title: Use of massively parallel signature sequencing to study genes expressed during the plant defense response.
abstract: Massively parallel signature sequencing is a sequencing-based method that provides quantitative gene expression data for nearly all transcripts in a particular ribonucleic acid sample. Although the sequencing technology is practiced as a service by a California-based company, we have developed methods for the handling and analysis of these data. This chapter describes the steps involved in obtaining data from massively parallel signature sequencing, aligning the signatures to genomic sequence, identifying novel transcripts, and performing quantitative analyses of genes expressed under conditions such as disease treatments.
authors.affiliation: Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, USA.
authors.forename: Blake C
authors.initials: BC
authors.lastname: Meyers
authors.forename: Christian D
authors.initials: CD
authors.lastname: Haudenschild
authors.forename: Kalyan
authors.initials: K
authors.lastname: Vemaraju
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000276:immunology*; D030541:Databases, Genetic; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D017343:Genes, Plant / Q000235:genetics*; D010935:Plant Diseases / Q000235:genetics* / Q000276:immunology; D012333:RNA, Messenger / Q000032:analysis / Q000235:genetics; D018749:RNA, Plant / Q000032:analysis / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D014584:User-Computer Interface
chemical_list: D012333:RNA, Messenger; D018749:RNA, Plant