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Infigen, Inc.,5 DeForest, Wisconsin 53532
Department of Biomedical Sciences,6 Cornell University, Ithaca, New York 14853-6401
Department of Biology,7 University of Pennsylvania, Philadelphia, Pennsylvania 19104-6018
Virginia Bioinformatics Institute and Department of Statistics,8 Virginia Tech, Blacksburg, Virginia 24061
NuPotential, LLC,9 Baton Rouge, Louisiana 70808-4124
Using an interwoven-loop experimental design in conjunction with highly conservative linear mixed model methodology using estimated variance components, 18 genes differentially expressed between nuclear transfer (NT)- and in vitro fertilization (IVF)-produced embryos were identified. The set is comprised of three intermediate-filament protein genes (cytokeratin 8, cytokeratin 19, and vimentin), three metabolic genes (phosphoribosyl pyrophosphate synthetase 1, mitochondrial acetoacetyl-coenzyme A thiolase, and 
-glucosidase), two lysosomal-related genes (prosaposin and lysosomal-associated membrane protein 2), and a gene associated with stress responses (heat shock protein 27) along with major histocompatibility complex class I, nidogen 2, a putative transport protein, heterogeneous nuclear ribonuclear protein K, mitochondrial 16S rRNA, and ES1 (a zebrafish orthologue of unknown function). The three remaining genes are novel. To our knowledge, this is the first report comparing individual embryos produced by NT and IVF using cDNA microarray technology for any species, and it uses a rigorous experimental design that emphasizes statistical significance to identify differentially expressed genes between NT and IVF embryos in cattle.
2 Correspondence: Kenneth J. Eilertsen, Pennington Biomedical Research Center, 6400 Perkins Road, Baton Rouge, LA 70808-4124. FAX: 225 763 0273; eilertkj{at}pbrc.edu
3 Current Address: Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, Iowa City, IA 52242
4 Current Address: Pennington Biomedical Research Center, Stem Cell Biology Group, 6400 Perkins Road, Baton Rouge, LA 70808-4124
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