Development of a porcine brain cDNA library, EST database, and microarray resource

Abstract

Recent developments in expressed sequence tag (EST) and cDNA microarray technology have had a dramatic impact on the ability of scientists to study responses of thousands of genes to internal and external stimuli. In neurobiology, studies of the human brain have been expanding rapidly by use of functional genomics techniques. To enhance these studies and allow use of a porcine brain model, a normalized porcine brain cDNA library (PBL) has been generated and used as a base for EST discovery and microarray generation. In this report, we discuss initial sequence analysis of 965 clones from this resource. Our data revealed that library normalization successfully reduced the number of clones representing highly abundant cDNA species and overall clone redundancy. Cluster analysis revealed over 800 unique cDNA species representing a redundancy rate for the normalized library of 6.9% compared with 29.4% before normalization. Sequence information, BLAST results, and TIGR cluster matches for these ESTs are publicly available via a web-accessible database (http://nbfgc.msu.edu). A cDNA microarray was created using 877 unique porcine brain EST amplicons spotted in triplicate on glass slides. This microarray was assessed by performing a series of experiments designed to test hybridization efficiency and false-positive rate. Our results indicate that the PBL cDNA microarray is a robust tool for studies of brain gene expression using swine as a model system.