title: Microarray analysis using disiloxyl 70mer oligonucleotides.
abstract: DNA microarray technology has evolved dramatically in recent years, and is now a common tool in researchers' portfolios. The scope of the technique has expanded from small-scale studies to extensive studies such as classification of disease states. Technical knowledge regarding solid phase microarrays has also increased, and the results acquired today are more reliable than those obtained just a few years ago. Nevertheless, there are various aspects of microarray analysis that could be improved. In this article we show that the proportions of full-length probes used significantly affects the results of global analyses of transcriptomes. In particular, measurements of transcripts in low abundance are more sensitive to truncated probes, which generally increase the degree of cross hybridization and loss of specific signals. In order to improve microarray analysis, we here introduce a disiloxyl purification step, which ensures that all the probes on the microarray are at full length. We demonstrate that when the features on microarrays consist of full-length probes the signal intensity is significantly increased. The overall increase in intensity enables the hybridization stringency to be increased, and thus enhance the robustness of the results.
authors.affiliation: School of Biotechnology, Department of Gene Technology, KTH, Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden.
authors.forename: Marcus Gry
authors.initials: MG
authors.lastname: Björklund
authors.forename: Christian
authors.initials: C
authors.lastname: Natanaelsson
authors.forename: Amelie Eriksson
authors.initials: AE
authors.lastname: Karlström
authors.forename: Yong
authors.initials: Y
authors.lastname: Hao
authors.forename: Joakim
authors.initials: J
authors.lastname: Lundeberg
mesh_terms: D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015345:Oligonucleotide Probes / Q000138:chemical synthesis / Q000737:chemistry*; D012833:Siloxanes / Q000737:chemistry
chemical_list: D015345:Oligonucleotide Probes; D012833:Siloxanes