Methodology article
Gene expression profiling to characterize sediment toxicity – a pilot study using Caenorhabditis elegans whole genome microarrays
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* Corresponding author: Stephen R Stürzenbaum stephen.sturzenbaum@kcl.ac.uk
- † Equal contributors
1 Humboldt-Universität zu Berlin, Department of Biology – Freshwater and Stress Ecology, Spaethstr. 80/81, 12437 Berlin, Germany
2 School of Biomedical & Health Sciences, Pharmaceutical Science Division, King's College London, 150 Stamford Street, London, SE1 9NH, UK
3 Ecossa (ecological sediment & soil assessment), Giselastr. 6, 82319 Starnberg, Germany
4 Federal Institute of Hydrology, Department Biochemistry and Ecotoxicology, Am Mainzer Tor 1, 56068 Koblenz, Germany
BMC Genomics 2009, 10:160 doi:10.1186/1471-2164-10-160
Published: 14 April 2009Additional files
Additional file 1:
Differentially regulated genes due to the exposure to the Elbe sediment. Significantly changing transcripts in C. elegans exposed to the Elbe (E) sediment [ANOVA, p < 0.05 without multiple sample correction, fold-change to reference sediment Danube (D) > 1.4 (up-regulated) or < 0.7 (down-regulated)].
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Additional file 2:
Differentially regulated genes due to the exposure to the Rhine sediment. Significantly changing transcripts in C. elegans exposed to the Rhine (R) sediment [ANOVA, p < 0.05 without multiple sample correction, fold-change to reference sediment Danube (D) > 1.4 (up-regulated) or < 0.7 (down-regulated)].
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Additional file 3:
List of all differentially regulated GO categories. Biological GO processes overrepresented in sediment exposed nematodes using the Danube sediment sample as reference.
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Additional file 4:
Molecular functions – partial GO tree. Partial GO tree presenting relevant molecular functions which were found to be overrepresented in C. elegans exposed to Elbe and/or Rhine sediments.
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Additional file 5:
Cellular components – partial GO tree. Partial GO tree presenting relevant cellular components which were found to be overrepresented in C. elegans exposed to Elbe and/or Rhine sediments.
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Additional file 6:
Overlapping differentially regulated genes of Elbe and Rhine. C. elegans transcripts that significantly changed in response to both Elbe and Rhine sediment exposure [ANOVA, p < 0.05 without multiple sample correction, fold-change to reference sediment Danube > 1.4 (up-regulated) or < 0.7 (down-regulated), for color code see below].
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Additional file 7:
Description of 58 differentially expressed genes involved in several reproduction associated, aging regulating and/or developmental processes. Identification, direction of change and description of all 58 genes which belong to one or more of the selected GO categories.
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Additional file 8:
Overlapping differentially regulated genes of selected toxico- genomic studies in C. elegans. C. elegans' transcripts significantly changed in response to sediment exposures (this study) and PCB52 [11], Cd [12] and two humic substances [10].
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Additional file 9:
Principal component analysis (PCA) including a liquid medium laboratory control. PCA of significantly changing genes in C. elegans exposed to three river sample sediments: Danube (red), Elbe (yellow) and Rhine (blue) or S-basal, an artificial laboratory control (black). Note that PCA analysis identifies that the laboratory control exposure clusters distinctly separate from the three sediment exposures when laboratory control (A) or the Danube sediment (B) is used as the baseline dataset.
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