title: Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA.
abstract: MPSS (massively parallel signature sequencing) is a sequencing-based technology that uses a unique method to quantify gene expression level, generating millions of short sequence tags per library. We have created a series of databases for four species (Arabidopsis, rice, grape and Magnaporthe grisea, the rice blast fungus). Our MPSS databases measure the expression level of most genes under defined conditions and provide information about potentially novel transcripts (antisense transcripts, alternative splice isoforms and regulatory intergenic transcripts). A modified version of MPSS has been used to perform deep profiling of small RNAs from Arabidopsis, and we have recently adapted our database to display these data. Interpretation of the small RNA MPSS data is facilitated by the inclusion of extensive repeat data in our genome viewer. All the data and the tools introduced in this article are available at http://mpss.udel.edu.
authors.affiliation: Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19714, USA.
authors.forename: Mayumi
authors.initials: M
authors.lastname: Nakano
authors.forename: Kan
authors.initials: K
authors.lastname: Nobuta
authors.forename: Kalyan
authors.initials: K
authors.lastname: Vemaraju
authors.forename: Shivakundan Singh
authors.initials: SS
authors.lastname: Tej
authors.forename: Jeremy W
authors.initials: JW
authors.lastname: Skogen
authors.forename: Blake C
authors.initials: BC
authors.lastname: Meyers
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D032461:Chromosomes, Plant; D030561:Databases, Nucleic Acid; D005091:Exons; D018745:Genome, Plant; D023281:Genomics; D020407:Internet; D020082:Magnaporthe / Q000235:genetics; D035683:MicroRNAs / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012275:Oryza / Q000235:genetics; D012333:RNA, Messenger / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D034741:RNA, Small Interfering / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic; D014584:User-Computer Interface; D027843:Vitis / Q000235:genetics
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D018749:RNA, Plant; D034741:RNA, Small Interfering