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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
Metabolomic profiles in short day, after bolting, single leaf analysis, Arabidopsis thaliana
LeafPosition, MaterialArabidopsis136986
15 experiment(s)
Metabolomic profiles in short day, after bolting, single leaf analysis, Arabidopsis thaliana contact: kopka@mpimp-golm.mpg.de description: Metabolomic profiles in short or long day, before and after bolting, single leaf analysis, Arabidopsis thaliana start date: 2012-01-18 experiment Id: 7e182921-2b1c-4276-9495-2505417eb21d 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
  • published first: GMD 2014.01.16
  • submission to GMD: Alexander Erban / MPIMP
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observation point: OP 1 observation time: 77.06:00:00 [days . hours : minutes : seconds]
TimeNameValueDurationUnit
initiationTotal Light100%16:00:00 
initiationTotal Light0%08:00:00 
initiationTypeAgar  
initiationType2MS  
initiationContainerPetri dish  
07dTotal Light100%08:00:00 
07dTotal Light0%16:00:00 
14dTypePotting soil  
14dTypeStender AG, Scharmbeck, Germany  
14dPlants/Container1  
14dContainerPot  
14dContainerPot size diameter 6cm  
12 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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