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MB Sample ID: SA032594

Local Sample ID:WT-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

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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 IDMB Sample IDFactor Level IDLevel ValueFactor Name
WT-6SA032594FL007268Wild-typeGenotype

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
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