Data files

We constructed a logic-based model to unravel mechanisms underlying pancreatic cancer and fibrosis. Model was calibrated with expression data and simulated for stimulus response and perturbation analysis to identify disease markers. Disease markers predicted by the model are validated through patient data using KM survival plot (which stratify patient into short and long survival) and box plot (expression level of the markers in normal vs. pancreatic patients). In vitro validations of the model ...

Salmon feed switch experiment: Lipid class quantitation for liver tissue samples (POS mode).

Lipid class abbreviations used: CE, cholesterol esters FC, free cholesterol Cer, ceramides HexCer, hexosyl ceramides (ie. galactosyl and glucosyl ceramides) MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols SM, sphingomyelins.

Salmon feed switch experiment: Lipid class quantitation for muscle tissue samples (POS mode).

Lipid class abbreviations used: CE, cholesterol esters FC, free cholesterol Cer, ceramides HexCer, hexosyl ceramides (ie. galactosyl and glucosyl ceramides) MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols SM, sphingomyelins.

Salmon feed switch experiment: Lipidomic data (POS mode) of gut tissue samples.

Salmon feed switch experiment: Lipidomic data (POS mode) of muscle tissue samples.

Salmon feed switch experiment: Lipid identification for muscle tissue samples (POS mode).

Lipid abbreviations used: CE, cholesterol esters Cer, ceramides GalCer, galactosyl ceramides GluCer, glucosyl ceramides MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols PI, phosphatidylinositols PS, phosphatidylserines SM, sphingomyelins.

The 'O-' ...

Salmon feed switch experiment: Lipid identification for liver tissue samples (POS mode).

Lipid abbreviations used: CE, cholesterol esters Cer, ceramides GalCer, galactosyl ceramides GluCer, glucosyl ceramides MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols PI, phosphatidylinositols PS, phosphatidylserines SM, sphingomyelins.

The 'O-' ...

Salmon feed switch experiment: Lipid identification for gut tissue samples (POS mode).

Lipid abbreviations used: CE, cholesterol esters Cer, ceramides GalCer, galactosyl ceramides GluCer, glucosyl ceramides MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols PI, phosphatidylinositols PS, phosphatidylserines SM, sphingomyelins.

The 'O-' prefix ...

Salmon feed switch experiment: Lipid class quantitation for gut tissue samples (POS mode).

Lipid class abbreviations used: CE, cholesterol esters FC, free cholesterol Cer, ceramides HexCer, hexosyl ceramides (ie. galactosyl and glucosyl ceramides) MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols SM, sphingomyelins.

Salmon feed switch experiment: Lipidomics data (POS mode) of liver samples.

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¶m=GPCho%2812%3A0%2F22%3A1%29 Description GPCho(12:0/22:1) Neutral mass ...

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 ...

Excel file summarizing:

• Name of the RNAseq study
• Orion path were the .fastq files are stored
• Year the libraries were sequenced
• short description

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 ...