Development and testing of a high-density cDNA microarray resource for cattle

Abstract

A cDNA microarray resource has been developed with the goal of providing integrated functional genomics resources for cattle. The National Bovine Functional Genomics Consortium's (NBFGC) expressed sequence tag (EST) collection was established in 2001 to develop resources for functional genomics research. The NBFGC EST collection and microarray contains 18,263 unique transcripts, derived from many different tissue types and various physiologically important states within these tissues. The NBFGC microarray has been tested for false-positive rates using self-self hybridizations and was shown to yield robust results in test microarray experiments. A web-accessible database has been established to provide pertinent data related to NBFGC clones, including sequence data, BLAST results, and ontology information. The NBFGC microarray represents the largest cDNA microarray for a livestock species prepared to date and should prove to be a valuable tool in studying genome-wide gene expression in cattle.

Gene expression profiling of bovine preovulatory follicles: gonadotropin surge and prostanoid-dependent up-regulation of genes potentially linked to the ovulatory process

“…Then, the mixture was applied to microarray slides for hybridization. A previously described bovine cDNA array containing ESTs representing w15 200 unique genes (Suchyta et al 2003) was utilized. Slides were hybridized for 18 h using step down temperatures from 65 to 42 8C in a sealed GeneTAC HybStation hybridization chamber (Genomic Solutions Inc., Ann Arbor, MI, USA).…”

“…SSC and deionized water, dried by brief centrifugation and further cleaned with compressed air and scanned using GeneTAC LSIV microarray scanner and GeneTAC LS software (Genomic solutions). GeneTAC Integrator 4.0 software was used to process array images, align spots, integrate robot-spotting files with the microarray image, and to export spot intensity data in a Microsoft Excel format as described previously (Suchyta et al 2003, Yao et al 2004.…”

A genômica funcional no âmbito da produção animal: estado da arte e perspectivas

“…De maneira que a genômica teve seu início somente no final da década de 80, após o método de Sanger ter sido modificado para permitir o seqüenciamento de forma automatizada e integrada a um sistema de leitura computadorizado (Venter et al, 2001), possibilitando que este processo fosse realizado em plataforma de larga escala e alta performance.…”

“…Além disso, as bibliotecas de cDNA produzidas nestes projetos fornecem o substrato para a confecção das lâminas de microarrays utilizadas nos ensaios de expressão gênica (Suchyta et al, 2003).…”

Annotation and <i>in silico</i> localization of the Affymetrix GeneChip Porcine Genome Array

“…Functional genomics provides new opportunities for determining the molecular processes underlying phenotypic variation towards developmental and reproduction traits, growth, immune response and host-pathogen interaction (BAI et al 2003, BAND et al 2002, BERNARD et al 2007, COGBURN et al 2003, MOSER et al 2004, PONSUKSILI et al 2007, 2008a, 2008b, SUCHYTA et al 2003, TUGGLE et al 2007. Currently several whole genome expression microarrays for pigs are available including consortium arrays like the »Pigoligoarray« (http://www.pigoligoarray.org) or commercial microarrays like the Agilent Porcine Gene Expression Microarray (Agilent Technologies; http://www.chem.agilent.com) and the Affymetrix GeneChip Porcine Genome Array (Affymetrix, http://www.affymetrix.com).…”