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MB Sample ID: SA000013
| Local Sample ID: | LabF_115873 |
| Subject ID: | SU000001 |
| Subject Type: | Plant |
| Subject Species: | Arabidopsis thaliana |
| Taxonomy ID: | 3702 |
| Genotype Strain: | Wassilewskija (Ws) | fatb-ko KD; At1g08510 |
| Species Group: | Plant |
Select appropriate tab below to view additional metadata details:
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:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| LabF_115873 | SA000013 | FL000003 | Control - Non-Wounded | Plant Wounding Treatment |
| LabF_115873 | SA000013 | FL000003 | Wassilewskija (Ws) | Arabidopsis Genotype |
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 |
