title: Transcript profiling in Arabidopsis with genome tiling microarrays.
abstract: Microarray technology is at present a standardized workflow for genome-wide expression analysis. Whole-genome tiling microarrays have emerged as an important platform for flexible and comprehensive expression profiling. In this chapter we describe a detailed standardized workflow for experiments assessing the transcriptome of Arabidopsis using tiling arrays and provide useful hints for critical steps from experimental design to data analysis. Although the protocol is optimized for AGRONOMICS1 arrays, it can readily be adapted to other tiling arrays. AGRONOMICS1 is the first platform that enables strand-specific expression analysis of the Arabidopsis genome with a single array. Moreover, it includes all perfect match probes from the original ATH1 array, allowing readily integration with the large existing ATH1 knowledge base. This workflow is designed for the analysis of raw data for any number of samples and it does not pose any particular hardware requirements.
authors: Plant Biotechnology, Department of Biology, ETH Zurich, Zurich, Switzerland.
authors: Diana
authors: D
authors: Coman
authors: Wilhelm
authors: W
authors: Gruissem
authors: Lars
authors: L
authors: Hennig
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D018076:DNA, Complementary / Q000235:genetics; D020869:Gene Expression Profiling / Q000295:instrumentation / Q000379:methods*; D018745:Genome, Plant; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation / Q000379:methods*; D018749:RNA, Plant / Q000235:genetics / Q000302:isolation & purification
chemical_list: D018076:DNA, Complementary; D018749:RNA, Plant