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Table 3 The over- and under-amplified loci.

From: Statistical evaluation of transcriptomic data generated using the Affymetrix one-cycle, two-cycle and IVT-Express RNA labelling protocols with the Arabidopsis ATH1 microarray

Probe ID

current 1-cyc vs. 2-cyc

current IVT-E vs. 2-cyc

Stepanova vs. Birnbaum

AGI code

Description

247762_at

16.4

39.8

2.4

AT5G59170

Proline-rich family protein.

249552_s_at

19.7

25.9

1.8

AT5G38250

AT5G38240

AT5G38250, serine/threonine protein kinase, putative; AT5G38240, serine/threonine protein kinase, putative.

251127_at

3.4

8.3

2.1

AT5G01080

Beta-galactosidase.

252971_at

10.9

22.5

1.6

AT4G38770

PRP4 (PROLINE-RICH PROTEIN 4).

255138_at

12.5

14.2

1.8

AT4G08380

Proline-rich extensin-like family protein.

262566_at

28.2

63.1

3.0

AT1G34310

ARF12 (AUXIN RESPONSE FACTOR 12); transcription factor.

266152_s_at

14.3

17.2

2.8

AT3G31908

AT3G32377

AT2G12050

AT3G31908, pseudogene, similar to aintegumenta-like protein; AT3G32377, pseudogene, similar to aintegumenta-like protein; AT2G12050, pseudogene, embryogenesis protein-related, similar to BABY BOOM (A. thaliana).

266154_at

39.1

47.1

3.0

AT2G12190

Cytochrome P450, putative.

245513_at

4.4

4.0

3.2

AT4G15780

ATVAMP724 (Arabidopsis thaliana vesicle-associated membrane protein 724).

245665_at

4.8

5.1

2.4

AT1G28250

Similar to hypothetical protein [Oryza sativa (japonica cultivar-group)] (GB:BAC84779.1).

246210_at

8.0

6.9

2.3

AT4G36420

Ribosomal protein L12 family protein.

249583_at

5.4

5.8

1.8

AT5G37770

TCH2 (TOUCH 2); calcium ion binding.

250226_at

7.4

6.6

3.6

AT5G13780

GCN5-related N-acetyltransferase, putative.

250935_at

9.0

8.9

39.7

AT5G03240

UBQ3 (POLYUBIQUITIN 3); protein binding.

253189_at

8.3

6.0

5.8

no_match

No_match.

253464_at

6.8

4.7

3.4

AT4G32030

Unknown protein.

253545_at

5.4

7.4

4.0

AT4G31310

Avirulence-responsive protein-related/avirulence induced gene (AIG) protein-related.

256092_at

9.8

12.4

8.3

AT1G20696

HMGB3 (HIGH MOBILITY GROUP B 3); transcription factor.

256231_at

9.4

9.5

5.3

AT3G12630

Zinc finger (AN1-like) family protein.

258001_at

5.5

6.2

9.8

AT3G28950

Avirulence-responsive protein-related/avirulence induced gene (AIG) protein-related.

258397_at

6.1

6.1

1.9

AT3G15357

Unknown protein.

258958_at

7.0

10.4

4.6

AT3G01390

VMA10 (VACUOLAR MEMBRANE ATPASE 10).

259095_at

5.9

6.2

1.7

AT3G05020

ACP1 (ACYL CARRIER PROTEIN 1).

262295_at

7.7

4.9

4.4

AT1G27650

ATU2AF35A; RNA binding.

263878_s_at

4.7

4.4

3.8

AT3G18140

AT2G22040

AT3G18140, transducin family protein/WD-40 repeat family protein; AT2G22040, transducin family protein/WD-40 repeat family protein.

264566_at

6.8

4.6

5.6

AT1G05270

TraB family protein.

264702_at

5.3

5.3

3.0

AT1G70190

Ribosomal protein L12 family protein.

265103_at

12.9

4.2

3.9

AT1G31070

UDP-N-acetylglucosamine pyrophosphorylase-related.

265443_at

6.4

6.7

3.0

AT2G20750

ATEXPB1 (ARABIDOPSIS THALIANA EXPANSIN B1).

266074_at

5.1

8.1

1.7

AT2G18740

Small nuclear ribonucleoprotein E, putative/snRNP-E, putative/Sm protein E, putative.

266125_at

6.9

6.3

1.8

AT2G45050

Zinc finger (GATA type) family protein.

267064_at

6.8

7.9

2.9

AT2G41110

CAM2 (CALMODULIN-2); calcium ion binding.

AFFX-Athal-GAPDH_5_s_at

13.4

8.3

11.8

AT3G04120

GAPC (GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE C SUBUNIT); glyceraldehyde-3-phosphate dehydrogenase.

  1. Loci classed as over- (above the break line) and under-amplified (below the break line) in both the data from this study and in independent one-cycle vs. two-cycle root data sets. Numbers represent the fold change in the comparison. Where several AGI codes are given for a particular probe ID, more than one transcript is likely to hybridise to the probes