title: Spotted long oligonucleotide arrays for human gene expression analysis.
abstract: DNA microarrays produced by deposition (or 'spotting')of a single long oligonucleotide probe for each gene may be an attractive alternative to other types of arrays. We produced spotted oligonucleotide arrays using two large collections of approximately 70-mer probes, and used these arrays to analyze gene expression in two dissimilar human RNA samples. These samples were also analyzed using arrays produced by in situ synthesis of sets of multiple short (25-mer) oligonucleotides for each gene (Affymetrix GeneChips). We compared expression measurements for 7344 genes that were represented in both long oligonucleotide probe collections and the in situ-synthesized 25-mer arrays. We found strong correlations (r = 0.8-0.9) between relative gene expression measurements made with spotted long oligonucleotide probes and in situ-synthesized 25-mer probe sets. Spotted long oligonucleotide arrays were suitable for use with both unamplified cDNA and amplified RNA targets, and are a cost-effective alternative for many functional genomics applications. Most previously reported evaluations of microarray technologies have focused on expression measurements made on a relatively small number of genes. The approach described here involves far more gene expression measurements and provides a useful method for comparing existing and emerging techniques for genome-scale expression analysis.
authors.affiliation: Department of Medicine, University of California, San Francisco, San Francisco, California 94143, USA.
authors.forename: Andrea
authors.initials: A
authors.lastname: Barczak
authors.forename: Madeleine Willkom
authors.initials: MW
authors.lastname: Rodriguez
authors.forename: Kristina
authors.initials: K
authors.lastname: Hanspers
authors.forename: Laura L
authors.initials: LL
authors.lastname: Koth
authors.forename: Yu Chuan
authors.initials: YC
authors.lastname: Tai
authors.forename: Benjamin M
authors.initials: BM
authors.lastname: Bolstad
authors.forename: Terence P
authors.initials: TP
authors.lastname: Speed
authors.forename: David J
authors.initials: DJ
authors.lastname: Erle
mesh_terms: D002460:Cell Line; D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data; D020869:Gene Expression Profiling / Q000379:methods* / Q000706:statistics & numerical data; D005796:Genes / Q000235:genetics; D006801:Humans; D020014:K562 Cells / Q000737:chemistry / Q000378:metabolism; D021141:Nucleic Acid Amplification Techniques; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000706:statistics & numerical data; D015345:Oligonucleotide Probes / Q000235:genetics; D012680:Sensitivity and Specificity
chemical_list: D015345:Oligonucleotide Probes