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 |
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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 |
