BMC Genomics 2009, 10:150 http://www.biomedcentral.com/1471-2164/10/150 fied by increasing the temperature from 55°C to 95°C to construct melting curves. Values were expressed by calcu- lating the 2(-ΔCt) value, where the threshold cycle Ct repre- sents the fractional cycle at which the fluorescence passes a fixed threshold, and ΔCt represents the differences between the Ct of the gene of interest and that of the housekeeping gene Rps16, coding for ribos- omal protein S16 sub-unit. Each value represented the average of 3 replicate measurements. number Genomic sequencing Genomic DNA was extracted from hearts of adult C57BL/ 6J and C57.YA using the DNeasy blood & tissue commercial kit (Qiagen Canada, Mississauga, ON). Primers were designed to amplify ~1 kb of upstream promoter, each exon (including 30 bp of intron flanking sequences as well as ~1 kb of the 3'-unstranslated region) of the Ddx3y and Eif2s3y genes. Amplicons were then sequenced at the McGill Genome Discovery Centre. Abbreviations chrY: chromosome Y; ChrYC57: chrY from the C57BL/6J mouse strain; ChrYA : chrY from the A/J mouse strain; CM: cardiomyocyte; CX: castration; FDR: false discovery rate; KEGG: Kyoto Encyclopedia of Genes and Genomes. Authors' contributions BL and RAV contributed equally to the manuscript. All authors were involved in the interpretation of the data and the writing of the manuscript. BL performed all exper- imental manipulations on animals, the isolation of cardi- omyocytes and measurement of their size, extracted RNA from hearts or other tissues, and performed all RT-PCR experiments. RAV and GAC performed the statistical design and analysis of the microarray experiments. CFD was responsible for the overall design, conception and conduct of the study, and coordinated the writing of the manuscript. Additional material Additional file 1 List of 249 interaction genes. List of 249 interaction genes (with signif- icant interaction between the effects of strain and surgery). Fold change (FC) was calculated as the ratio of mean expression of either: 1) C57BL/ 6J over C57.YA mice (Strain); or 2) Castrated over sham-operated (Treat- ment) mice. Ratios below 1 are expressed as the negative of the inverse ratio (e.g. a ratio of 0.75 is equivalent to a -1.3 FC). FC equal or higher than 1.5 are formatted in bold. For genes represented by multiple probes in the microarray, only the probe with the lowest p-value for the interac- tion term is included. P-values for the interaction between strain and treatment effects are adjusted for multiple comparisons with an FDR transformation (see methods). Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-150-S1.xls] Additional file 2 Differential expression of genes in selected KEGG pathways. Differen- tial expression of genes in selected KEGG pathways. Fold change (FC) was calculated as the ratio of mean expression in CX vs. sham-operated group. Ratios below 1 are expressed as the negative of the inverse ratio (e.g. a ratio of 0.75 is equivalent to a -1.3 FC). P-values for the interaction between strain and treatment effects are adjusted for multiple comparisons with an FDR transformation (see methods). P-values less than 0.1 are in bold. For genes represented by multiple probes in the microarray, only the probe with the lowest p-value for the interaction term is included. Genes are sorted by p-values within pathways. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-150-S2.xls] Additional file 3 Primers used for RT-PCR amplification of chr Y mRNA transcripts. Primers used for RT-PCR amplification of chr Y mRNA transcripts. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-150-S3.doc] Acknowledgements This work has been supported by grant MOP-64391 from the Canadian Institutes for Health Research (CIHR) and in part by the NIGMS Centers of Excellence in Systems Biology Program grant GM076468. We thank the "Genome Quebec Innovation Centre" for performing the Illumina Bead- Chip hybridization experiments, and thank in particular Isabelle Guillet for excellence of the service provided. References 1. Jobling MA, Tyler-Smith C: The human Y chromosome: an evo- lutionary marker comes of age. Nat Rev Genet 2003, 4:598-612. 2. Polanco JC, Koopman P: Sry and the hesitant beginnings of male development. Dev Biol 2007, 302:13-24. 3. Graves JA: Sex chromosome specialization and degeneration in mammals. Cell 2006, 124:901-914. 4. Lahn BT, Page DC: Functional coherence of the human Y chro- mosome. Science 1997, 278:675-680. 5. 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