SEEK ID: https://fairdomhub.org/people/626
Location:
Norway
ORCID:
https://orcid.org/0000-0001-9533-3227
Joined: 5th Feb 2016
Expertise: Bioinformatics
Tools: Not specified
Related items
- Programmes (1)
- Projects (2)
- Institutions (1)
- Assays (1)
- Data files (6+6)
- SOPs (1)
- Publications (1)
- Presentations (0+2)
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
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
Organisms: Danio rerio, Salmo salar, Oncorhynchus mykiss
Towards the Digital Salmon: From a reactive to a pre-emptive research strategy in aquaculture (DigiSal)
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. Project DigiSal will lay the foundations for a Digital Salmon: an ensemble of mathematical descriptions of salmon physiology, combining ...
Programme: The Digital Salmon
Public web page: http://tinyurl.com/digisal
Organisms: Danio rerio, Salmo salar, Oncorhynchus mykiss
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) ...
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: 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
Read counts for each sample
Creators: Graceline Tina Kirubakaran, Gareth Gillard, Fabian Grammes
Submitter: Graceline Tina Kirubakaran
FPKMs or Fragments Per Kilobase of exon per Million reads . Fragment means fragment of DNA, so the two reads that comprise a paired-end read count as one. Per kilobase of exon means the counts of fragments are then normalized by dividing by the total length of all exons in the gene (or transcript). This bit of magic makes it possible to compare Gene A to Gene B even if they are of different lengths. Per million reads means this value is then normalized against the library size. This bit of magic ...
Creators: Graceline Tina Kirubakaran, Fabian Grammes, Gareth Gillard
Submitter: Graceline Tina Kirubakaran
Column 1: Row numbers Column 2: Sample id (See below) Column 3: Water (Fish from salt water or fresh water) Column 4: Tissue (Liver or Gut) Column 5: Feed (MA- Marine oil, VO- Vegetable oil) Column 6: Day Column 7: Count file location
Column 2 explained: The freshwater fish have no tank numbers and saltwater fish do have tank numbers eg : 69-D0-MA-G-1 - > 69 well position (id given when sequncing), Day 0, Marine oil, Gut, Fish number 1 147-D16-VO-MA-L-6 -> 147 well position, Day 16, Vegetable ...
Creators: Graceline Tina Kirubakaran, Gareth Gillard
Submitter: Graceline Tina Kirubakaran
FPKMs or Fragments Per Kilobase of exon per Million reads . Fragment means fragment of DNA, so the two reads that comprise a paired-end read count as one. Per kilobase of exon means the counts of fragments are then normalized by dividing by the total length of all exons in the gene (or transcript). This bit of magic makes it possible to compare Gene A to Gene B even if they are of different lengths. Per million reads means this value is then normalized against the library size. This bit of magic ...
Creators: Graceline Tina Kirubakaran, Gareth Gillard, Fabian Grammes
Submitter: Graceline Tina Kirubakaran
Read counts for each sample
Creators: Graceline Tina Kirubakaran, Fabian Grammes, Gareth Gillard
Submitter: Graceline Tina Kirubakaran
Creators: Graceline Tina Kirubakaran, Gareth Gillard, Fabian Grammes, Jon Olav Vik
Submitter: Graceline Tina Kirubakaran
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: Sahar Hassani, Inga Leena Angell, Jon Olav Vik, Graceline Tina Kirubakaran, Gareth Gillard, Arne Gjuvsland, Fabian Grammes, Hanne Hellerud Hansen, Thomas Harvey, Torgeir R. Hvidsten, Vitor Martins dos Santos, Dominic Nanton, Stuart Owen, Jacob Seilø Torgersen, Sandve Simen, Lars Snipen, Natalie Stanford, Kristil Sundsaasen, Kristina Vagonyte-Hallan, Dagmar Waltemath, Jesse van Dam, RAGNHILD ÅNESTAD
Submitter: Inga Leena Angell
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.