Jianbo Yao | PubMed Health

PubMed2003

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

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.

Animals↗

PubMed2002

Generation of expressed sequence tags from a normalized porcine skeletal muscle cDNA library.

Recent developments in microarray technologies permit scientists to analyze expression of thousands of genes simultaneously in diverse biological systems. In an effort to provide integrated resources for application of microarray technologies to studies of skeletal muscle growth and development in swine, we have constructed a normalized cDNA library from porcine skeletal muscle. The effectiveness of normalization was evaluated by DNA sequencing of clones randomly picked from the library before and after normalization, and also by Southern blot hybridization using probes representing abundant transcripts. Our data suggests that the normalization procedure successfully reduced the highly abundant cDNA species in the normalized library. To date, a total of 782 EST (expressed sequence tag) sequences have been generated from this normalized library (687 ESTs) and the original library (95 ESTs). The sequence information of these ESTs plus their BLAST results has been made available through a web accessible database (http://nbfgc.msu.edu). Cluster analysis of the data indicates that a total of 742 unique sequences are present in this collection. BLASTN search of the 742 EST sequences against the public database (dbEST) revealed that 139 had no significant matches (E-value > 10(-15)) to porcine ESTs already entered in the database, suggesting the possibility of their specific expression in porcine skeletal muscle. Generation of non-redundant ESTs from this library will allow us to construct cDNA microarrays for identification of gene expression changes that regulate muscle growth and affect meat quality in swine.

Animals↗