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MB Sample ID: SA028929
| Local Sample ID: | 236 |
| Subject ID: | SU000583 |
| Subject Type: | Plant |
| Subject Species: | Solanum lycopersicum |
| Taxonomy ID: | 4081 |
| Genotype Strain: | S. lycopersicum X S. pimpinellifolium |
| Age Or Age Range: | Dry Seeds - 6 hours Imbibed Seeds |
| Species Group: | Plant |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU000583 |
| Subject Type: | Plant |
| Subject Species: | Solanum lycopersicum |
| Taxonomy ID: | 4081 |
| Genotype Strain: | S. lycopersicum X S. pimpinellifolium |
| Age Or Age Range: | Dry Seeds - 6 hours Imbibed Seeds |
| Species Group: | Plant |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 236 | SA028929 | FL007044 | 6hImbibedSeeds | Treatment |
Collection:
| Collection ID: | CO000577 |
| Collection Summary: | None |
| Collection Protocol ID: | SL_COL_PROT |
| Collection Protocol Filename: | SL_COL_PROT.pdf |
| Sample Type: | Seeds |
| Volumeoramount Collected: | 30 mg |
Treatment:
| Treatment ID: | TR000597 |
| Treatment Summary: | In this study the F8 population of 100 Recombinant Inbred Lines (RILs) obtained from a cross between Solanum lycopersicum X Solanum pimpinellifolium were intelligently allocated to two sub-populations optimized for the distribution of parental alleles using the R-procedure DesignGG (Li et al., 2009; Joosen et al., 2013); hence 50 RIL lines were used for dry seeds and 50 lines for 6h imbibed seeds |
| Treatment: | Metabolites were extracted from dry and 6 hour imbibed seeds |
| Treatment Route: | Seed |
| Plant Growth Location: | The S. lycopersicum × S. pimpinellifolium RIL population was grown twice under controlled conditions in the greenhouse facilities at Wageningen University, in the Netherlands. |
| Plant Plot Design: | RCBD |
| Plant Light Period: | 16h light and 8h dark (long-day conditions) |
| Plant Humidity: | 30% RH |
| Plant Temp: | The day and night temperatures were maintained at 25 °C and 15 °C, respectively |
| Plant Watering Regime: | Watered Daily |
| Plant Nutritional Regime: | All the RILs were uniformly supplied with the basic dose of fertilizer |
| Plant Growth Stage: | Seeds were extracted from healthy fruits and treated with 1% hydrochloric acid (HCL) to remove the large pieces of the pulp that were sticking onto the seeds. |
| Plant Storage: | The cleaned seeds were dried for 3d at 20 °C and were stored in a cool, dry storage room (13 °C and 30% RH) in paper bags |
Sample Preparation:
| Sampleprep ID: | SP000590 |
| Sampleprep Summary: | The extraction method is modified from the method previously described by (Roessner et al., 2000). Approximately a bulk of approximately 70-100 seeds (30mg) seeds were homogenized in 2 ml tubes with 2 iron balls (2.5mm), pre-cooled in liquid nitrogen. For the homogenization the micro-dismembrator (Sartorius) is used at 1500 rpm. 700μl methanol/ chloroform (4:3) was added together with the standard (0.2mg/ml ribitol) and mixed thoroughly. After 10 minutes sonication, 200μl MQ was added to the mixture followed by vortexing and centrifuging (5 mins 13,500rpm). Methanol phase was collected in a glass vial. 500μl methanol/chloroform was added to the remaining organic phase and kept on ice for 10 minutes. 200μl MQ was added followed by vortexing and centrifuging (5 mins 13,500rpm). Again, the methanol phase was collected and mixed with the other collected phase. 100μl was dried overnight in a speedvac (35°C Savant SPD121). The GC-TOF-MS method was previously described by (Carreno-Quintero et al., 2012) with some minor modifications. Detector voltage was set at 1600V. Raw data was processed using the chromaTOF software 2.0 (leco instruments) and further processed using the Metalign software (Lommen, 2009), to extract and align the mass signals. A signal-to-noise ratio of 2 was used. The output was further processed by the Metalign Output Transformer (METOT; Plant Research International, Wageningen) and the mass signals that were present in less than 3 RILs were discarded. Out of all the mass signals, centrotypes are formed using the MSclust program (Tikunov et al., 2011). This resulted in 160 unique centrotypes (representative masses). The mass spectra of these centrotypes were used for identification by matching to an in-house constructed library, the NIST05 (National Institute of Standards and Technology, Gaithersburg, MD, USA; http://www.nist.gov/srd/mslist.htm) and Golm libraries (http://csbdb.mpimp-golm.mpg.de/csbdb/gmd/gmd.html)). This identification is based on spectra similarity and comparison with retention indices calculated by using a 3rd order polynomial function (Strehmel et al., 2008). |
| Sampleprep Protocol Filename: | SL_COL_PROT.pdf |
| Processing Method: | For the homogenization the micro-dismembrator (Sartorius) is used at 1500 rpm |
| Cell Type: | Seeds |
Combined analysis:
| Analysis ID | AN000862 | AN000863 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | GC | GC |
| Chromatography system | Agilent 6890N | Agilent 6890N |
| Column | Zebron Z-guard guard GC Cap 5m x 0.1mm | Zebron Z-guard guard GC Cap 5m x 0.1mm |
| MS Type | EI | EI |
| MS instrument type | GC x GC-TOF | GC x GC-TOF |
| MS instrument name | Agilent | Agilent |
| Ion Mode | POSITIVE | POSITIVE |
| Units | Peak Area | Peak Area |
Chromatography:
| Chromatography ID: | CH000613 |
| Chromatography Summary: | Untargetted GC-TOF-MS |
| Methods Filename: | SL_COL_PROT.pdf |
| Chromatography Comments: | Detector voltage: 1600 |
| Instrument Name: | Agilent 6890N |
| Column Name: | Zebron Z-guard guard GC Cap 5m x 0.1mm |
| Column Temperature: | 300°C |
| Flow Rate: | 1ml/min |
| Injection Temperature: | 70°C |
| Internal Standard: | Ribitol |
| Retention Index: | 1000-3100 |
| Retention Time: | 300-1800 sec |
| Sample Injection: | 2µL |
| Solvent A: | 20mg 0-methylhydroxylamine hydrochloride/ml pyridine |
| Solvent B: | MSTFA (derivatization agent) |
| Analytical Time: | 1800sec |
| Oven Temperature: | 70->300 |
| Running Voltage: | 1600 |
| Time Program: | 1800 sec |
| Transferline Temperature: | 270°C |
| Washing Buffer: | CHCl3 |
| Target Sample Temperature: | 40°C |
| Sample Syringe Size: | 25°C |
| Randomization Order: | Yes |
| Chromatography Type: | GC |
MS:
| MS ID: | MS000763 |
| Analysis ID: | AN000862 |
| Instrument Name: | Agilent |
| Instrument Type: | GC x GC-TOF |
| MS Type: | EI |
| MS Comments: | Dry Seed condition |
| Ion Mode: | POSITIVE |
| MS ID: | MS000764 |
| Analysis ID: | AN000863 |
| Instrument Name: | Agilent |
| Instrument Type: | GC x GC-TOF |
| MS Type: | EI |
| MS Comments: | 6 hours Imbibed Seeds |
| Ion Mode: | POSITIVE |
