SE45:/S01/M01

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Sample Set Information

ID SE45
Title Metabolomic Characterization of Knockout Mutants in Arabidopsis: Development of a Metabolite Profiling Database for Knockout Mutants in Arabidopsis
Description Despite recent intensive research efforts in functional genomics, the functions of only a limited number of Arabidopsis (Arabidopsis thaliana) genes have been determined experimentally, and improving gene annotation remains a major challenge in plant science. As metabolite profiling can characterize the metabolomic phenotype of a genetic perturbation in the plant metabolism, it provides clues to the function(s) of genes of interest. We chose 50 Arabidopsis mutants, including a set of characterized and uncharacterized mutants, that resemble wild-type plants. We performed metabolite profiling of the plants using gas chromatography-mass spectrometry. To make the data set available as an efficient public functional genomics tool for hypothesis generation, we developed the Metabolite Profiling Database for Knock-Out Mutants in Arabidopsis (MeKO). It allows the evaluation of whether a mutation affects metabolism during normal plant growth and contains images of mutants, data on differences in metabolite accumulation, and interactive analysis tools. Nonprocessed data, including chromatograms, mass spectra, and experimental metadata, follow the guidelines set by the Metabolomics Standards Initiative and are freely downloadable. Proof-of-concept analysis suggests that MeKO is highly useful for the generation of hypotheses for genes of interest and for improving gene annotation. MeKO is publicly available at http://prime.psc.riken.jp/meko/.
Authors Atsushi Fukushima, Miyako Kusano, Ramon Francisco Mejia, Mami Iwasa, Makoto Kobayashi, Naomi Hayashi, Akiko Watanabe-Takahashi, Tomoko Narisawa, Takayuki Tohge, Manhoi Hur, Eve Syrkin Wurtele, Basil J. Nikolau, Kazuki Saito, RIKEN CSRS
Reference Fukushima et al. (2014) Plant Physiology 165:948-961 (PMID: 24828308)
Comment The raw data files are available at DropMet web site in PRIMe database, MetaboLights (Salek et al., 2013) (accession no. MTBLS47), and The MetabolomeExpress (Carroll et al., 2010).


Link icon article.png

Link icon database.png

Link icon database.png Link icon dropmet.png

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

Link icon database.png Link MetaboLights.png

Related data are deposited in MetaboLights.

Link icon database.png Link MetabolomeExpress.png

Related data are deposited in MetabolomeExpress.

Sample Information

ID S01
Title Arabidopsis (Aerial parts,ecotype: Col-0 or Col)
Organism - Scientific Name Arabidopsis thaliana
Organism - ID NCBI taxonomy:3702
Compound - ID
Compound - Source
Preparation All mutants were purchased from the Arabidopsis Biological Resource Center (ABRC, https://abrc.osu.edu/).
Sample Preparation Details ID SS01
Comment


The mutants used in this study
Line AGI or ID Background Germplasm / StockID
aat2-2 AT5G19550 Col CS3971
aba1-5 AT5G67030 Col CS155
aba1-6 AT5G67030 Col-0 CS3772
aba2-1 AT1G52340 Col CS156
aba2-3 AT1G52340 Col CS156
aba3-1 AT1G16540 Col CS157
amt1-1 AT4G13510 Col CS6168
cim10 CIM10 Col CS6574
cim11 CIM11 Col CS6575
cim13 CIM13 Col CS6576
cim14 CIM14 Col CS6577
cim6 CIM6 Col CS6571
cim7 CIM7 Col CS6572
cim9 CIM9 Col CS6573
cla-1S AT4G15560 Col CS16003
cob-2 AT5G60920 Col CS8542
eto1-1 AT3G51770 Col CS3072
eto3 AT3G49700 Col CS8060
fad5-1 AT3G15850 Col CS206
fad6-1 AT4G30950 Col CS207
fah1-2 AT4G36220 Col CS6172
fur1-1 AT4G05120 Col CS3729
fus6-1S AT3G61140 Col CS16057
gsr1-1 GSR1 Col CS6391
ixr1-1 AT5G05170 Col CS6201
ixr1-2 AT5G05170 Col CS6202
mur1-1 AT3G51160 Col CS6243
mur1-2 AT3G51160 Col CS6244
mur2-1 AT2G03220 Col CS8565
mur3-2 AT2G20370 Col CS8567
mur4-2 AT1G30620 Col CS8569
mur5-1 MUR5 Col CS8572
mur6-1 MUR6 Col CS8573
mur7-1 MUR7 Col CS8574
mur8-1 MUR8 Col CS8575
mur9-1 MUR9 Col CS8576
mur11-1 MUR11 Col CS8579
pac-1S AT2G48120 Col CS16058
pad2-1 AT4G23100 Col CS3804
pad3-1 AT3G26830 Col CS3805
pad4-1 AT3G52430 Col CS3806
pap1-D AT1G56650 Col CS3884
phyB-9 AT2G18790 Col CS6217
prc1-1 AT5G64740 Col CS297
rsw1-1 AT4G32410 Col CS6554
rsw2-1 AT5G49720 Col CS6555
rsw3-1 AT5G63840 Col CS6556
sng1-1 AT2G22990 Col CS3737
tbr-1 AT5G06700 Col CS3741
vtc1-1 AT2G39770 Col-0 CS8326

Sample Preparation Details Information

ID SS01
Title Sample Preparation
Description <Growth condition>

Sterilized seeds were stratified at 5°C for 2 days and then sown on Murashige and Skoog medium containing 1% sucrose. Seedlings of Arabidopsis Col-0 and the mutants were cultivated in controlled growth chambers at 22°C under 16-h light and 8-h dark conditions for 18 days (light strength approximately 80 photosynthetic photon flux).


<Sampling and sampling date>

The leaves were harvested September- through December 2008


<Metabolism quenching method>

The aerial part of each sample was harvested. All plant materials were frozen immediately in liquid nitrogen to quench enzymatic activity.


The all raw data are also available in MetaboLights (Salek et al., 2013) (accession no. MTBLS47), and The MetabolomeExpress (Carroll et al., 2010).

Comment_of_details


Link icon database.png Link MetaboLights.png

Related data are deposited in MetaboLights.

Link icon database.png Link MetabolomeExpress.png

Related data are deposited in MetabolomeExpress.

Analytical Method Information

ID M01
Title GC-TOF MS
Method Details ID MS01
Sample Amount 1 μL
Comment


Analytical Method Details Information

ID MS01
Title GC-TOF/MS
Instrument GC Agilent 6890N gas chromatograph / MS Pegasus IV TOF mass spectrometer
Instrument Type
Ionization EI
Ion Mode Positive
Description <Sample processing and extraction>

Each sample was extracted at a concentration of 5 mg flesh weight (FW) of tissues per ml extraction medium (methanol / chloroform/water [3:1:1 v/v/v]) containing 10 stable isotope reference compounds:

• [2H4]-succinic acid

• [13C5,15N]-glutamic acid

• [2H7]-cholesterol

• [13C3]-myristic acid

• [13C5]-proline

• [13C12]-sucrose

• [13C4]-hexadecanoic acid

• [2H4]-1,4-butanediamine

• [2H6]-2-hydoxybenzoic acid

• [13C6]-glucose

using a Retsch mixer mill MM310 at a frequency of 30 Hz for 3 min at 4°C. Each isotope compound was adjusted to a final concentration of 15 ng µl-1 for each 1-µl injection. After 5-min centrifugation at 15,100 × g, a 100 µl aliquot of the supernatant was drawn and transferred into a glass insert vial. The extracts were evaporated to dryness in an SPD2010 SpeedVac® concentrator from ThermoSavant (Thermo Electron Corporation, Waltham, MA, USA). For methoximation, 30 µl of methoxyamine hydrochloride (20 mg/ml in pyridine) was added to the sample. After 24 h of derivatization at room temperature, the sample was trimethylsilylated for 1 h using 30 µl of MSTFA with 1% TMCS at 37°C with shaking. For methoximation, 30 µl of methoxyamine hydrochloride (20 mg ml-1 in pyridine) were added to the sample. After 24 h of derivatization at room temperature, the sample was trimethylsilylated for 1 h using 30 µl of MSTFA at 37°C with shaking. After silylation 30 µl of n-heptane were added. All derivatization steps were performed in the vacuum glove box VSC-100 (Sanplatec, Japan) filled with 99.9995% (G3 grade) of dry nitrogen.

<GC-TOF/MS conditions>
Using the splitless mode by an CTC CombiPAL auto-sampler (CTC analytics, Zwin-gen, Switzerland), 1 µl of each sample was injected into an Agilent 6890N gas chromatograph (Agilent Technologies, Wilmingston, USA) featuring a 30 m x 0.25 mm inner diameter fused-silica capillary column with a chemically bound 0.25-µl film Rtx-5 Sil MS stationary phase (RESTEK, Bellefonte, USA) for metabolome analysis. Helium was delivered as the carrier gas at a constant flow rate of 1 ml min-1. The temperature program for metabolome analysis started with a 2-min isothermal step at 80°C followed by temperature ramping of 30°C to a final temperature of 320°C, which was maintained for 3.5 min. The transfer line and the ion source temperatures were 250 and 200°C, respectively. Ions were generated with a 70-eV electron beam at an ionization current of 2.0 mA. Data acquisition was on a Pegasus IV TOF MS instrument (LECO, St. Joseph, MI, USA) at an acquisition rate of 30 spectra s-1 in the mass range of a mass-to-charge ratio of m/z = 60-800. The solvent delay was 237 sec. Alkane standard mixtures (C8-C20 and C21-C40) were purchased from Sigma-Aldrich (Tokyo, Japan) and used for calculating the retention index (RI). The normalized response for calculating the signal intensity of each metabolite from the mass-detector response was obtained with each selected ion current unique in each metabolite MS spectrum to normalize the peak response. For quality control, we injected methylstearate in every 6 samples. Quality control (QC) samples were prepared by mixing 100 μl of extracts of each wild-type sample. We run six QC samples per batch (30 samples in total).

Comment_of_details
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