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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000591 |
| Study Title | Metablomic profiling in acc1-5 mutant and wild type arabidiopsis |
| Study Summary | This 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 |
| Department | London Research and Development Centre |
| Laboratory | Renaud |
| Last Name | Renaud |
| First Name | Justin |
| Address | 1391 Sandford street, London, Ontario, Canada |
| justin.renaud@agr.gc.ca | |
| Phone | 519-953-6698 |
| Submit Date | 2017-03-12 |
| Publications | Chen, Chen, et al. "Cytosolic acetyl-CoA promotes histone acetylation predominantly at H3K27 in Arabidopsis." Nature Plants (2017): 1. |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2017-10-25 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |
|---|---|---|
| SA032598 | ACC1-6 | acc1-knockout mutant |
| SA032599 | ACC1-7 | acc1-knockout mutant |
| SA032600 | ACC1-5 | acc1-knockout mutant |
| SA032601 | ACC1-1 | acc1-knockout mutant |
| SA032602 | ACC1-2 | acc1-knockout mutant |
| SA032603 | ACC1-3 | acc1-knockout mutant |
| SA032604 | ACC1-4 | acc1-knockout mutant |
| SA032591 | WT-7 | Wild-type |
| SA032592 | WT-1 | Wild-type |
| SA032593 | WT-5 | Wild-type |
| SA032594 | WT-6 | Wild-type |
| SA032595 | WT-2 | Wild-type |
| SA032596 | WT-3 | Wild-type |
| SA032597 | WT-4 | Wild-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: | 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 |
