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Metabolite Profiling Experiments

The GC-MS metabolite profiling experiments given below are made publicly available to get feedback from the community. The relative metabolite concentrations are normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol). Although these details are accessible within the GMD, they are not made available on the web site so far. For these details please refer to the publication. As it is our intention to increase the breadth GMD’s experiment repository in terms of organisms, organs and stresses, we actively work on cross experiment normalisation and thus, profile data and data representation might change in the future without any further notice. For maximal quality assessment, all experiments are described using the XEML framework (see tree below), while the GC-MS chromatograms are processed using the TagFinder software.
Title
Factor(s)GenusAccessionsReplica GroupsSamplesMetabolites
Mining for metabolic responses to long-term salt stress: a case study on the model legume Lotus japonicus (C)
SaltLotus1740105
15 experiment(s)
Mining for metabolic responses to long-term salt stress: a case study on the model legume Lotus japonicus (C) contact: kopka@mpimp-golm.mpg.de description: Mining for robust transcriptional and metabolic responses to long-term salt stress: a case study on the model legume Lotus japonicus. Translational genomics, the use of model species to generate knowledge about biological processes and the functions of genes, offers great promise to biotechnologists. Few studies have sought robust responses of model plants to environmental stresses, such as salinity, by altering the stress dosage or by repeating experiments in consecutive years and/or different seasons.We mined our published and unpublished data on legume salt acclimation for robust system features at the ionomic, transcriptomic and metabolomic levels. We analysed data from the model legume Lotus japonicus, obtained through six independent, longterm, non-lethal salt stress experiments which were carried out over two consecutive years. Best possible controlled greenhouse conditions were applied and two main questions asked: how reproducible are results obtained from physiologically meaningful salinity experiments, and what degree of bias may be expected if conclusions are drawn from less well-repeated sampling?A surprisingly large fraction of the transcriptional and metabolic responses to salt stress were not reproducible between experiments. A core set of robust changes was found that was shared between experiments. Many of these robust responses were qualitatively and quantitatively conserved between different accessions of the same species, indicating that the robust responses may be a sound starting point for translational genomics. start date: 2006-01-01 experiment Id: cdb1fa79-b1a7-4e18-9caf-54eb2f3bb6a1 links: metabolite profile  MapMan pathway  XEML experimental description  ISA-Tab export  TagList Metabolite raw export  TagList Metabolite norm export  TagList Analyte raw export  TagList Analyte norm export  TagList MST raw export
  • 6308if - C
  • doi: 10.1111/j.1365-3040.2009.02047.x
  • doi: 10.1111/j.1365-313X.2007.03381.x
  • Sanchez, D. H., Lippold, F., Redestig, H., Hannah, M. A., Erban, A., Krämer, U., Kopka, J. and Udvardi, M. K. (2008), Integrative functional genomics of salt acclimatization in the model legume Lotus japonicus. The Plant Journal, 53: 973–987. doi: 10.1111/j.1365-313X.2007.03381.x
  • SANCHEZ, D. H., SZYMANSKI, J., ERBAN, A., UDVARDI, M. K. and KOPKA, J. (2010), Mining for robust transcriptional and metabolic responses to long-term salt stress: a case study on the model legume Lotus japonicus. Plant, Cell & Environment, 33: 468–480. doi: 10.1111/j.1365-3040.2009.02047.x
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observation point: OP 2 observation time: 32.00:00:00 [days . hours : minutes : seconds]
TimeNameValueDurationUnit
initiationSalt0 mM
08dSalt50 mM
2 experimental conditions(s)
This tree schematises the experimental design of a single metabolite profiling experiment with the x-axis representing the time scale. Branches of the tree are used to describe the plant’s environmental condition. Recorded environmental conditions are either given to describe the general experimental setup and to support cross experiment comparisons, or to indicate the specific stress type. A “salt stress experiment” is described using different salt concentrations. Clicking the nodes of the tree, quantitative environmental conditions (e.g. temperature, salt concentrations, humidity, etc.) describing the plant’s environment can be inspected in the right table. Unfortunately, due to the limitations of the current html based visualisation, the scaling of the tree's branches is not proportional to the real length of time. Green tagged observation points (OP) represent sampling time points. Results in the data analysis (see heat map or MapMan links in table on top) correspond to these observation points. Please note that observation point names (OP1, OP2, etc.) do not relate to each other. Instead, use the description of the observation points to identify potential candidates for cross experiment profile comparison.
service last updated 31/08/2021 © 2008-2014 Golm Metabolome Database - All rights reserved
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