title: An expression atlas of rice mRNAs and small RNAs.
abstract: Identification of all expressed transcripts in a sequenced genome is essential both for genome analysis and for realization of the goals of systems biology. We used the transcriptional profiling technology called 'massively parallel signature sequencing' to develop a comprehensive expression atlas of rice (Oryza sativa cv Nipponbare). We sequenced 46,971,553 mRNA transcripts from 22 libraries, and 2,953,855 small RNAs from 3 libraries. The data demonstrate widespread transcription throughout the genome, including sense expression of at least 25,500 annotated genes and antisense expression of nearly 9,000 annotated genes. An additional set of approximately 15,000 mRNA signatures mapped to unannotated genomic regions. The majority of the small RNA data represented lower abundance short interfering RNAs that match repetitive sequences, intergenic regions and genes. Among these, numerous clusters of highly regulated small RNAs were readily observed. We developed a genome browser (http://mpss.udel.edu/rice) for public access to the transcriptional profiling data for this important crop.
authors.affiliation: Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA.
authors.forename: Kan
authors.initials: K
authors.lastname: Nobuta
authors.forename: R C
authors.initials: RC
authors.lastname: Venu
authors.forename: Cheng
authors.initials: C
authors.lastname: Lu
authors.forename: André
authors.initials: A
authors.lastname: Beló
authors.forename: Kalyan
authors.initials: K
authors.lastname: Vemaraju
authors.forename: Karthik
authors.initials: K
authors.lastname: Kulkarni
authors.forename: Wenzhong
authors.initials: W
authors.lastname: Wang
authors.forename: Manoj
authors.initials: M
authors.lastname: Pillay
authors.forename: Pamela J
authors.initials: PJ
authors.lastname: Green
authors.forename: Guo-liang
authors.initials: GL
authors.lastname: Wang
authors.forename: Blake C
authors.initials: BC
authors.lastname: Meyers
mesh_terms: D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D018745:Genome, Plant / Q000235:genetics; D012275:Oryza / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics*; D012342:RNA, Small Nuclear / Q000235:genetics*; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic
chemical_list: D012333:RNA, Messenger; D018749:RNA, Plant; D012342:RNA, Small Nuclear