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Strategies for Undertaking Expressed Sequence Tag (EST) Projects

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Expressed Sequence Tags (ESTs)

Part of the book series: Methods in Molecular Biology ((MIMB,volume 533))

Abstract

Complementary DNA (cDNA) sequencing can be used to sample an organism’s transcriptome, and the generated EST sequences can be used for a variety of purposes. They are especially important for enhancing the utility of a genome sequence or for providing a gene catalog for a genome that has not or will not be sequenced. In planning and executing a cDNA project, several criteria must be considered. One should clearly define the project purpose, including organism tissue(s) choice, whether those tissues should be pooled, ability to acquire adequate amounts of clean and well-preserved tissue, choice of type(s) of library, and construction of a library (or libraries) that is compatible with project goals. In addition, one must possess the skills to construct the library (or libraries), keeping in mind the number of clones that will be necessary to meet the project requirements. If one is inexperienced in cDNA library construction, it might be wise to outsource the library production and/or sequence and analysis to a sequencing center or to a company that specializes in those activities. One should also be aware that new sequencing platforms are being marketed that may offer simpler protocols that can produce cDNA data in a more rapid and economical manner. Of course, the bioinformatics tools will have to be in place to de-convolute and aid in data analysis for these newer technologies. Possible funding sources for these projects include well-justified grant proposals, private funding, and/or collaborators with available funds.

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Acknowledgments

This work was supported by the National Human Genome Research Institute (Grant U54 HG003079).

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Authors and Affiliations

  1. Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA

    Sandra W. Clifton & Makedonka Mitreva

Authors
  1. Sandra W. Clifton
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  2. Makedonka Mitreva
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Editors and Affiliations

  1. Molecular Structure and Function Hospital for Sick Children, Departments of Biochemistry & Molecular Genetics, University of Toronto, Toronto, ON, Canada

    John Parkinson

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Clifton, S.W., Mitreva, M. (2009). Strategies for Undertaking Expressed Sequence Tag (EST) Projects. In: Parkinson, J. (eds) Expressed Sequence Tags (ESTs). Methods in Molecular Biology, vol 533. Humana Press. https://doi.org/10.1007/978-1-60327-136-3_2

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  • DOI: https://doi.org/10.1007/978-1-60327-136-3_2

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-759-4

  • Online ISBN: 978-1-60327-136-3

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