Summary of study ST000591

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, 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.
Institute
Agriculture and Agri-Food Canada
DepartmentLondon Research and Development Centre
LaboratoryRenaud
Last NameRenaud
First NameJustin
Address1391 Sandford street, London, Ontario, Canada
Emailjustin.renaud@agr.gc.ca
Phone519-953-6698
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
Analysis Type DetailLC-MS
Release Date2017-10-25
Release Version1
Justin Renaud Justin Renaud
https://dx.doi.org/10.21228/M86W3V
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

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
Department:Chemistry
Laboratory:Renaud
Last Name:Renaud
First Name:Justin
Address:1391 Sandford Street
Email:justin.renaud@agr.gc.ca
Phone:519-953-6698
Funding Source:Natural Science and Engineering Research Council of Canada (R4019A01) and Agriculture and Agri-Food Canada A-base

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:

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
SA032591WT-7Wild-type
SA032592WT-1Wild-type
SA032593WT-5Wild-type
SA032594WT-6Wild-type
SA032595WT-2Wild-type
SA032596WT-3Wild-type
SA032597WT-4Wild-type
Showing results 1 to 14 of 14

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:5 mM ammonium acetate, pH = 4.00
Solvent B:B = 90% acetonitrile, 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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