Effects of elevated seawater pCO2 on gene expression patterns in the gills of the green crab, Carcinus maenas
1 Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada R3T2N2
2 Biological Oceanography, Leibniz-Institute of Marine Sciences (IFM-GEOMAR) Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
3 Marine Ecology, Leibniz-Institute of Marine Sciences (IFM-GEOMAR) Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
4 Center for Marine Functional Genomics, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672 USA
5 Paris-Lodron-Universität Salzburg, FB Organismische Biologie, Hellbrunnerstr. 34, 5020 Salzburg, Austria
BMC Genomics 2011, 12:488 doi:10.1186/1471-2164-12-488Published: 6 October 2011
Additional File 1:
Table S1. Annotation details on transcripts for the Carcinus maenas the microarray assay applied in this study. Annotation results on transcripts for the Carcinus maenas microarray assay applied in this study from a newly performed bioinformatic analysis conducted with the internet portal Blast2GO  in 2009 by the authors of this study, compared to a first annotation provided by Towle et al. . Included are the sequence length of the aligned sequence (= seq. length), the number of hits for the transcript (= #hits), the mean similarity of the alignment (= mean sim), the number of Gene Ontology (GO) terms assigned to that blast hit (= #GOs), a description of the assigned GOs (= GOs), Enzyme Codes (= EC), results of the InterProScan, the exact hit description of the best hit, as well as the accession number (= hit ACC, E-value, similarity, score, alignment length and number of positive matches bases of the best hit.
Table S2. Details on primers for quantitative real-time polymerase chain reaction (qRT-PCR) to assess responses of Carcinus maenas to hypercapnia. Primer sequences (5' → 3') and descriptions of the targeted genes used in the real-time polymerase chain reaction (qRT-PCR) in the short- and long-term hypercapnia experiments on Carcinus maenas. Numbers ('no.') are according to the numbers used in Figure 4 and Additional File 2 Figure S1. Accession numbers (ACC. no.) refer to the ESTs generated for the C. maenas microarray by Towle et al.  and the database GenBank (NCBI). R2 and efficiency were tested in a qRT-PCR dilution series (for details, see Material & Methods).
Table S3. Transcripts significantly regulated in response to hypercapnia in Carcinus maenas. Transcripts significantly regulated in response to hypercapnia in Carcinus maenas as identified by variance-based linear modelling (F-test) and sign test. Out of 1634 genes, 678 were identified by sign test, 578 genes were identified by F-test, and 378 were identified to be affected by both statistical tests. Transcripts are sorted alphabetically after the accession number (ACC. no., database GenBank (NCBI)). Bold and underlined = significantly regulated as identified by sign test, p < 0.05; bold = significantly regulated as identified by both statistical tests (sign test and F test, p < 0.05); italic = differentially expressed as identified by F-Test. Accession numbers refer to the ESTs generated for the C. maenas microarray by Towle et al. . Values are given as median and median deviation (MD).
Table S4. Significantly regulated transcripts associated with a cellular stress-response in Carcinus maenas when exposed to hypercapnia. Significantly regulated transcripts in the short-term hypercapnia study on Carcinus maenas associated with a cellular stress-response acoording to . Bold and underlined (values) = significantly regulated (sign test, p < 0.05), bold (ACC. no.) = transcripts identified to be significantly regulated by both tests (sign test and F-test, p < 0.05). Accession numbers (ACC. no.) refer to the GenBank database (NCBI).
Table S5. Significantly up-regulated transcripts in the short-term hypercapnia study associated with structural molecule activity in gills of Carcinus maenas. Transcripts identified to be responsible for the over-representation of the GO-term "structural modification" (GO:0005198) in Carcinus maenas gills exposed to hypercapnia (enrichment analysis with Fisher's exact test). Bold and underlined (values) = significantly regulated as identified by sign test (p < 0.05); bold (ACC. no.) = identified to be significantly regulatd by both tests (sign test and F-test, p < 0.05). Accession numbers (ACCs) refer to the database GenBank (NCBI).
Table S6. Details on transcripts of special interest identified by microarray analysis on gills of Carcinus maenas after exposure to short-term hypercapnia. Identification and details on transcripts of special interest identified by microarray analysis, after an additional NCBI blastx. * = NCBI blastn; ** = see Towle et al.  for details. Accession numbers (ACC. no.) refer to the database GenBank (NCBI).
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Additional file 2:
figure S1. Comparison of distinct transcripts of the microarray analysis vs. qRT-PCR for the response of Carcinus maenas to short-term hypercapnia. Comparison of the regulation of distinct transcripts of gill 9 for the Carcinus maenas response to short-term hypercapnia (1 week, April 2009) in the microarray analysis with results of the qRT-PCR experiment performed on the respective genes from the short-term incubation conducted in April 2010. In 7 of 8 cases, both techniques show the same tendency in regulation. Values represent median log2-ratios with median deviation (error bars). Transcript numbers according to Additional File 1 Table S2. Senesc. ass. prot = senescence-associated protein, put. syntaxin = putative Syntaxin binding protein 2, gCA = glycosyl-phosphatidylinositol-linked carbonic anhydrase VII, prot. inh. = hemozyte kazal-type proteinase inhibitor, K-channel = hyperpolarization activated cyclic nucleotide-gated potassium channel 2, NKA = Na+/K+-ATPase alpha subunit, Cl-channel (Ca-act.) = calcium acitvated chloride channel.
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