Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA

By Mayumi Nakano, K. Nobuta, Kalyan Vemaraju, Shivakundan Singh Tej, Jeremy W. Skogen, Blake C. Meyers. Nucleic Acids Res., 2005

310 citations recorded by the source corpus.

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 .

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/6d26ef87468ba46e6c79a0ce557ecb23924f3753

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Citations in the corpus

Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. (2008, methodology): “…profiling has already been realized in a few organisms (Rajagopalan et al. 2006; Fahlgren et al. 2007; Kasschau et al. 2007; Yao et al. 2007) using the massively parallel signature sequencing (MPSS) methodology (Nakano et al. 2006) and more recently the Roche/454 platform (Margulies et al. 2005).”
High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes (2007, background): “Twenty-two predicted miRNAs that were sequenced at least two times, or that had miRNA* sequences represented in the ASRP or MPSS databases [33], failed at the target validation step (Table 2).”
Global identification of microRNA–target RNA pairs by parallel analysis of RNA ends (2008, result): “Interestingly, signatures from both libraries matched to introns and intergenic regions ( Supplementary Table 1 online), suggesting that the latter regions are transcriptionally active but potentially derived from unannotated transcripts, in accordance with previous transcript profiling report”
The TIGR Rice Genome Annotation Resource: improvements and new features (2006, methodology): “Quantitative transcript data are available through a massively parallel signature sequencing project [MPSS (20)] and a serial analysis of gene expression (SAGE) project [(21), http://www.”
Gene Expression Profiling of Plants under Salt Stress (2011, background): “In one study, MPSS libraries were constructed for rice under various abiotic stresses, including salt stress (Nakano et al., 2006).”