Computational protocol: Cultivar-Specific Changes in Primary and Secondary Metabolites in Pak Choi (Brassica Rapa, Chinensis Group) by Methyl Jasmonate

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Protocol publication

[…] All analyses were done with three biological replications (three plants per replication). Univariate analysis of variance (ANOVA) and Student’s t-test were performed using JMP Pro 12 (SAS Institute, Cary, NC, USA) to determine the MeJA effect on primary and secondary metabolites and gene expression changes. For primary metabolite data, raw data files were converted to CDF format (*.cdf) using the Leco ChromaTOF software program (Version 4.44, Leco Corp, Warrendale, PA, USA). After conversion, the MS data were processed using the metAlign software package (Available online: http://www.metalign.nl) to obtain a data matrix containing retention times, accurate masses and normalized peak intensities. The resulting data were exported to Excel (Microsoft, Redmond, WA, USA) for further analysis using MetaboAnalyst 3.0 (Available online: http://www.metaboanalyst.ca/faces/home.xhtml). […]

Pipeline specifications

Software tools JMP Pro, ChromaTOF, MetAlign, MetaboAnalyst
Applications Miscellaneous, MS-based untargeted metabolomics
Organisms Brassica rapa
Chemicals Amino Acids, Carbohydrates, Carbon, Glucosinolates, Isothiocyanates