Data files

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 ...

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 ...

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 ...

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 ...

A file which combine previous metabolomics samples ID to new sample ID file (https://fairdomhub.org/data_files/1330)

Information for salmon genes, including transcript length used for calculating transcrip per million (TPM) value

Read counts for each sample

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 ...

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 ...

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

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 ...

Read counts for each sample

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 ...

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. ...

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...

FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

FASTQ file made from AB1 files. Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq