Table 1.
Overview of experiments involving 373 Affymetrix rice genome microarrays used for the global analysis in this study.
| Sample description | Ref | GEO/other accession | Reps | Arrays | Tissue |
|---|---|---|---|---|---|
| DEVELOPMENT/TISSUE | |||||
| Dry seed and aerobic germination (up to 24 h) cv. Amaroo | [25] | E-MEXP-1766 | 3 | 15 | Dry and germinating seed |
| Dry seed and anaerobic germination (up to 24 h) and switch conditions cv. Amaroo | [21] | E-MEXP-2267 | 3 | 36 | Imbibed seed |
| Aerobic and anaerobic grown coleoptiles cv. Nipponbare | [27] | GSE6908 | 2 | 4 | Coleoptile |
| Embryo, endosperm, leaf and root from 7-d seedling, 10-d seedling cv. Zhonghua | [28] | GSE11966 | 2 | 10 | Embryo, endosperm, leaf and root from 7-d seedling, 10-d seedling |
| Stigma, Ovary+7 single arrays cv. Nipponbare | [29] | GSE7951 | 1-3 | 13 | Stigma, ovary+7 single arrays |
| Mature leaf, young leaf, semi apical meristem, inflorescence, seed cv. IR64 | [30] | GSE6893 | 3 | 45 | Mature leaf, young leaf, semi apical meristem, inflorescence, seed |
| ABIOTIC STRESS | |||||
| Drought, salt, cold stress cv. IR64 | [30] | GSE6901 | 3 | 12 | Seedling |
| Heat stress cv. Zhonghua | [31] | GSE14275 | 3 | 6 | Seedling |
| Salt stress on 2 cultivars; indica, FL478 (salt tolerant), indica, IR29 (salt sensitive) | [32] | GSE3053 | 3 | 11 | Crown and growing point |
| Salt stress on 4 cultivars; japonica, m103 (salt sensitive), indica, IR29 (salt sensitive), japonica, Agami (salt tolerant), indica, IR63731 (salt tolerant) | [33] | GSE4438 | 3 | 24 | Panicle initiation stage |
| Salt stress on root using 4 cultivars; FL478 (salt tolerant), IR29 (salt sensitive), IR63731 (salt tolerant), Pokkali (salt tolerant) | Not found | GSE14403 | 3 | 23 | Root |
| Fe and P treatments cv. Nipponbare | [34] | GSE17245 | 2 | 16 | Root |
| Arsenate treatment cv. Azucena | [35] | GSE4471 | 3 | 12 | Seedling |
| Physical stress at roots tips cv. Bala | [35] | GSE10857 | 3 | 12 | Root tip |
| BIOTIC STRESS | |||||
| S.Hermonthica plant parasite infection cv. Nipponbare (resistant), IAC165 (susceptible) | [36] | GSE10373 | 2 | 24 | Root |
| M.grisea blast fungus infection cv. Nipponbare | [37] | GSE7256 | 2 | 8 | Leaf |
| Rice stripe virus infection cv. WuYun3, KT95-418 | Not found | GSE11025 | 3 | 12 | Seedling |
| Infection with bacteria X.Oryzae pv. oryzicola and oryzae cv. Nipponbare | Not found | GSE16793 | 4 | 60 | Whole-plant tissue |
| HORMONE TREATMENT | |||||
| Cytokinin treatment on root and leaf cv. Nipponbare | [38] | GSE6719 | 3 | 24 | Root, 2-week old seedlings |
| Indole-3-actetic acid and benzyl aminopurine treatment cv. IR64 | [39] | GSE5167 | 2 | 6 | Seedling |
The microarray experiments are classified as development/tissue, abiotic stress, biotic stress or hormone treatment respectively, depending on the purpose of the experiment. For each microarray dataset; the sample/experimental description, the respective cultivar (cv.), the corresponding publication (Ref - where available), public Gene Expression Omnibus (GSE) identifier or MIAME Genexpress identifier (E-MEXP), the number of biological replications carried out (Reps), the number of microarrays carried out in that experimental dataset and the tissues analysed are shown.