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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.