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

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 prob...

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Detalles Bibliográficos
Autores principales: Garbe, John R., Elsik, Christine G., Antoniou, Eric, Reecy, James M., Clark, Karl J., Venkatraman, Anand, Kim, Jae-Woo, Schnabel, Robert D., Michael Dickens, C., Wolfinger, Russell D., Fahrenkrug, Scott C., Taylor, Jeremy F.
Formato: Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3010673/
https://www.ncbi.nlm.nih.gov/pubmed/21197395
http://dx.doi.org/10.1155/2010/453638
Descripción
Sumario: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.