Open Access Research article

Transcriptomic assessment of resistance to effects of an aryl hydrocarbon receptor (AHR) agonist in embryos of Atlantic killifish (Fundulus heteroclitus) from a marine Superfund site

Marjorie F Oleksiak1, Sibel I Karchner2, Matthew J Jenny23, Diana G Franks2, David B Mark Welch4 and Mark E Hahn2*

  • * Corresponding author: Mark E Hahn mhahn@whoi.edu

  • † Equal contributors

Author Affiliations

1 Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149 USA

2 Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA

3 University of Alabama, Department of Biological Sciences, Box 870344, Tuscaloosa, AL 35487-0344 USA

4 Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02568 USA

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BMC Genomics 2011, 12:263  doi:10.1186/1471-2164-12-263

Published: 24 May 2011

Additional files

Additional file 1:

Figure S1. Loop design for microarray hybridizations. See text for details.

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Additional file 2:

Table S1. Significant differently expressed genes: Results from 2-way ANOVA. Genes significantly differently expressed at 5, 10 and 15 days post-fertilization. Gene, function, relative fold-differences and p-values are reported. A gene with a positive fold-difference is more highly expressed in population/treatment listed first, and a gene with a negative fold-difference is more highly expressed in the population/treatment listed last. Significant p-values are in bold. NBH: New Bedford Harbor (PCB-contaminated site); SC: Scorton Creek (reference site). Unannotated genes are denoted by UnAn and a unique number. Some of the unannotated probes were subsequently annotated after extension using the 454 databases (EST and shotgun libraries); see Table S4 (Additional file 6) for details.

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Additional file 3:

Figure S2. Volcano plots illustrating gene expression differences at 5, 10, and 15 dpf. Significances of differences are plotted as -log10(p-values) against log2 differences in expression. Gene expression differences between A. NBH PCB and NBH DMSO treated embryos, B. NBH DMSO and SC DMSO treated embryos, C. SC PCB and NBH DMSO treated embryos, D. NBH PCB and SC DMSO treated embryos, E. SC PCB and NBH PCB treated embryos, and F. SC PCB and SC DMSO treated embryos. Dashed line demarks the FDR p-value of < 0.01 (p < 0.00669).

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Additional file 4:

Table S2. Differential gene expression and PCB inducibility in pairwise comparisons of NBH and SC embryos at 5, 10, and 15 dpf. Genes with significant differences in pairwise comparisons of gene expression are included. Gene expression ratios are indicated. A gene with a positive fold-difference is more highly expressed in the population/treatment listed first, and a gene with a negative fold-difference is more highly expressed in the population/treatment listed last. Genes are listed in order of ratios in the reference population (SC) comparison with tolerant population (SC). Ratios with significant p-values are in bold. See Table S1 (Additional file 2) for a list of all genes significant in the ANOVA analysis. NBH: New Bedford Harbor; SC: Scorton Creek; PCB: PCB-126; DMSO: dimethylsulfoxide. Unannotated genes are denoted by UnAn and a unique number. Some of the unannotated probes were subsequently annotated after extension using the 454 database; see Table S4 (Additional file 6) for details.

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Additional file 5:

Table S3. Mean fold change in gene expression in pairwise comparisons.

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Additional file 6:

Table S4. Probes annotated as a result of 454 sequencing. Microarray probe sequences were used in blast searches against the 454 sequence data (EST and shotgun libraries). The probe sequences that were extended with the matching reads were used to search GenBank using blast to obtain the annotations.

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Additional file 7:

Figure S3. Possible scenarios comparing the response of SC and NBH fish to PCB.

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