Summary of Study ST000591

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR000432. The data can be accessed directly via it's Project DOI: 10.21228/M86W3V This work is supported by NIH grant, U2C- DK119886.


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Study IDST000591
Study TitleMetablomic profiling in acc1-5 mutant and wild type arabidiopsis
Study SummaryThis experiment tests the metabolic consequence of a mutation at the ACC1 gene (At1g36160). The allele of acc1-5 bearing an EMS mutation, which cause a single amino acid substitution from aspartic acid to asparagine. Seedlings from both the acc1-5 mutant and the wild type were harvested and analyzed via HILIC LC-MS. Of particular interest are metabolites which would be affected by depletion of malonyl-CoA pools (flavenoids) and primary metabolites.
Agriculture and Agri-Food Canada
DepartmentLondon Research and Development Centre
Last NameRenaud
First NameJustin
Address1391 Sandford street, London, Ontario, Canada
Submit Date2017-03-12
PublicationsChen, Chen, et al. "Cytosolic acetyl-CoA promotes histone acetylation predominantly at H3K27 in Arabidopsis." Nature Plants (2017): 1.
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2017-10-25
Release Version1
Justin Renaud Justin Renaud application/zip

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Project ID:PR000432
Project DOI:doi: 10.21228/M86W3V
Project Title:Understanding the effects of acetyl-CoA carboxylase (ACC1) upon the metabolite profiles of Arabidopsis
Project Type:Single gene knockout impact on Arabidopsis metabolites
Project Summary:The arabidopsis gene, acetyl-CoA carboxylase1 (ACC1) catalyzes the carboxylation of acetyl-CoA to malonyl-CoA. When this gene malfunctions, there are elevated levels of acetyl-CoA which have been shown to increase levels of histone acetylation. This project aims to understand how a malfunctioning ACC1 effects the levels of primary metabolites by comparing to metabolite profiles of wild type Arabidopsis grown under identical conditions.
Institute:Agriculture and Agri-Food Canada
Last Name:Renaud
First Name:Justin
Address:1391 Sandford Street
Funding Source:Natural Science and Engineering Research Council of Canada (R4019A01) and Agriculture and Agri-Food Canada A-base


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


Subject type: Plant; Subject species: Arabidopsis thaliana (Factor headings shown in green)

mb_sample_id local_sample_id Genotype
SA032598ACC1-6acc1-knockout mutant
SA032599ACC1-7acc1-knockout mutant
SA032600ACC1-5acc1-knockout mutant
SA032601ACC1-1acc1-knockout mutant
SA032602ACC1-2acc1-knockout mutant
SA032603ACC1-3acc1-knockout mutant
SA032604ACC1-4acc1-knockout mutant
Showing results 1 to 14 of 14


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 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 instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Units Peak area


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 ID:MS000805
Analysis ID:AN000906
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
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.
Capillary Temperature:250°C
Collision Energy:-
Dry Gas Flow:30 units
Fragmentation Method:HCD
Ion Source Temperature:450
Ion Spray Voltage:3.9 kV
Mass Accuracy:<5 ppm
Scanning Range:93-1400