Data for DIMet Galaxy (Bioprotocol)

Dataset for the DIMet Galaxy step-by-step use case, in preparation for submission to the Bioprotocol journal.

This dataset was originally published by Guyon J, et al., 2022. The subset of it, with exclusively LDHAB KO and Control samples at 0h, 24h and 48h,  is the main file of the present Zenodo record. Also, the Differentially expressed genes (DEG) when comparing LDHAB KO vs. Control at 0 h and 48 h are available and explained in the 'Instructions for users' below.

The present dataset serves for demonstrating the step-by-step usage of the Galaxy versions of TraceGroomer and DIMet tools.

Instructions for users:

• Please download and unzip the entire folder, in your machine.
• Take into account the files description below
  • 'dimet_bioprotocol/' folder: 
    

    Type of file	File name
    Labeled metabolomics data as received from Metabolomics facility (main file)	isocor_LDHABKO_Ctrl.tsv
    Samples metadata (the file that explains the experimental setup)	metadata_LDHABKO_Ctrl.tsv

  • 'dimet_bioprotocol/metabologram_data/' subfolder: 

    Type of file	File name
    file of DEG at T0 (0 h)	LDHABKO_Ctrl_0h_DEG.tsv
    file of DEG at T48 (48 h)	LDHABKO_Ctrl_48h_DEG.tsv
    file with pathways* for metabolites	pathways_metabolites_custom.tsv
    file with pathways* for transcripts (or genes)	pathways_genes_list_custom.tsv

    *the lists of pathways in the file are disposed in columns, for each column: the top cell is the name of the pathway, whereas the rest of the cells are the elements belonging to that pathway.

For any inquiries or help, contact Johanna Galvis.