Summary of Study ST000001

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR000001. The data can be accessed directly via it's Project DOI: 10.21228/M8159B This work is supported by NIH grant, U2C- DK119886.


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Study IDST000001
Study TitleFatb Induction Experiment (FatBIE)
Study TypeGenotype treatment
Study SummaryThis experiment tests the consequence of a mutation at the FatB gene (At1g08510) in the wound-response of Arabidopsis. The FatB mutant allele (fatb KD J. Ohlrogge (Plant Cell 2003, Vol 15, 1020-1033)) was obtained from Dr. Katayonn Dehesh, University of California, Davis, Davis, CA. This allele is in the Ws background.The standardized growth conditions are as follows: 1. Seeds (between 14 and 16) are sown on media in 100 x 100 x 15mm square Falcon Petri Dishes (Fisher Scientific, catalogue #08-757-11A). Seeds were arranged on the plates in a single horizontal line at the 1-cm mark from the top of the plate.2. Each plate contains between 20 and 25-ml of sterile MS media containing 0.1% (w/v) sucrose.3. Prior to sowing, seeds were sterilized by treating for 1 minute at room temperature with a 300-l solution of 50% (v/v) ethanol, this solution was removed and replaced with a 300-l solution consisting of 1% (v/v) Tween 20 (Fischer BioReagents, catalogue #BP33750), and 50% (v/v) bleach solution (Clorox), and incubated at room temperature for 10-minutes. The seeds were then washed with three changes of 0.3-ml of sterile water.
University of California, Davis
DepartmentDavis Genome Center
Last NameKind
First NameTobias
Address451 E. Health Sci. Drive, Davis, CA 95616, USA
Submit Date2013-01-15
Num Groups4
Total Subjects24
Raw Data AvailableNo
Analysis Type DetailGC-MS
Release Date2013-02-14
Release Version1
Tobias Kind Tobias Kind application/zip

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Project ID:PR000001
Project DOI:doi: 10.21228/M8159B
Project Title:FatB Gene Project
Project Type:Genotype treatment
Project Summary:Experiment to test the consequence of a mutation at the FatB gene (At1g08510) in the wound-response of Arabidopsis
Institute:University of California, Davis
Department:Davis Genome Center
Last Name:Fiehn
First Name:Oliver
Address:451 E. Health Sci. Drive, Davis, CA, 95616, USA
Publications:Quality control for plant metabolomics: reporting MSI-compliant studies. DOI: 10.1111/j.1365-313X.2007.03387.x PubMed


Subject ID:SU000001
Subject Type:Plant
Subject Species:Arabidopsis thaliana
Taxonomy ID:3702
Genotype Strain:Wassilewskija (Ws) | fatb-ko KD; At1g08510
Species Group:Plant


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

mb_sample_id local_sample_id Arabidopsis Genotype Plant Wounding Treatment
SA000019LabF_115904fatb-ko KD; At1g08510 Control - Non-Wounded
SA000020LabF_115909fatb-ko KD; At1g08510 Control - Non-Wounded
SA000021LabF_115914fatb-ko KD; At1g08510 Control - Non-Wounded
SA000022LabF_115919fatb-ko KD; At1g08510 Control - Non-Wounded
SA000023LabF_115924fatb-ko KD; At1g08510 Control - Non-Wounded
SA000024LabF_115929fatb-ko KD; At1g08510 Control - Non-Wounded
SA000007LabF_115842fatb-ko KD; At1g08510 Wounded
SA000008LabF_115847fatb-ko KD; At1g08510 Wounded
SA000009LabF_115852fatb-ko KD; At1g08510 Wounded
SA000010LabF_115857fatb-ko KD; At1g08510 Wounded
SA000011LabF_115862fatb-ko KD; At1g08510 Wounded
SA000012LabF_115867fatb-ko KD; At1g08510 Wounded
SA000013LabF_115873Wassilewskija (Ws) Control - Non-Wounded
SA000014LabF_115878Wassilewskija (Ws) Control - Non-Wounded
SA000015LabF_115883Wassilewskija (Ws) Control - Non-Wounded
SA000016LabF_115888Wassilewskija (Ws) Control - Non-Wounded
SA000017LabF_115893Wassilewskija (Ws) Control - Non-Wounded
SA000018LabF_115898Wassilewskija (Ws) Control - Non-Wounded
SA000001LabF_115811Wassilewskija (Ws) Wounded
SA000002LabF_115816Wassilewskija (Ws) Wounded
SA000003LabF_115821Wassilewskija (Ws) Wounded
SA000004LabF_115826Wassilewskija (Ws) Wounded
SA000005LabF_115831Wassilewskija (Ws) Wounded
SA000006LabF_115836Wassilewskija (Ws) Wounded
Showing results 1 to 24 of 24


Collection ID:CO000001
Sample Type:Plant
Volumeoramount Collected:50 mg


Treatment ID:TR000001
Treatment Route:Wounded
Treatment Dose:Ten punches
Treatment Doseduration:3 min wounding period; 2 h response perioid before harvest
Plant Growth Support:Fourteen to sixteen seeds were sown on 2025 ml of sterile Murashige and Skoog basal salt mixture (MS medium) containing 0.1% w/v sucrose and 1 liquid vitamin solution (Sigma, containing 15 g l)1 bacto agar (BD) in 100 100 15 mm square Falcon Petri dishes (Thermo Fisher Scientific; http:// Seeds were arranged on the plates in a single horizontal line 1 cm from the top of the plate. Prior to sowing, seeds were sterilized by treating for 1 min at room temperature with 300 ll of 50% v/v ethanol; this solution was then removed and replaced by 300 ll of a solution consisting of 1% v/v Tween-20 (Thermo Fisher Scientific) and 50% v/v bleach (Clorox; http://www.clorox. com), and incubated at room temperature for 10 min. The seeds were then washed with three changes of 0.3 ml of sterile water. After sowing the seeds, the plates were wrapped using micropore tape (3 M Health Care;, and then stored horizontally for 4 days at 4 C in the dark. On the 5th day, plates were moved to the growth room, and held in a vertical position in Plexiglass holders for 12 days.
Plant Growth Location:Controlled-environment facility at Iowa State University, Nikolau laboratory.
Plant Plot Design:Each genotype and replicate were grown on individual plates and placed randomly in the Plexiglass holders.
Plant Light Period:24 h day at 82 micromol/m**2 s (light source Sylvania;, F34CW/SS/ECO/RP)
Plant Humidity:Day 100%, night 100%
Plant Temp:Day 24 C, night 24 C
Plant Watering Regime:No further watering, plates remained closed
Plant Nutritional Regime:MS medium without further fertilizers
Plant Estab Date:2006-09-25
Plant Harvest Date:2006-10-11
Plant Growth Stage:Boyes 1.11.4
Plant Metab Quench Method:Immersion in liquid nitrogen within 1 min after harvest
Plant Harvest Method:Petri plates were opened and the aerial portions of the plants were cut
Plant Storage:-70 C for 1 day, then shipping on dry ice and storage at -80 C for 2 weeks

Sample Preparation:

Sampleprep ID:SP000001
Processing Storage Conditions:Frozen tissues were kept in 2 ml round-bottomed Eppendorf tubes equipped with one 3 mm diameter steel ball, and homogenized using a Retsch ( ball mill for 30 sec at 25/sec
Extraction Method:Ground tissue powder was kept in liquid nitrogen between homogenization and extraction. The extraction solvent was prepared by mixing isopropanol/ acetonitrile/water at the volume ratio 3:3:2 and degassing this mixture by directing a gentle stream of nitrogen through the solvent for 5 min. The solvent was cooled to )20 C prior to extraction. Randomly processing all samples of the study, 1 ml of cold solvent per 20 mg of ground tissue was added, vortexed for 10 sec, and shaken at 4 C for 5 min to extract metabolites and simultaneously precipitate proteins. After centrifugation at 12 800 g for 2 min, 90% of the supernatant was removed, taking are not to remove any residues from the pellet
Extract Concentration Dilution:The supernatant was separated into two equal aliquots and concentrated to dryness in a Centrivap cold trap vacuum concentrator (http://www. at room temperature for 4 h
Extract Cleanup:In order to fractionate complex lipids and waxes, the residue was re-suspended in 500 ll 50% aqueous acetonitrile and centrifuged at 12 800 g for 2 min. The supernatant was transferred to a 1.5 ml Eppendorf tube and concentrated to dryness in a vacuum concentrator
Extract Storage:Dried extracts can be kept under nitrogen at -80 C for up to 4 weeks. In the study presented here, extracts were immediately derivatized for GCTOF mass spectrometry
Organ Specification:Rosette leaf
Cell Type:Arial portion

Combined analysis:

Analysis ID AN000001
Analysis type MS
Chromatography type GC
Chromatography system Agilent 6890N
MS Type EI
MS instrument type GC-TOF
MS instrument name Leco Pegasus III GC TOF
Units Peak height


Chromatography ID:CH000001
Methods Filename:nihms161442.pdf
Instrument Name:Agilent 6890N
Chromatography Type:GC


MS ID:MS000001
Analysis ID:AN000001
Instrument Name:Leco Pegasus III GC TOF
Instrument Type:GC-TOF
MS Type:EI