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Table 1 Overview of experiments involving 373 Affymetrix rice genome microarrays used for the global analysis in this study.

From: Defining reference genes in Oryza sativausing organ, development, biotic and abiotic transcriptome datasets

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

  1. 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.
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BMC Plant Biology

ISSN: 1471-2229

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