SE55:/S01
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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 |
