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Sample Set Information

Title Toward genome-wide metabolotyping and elucidation of metabolic system: metabolic profiling of large-scale bioresources
Description We established a novel methodology, termed widely targeted metabolomics, which can generate thousands of metabolome data points in a high-throughput manner. We previously conducted a targeted metabolite analysis of large-scale Arabidopsis bioresources, namely transposon-tagged mutants and accessions, to make a smaller dataset of metabolite accumulation. In this paper, we release approximately 3,000 metabolic profiles obtained by targeted analysis for 36 metabolites and discuss the possible regulation of amino acid accumulation.
Authors Masami Yokota Hirai, Yuji Sawada, Shigehiko Kanaya, Takashi Kuromori, Masatomo Kobayashi, Romy Klausnitzer, Kosuke Hanada, Kenji Akiyama, Tetsuya Sakurai, Kazuki Saito, Kazuo Shinozaki
Reference Hirai YM et al. (2010) Journal of Plant Research 123: 291-298

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The raw data files are available at DROP Met web site in PRIMe database of RIKEN.

Sample Information

ID S01
Title Seeds of transposon-tagged mutants and Seeds of 225 accessions of Arabidopsis
Organism - Scientific Name Arabidopsis thaliana
Organism - ID NCBI taxonomy:3702
Compound - ID
Compound - Source
Preparation Seeds of transposon-tagged mutants were analyzed for metabolic profiling. From the Ds transposon singlecopy insertion lines that we previously established (Kuromori et al. 2006), we used 2,656 knockout mutants in which the Ds transposon was homozygously inserted into the coding regions. For each gene mutant, seeds were harvested from an F3 individual plant described in Kuromori et al. (2006). Briefly, F3 seeds were sown on agarsolidified MS medium containing 3% w/v sucrose and 20 lg mL-1 hygromycin. After stratification at 4℃ for 1 week, plants were grown for 3 weeks under a 16-h light/8-h dark cycle at 22℃, transferred to soil and grown under the same conditions with application of 2,000-fold diluted Hyponex (Hyponex Japan Co Ltd., Osaka, Japan) until seed maturity.
Sample Preparation Details ID SS01

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Sample Preparation Details Information

Title Sample Preparation
Description Seeds of 225 accessions of Arabidopsis were also analyzed for metabolic profiling. Seeds of each accession were sown on soil and germinated plants were grown in a greenhouse under natural light at 22℃ with application of 2,000-fold-diluted Hyponex until flowering finished. Then seeds were desiccated on plants for 1.5–2 months, harvested, and then stored at 4℃ and 20% humidity until use.

Analytical Method Information

ID M01
Title Metabolic profiling
Method Details ID MS01
Sample Amount N.A.
Comment Not written in the paper.

Analytical Method Details Information

Instrument UPLC (Waters)-quadrupole MS and ZQ mass spectrometers (Waters)
Instrument Type
Ionization ESI
Ion Mode Positive (amino acid analysis) and negative (glucosinolates and flavonoid analysis)
Description A total of 200 seeds of each independent mutant and accession were homogenized using a mixer mill MM 200 (Retsch) in 80 μL of extraction buffer [40% acetonitrile in H2O with 25 μM hydroxyphenyl–glucosinolate (GSL) and 50 μM norleucine as internal standards].The extracts were diluted with 500 lL of LC–MS grade H2O and centrifuged (1,000 g) for 5 min. The supernatants were filtered through a CAPTIVA 0.45μlm filter (Varian).

Thirty-six metabolites (17 amino acids, 18 GSLs, and 1 flavonoid; Table S1) were separated on UPLC through a reverse phase column (50 9 2.1 mm,HSS T3 1.8 μm; Waters) (Table S1) and detected using ZQ mass spectrometers (Waters) with an electrospray ionization (ESI) interface (positive mode for amino acid analysis; negative mode for glucosinolates and flavonoid analysis; capillary voltage, +3.0 and -3.0 keV; cone voltage, +25 and -40 V; source temperature, 120℃; desolvation temperature, 350℃; cone gas flow, 50 L/h; desolvation gas flow, 600 L/h).


Data Analysis Information

ID D01
Title High-throughput amino acid and glucosinolate analysis
Data Analysis Details ID DS01
Recommended decimal places of m/z Default

Data Analysis Details Information

Title High-throughput amino acid and glucosinolate analysis
Description MassLynx software version 4.0 (Waters) was used to control all instruments and calculate peak areas. The analytical error of this analysis using UPLCquadrupole MS is less than 10% (data not shown); thus, we did not perform an analytical replicate in this study.
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