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MB Sample ID: SA032598
Local Sample ID: | ACC1-6 |
Subject ID: | SU000614 |
Subject Type: | Plant |
Subject Species: | Arabidopsis thaliana |
Taxonomy ID: | 3702 |
Genotype Strain: | Col-0 |
Age Or Age Range: | 12 Days after germination |
Weight Or Weight Range: | 50 mg |
Species Group: | Plant |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU000614 |
Subject Type: | Plant |
Subject Species: | Arabidopsis thaliana |
Taxonomy ID: | 3702 |
Genotype Strain: | Col-0 |
Age Or Age Range: | 12 Days after germination |
Weight Or Weight Range: | 50 mg |
Species Group: | Plant |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
ACC1-6 | SA032598 | FL007269 | acc1-knockout mutant | Genotype |
Collection:
Collection ID: | CO000608 |
Collection Summary: | Arabidopsis seeds obtained from the Arabidopsis Biological Resource Center (ABRC) at the Ohio State University were grown in half strength of Murashige and Skoog (½ MS) medium (0.5XMS salts, 1.5% [w/v] sucrose, and 0.8% agar [pH 5.8]) or soil under 16h/8h light/dark cycle at 23°C. Plants were harvested 12 days after germination. 50 mg of each plant (7 mutants, 7 wild type) were ground in liquid N2 using ball mill and immediately extracted following collection protocol. |
Collection Protocol Filename: | collection_protocol.pdf |
Sample Type: | Seedlings |
Collection Location: | London, Ontario |
Collection Frequency: | Single |
Treatment:
Treatment ID: | TR000628 |
Treatment Summary: | Effects of single gene knockout on arabidopsis metabolites compared to wild-type control. 7 replicates of wild-type, 7-replicates of acc1-5 knockout. |
Sample Preparation:
Sampleprep ID: | SP000621 |
Sampleprep Summary: | 50 mg of 12 DAG WT and acc1-5 seedlings were collected and grinded in liquid N2 using a ball-mill. The fine powders were suspended in 1 mL ice cooled methanol: water (4:1) by vortex. The mixtures were sonicated in water bath sonicator for 15 mins and followed by centrifugation at 11,000g for 10 mins at 4 °C. 700 µL of the supernatant was transferred into fresh tubes and evaporated to dryness using a vacufuge at ambient temperature. The residue was re-dissolved in 1:1 mixture of methanol: water and vortexed vigorously. All samples were filtered using 0.2 μm PTFE syringe filter (Whatman) and 5 µL of 1 µg/mL 13C6 phenylalanine internal standard (Cambridge Isotopes, Tewksbury, USA) were added to all samples |
Combined analysis:
Analysis ID | AN000906 |
---|---|
Analysis type | MS |
Chromatography type | HILIC |
Chromatography system | Agilent 1290 |
Column | SeQuant ZIC-pHILIC (100 x 2.1mm,3.5um) |
MS Type | ESI |
MS instrument type | Orbitrap |
MS instrument name | Thermo Q Exactive Orbitrap |
Ion Mode | POSITIVE |
Units | Peak area |
Chromatography:
Chromatography ID: | CH000643 |
Chromatography Summary: | Samples were resolved using HILIC column |
Instrument Name: | Agilent 1290 |
Column Name: | SeQuant ZIC-pHILIC (100 x 2.1mm,3.5um) |
Column Temperature: | 30C |
Flow Gradient: | 87% B for 5 minutes, decreased to 55% over 8 minutes and held for 4 minutes before returning to 87% over 3 minute |
Flow Rate: | 0.3 ml min-1 |
Internal Standard: | 13C6 phenylalanine internal standard |
Solvent A: | 100% water; 5 mM ammonium acetate, pH 4 |
Solvent B: | 90% acetonitrile/10% water; 0.1% formic acid |
Chromatography Type: | HILIC |
MS:
MS ID: | MS000805 |
Analysis ID: | AN000906 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | High resolution 140k for sample comparison. The automatic gain control (AGC) and maximum injection time (IT) were 3×106 and 524 ms respectively. |
Ion Mode: | POSITIVE |
Capillary Temperature: | 250°C |
Collision Energy: | - |
Dry Gas Flow: | 30 units |
Fragmentation Method: | HCD |
Ion Source Temperature: | 450 |
Ion Spray Voltage: | 3.9 kV |
Ionization: | ESI |
Mass Accuracy: | <5 ppm |
Dataformat: | .raw |
Scanning Range: | 93-1400 |