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Table 3 Transcripts at higher levels in stationary (high-toxin-producing) as compared to late-exponential (low-toxin-producing) phase in Pseudo-nitzschia multiseries ( Ps-n ) as determined by cDNA microarray analysis

From: Gene expression studies for the analysis of domoic acid production in the marine diatom Pseudo-nitzschia multiseries

  

Fold changea

 

Stationary versus late-exponential phase

Ps-n NR Identifier

JGI Ps-n Genome hit

Non-axenic

Non-axenic

Axenic

Predicted gene product

 

Scaffold:Start-End

Expt. 1

Expt. 2

Expt.

 

PSN0011

481:47438-49830

3.99 ± 0.96

3.46 ± 1.90

2.19 ± 0.37

Cycloisomerase (pfam10282 lactonase/lactonizing enzyme),

COG2706 (3-carboxymuconate cyclase)

PSN0072

269:13929-16593

3.40 ± 0.38

3.39 ± 0.32

2.01 ± 0.24

SLC6, Sodium and Chloride-dependent amino acid transporter

PSN0014

2396:2127-4845

4.64 ± 0.89

4.10 ± 0.89

2.14 ± 0.27

Acyl-CoA synthetase with transit peptide

PSN0016

37:106113-109070

3.78 ± 0.27

3.01 ± 0.29

3.11 ± 0.50

Phosphoenolpyruvate carboxykinase, ATP-

dependent with transit peptide (PEPCK)

PSN0025

155:75271-76268

6.65 ± 1.56

7.07 ± 1.75

4.18 ± 0.57

Small heat shock protein with alpha-crystallin

domain, chloroplastic (sHSP)

PSN0052

70:256654-258177

3.89 ± 0.59

2.61 ± 0.21

1.57 ± 0.01

Mitochondrial carrier protein

PSN0015

66:296511-298386

3.19 ± 0.57

3.15 ± 0.43

1.86 ± 0.17

Aldo-keto reductase with signal peptide

PSN0042

21:457033-458813

5.47 ± 0.75

7.52 ± 1.69

3.37 ± 0.50

Predicted protein with signal peptide

6H1

117:15135-16102

5.45 ± 0.55

3.76 ± 0.00

2.57 ± 0.04

Predicted protein with signal or transit peptide

73D12

1312:10048-11278

3.45 ± 0.11

4.01 ± 0.03

1.63 ± 0.07

Ps-n specific, no hits in NR or Swissprot

46A5

447:56474-57752

4.36 ± 0.00

4.61 ± 0.11

1.73 ± 0.02

Ps-n specific, no hits in NR or Swissprot

17F11

303:41858-44529

5.42 ± 0.18

6.02 ± 0.85

2.07 ± 0.06

Predicted protein with glycosyltransferase domain

PSN1428b

95:293619-297233

2.22 ± 0.26

1.86 ± 0.20

1.81 ± 0.37

NAD-specific glutamate dehydrogenase (GDH)

  1. aThe fold-change data presented are the average of all of the cDNA clones that were printed on the array for each transcript. The number of cDNA clones for each transcript was: PSN0011 (21), PSN0072 (3), PSN0014 (14), PSN0016 (14), PSN0025 (5), PSN0052 (4), PSN0015 (7), PSN0042 (4), 6H1 (1), 73D12 (1), 46A5 (1), 17F11 (1), PSN1428 (2). Each clone was printed on the array twice.
  2. bPSN1428 was included as a gene of interest in RT-qPCR analysis, below, although it did not meet our statistical criteria for the original microarray analysis. Please see Methods for statistical analysis, and Additional file1 for FDR and LDFR data.
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BMC Molecular Biology

ISSN: 1471-2199

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