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| Status |
Public on Sep 30, 2012 |
| Title |
Transcriptome analysis of annotated coding genes and sORF in 16 organs and 17 environmental conditions at A. thaliana |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by array
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| Summary |
There are 16 organ samples (dry seeds, 24H imbibed seeds, 48H imbibed seeds, juvenile rosette, adult rosette, senescence leaves, cauline leaves, stems, young buds, mature flower buds, flowers, young siliques, mature siliques and old siliques) with triplicates. There are 17 samples of different environmental samples (0 h white, 1 h white, 6 h white, 24 h white, dark, blue, far-red and red lights, control, cold 2h, cold 6h, hot 2h, hot 6h, NaCl 2h, NaCl 6h, dry 2h and dry 6h) with triplicates.
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| Overall design |
For 12 organs, three lines of plants were grown in soil under the long-day conditions of 16 hours light at 22℃. Samples were collected from each of juvenile rosette leaves, adult rosette leaves, cauline leaves, stems, young flower buds (sepals were closed and petals are not visible), mature flower buds (petals are visible), flowers, young siliques filled with white seeds, mature siliques filled with green seeds, old yellowing siliques (2-month-old) and senescence rosettes. Root tissues were collected from 2-week-old plants growing on 1% agar plates containing Murashige and Skoog (MS). Callus were collected from cultured CIM (callus induction medium) containing B5 medium supplemented with 20 g liter–1 glucose, 0.5 mg liter–1 2,4-D, and 0.1 mg liter–1 kinetin. Dry seed was defined to be after-ripened seeds for 4 weeks. Imbibed seeds are collected from seeds imbibed on the moistened paper for 24 and 48 hours under the continuous light at 22℃. In light irradiations, wild type (WT) seeds were plated on MS plates. For the time course experiment of white light, the plates were placed at 4°C in darkness for at least 2 days prior to receiving 6 h red light irradiation to synchronize germination. Then, plates were placed in the dark for 3 days and then exposed to white fluorescent light (100 μmol m–2 s–1) for 1, 6 and 24 h. For monochromatic light experiment, WT seedlings were grown in continuous red light, blue light, far-red light, or darkness for 6 days after red light irradiation. The light intensity used was 0.17 μmol m–2 s–1 for red light, 1.16 μmol m–2 s–1 for blue light and 0.53 μmol m–2 s–1 for far-red light. All abiotic stress samplings were collected from plants grown for 2 weeks on MS plates under 2 and 6 hours of abiotic stress conditions at the continuous light at 22℃. For drought stress treatment, plants were transferred and dehydrated onto the dried filter paper in the covered plastic dishes. For heat and cold stress treatments, the covered plastic dishes with plants were transferred directly from 22 to 37 and 2℃ respectively. For salinity stress treatment, plants were transferred onto the filter paper moistened with MS plates including 200mM NaCl.
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| Contributor(s) |
Hanada K, Higuchi M, Okamoto M, Yoshizumi T, Shimizu M, Tanaka M, Horii Y, Kawashima M, Matsui K, Toyoda T, Shinozaki K, Seki M, Matsui M |
| Citation(s) |
23341627 |
| Submission date |
Dec 06, 2011 |
| Last update date |
Feb 04, 2013 |
| Contact name |
Kousuke Hanada |
| E-mail(s) |
kohanada@bio.kyutech.ac.jp
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| Organization name |
Kyushu Institute Technology
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| Department |
Department of Bioscience and Bioinformatics
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| Street address |
680-4 Kawazu
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| City |
Iizuka |
| State/province |
Fukuoka |
| ZIP/Postal code |
820-8502 |
| Country |
Japan |
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| Platforms (1) |
| GPL14937 |
Agilent-022830 RIKEN_AT_sORF0902 |
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| Samples (99)
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| Relations |
| BioProject |
PRJNA149703 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE34188_RAW.tar |
611.5 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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