Open Access Research article

Revealing genes associated with vitellogenesis in the liver of the zebrafish (Danio rerio) by transcriptome profiling

Liraz Levi12, Irena Pekarski1, Ellen Gutman3, Paolo Fortina34, Terry Hyslop5, Jakob Biran2, Berta Levavi-Sivan2 and Esther Lubzens1*

Author Affiliations

1 Department Marine Biology and Biotechnology, Israel Oceanographic and Limnological Research, Haifa, Israel

2 Department of Animal Sciences, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, Rehovot 76100, Israel

3 Department of Cancer Biology, Kimmel Cancer Center, Thomas Jefferson University Jefferson Medical College, Philadelphia, PA 19107, USA

4 Department of Experimental Medicine, University La Sapienza, Roma, Italy

5 Division of Biostatistics, Thomas Jefferson University Jefferson Medical College, PA 19107, USA

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BMC Genomics 2009, 10:141  doi:10.1186/1471-2164-10-141

Published: 31 March 2009

Additional files

Additional file 1:

Significantly different transcripts among the five tested groups. List of 2, 523 genes corresponding to the significantly different transcripts found by SAM analysis.

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Additional file 2:

Detailed lists of genes that were found to be regulated in this study. Detailed lists of gene accession numbers and gene names in groups 1–9 as they appear in Figures 6 and 7.

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Additional file 3:

Genes in selected GO terms. This table represents SAM values and E2 regulation of genes in selected functions for the five tested groups.

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Additional file 4:

Primers used for chip validation. List of primers used in real-time PCR for microarray validation.

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Additional file 5:

Validation of microarray results by real-time PCR. The graphs in the figure indicate the correlation between the microarray results and real-time PCR results of 16 selected genes, represented by the R2 value in each graph. The expression levels of the following 16 genes genes were normalized to ef1a: 1) retinoic acid receptor alpha a (raraa); 2) estrogen receptor alpha gene (esr1); 3) retinol dehydrogenase 10 (rdh10); 4) retinol dehydrogenase 14 (rdh14); 5) dehydrogenase/reductase (SDR family) member 10 (dhrs10); 6) stearoyl-desaturase (sCd); 7) fatty acid desaturase 2 (fads2); 8) alcohol dehydrogenase 5 (adh5); 9) vitellogenin 1 (vtg1); 10) vitellognin 3 (vtg3); 11) insulin-like growth factor 1 (igf1); 12) nothepsin (nots); 13) alcohol dehydrogenase 8b (adh8b); 14) cytochrome p450, family 1, subfamily a1 (cyp1a1); 15) cytochrome P450, family 2, subfamily K, polypeptide 6 (cyp2k6) and 16) steroidogenic acute regulatory protein (star).

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