SE55:/S01/M01/D01
From Metabolonote
Sample Set Information
| ID | SE55 |
|---|---|
| Title | AtMetExpress development: a phytochemical atlas of arabidopsis development |
| Description | We analyzed phytochemical accumulation during development of the model plant Arabidopsis (Arabidopsis thaliana) using liquid chromatography-mass spectrometry in samples covering many growth stages and organs. We also obtained tandem mass spectrometry spectral tags of many metabolites as a resource for elucidation of metabolite structure. These are part of the AtMetExpress metabolite accumulation atlas. Based on the dataset, we detected 1,589 metabolite signals from which the structures of 167 metabolites were elucidated. The integrated analyses with transcriptome data demonstrated that Arabidopsis produces various phytochemicals in a highly tissue-specific manner, which often accompanies the expression of key biosynthesis-related genes. We also found that a set of biosynthesis-related genes is coordinately expressed among the tissues. These data suggested that the simple mode of regulation, transcript to metabolite, is an origin of the dynamics and diversity of plant secondary metabolism. |
| Authors | Fumio Matsuda, Masami Yokota Hirai, Eriko Sasaki, Kenji Akiyama, Keiko Yonekura-Sakakibara, Nicholas J. Provart, Tetsuya Sakurai, Yukihisa Shimada, Kazuki Saito |
| Reference | Matsuda F et al. (2010) Plant Physiology 152: 566-578 |
| Comment |
The raw data files are available at DROP Met web site in PRIMe database of RIKEN.
Sample Information
| ID | S01 |
|---|---|
| Title | Arabidopsis (accession Columbia-0; Lehle Seeds) |
| Organism - Scientific Name | Arabidopsis thaliana |
| Organism - ID | NCBI taxonomy:3702 |
| Compound - ID | |
| Compound - Source | |
| Preparation | Seeds of Arabidopsis thaliana Col-0 was obtained from the ABRC. A. thaliana seedlings were grown under the following conditions.
See the table below. |
| Sample Preparation Details ID | SS01 |
| Comment |
| Sample name |
Corresponding microarray data in AtGenExpress |
Tissue | Age | Photoperiod | Substrate |
|---|---|---|---|---|---|
| ATME_ 1 | ATGE_ 1 | cotypedons | 10 days | continuous light | soil |
| ATME_ 7 | ATGE_ 7 | seedling,green parts | 10 days | continuous light | soil |
| ATME_ 9 | ATGE_ 9 | root | 21 days | continuous light | soil |
| ATME_ 10 | ATGE_ 10 | rosette leaf #4, 1 cm long |
14 days | continuous light | soil |
| ATME_ 12 | ATGE_ 12 | rosette leaf #2 | 21 days | continuous light | soil |
| ATME_ 13 | ATGE_ 13 | rosette leaf #4 | 21 days | continuous light | soil |
| ATME_ 14 | ATGE_ 14 | rosette leaf #6 | 21 days | continuous light | soil |
| ATME_ 15 | ATGE_ 15 | rosette leaf #8 | 21 days | continuous light | soil |
| ATME_ 16 | ATGE_ 16 | rosette leaf #10 | 21 days | continuous light | soil |
| ATME_ 19 | ATGE_ 19 | leaf7, petiole | 21 days | continuous light | soil |
| ATME_ 20 | ATGE_ 20 | leaf7, proximal half | 21 days | continuous light | soil |
| ATME_ 21 | ATGE_ 21 | leaf7, distal half | 21 days | continuous light | soil |
| ATME_ 25 | ATGE_ 25 | leaf, senescing | 35 days | continuous light | soil |
| ATME_ 26 | ATGE_ 26 | cauline leaves | 28 days | continuous light | soil |
| ATME_ 27 | ATGE_ 27 | stem, 2nd internode | 28 days | continuous light | soil |
| ATME_ 28 | ATGE_ 28 | 1st node | 28 days | continuous light | soil |
| ATME_ 29 | ATGE_ 29 | shoot apex, inflorescence (after bolting) |
28 days | continuous light | soil |
| ATME_ 32 | ATGE_ 32 | flowers stage 10/11 |
28 days | continuous light | soil |
| ATME_ 33 | ATGE_ 33 | flowers stage 12 | 28 days | continuous light | soil |
| ATME_ 39 | ATGE_ 39 | flowers stage 15 | 28 days | continuous light | soil |
| ATME_ 41 | ATGE_ 41 | flowers stage 15, sepals |
28 days | continuous light | soil |
| ATME_ 42 | ATGE_ 42 | flowers stage 15, petals |
28 days | continuous light | soil |
| ATME_ 45 | ATGE_ 45 | flowers stage 15, carpels |
28 days | continuous light | soil |
| ATME_ 76 | ATGE_ 76 | siliques, w/seeds stage 3 |
28 days | long day (16/8) | soil |
| ATME_ 77 | ATGE_ 77 | siliques, w/seeds stage 4 |
28 days | long day (16/8) | soil |
| ATME_ 78 | ATGE_ 78 | siliques, w/seeds stage 5 |
28 days | long day (16/8) | soil |
| ATME_ 91 | ATGE_ 91 | leaf | 15 days | long day (16/8) | 1x MS agar, 1% sucrose |
| ATME_ 92 | ATGE_ 92 | flower | 28 days | long day (16/8) | soil |
| ATME_ 93 | ATGE_ 93 | root | 15 days | long day (16/8) | 1x MS agar, 1% sucrose |
| ATME_ 95 | ATGE_ 95 | root | 08 days | continuous light | 1x MS agar, 1% sucrose |
| ATME_ 96 | ATGE_ 96 | seedling,green parts | 08 days | continuous light | 1x MS agar |
| ATME_ 97 | ATGE_ 97 | seedling,green parts | 08 days | continuous light | 1x MS agar, 1% sucrose |
| ATME_ 98 | ATGE_ 98 | root | 21 days | continuous light | 1x MS agar |
| ATME_ 99 | ATGE_ 99 | root | 21 days | continuous light | 1x MS agar, 1% sucrose |
| ATME_101 | ATGE_101 | seedling,green parts | 21 days | continuous light | 1x MS agar, 1% sucrose |
| ATME_ 84 | RIKEN-NAKABAYASHI | seed, mature | 16 wk | long day (16/8) | soil |
Sample Preparation Details Information
| ID | SS01 |
|---|---|
| Title | Sample Preparation |
| Description | Collected sample tissues were weighed and stored at -80℃ until analysis. |
| Comment_of_details |
Analytical Method Information
| ID | M01 |
|---|---|
| Title | Metabolic profiling Analysis Using LC-ESI-MS |
| Method Details ID | MS01 |
| Sample Amount | 3 μL |
| Comment |
Analytical Method Details Information
| ID | MS01 |
|---|---|
| Title | Metabolic profiling Analysis Using LC-ESI-MS |
| Instrument | Waters Acquity UPLC system and Waters Q-TOF Premier |
| Instrument Type | UPLC-QTOF-MS |
| Ionization | ESI |
| Ion Mode | Negative |
| Description | The frozen tissues were homogenized in five volumes of 80% aqueous methanol containing 0.1% acetic acid, 0.5 mg/L of lidocaine, and d-camphor sulfonic acid (Tokyo Kasei) using a mixer mill (MM 300, Retsch) with a zirconia bead for 6 min at 20 Hz. Following centrifugation at 15,000g for 10 min and filtration (Ultrafree-MC filter, 0.2 mm, Millipore), the sample extracts were applied to an HLB mElution plate (Waters) equilibrated with 80% aqueous methanol containing 0.1% acetic acid.
Metabolome analysis was performed with an LC-ESI-Q-TOF/MS system equipped with an ESI interface (HPLC: Waters Acquity UPLC system; MS: Waters Q-TOF Premier) operated under previously described conditions (Matsuda et al., 2009). In the negative ion mode, the MS conditions were as follows: capillary voltage: +3.0 keV; cone voltage: 22.5 V; source temperature: 120℃; desolvation temperature: 450℃; cone gas flow: 50 L/h; desolvation gas flow: 800 L/h; collision energy: 2 V; detection mode: scan (m/z 100–2,000; dwell time: 0.45 s; interscan delay: 0.05 s, centroid); dynamic range enhancement mode: on. The scans were repeated for 19.5 min in a single run. |
| Comment_of_details |
Data Analysis Information
| ID | D01 |
|---|---|
| Title | Profiling by MetAlign and MS2T-based peak annotation |
| Data Analysis Details ID | DS01 |
| Recommended decimal places of m/z | Default |
| Comment |
Data Analysis Details Information
| ID | DS01 |
|---|---|
| Title | Profiling by MetAlign and MS2T-based peak annotation |
| Description | The scans were repeated for 19.5 min in a single run. The raw data were recorded with the aid of MassLynx version 4.1 software (Waters).The raw chromatogram data were processed to produce a data matrix consisting of 1,589 metabolite signals (773 from positive and 816 from negative ion mode; Supplemental Data S1) using MetAlign (Lommen, 2009). The parameters used for data processing were as follows: maximum amplitude, 10,000; peak slope factor, 1; peak threshold factor, 6; average peakwidth at half weight, 8; scaling options, none; maximum shift per scan, 35; select min nr per peak set, 4. The data matrix generated by MetAlign was processed with inhouse software written in Perl/Tk (Matsuda et al., 2009). By this procedure, the metabolite signals eluted before 0.85 min and after 12.0 min were discarded, original peak intensity values were divided with those of the internal standards (lidocaine: m/z = 235 [M + H]+, eluted at 4.19 min; camphor-10-sulfonic acid: m/z = 231 [M 2 H]2, eluted at 3.84 min, for the positive and negative ion modes, respectively) to normalize the peak intensity values, discarding low-intensity data (under signal-to-noise ratio , 5), and isotope peaks were removed by employing specific parameters (rthres . 0.8, DRt = 0.5 s, and Dm/z = 2 D). Metabolite signals were assigned unique accession codes, such as adn031026 (representing AtMetExpress Development negative ion mode data, peak number 31026).
MS2T data were acquired from nine tissues of Arabidopsis and processed to create 36 MS2T libraries using previously described methods (Matsuda et al., 2009). Each MS2T entry was assigned a unique accession code, such as ATH10n03690, in which ATH10n is the name of the library and 03690 is the entry number. A total of 36 MS2T libraries with 476,120 accession codes were created in this study (Supplemental Table S2). The MS2T libraries contain a high volume of redundant and low-quality data (Matsuda et al., 2009). Since the metabolic profile data and the MS2T libraries were acquired using compatible analytical conditions, a metabolite signal obtained in the profile can be tagged with MS2Ts obtained from a corresponding metabolite with identical unit mass eluting at a similar retention time. By this method, approximately 95% of the metabolite signals were tagged with at least one MS2T. The mean number of MS2Ts tagged to each metabolite peak was 13.5. |
| Comment_of_details |
