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MB Sample ID: SA015469
| Local Sample ID: | AB33_I_3 |
| Subject ID: | SU000373 |
| Subject Type: | Plant |
| Subject Species: | Cynodon transvaalensis |
| Taxonomy ID: | 75728 |
| Genotype Strain: | AB03, AB33, and AB39 |
| Age Or Age Range: | 4 month old plant clones |
| Subject Comments: | (African Bermudagrass,C. transvaalensis) |
| Species Group: | Plant |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU000373 |
| Subject Type: | Plant |
| Subject Species: | Cynodon transvaalensis |
| Taxonomy ID: | 75728 |
| Genotype Strain: | AB03, AB33, and AB39 |
| Age Or Age Range: | 4 month old plant clones |
| Subject Comments: | (African Bermudagrass,C. transvaalensis) |
| Species Group: | Plant |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| AB33_I_3 | SA015469 | FL003453 | AB33 | Plant genotype |
| AB33_I_3 | SA015469 | FL003453 | inoc | Nematode inoculation |
Collection:
| Collection ID: | CO000367 |
| Collection Summary: | Rinsed roots were cut off the plant, placed into paper envelopes, and immediately placed into liquid nitrogen. Roots were stored at -80°C until freeze-drying. Freeze-dried roots were held at room temperature in ziploc bags with silica gel packets. They were then frozen in liquid nitrogen and ground to a powder in a tissue homogenizer with ball bearings (Geno/Grinder 2010), and then stored in 2 ml snap-cap plastic tubes at room temperature. |
| Sample Type: | plant root tissue |
| Collection Method: | whole plant destruction |
| Collection Location: | greenhouse |
| Collection Frequency: | once |
| Collection Duration: | 1-2 minutes to cut off and rinse the roots prior to placement into liquid nitrogen |
| Collection Time: | 136 days after inoculation |
| Volumeoramount Collected: | 0.2-0.5 grams of root tissue, dry weight |
| Storage Conditions: | 1)-80C until freeze-drying. 2) Held at room temperature in ziploc bags with silica packets. 3) Frozen in liquid nitrogen and ground using a Geno/Grinder 2010. 4) Transferred to 2 mL tubes and held at room temperature. |
| Collection Vials: | Paper coin envelopes |
| Storage Vials: | 2 ml snap-cap plastic tubes |
| Collection Tube Temp: | liquid nitrogen (-196°C) |
| Additives: | none |
Treatment:
| Treatment ID: | TR000387 |
| Treatment Summary: | Plants clones propagated by stolons were allowed to establish for 30 days in 4 cm diameter conetainers filled with sand. Fifty sting nematodes (mixed age and gender) were added to each conetainer and allowed to grow and reproduce for 90 days. Nematodes were then rinsed off of roots for quantification, and plant roots were frozen in liquid nitrogen and stored at -80C until they were freeze-dried.Freeze-dried roots were ground to a powder and then submitted for global metabolomic analysis. |
| Treatment: | Biotic |
| Treatment Compound: | Sting nematode, Belonolaimus longicaudatus |
| Plant Growth Support: | sand in conetainers- 4 cm wide, 30 cm deep |
| Plant Growth Location: | temperature controlled greenhouse |
| Plant Plot Design: | complete randomized design |
| Plant Light Period: | Natural lighting, ca. 11:13 Light:Dark |
| Plant Humidity: | ca.50%RH |
| Plant Temp: | 25°C |
| Plant Watering Regime: | Twice daily for 5 min |
| Plant Nutritional Regime: | Weekly liquid fertilizer of 24-8-16 (N-P-K) |
| Plant Estab Date: | 2015-09-24 |
| Plant Harvest Date: | 2016-04-02 |
| Plant Growth Stage: | non-reproductive |
| Plant Metab Quench Method: | liquid nitrogen, followed by storage at -80°C |
| Plant Harvest Method: | rinsed roots were cut off the plant and placed into paper envelopes |
| Plant Storage: | 1)-80C until freeze-drying. 2) Held at room temperature in ziploc bags with silica packets. 3) Frozen in liquid nitrogen and ground using a Geno/Grinder 2010. 4) Transferred to 2 mL tubes and held at room temperature. |
Sample Preparation:
| Sampleprep ID: | SP000380 |
| Sampleprep Summary: | none |
| Sampleprep Protocol Filename: | Maize_Tissue_sample_prep.pdf |
Combined analysis:
| Analysis ID | AN000575 | AN000576 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Scientific-Dionex Ultimate 3000 | Thermo Scientific-Dionex Ultimate 3000 |
| Column | ACE Excel 2 C18-PFP (100 x 2.1mm, 2um) | ACE Excel 2 C18-PFP (100 x 2.1mm, 2um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | peak area | peak area |
Chromatography:
| Chromatography ID: | CH000411 |
| Chromatography Summary: | See document |
| Methods Filename: | Metabolomics_LCMSProtocol.pdf Appendix_A_-_Internal_Standard_Prep_GLCMS.pdf |
| Instrument Name: | Thermo Scientific-Dionex Ultimate 3000 |
| Column Name: | ACE Excel 2 C18-PFP (100 x 2.1mm, 2um) |
| Flow Rate: | 0.350mL/min-0.600mL/min |
| Internal Standard: | Appendix A - Internal Standard Prep GLCMS.pdf |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS000511 |
| Analysis ID: | AN000575 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | HESI |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | Metabolomics_LCMSProtocol.pdf |
| MS ID: | MS000512 |
| Analysis ID: | AN000576 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | HESI |
| Ion Mode: | NEGATIVE |
| Analysis Protocol File: | Metabolomics_LCMSProtocol.pdf |
