast database.

Salmon feed experiment: Lipidomic data (NEG mode) of muscle samples from fresh water sampling.

Salmon feed experiment: Lipidomic data (NEG mode) of liver samples from fresh water sampling.

Negative mode lipidomics of liver samples from saltwater sampling.

Extraction procedure and lipid analysis.

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 ...

Source: Tom Harvey [E- mail from Jon Olav 19 May 2016]

Use this template when you upload RNA sequencing data. Email : 31 May 2016 More columns need to be added PE/SE etc?

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.

Describes how the DNA was isolated from salmon intestinal samples before preparations of 16S rRNA gene amplicons for the Illumina MiSeq system.

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 ...

DigiSal Metabolomics and Lipidomics Update

Conclusion: * Organic acid test ok * Next 1. Analyze all samples for OA (or selection? – include days and feed variation) 2. Then aminoacids? 3. Evaluate results – choose some samples for CapIC?

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 ...