SE59:/S01/M01/D01
Sample Set Information
| ID | SE59 |
|---|---|
| Title | Alternation of flavonoid accumulation under drought stress in Arabidopsis thaliana |
| Description | We reported that flavonoids, a class of specialized metabolites, including flavonols and anthocyanins with strong radical scavenging activity contributed to the mitigation of oxidative and drought stress in Arabidopsis thaliana (Arabidopsis). However, the behavior of flavonoids during drought stress is still not well documented. Herein we investigated the time-series alternation of flavonoids in the aerial part of Arabidopsis (wild type, Col-0) during drought stress by LC-QTOF-MS. The drastic alternation of 5 flavonols and 5 anthocyanins was revealed together with changes in marker metabolites of drought stress, e.g., proline, raffinose, and galactinol. These findings indicate that flavonols and anthocyanins can mitigate drought stress. |
| Authors | Ryo Nakabayashi, Tetsuya Mori, and Kazuki Saito |
| Reference | Nakabayashi R et al. (2014) Plant Signaling & Behavior 9: e29518 |
| Comment |
The raw data files are available at DROP Met web site in PRIMe database of RIKEN.
Sample Information
| ID | S01 |
|---|---|
| Title | Arabidopsis |
| Organism - Scientific Name | Arabidopsis thaliana |
| Organism - ID | NCBI taxonomy:3702 |
| Compound - ID | |
| Compound - Source | |
| Preparation | Treatment dose or intensity levels: The plants vertically grown in GM plates were incubated in 24-well plates (TPP, http://www.tpp.ch/index.php) and each plant was put in a well with 3 ml water.
Treatment time, time intervals and duration before harvest: 0 day Harvest date, time: no information Plant growth stage: 3 weeks (GM plate) + 0 day (treatment) Metabolism quenching method: Freezing with liquid N2 Harvest method: After removing root, the samples were immediately frozen with liquid nitrogen and lyophilized at −55 °C. Sample strage: The lyophilized materials were stored at −80 °C. Reprecate sampling and analyses: n=3 Tissue harvesting method: Time from tissue resection to liquid N2 freezing was one minute. Tissues were pooled in tube. |
| Sample Preparation Details ID | SS01 |
| Comment |
Sample Preparation Details Information
| ID | SS01 |
|---|---|
| Title | Drought stress |
| Description | Three-week-old plants vertically grown on GM plates were incubated in 24-well plates (TPP, http://www.tpp.ch/index.php). Each plant was put in a well with 3 ml water. Three-week-old plants were exposed to drought stress by stopping watering.The aerial samples were harvested at the time points of DAD 0, 3, and 5. |
| Comment_of_details | DAD, days after drought. |
Analytical Method Information
| ID | M01 |
|---|---|
| Title | LC-QTOF-MS |
| Method Details ID | MS01 |
| Sample Amount | N.A. |
| Comment | Not written in the paper. |
Analytical Method Details Information
| ID | MS01 |
|---|---|
| Title | Untargeted metabolomic analysis of LC-QTOF-MS |
| Instrument | LC, Waters Acquity UPLC system; MS, Waters Xevo G2 Q-Tof |
| Instrument Type | UPLC-QTOF-MS |
| Ionization | ESI |
| Ion Mode | Positive |
| Description | Tissue processing method: The lyophilized materials were ground using a mixer mill (MM300, Retsch) with zirconia beads for 2 min at 18 Hz and 4 °C.
Storage condition prior to extraction or further processing: The lyophilized powder materials were stored at −80 °C. Extraction method: The freeze-dried samples were extracted with 50 ml of 80% MeOH containing 2.5 mM lidocaine per mg dry weight using a mixer mill (MM300, Retsch) with zirconia beads for 10 min at 20 Hz and 4 °C. Extract cleanup and/or Additional manipulation: After centrifugation for 10 min, the supernatant was filtered using an HLB mElution plate (Waters). Extract storage and/or relocate: not storaged Chromatography instrument description: LC, Waters Acquity UPLC system Separation column and pre/guard column: column, Acquity BEH C18 (1.7 μm, 2.1 mm x 100 mm, Waters) Separation parameter: solvent system, solvent A (water with 0.1% formic acid) and solvent B (acetonitrile with 0.1% formic acid) Instrument description: Waters Xevo G2 Q-Tof Sample introduction and delivery: From LC Ionization source: ESI positive. column temperature, 40 °C; MS detection: capillary voltage, +3.0 keV, cone voltage, 25.0 V, source temperature, 120 °C, desolvation temperature, 450 °C, cone gas flow, 50 l/h; desolvation gas flow, 800 l/h; collision energy, 6 V; MS/MS detection: collision energy, rampled from 10 to 50V Mass analyzer description and acquisition mode: quadrupole-time-of-flight Data acquisition parameters: MS: mass range, m/z 100‒1500; scan duration, 0.1 sec; interscan delay, 0.014 sec; data acquisition, centroid mode. MS/MS: m/z 50–1500; scan duration, 0.02 sec; inter-scan delay, 0.014 sec; data acquisition, centroid mode; MS/MS spectra of the top 10 ions (> 1000 counts) in an MS scan were automatically obtained. |
| Comment_of_details |
Data Analysis Information
| ID | D01 |
|---|---|
| Title | Data analysis |
| Data Analysis Details ID | DS01 |
| Recommended decimal places of m/z | Default |
| Comment |
Data Analysis Details Information
| ID | DS01 |
|---|---|
| Title | Data analysis |
| Description | <Untargeted metabolomic analysis of LC-QTOF-MS> The untargeted metabolomic analysis using LC-QTOF-MS and the metabolome data processing of alignment, de-isotoping, noise cutting, and normalization was conducted as previously described. |
| Comment_of_details |
The raw data files are available at DROP Met web site in PRIMe database of RIKEN.
