Data files
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This is the fatty acid profile data from the freshwater portion of the feed switch trial. The last column has the sample ID eg: D0_MA-L-1/9_6 (Day 0, MA- Marine oil, L-liver, 1/9 sept 1, fish number 6
Fatty acid Systematic Name C14:0 Myristic acid myristin-syre C16:0 Palmitic acid palmitin-syre C16:1n7 Palmitoleic palmitolein-syre C17:0 C17:1 C18:0 stearic acid stearin-syre 18:1n9c oleic acid olje-syre C18:2n6c linoleic acid linolsyre C20:1 eicosenoic acid C18:3n3 linolenic acid linolensyre C20:2 ...
Creators: Graceline Tina Kirubakaran, Inga Leena Angell, Thomas Harvey, Jon Olav Vik, Magny Sidsel Thomassen
Submitter: Graceline Tina Kirubakaran
Fatty acid Systematic Name
C14:0 Myristic acid myristin-syre C16:0 Palmitic acid palmitin-syre C16:1n7 Palmitoleic palmitolein-syre C17:0 C17:1 C18:0 stearic acid stearin-syre 18:1n9c oleic acid olje-syre C18:2n6c linoleic acid linolsyre C20:1 eicosenoic acid C18:3n3 linolenic acid linolensyre C20:2 eicosadienoic C22:1 cetoleic acid cetolein-syre C20:3n3 eicosatrienoic acid C20:4n6 arachidonic acid arakidon-syre ARA C22:2 C20:5n3 eicosapentaenoic acid EPA C24:1 nervonic acid C22:5n3 docosapentaenoic ...
Creators: Thomas Harvey, Magny Sidsel Thomassen
Submitter: Thomas Harvey
This is the fatty acid profile data from the freshwater portion of the feed switch trial. eg: D0_MA_M_6 (Day 0, MA- Marine oil, L-liver, fish number 6)
Fatty acid Systematic Name C14:0 Myristic acid myristin-syre C16:0 Palmitic acid palmitin-syre C16:1n7 Palmitoleic palmitolein-syre C17:0 C17:1 C18:0 stearic acid stearin-syre 18:1n9c oleic acid olje-syre C18:2n6c linoleic acid linolsyre C20:1 eicosenoic acid C18:3n3 linolenic acid linolensyre C20:2 eicosadienoic C22:1 cetoleic acid cetolein-syre ...
Creators: None
Submitter: Yang Jin
This is the fatty acid profile data from the seawater portion of the feed switch trial. eg: D0_MA_M_6 (Day 0, MA- Marine oil, Muscle, fish number 6)
Fatty acid Systematic Name C14:0 Myristic acid myristin-syre C16:0 Palmitic acid palmitin-syre C16:1n7 Palmitoleic palmitolein-syre C17:0 C17:1 C18:0 stearic acid stearin-syre 18:1n9c oleic acid olje-syre C18:2n6c linoleic acid linolsyre C20:1 eicosenoic acid C18:3n3 linolenic acid linolensyre C20:2 eicosadienoic C22:1 cetoleic acid cetolein-syre ...
Creators: None
Submitter: Yang Jin
Fatty acid methyl ester (FAME) analysis showing which fatty acids were in the samples, though not what specific lipids they were part of (triacylglycerides, phospholipids, etc.) https://en.wikipedia.org/wiki/Fatty_acid_methyl_ester
Values in Ark1!A2:AO21 are probably mass percent of total FAME, including C19:0 added for calibration. Sample identifiers are lab-local; GSF1 identifiers are in Ark5!A4:U22 but suffer from typos. Use caution and see below.
This workbook is a mess:
- Results appear in ...
Creators: Magny Sidsel Thomassen, Sandve Simen, Jacob Seilø Torgersen, Jon Olav Vik, Arne Gjuvsland
Submitter: Magny Sidsel Thomassen
Results of gas chromatography of fatty acid composition of feeds used in Study "GSF1: Salmon feed-switch experiment vegetable and fish oil 2015-2016", https://fairdomhub.org/studies/144.
Feed samples are identified by their EWOS feed number. Fatty acids are identified by ChEBI ID. Numbers in table are mass percentage of lipid fraction.
Details on recipes, pellet size etc for each feed ID are in https://fairdomhub.org/data_files/1308.
(The above clarifications required some detective work, which ...
Creators: Jon Olav Vik, Magny Sidsel Thomassen, Graceline Tina Kirubakaran
Submitter: Jon Olav Vik
At the GenoSysFat startup meeting 2015-04-22, Dominic Nanton of EWOS described the feeds they made for GenoSysFat.
Describes recipes with linseed oil (LNO) and palm oil (PO) to provide the 18:3n-3 precursor to EPA and DHA and match saturation of 100% fish oil (FO) control diet at ca 0.7 mass% EPA+DHA.
Page 2: Overview Page 3-4: Description of feeds. Feed no., Code, Initial fish weight (g), Feed size (mm), Fish number (3000), Feed (kg) Page 5-7: Feed formulations. Feed number, Feed name, Feed size ...
Creators: Jon Olav Vik, Dominic Nanton
Submitter: Jon Olav Vik
A file which combine previous metabolomics samples ID to new sample ID file (https://fairdomhub.org/data_files/1330)
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
Information on samples submitted for RNAseq
Rows are individual samples
Columns are: ID Sample Name Date sampled Species Sex Tissue Geographic location Date extracted Extracted by Nanodrop Conc. (ng/µl) 260/280 260/230 RIN Plate ID Position Index name Index Seq Qubit BR kit Conc. (ng/ul) BioAnalyzer Conc. (ng/ul) BioAnalyzer bp (region 200-1200) Submission reference Date submitted Conc. (nM) Volume provided PE/SE Number of reads Read length
Creator: Thomas Harvey
Submitter: Thomas Harvey
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
List of 40 proteins as targets for pilot proteomics analysis of feed-switch samples (of liver, I presume).
E-mail from Simen Rød Sandve to Morten Skaugen 2015-08-11:
On Tue, Aug 11, 2015 at 10:01 AM, Simen Rød Sandve wrote: Please find attached an excel table with 40 proteins of interest (names, annotation, and protein sequence). I know we mentioned 20 proteins as a nice number to aim for in the targeted analyses – but we couldn't really seem to agree on a smaller subset . Please see if its ...
Creators: Jon Olav Vik, Simen Rød Sandve
Submitter: Jon Olav Vik
Path to this file: orion:~jonvi/genosysfat/SRS_lakselever_pilot.sf3 Attempt at workaround because the "Remote URL" field only accepts http, https, ftp: ftp://10.209.0.221/mnt/users/jonvi/genosysfat/SRS_lakselever_pilot.sf3
This file resides on the "orion" server (currently 10.209.0.221) at Cigene, which is only reachable from within NMBU network, e.g. via vpn.nmbu.no (as username@nmbu.no).
It is a 190 MB binary file to be viewed e.g. by Scaffold, http://www.proteomesoftware.com/products/scaffold/download. ...
Creators: Jon Olav Vik, Morten Skaugen, Simen Rød Sandve
Submitter: Jon Olav Vik
FASTA file of representative sequences for operational taxonomic units in gut microbiota analyses from feed-switch experiment at Solbergstrand Sept 2015.
(Knut Rudi --> Jon Olav Vik 20160126, email subject "metadata for alle fisk".)
File contents look like this:
OTU_1 1..446 -GTCC---GCCCTACGGGAT... OTU_2 1..446 -GTCC--GCCC-TACGGGAT... ... OTU_439 1..472 ----ATGTCACCTACGGGAT...
Creators: Jon Olav Vik, Knut Rudi
Submitter: Jon Olav Vik
FASTA file of representative sequences for operational taxonomic units in gut microbiota analyses from feed-switch experiment at Solbergstrand January 2016.
Creators: Inga Leena Angell, Jon Olav Vik, Graceline Tina Kirubakaran, Sahar Hassani
Submitter: Inga Leena Angell
Gut microbiota analysis of fish sampled in january 2016. The data is found in row 335-548 and downwards (Sheet 1). The first 16 colums contain information about the fish, and the following columns (From R to AJO) each represent an OTU (Operational taxonomic unit) with the given taxonomy for each OTU presented in the bottom row. Sequencing depth was kept at 13000 sequences per sample, thus the numbers presented in the OTU columns represent the number of sequences matching the specific OTU from the ...
Creators: Inga Leena Angell, Jon Olav Vik, Graceline Tina Kirubakaran, Sahar Hassani
Submitter: Inga Leena Angell
Gut microbiota analysis of the fish whose gross phenotypes are listed in https://fairdomhub.org/data_files/1244. Besides identification of the fish, the data are a 130 x 435 matrix showing amounts of operational taxonomic units (OTUs), one row per fish and one column per OTU (https://en.wikipedia.org/wiki/Operational_taxonomic_unit). Sequences that characterize each OTU are in https://fairdomhub.org/data_files/1317. Amounts are measured as the number out of 2000 sequences examined that contain a ...
Creators: Inga Leena Angell, Jon Olav Vik, Graceline Tina Kirubakaran, Sahar Hassani
Submitter: Inga Leena Angell
Combined taxonomy table of abundance of OTUs (Operational Taxonomy Units) in both freshwater and saltwater samples from 16S V3-V4 Illumina sequencing of gut microbiota. Primers used for sequencing are given in https://fairdomhub.org/sops/270 The OTUs are presented in number of counts per sample (n=349). Each row represent one sample. Raw data are available in the Sequence Read Archive database under accession number SRP119730 (https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP119730).
Creators: Inga Leena Angell, Lars Snipen, Jon Olav Vik
Submitter: Inga Leena Angell