Transcriptome analysis in maritime pine

Laser Capture Microdisection. Source: http://www.eplantscience.com

Laser Capture Microdisection. Source: http://www.eplantscience.com

The combination of laser capture microdissection (LCM) and next-generation sequencing is a powerful tool with which to resolve the entire transcriptome of specific cell types and tissues. Canas et al. Tree Physiol (2014) doi: 10.1093/treephys/tpt113  have developed a protocol for transcriptomic analyses of conifer tissue types using LCM and 454 pyrosequencing.

Fang J. & Schneider B.  Laser Microdissection: a sample preparation technique for plant micrometabolic profiling. Phytochemical Analysis (2013). Online 23 Sep., DOI: 10.1002/pca.2477. This paper provides an introduction to LMD methodology and a concise review of recent applications of LMD in the high-resolution analysis of metabolites in different plant materials.

Bailey-Serres. Microgenomics: Genome-Scale, Cell-Specific Monitoring of Multiple Gene Regulation Tiers. Annual Review of Plant Biology (2013) 64: 293-325. This review surveys the advantages and applications of microgenomics technologies that enable panoramic quantitation of cell-type-specific expression in plants, focusing on the importance of querying gene activity at multiple steps in the continuum, from histone modification to selective translation.

Ronaghi. Pyrosequencing Sheds Light on DNA Sequencing. Genome Research (2001) 11: 3-11. Pyrosequencing has emerged as a new sequencing methodology. This technique is a widely applicable, alternative technology for the detailed characterization of nucleic acids. Pyrosequencing has the potential advantages of accuracy, flexibility, parallel processing, and can be easily automated.This article considers key features regarding different aspects of pyrosequencing technology, including the general principles, enzyme properties, sequencing modes, instrumentation, and potential applications.

 
Marsh (edt.) Pyrosequencing® Protocols, Methods in Molecular Biology™ (2007) 373: 15-23. Pyrosequencing® is a unique system that allows the analysis of genetic variations including single-nucleotide polymorphisms, indels and short repeats, as well as assessing RNA allelic imbalance, DNA methylation status, and gene copy number. Advances in methodology, including multiplex and universal primer applications, have reduced assay cost and improved throughput. This chapter briefly reviews some of the many applications for Pyrosequencing technology.
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