Methods for analysis of gene expression in plants using MPSS.
Kan Nobuta1, Kalyan Vemaraju, Blake C Meyers
1Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
Methods in Molecular Biology (Clifton, N.J.)
|February 22, 2008
Summary
Massively parallel signature sequencing (MPSS) technology enables deep profiling of mRNA and small RNA. MPSS databases provide absolute gene expression levels and identify novel transcripts across multiple species.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Massively parallel signature sequencing (MPSS) is a high-throughput sequencing technology.
- MPSS is suitable for deep profiling of messenger RNA (mRNA) and small RNA through cDNA tag sequencing.
Purpose of the Study:
- To present MPSS databases for mRNA and small RNA expression analysis.
- To highlight analytical tools for interpreting MPSS expression data.
Main Methods:
- MPSS technology was used to sequence cDNA tags from various libraries.
- Databases were created for four species: Arabidopsis, rice, grape, and Magnaporthe grisea.
- Web interface with tools like Gene Analysis (GA), Chromosome Viewer (CV), and Library Analysis (LIBAN) was developed.
Main Results:
- MPSS databases provide absolute gene expression levels for samples.
- Databases offer insights into novel transcripts, including antisense transcripts, alternative splice isoforms, and regulatory intergenic transcripts.
- MPSS-derived Arabidopsis small RNA samples were used to build an extensive database.
Conclusions:
- MPSS databases offer comprehensive gene expression profiling.
- The provided analytical tools facilitate the interpretation of MPSS expression data.
- These resources support research in genomics and transcriptomics across different species.
