title: Design of tiling arrays and their application to bacterial transcriptome analysis.
abstract: Whole-genome sequencing and annotation have clarified total gene number and structure in a variety of organisms. Microarrays have facilitated transcriptome analysis through the use of probes that target a large number of genes based on genomic information. However, microarrays are limited in that they can only examine known or predicted genes; non-annotated genes and noncoding regions cannot be accounted for.Recent advances in technology have led to the design of tiling arrays, which contain a vastly increased number of spotted probes, and at higher density. Tiling arrays cover the entire genome of a prokaryotic species in an unbiased fashion by designing a large number of probes. Upon hybridization of total RNA, all the transcribed regions of the genome, irrespective of gene annotation, can be detected. As opposed to next-generation sequencing, tiling arrays are cost-effective, easy to analyze, and have been used for experiments as diverse as transcriptome analysis, ChIP-chip, and DNA sequence variation detection. In this chapter, the methods for bacterial tiling array slide design, RNA sample preparation, hybridization, and data analysis are described.
authors: Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan.
authors: Takeshi
authors: T
authors: Akama
authors: Kazuaki
authors: K
authors: Nakamura
authors: Akito
authors: A
authors: Tanoue
authors: Koichi
authors: K
authors: Suzuki
mesh_terms: D001419:Bacteria / Q000235:genetics*; D004269:DNA, Bacterial / Q000032:analysis / Q000235:genetics*; D020869:Gene Expression Profiling / Q000295:instrumentation / Q000379:methods*; D016680:Genome, Bacterial; D009693:Nucleic Acid Hybridization / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation / Q000379:methods*; D012329:RNA, Bacterial / Q000032:analysis / Q000235:genetics*; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods; D012984:Software
chemical_list: D004269:DNA, Bacterial; D012329:RNA, Bacterial