Summary of study ST001034

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000692. The data can be accessed directly via it's Project DOI: 10.21228/M8769J This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST001034
Study TitlePAMP-triggered changes in the exometabolome of Arabidopsis suspension cells
Study SummaryThe goal of this study was to determine how the exometabolome of defense-elicited Arabidopsis suspension cells inhibits virulence gene expression and growth of a plant pathogenic bacterium Pseudomonas syringae. Arabidopsis T87 suspension cells were treated with the pathogen-associated molecular pattern elf26 or a DMSO-control treatment for six hours, then incubated in fresh media for one hour. The conditioned medium (exudate) was collected from each culture by centrifugation and 0.22 um filter to remove plant cells. These samples are designated T=6 mock and T=6 elf26 in our experimental design. We also prepared samples in the same manner from control-treated cells except without any pre-treatment time prior to one hour exudate production. These samples are labeled T=0 mock. A total of seven biological replicates of each treatment condition were analyzed, with each replicate prepared from cells grown in separate flasks. The exudates were prepared in four independent experiments performed on separate days (1 biological replicate from first experiment, 2 biological replicates from each of the 3 remaining experiments). Four samples of the culture medium, one from each of the four independent experiments, are included.
Institute
Oregon State University
Last NameAnderson
First NameJeff
Address2082 Cordley Hall
Emailanderje2@oregonstate.edu
Phone541-737-4076
Submit Date2018-08-09
Raw Data AvailableYes
Raw Data File Type(s).cdf
Analysis Type DetailGC-MS
Release Date2019-03-06
Release Version1
Jeff Anderson Jeff Anderson
https://dx.doi.org/10.21228/M8769J
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000692
Project DOI:doi: 10.21228/M8769J
Project Title:PAMP-triggered changes in the exometabolome of Arabidopsis suspension cells
Project Summary:The goal of this study was to determine how the exometabolome of defense-elicited Arabidopsis suspension cells inhibits virulence gene expression and growth of a plant pathogenic bacterium Pseudomonas syringae. Arabidopsis T87 suspension cells were treated with the pathogen-associated molecular pattern elf26 or a DMSO-control treatment for six hours, then incubated in fresh media for one hour. The conditioned medium (exudate) was collected from each culture by centrifugation and 0.22 um filter to remove plant cells. These samples are designated T=6 mock and T=6 elf26 in our experimental design. We also prepared samples in the same manner from control-treated cells except without any pre-treatment time prior to one hour exudate production. These samples are labeled T=0 mock. A total of seven biological replicates of each treatment condition were analyzed, with each replicate prepared from cells grown in separate flasks. The exudates were prepared in four independent experiments performed on separate days (1 biological replicate from first experiment, 2 biological replicates from each of the 3 remaining experiments). Four samples of the culture medium, one from each of the four independent experiments, are included.
Institute:Oregon State University
Last Name:Anderson
First Name:Jeff
Address:2082 Cordley Hall, Corvallis, OR, 97331, USA
Email:anderje2@oregonstate.edu
Phone:541-737-4076
Funding Source:NSF 1557694

Subject:

Subject ID:SU001073
Subject Type:Plant
Subject Species:Arabidopsis thaliana
Taxonomy ID:3702

Factors:

Subject type: Plant; Subject species: Arabidopsis thaliana (Factor headings shown in green)

mb_sample_id local_sample_id treatment
SA069219170731dngsa21_2.cdfmedium only
SA069220170731dngsa07_2.cdfmedium only
SA069221170731dngsa14_2.cdfmedium only
SA069222170731dngsa04_2.cdfmedium only
SA069198170731dngsa01_2.cdfT=0
SA069199170731dngsa19_2.cdfT=0
SA069200170731dngsa20_2.cdfT=0
SA069201170731dngsa12_2.cdfT=0
SA069202170731dngsa13_2.cdfT=0
SA069203170731dngsa05_2.cdfT=0
SA069204170731dngsa06_2.cdfT=0
SA069205170731dngsa24_2.cdfT=6 elf26
SA069206170731dngsa18_2.cdfT=6 elf26
SA069207170731dngsa25_2.cdfT=6 elf26
SA069208170731dngsa03_2.cdfT=6 elf26
SA069209170731dngsa10_2.cdfT=6 elf26
SA069210170731dngsa11_2.cdfT=6 elf26
SA069211170731dngsa17_2.cdfT=6 elf26
SA069212170731dngsa02_2.cdfT=6 mock
SA069213170731dngsa23_2.cdfT=6 mock
SA069214170731dngsa22_2.cdfT=6 mock
SA069215170731dngsa16_2.cdfT=6 mock
SA069216170731dngsa08_2.cdfT=6 mock
SA069217170731dngsa09_2.cdfT=6 mock
SA069218170731dngsa15_2.cdfT=6 mock
Showing results 1 to 25 of 25

Collection:

Collection ID:CO001067
Collection Summary:Samples were 0.2 uM filtered and frozen in liquid nitrogen.
Sample Type:Cultured cells

Treatment:

Treatment ID:TR001087
Treatment Summary:Arabidopsis T87 suspension cells were treated with the pathogen-associated molecular pattern elf26 or a DMSO-control treatment for six hours, then incubated in fresh media for one hour. The conditioned medium (exudate) was collected from each culture by centrifugation and 0.22 um filter to remove plant cells.

Sample Preparation:

Sampleprep ID:SP001080
Sampleprep Summary:100 µL of each exudate sample was concentrated to dryness in a Centrivap cold trap vacuum concentrator (Labconco). Sample derivatization, chromatographic parameters, instrument parameters and data processing methods were as described [Fiehn et al. (2008) Quality control for plant metabolomics: reporting MSI-compliant studies. Plant J. 53:691–704].

Combined analysis:

Analysis ID AN001695
Analysis type MS
Chromatography type GC
Chromatography system Agilent 6890N
Column Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)
MS Type EI
MS instrument type GC x GC-TOF
MS instrument name Leco Pegasus IV TOF
Ion Mode POSITIVE
Units peak heights

Chromatography:

Chromatography ID:CH001194
Instrument Name:Agilent 6890N
Column Name:Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)
Chromatography Type:GC

MS:

MS ID:MS001570
Analysis ID:AN001695
Instrument Name:Leco Pegasus IV TOF
Instrument Type:GC x GC-TOF
MS Type:EI
Ion Mode:POSITIVE
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