SE45:/S01
From Metabolonote
lower pageM01
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). |
The raw data files are available at DROP Met web site in PRIMe database of RIKEN.
Related data are deposited in MetaboLights.
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 |
| 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).
The leaves were harvested September- through December 2008
The aerial part of each sample was harvested. All plant materials were frozen immediately in liquid nitrogen to quench enzymatic activity.
|
| Comment_of_details |
Related data are deposited in MetaboLights.
