custom design and analysis of high-density oligonucleotide bacterial tiling microarrays定制的设计和分析高密度寡核苷酸细菌花砖微阵列.pdfVIP

Custom Design and Analysis of High-Density Oligonucleotide Bacterial Tiling Microarrays 1,2 2 2 3 2,3 Gard O. S. Thomassen , Alexander D. Rowe , Karin Lagesen , Jessica M. Lindvall , Torbjørn Rognes * 1 Centre for Molecular Biology and Neuroscience (CMBN), Institute of Medical Microbiology, University of Oslo, Oslo, Norway, 2 Centre for Molecular Biology and Neuroscience (CMBN), Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway, 3 Department of Informatics, University of Oslo, Oslo, Norway Abstract Background: High-density tiling microarrays are a powerful tool for the characterization of complete genomes. The two major computational challenges associated with custom-made arrays are design and analysis. Firstly, several genome dependent variables, such as the genome’s complexity and sequence composition, need to be considered in the design to ensure a high quality microarray. Secondly, since tiling projects today very often exceed the limits of conventional array- experiments, researchers cannot use established computer tools designed for commercial arrays, and instead have to redesign previous methods or create novel tools. Principal Findings: Here we describe the multiple aspects involved in the design of tiling arrays for transcriptome analysis and detail the normalisation and analysis procedures for such microarrays. We introduce a novel design method to make two 280,000 feature microarrays covering the entire genome of the bacterial species Escherichia coli and Neisseria meningitidis, respectively, as well as the use of multiple copies of control probe-sets