Development and Application of Bovine and Porcine Oligonucleotide Arrays with Protein-Based Annotation

• Published in: BioMed research international Vol. 2010; no. 2010; pp. 1 - 11
• Main Authors: Wolfinger, Russell D., Fahrenkrug, Scott C., Taylor, Jeremy F., Schnabel, Robert D., Kim, Jae-Woo, Venkatraman, Anand, Clark, Karl J., Reecy, James M., Antoniou, Eric, Elsik, Christine G., Garbe, John R., Michael Dickens, C.
• Format: Journal Article
• Language: English
• Published: Cairo, Egypt Hindawi Publishing Corporation 2010
• ISSN: 2314-6133; 2314-6141
• DOI: 10.1155/2010/453638

The design of oligonucleotide sequences for the detection of gene expression in species with disparate volumes of genome and EST sequence information has been broadly studied. However, a congruous strategy has yet to emerge to allow the design of sensitive and specific gene expression detection probes. This study explores the use of a phylogenomic approach to align transcribed sequences to vertebrate protein sequences for the detection of gene families to design genomewide 70-mer oligonucleotide probe sequences for bovine and porcine. The bovine array contains 23,580 probes that target the transcripts of 16,341 genes, about 72% of the total number of bovine genes. The porcine array contains 19,980 probes targeting 15,204 genes, about 76% of the genes in the Ensembl annotation of the pig genome. An initial experiment using the bovine array demonstrates the specificity and sensitivity of the array.