Data files

Spreadsheet of weight, length and sex of fish sampled after feed switch between vegetable and marine oil, in September 2015 (freshwater) and January 2016 (seawater).

Spreadsheet columns are:

• Date (YYYY-MM-DD)
• Day (day zero is the day before first feeding with new feed)
• Inputter (person entering data into Excel)
• Tank (1, 2, 4, 5 with Atlantic salmon, 3 and 6 with rainbow trout)
• Section (tanks were divided in half using perforated walls)
• Treatment (explained in sheet "treatments")

...

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.

Positive mode metabolomics of muscle samples from saltwater sampling.

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

Columns: Compound 8.60_759.5784n Compound ID GPCho(12:0/22:1) Accepted? Adducts M+H, M+Na Formula C42H82NO8P Score 51,1 Fragmentation Score 62,1 Mass Error (ppm) 0,808672852 Isotope Similarity 94,59106017 Theoretical Isotope Distribution 100 - 47 - 12.5 - 2.39 - 0.367 Link http://nonlinear.com/redirect/outbound?p=lipidblast&param=GPCho%2812%3A0%2F22%3A1%29 Description GPCho(12:0/22:1) Neutral ...

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

Columns: Compound 8.60_759.5784n Compound ID GPCho(12:0/22:1) Accepted? Adducts M+H, M+Na Formula C42H82NO8P Score 51,1 Fragmentation Score 62,1 Mass Error (ppm) 0,808672852 Isotope Similarity 94,59106017 Theoretical Isotope Distribution 100 - 47 - 12.5 - 2.39 - 0.367 Link http://nonlinear.com/redirect/outbound?p=lipidblast¶m=GPCho%2812%3A0%2F22%3A1%29 Description GPCho(12:0/22:1) Neutral mass (Da) ...

Source code is at https://gitlab.com/digisal/GSF1_metabolomics/. The report loads smoothly in Chrome, but is very slow to load in Firefox.

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

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

Positive mode metabolomics of liver samples from saltwater sampling.

Positive mode metabolomics of the same muscle tissue sample at multiple levels of dilution.

Samples of 40 45 50 55 60 mg were diluted in the same volume, then analysed. The resulting data describe the same tissue at different levels of dilution. From this we can devise some numerical post-processing that would make all samples "similar" based on the mass of tissue. This post-processing could then be applied to later samples given their mass.

NOTE: Sample does not come from the salmon feed-switch ...

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 ...

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 ...

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 ...

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...

FASTA file of representative sequences for operational taxonomic units in gut microbiota analyses from feed-switch experiment at Solbergstrand January 2016.

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 ...

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 ...