Gene expression in normal tissues to validate the first generation porcine oligonucleotide microarray. Sus scrofa

Lung, liver, muscle (Semitendinosus), small intestine (duodenum; approximately 5 cm from stomach) were collected from six cross-bred white pigs (three 15 week old and three 17 week old). Total RNAs were isolated from these tissues to study gene expression by using the first generation of porcine long oligonucleotide microarray. In the experimental design, tissue samples from the six animals were assigned to six loops (three for younger animals and three for older animals). One sample from each of the four tissues from a single animal was used in each loop. The order of the tissues in each loop was varied so that all pairs of tissues were represented together on a slide an equal number of times. Dye balance was used throughout so that each tissue was measured an equal number of times with each dye. Data from 48 measurements from 24 slides were collected, with 12 measurements for each tissue. The mixed model included fixed effects for dye, tissue, animal age, and age-by-tissue interaction as well as random effects for slide, animal, and animal-by-tissue interaction. Genes with expression significantly higher in one tissue than in each of the others will be referred to as tissue-selective genes. To identify such genes, pair-wise comparisons of normalized signal intensities between tissues were conducted as part of our mixed model analyses for each gene. Keywords: repeat sample