'PACLIMS': A component LIM system for high-throughput functional genomic analysis

Nicole Donofrio, Ravi Rajagopalon, Douglas Brown, Stephen Diener, Donald Windham, Shelly Nolin, Anna Floyd, Thomas Mitchell, Natalia Galadima, Sara Tucker, Marc J. Orbach, Gayatri Patel, Mark Farman, Vishal Pampanwar, Cari Soderlund, Yong Hwan Lee, Ralph A. Dean

Research output: Contribution to journalArticle

25 Scopus citations

Abstract

Background: Recent advances in sequencing techniques leading to cost reduction have resulted in the generation of a growing number of sequenced eukaryotic genomes. Computational tools greatly assist in defining open reading frames and assigning tentative annotations. However, gene functions cannot be asserted without biological support through, among other things, mutational analysis. In taking a genome-wide approach to functionally annotate an entire organism, in this application the ∼11,000 predicted genes in the rice blast fungus (Magnaporthe grisea), an effective platform for tracking and storing both the biological materials created and the data produced across several participating institutions was required. Results: The platform designed, named PACLIMS, was built to support our high throughput pipeline for generating 50,000 random insertion mutants of Magnaporthe grisea. To be a useful tool for materials and data tracking and storage, PACLIMS was designed to be simple to use, modifiable to accommodate refinement of research protocols, and cost-efficient. Data entry into PACLIMS was simplified through the use of barcodes and scanners, thus reducing the potential human error, time constraints, and labor. This platform was designed in concert with our experimental protocol so that it leads the researchers through each step of the process from mutant generation through phenotypic assays, thus ensuring that every mutant produced is handled in an identical manner and all necessary data is captured. Conclusion: Many sequenced eukaryotes have reached the point where computational analyses are no longer sufficient and require biological support for their predicted genes. Consequently, there is an increasing need for platforms that support high throughput genome-wide mutational analyses. While PACLIMS was designed specifically for this project, the source and ideas present in its implementation can be used as a model for other high throughput mutational endeavors.

Original languageEnglish (US)
Article number94
JournalBMC bioinformatics
Volume6
DOIs
StatePublished - Apr 12 2005

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

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    Donofrio, N., Rajagopalon, R., Brown, D., Diener, S., Windham, D., Nolin, S., Floyd, A., Mitchell, T., Galadima, N., Tucker, S., Orbach, M. J., Patel, G., Farman, M., Pampanwar, V., Soderlund, C., Lee, Y. H., & Dean, R. A. (2005). 'PACLIMS': A component LIM system for high-throughput functional genomic analysis. BMC bioinformatics, 6, [94]. https://doi.org/10.1186/1471-2105-6-94