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Table 1 Overview of the 366 Affymetrix rice genome microarrays and 177 Affymetrix Arabidopsis genome arrays used for the global analysis in this study.

From: Common and distinct organ and stress responsive transcriptomic patterns in Oryza sativa and Arabidopsis thaliana

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]

  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 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.
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BMC Plant Biology

ISSN: 1471-2229

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