Data files

An initial choice of 5 widely spaced substrates enables a first, rough estimate of Km to inform the design of first-round experiments.

PhD thesis research by Joost W Aerts under supervision of Hans V. Westerhoff, Rob J van Spanning and Pascale Ehrenfreund

In this folder one has the: thesis summary a pdf of the thesis supplemental material per chapter, for chapters 3, 4, 6, and 7

Full list of detected miRNA which were found to be deregulated in PE-EVs.

CPM is a descriptive measures for the expression level of a gene.

Batch sample publishing

GPT Assay results for "Excision of mutagenic replication-blocking lesions suppresses cancer but promotes cytotoxicity and lethality in nitrosamine-exposed mice" by Kay et al. https://doi.org/10.1016/j.celrep.2021.108864

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.