Assays

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 ...

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.

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.

Differential expression analysis (using R package edgeR) on liver gene expression between salmon with all four fads2 genes knockout, only fads2d6b & fads2d6c knockout and wildtype. All salmon was given either a low-PUFA diet or a high-PUFA diet

Total lipids are extracted from tissues of white muscle, liver and whole brain from three fish per dietary treatment.

The three different CRISPR target sites within the elovl2 gene (T1-3) were characterised by Sanger sequencing, sequencing on average 8 clones per individual.

RNAseq is utilised to validate the SnpEff annotation predictions for aberrant splicing. For this purpose the percentage exon retention for exons 4, 6 and 7 are calculated using RNAseq data.

Stranded RNAseq libraries were prepared from 1µg total RNA from liver tissue using TruSeq Stranded mRNA library preparation kit (Illumina, San Diego, USA) using double unique indices (#20022371), according to the manufacturer's instruction (Part 15031057 Rev.E). Libraries were sequenced at the Norwegian Sequencing Centre (NSC). All libraries were pooled, and the same pool was sequenced on 4 flow cell lanes on a HiSeq 3000 machine (Illumina), generating 100bp single-end reads. RNA sequencing files ...