Table 1.
Overview of the 366 Affymetrix rice genome microarrays and 177 Affymetrix Arabidopsis genome arrays used for the global analysis in this study.
| Sample details | GEO/AT-EXP | Rep | No. Arrays | Tissue | Publications |
|---|---|---|---|---|---|
| Development - Rice | |||||
| Dry seed and aerobic germination (up to 24 h) cv. Amaroo | E-MEXP-1766 | 3 | 15 | Dry and germinating seed | [83] |
| Dry seed and anaerobic germination (up to 24 h) and switch conditions cv. Amaroo | E-MEXP-2267 | 3 | 36 | Imbibed seed | [84] |
| Aerobic and anaerobic grown coleoptiles cv. Nipponbare | GSE6908 | 2 | 4 | Coleoptile | [85] |
| Embryo, endosperm, leaf and root from 7-d seedling, 10 d seedling cv. Zhonghua | GSE11966 | 2 | 10 | Embryo, endosperm, leaf and root from 7-d seedling, 10-d seedling | [86] |
| Stigma, Ovary cv. Nipponbare | GSE7951 | 3 | 6 | Stigma, ovary | [87] |
| Mature leaf, young leaf, semi apical meristem, inflorescence, seed cv. IR64 | GSE6893 | 3 | 45 | Mature leaf, young leaf, semi apical meristem, inflorescence, seed | [39] |
| Abiotic stress - Rice | |||||
| Drought, salt, cold stress cv. IR64 | GSE6901 | 3 | 12 | Seedling | [39] |
| Heat stress cv. Zhonghua | GSE14275 | 3 | 6 | Seedling | [71] |
| Salt stress on 2 cultivars; indica, FL478 (salt tolerant), indica, IR29 (salt sensitive) | GSE3053 | 3 | 11 | Crown and growing point | [88] |
| Salt stress on 4 cultivars; japonica, m103 (salt sensitive), indica, IR29 (salt sensitive), japonica, Agami (salt tolerant), indica, IR63731 (salt tolerant) | GSE4438 | 3 | 24 | Panicle initiation stage | [89] |
| Salt stress on root using 4 cultivars; FL478 (salt tolerant), IR29 (salt sensitive), IR63731 (salt tolerant), Pokkali (salt tolerant) | GSE14403 | 3 | 23 | Root | - |
| Fe and P treatments cv. Nipponbare | GSE17245 | 2 | 16 | Root | [90] |
| Arsenate treatment cv. Azucena | GSE4471 | 3 | 12 | Seedling | [91] |
| Physical stress at roots tips cv. Bala | GSE10857 | 3 | 12 | Root tip | [92] |
| Biotic stress - Rice | |||||
| S. Hermonthica plant parasite infection cv. Nipponbare (resistant), IAC165 (susceptible) | GSE10373 | 2 | 24 | Root | [93] |
| M. grisea blast fungus infection cv. Nipponbare | GSE7256 | 2 | 8 | Leaf | [94] |
| Rice stripe virus infection cv. WuYun3, KT95-418 | GSE11025 | 3 | 12 | Seedling | - |
| Infection with bacteria X. Oryzae pv. oryzicola and oryzae cv. Nipponbare | GSE16793 | 4 | 60 | Whole-plant tissue | - |
| Hormone treatment - Rice | |||||
| Cytokinin treatment on root and leaf cv. Nipponbare | GSE6719 | 3 | 24 | Root, 2-week old seedlings | [95] |
| Indole-3-actetic acid and benzyl aminopurine treatment cv. IR64 | GSE5167 | 2 | 6 | Seedling | [96] |
| Development - Arabidopsis | |||||
| AtGenExpress developmental tissue microarray dataset (wildtype only) | E-AFMX-9 | 3 | 147 | Wild type, different tissues | [97] |
| Abiotic stress - Arabidopsis | |||||
| AtGenExpress global stress expression dataset (wildtype) | GSE5620, GSE5624, GSE5623, GSE5621, GSE5628 | 2 | 30 | Wild type, shoots | [80] |
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 set in each experiment an experimental description is given with the respective cultivar (cv.) indicated, public Gene Expression Omnibus (GSE) identifier or MIAME Genexpress identifier (E-MEXP), the number of biological replications carried out (Reps), the number of arrays carried out in that experiment, the tissues analysed are described and a reference (if published) is shown.