Summary of Study ST000001
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 PR000001. The data can be accessed directly via it's Project DOI: 10.21228/M8159B This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000001 |
| Study Title | Fatb Induction Experiment (FatBIE) |
| Study Type | Genotype treatment |
| Study Summary | This 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. |
| Institute | University of California, Davis |
| Department | Davis Genome Center |
| Laboratory | Fiehn |
| Last Name | Kind |
| First Name | Tobias |
| Address | 451 E. Health Sci. Drive, Davis, CA 95616, USA |
| tkind@ucdavis.edu | |
| Submit Date | 2013-01-15 |
| Num Groups | 4 |
| Total Subjects | 24 |
| Raw Data Available | No |
| Analysis Type Detail | GC-MS |
| Release Date | 2013-02-14 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| 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 |
| Laboratory: | Fiehn |
| Last Name: | Fiehn |
| First Name: | Oliver |
| Address: | 451 E. Health Sci. Drive, Davis, CA, 95616, USA |
| Email: | ofiehn@ucdavis.edu |
| Publications: | Quality control for plant metabolomics: reporting MSI-compliant studies. DOI: 10.1111/j.1365-313X.2007.03387.x PubMed |
Subject:
| Subject ID: | SU000001 |
| Subject Type: | Plant |
| Subject Species: | Arabidopsis thaliana |
| Taxonomy ID: | 3702 |
| Genotype Strain: | Wassilewskija (Ws) | fatb-ko KD; At1g08510 |
| Species Group: | Plant |
Factors:
Subject type: Plant; Subject species: Arabidopsis thaliana (Factor headings shown in green)
| mb_sample_id | local_sample_id | Arabidopsis Genotype | Plant Wounding Treatment |
|---|---|---|---|
| SA000019 | LabF_115904 | fatb-ko KD; At1g08510 | Control - Non-Wounded |
| SA000020 | LabF_115909 | fatb-ko KD; At1g08510 | Control - Non-Wounded |
| SA000021 | LabF_115914 | fatb-ko KD; At1g08510 | Control - Non-Wounded |
| SA000022 | LabF_115919 | fatb-ko KD; At1g08510 | Control - Non-Wounded |
| SA000023 | LabF_115924 | fatb-ko KD; At1g08510 | Control - Non-Wounded |
| SA000024 | LabF_115929 | fatb-ko KD; At1g08510 | Control - Non-Wounded |
| SA000007 | LabF_115842 | fatb-ko KD; At1g08510 | Wounded |
| SA000008 | LabF_115847 | fatb-ko KD; At1g08510 | Wounded |
| SA000009 | LabF_115852 | fatb-ko KD; At1g08510 | Wounded |
| SA000010 | LabF_115857 | fatb-ko KD; At1g08510 | Wounded |
| SA000011 | LabF_115862 | fatb-ko KD; At1g08510 | Wounded |
| SA000012 | LabF_115867 | fatb-ko KD; At1g08510 | Wounded |
| SA000013 | LabF_115873 | Wassilewskija (Ws) | Control - Non-Wounded |
| SA000014 | LabF_115878 | Wassilewskija (Ws) | Control - Non-Wounded |
| SA000015 | LabF_115883 | Wassilewskija (Ws) | Control - Non-Wounded |
| SA000016 | LabF_115888 | Wassilewskija (Ws) | Control - Non-Wounded |
| SA000017 | LabF_115893 | Wassilewskija (Ws) | Control - Non-Wounded |
| SA000018 | LabF_115898 | Wassilewskija (Ws) | Control - Non-Wounded |
| SA000001 | LabF_115811 | Wassilewskija (Ws) | Wounded |
| SA000002 | LabF_115816 | Wassilewskija (Ws) | Wounded |
| SA000003 | LabF_115821 | Wassilewskija (Ws) | Wounded |
| SA000004 | LabF_115826 | Wassilewskija (Ws) | Wounded |
| SA000005 | LabF_115831 | Wassilewskija (Ws) | Wounded |
| SA000006 | LabF_115836 | Wassilewskija (Ws) | Wounded |
| Showing results 1 to 24 of 24 |
Collection:
| Collection ID: | CO000001 |
| Collection Summary: | - |
| Sample Type: | Plant |
| Volumeoramount Collected: | 50 mg |
Treatment:
| Treatment ID: | TR000001 |
| Treatment: | Abiotic |
| 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, http://www.sigmaaldrich.com/) containing 15 g l)1 bacto agar (BD) in 100 100 15 mm square Falcon Petri dishes (Thermo Fisher Scientific; http:// www.thermofisher.com). 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; http://www.3m.com), 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; http://www.sylvania.com), 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 |
| Sampleprep Summary: | - |
| 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 (http://www.retch-us.com) 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. labconco.com) 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 |
| Column | |
| MS Type | EI |
| MS instrument type | GC-TOF |
| MS instrument name | Leco Pegasus III GC TOF |
| Ion Mode | POSITIVE |
| Units | Peak height |
Chromatography:
| Chromatography ID: | CH000001 |
| Methods Filename: | nihms161442.pdf |
| Instrument Name: | Agilent 6890N |
| Chromatography Type: | GC |
MS:
| MS ID: | MS000001 |
| Analysis ID: | AN000001 |
| Instrument Name: | Leco Pegasus III GC TOF |
| Instrument Type: | GC-TOF |
| MS Type: | EI |
| Ion Mode: | POSITIVE |
