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

Persistent Link:
http://hdl.handle.net/10150/610132
Title:
'PACLIMS': A component LIM system for high-throughput functional genomic analysis
Author:
Donofrio, Nicole; Rajagopalon, Ravi; Brown, Douglas; Diener, Stephen; Windham, Donald; Nolin, Shelly; Floyd, Anna; Mitchell, Thomas; Galadima, Natalia; Tucker, Sara; Orbach, Marc; Patel, Gayatri; Farman, Mark; Pampanwar, Vishal; Soderlund, Cari; Lee, Yong-Hwan; Dean, Ralph
Affiliation:
Department of Plant Pathology, Fungal Genomics Laboratory, North Carolina State University, Raleigh, NC, USA; Department of Plant Pathology, University of Arizona, Tucson, AZ, USA; Department of Plant Pathology, Plant Sciences Building, 1405 Veteran's Drive, University of Kentucky, Lexington, KY, 40546, USA; Arizona Genomics Computational Laboratory, University of Arizona, Tucson, AZ, USA; School of Agricultural Biotechnology, Seoul National University, Seoul, Korea
Issue Date:
2005
Publisher:
BioMed Central
Citation:
BMC Bioinformatics 2005, 6:94 doi:10.1186/1471-2105-6-94
Journal:
BMC Bioinformatics
Rights:
© 2005 Donofrio et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
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.
EISSN:
1471-2105
DOI:
10.1186/1471-2105-6-94
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2105/6/94

Full metadata record

DC FieldValue Language
dc.contributor.authorDonofrio, Nicoleen
dc.contributor.authorRajagopalon, Ravien
dc.contributor.authorBrown, Douglasen
dc.contributor.authorDiener, Stephenen
dc.contributor.authorWindham, Donalden
dc.contributor.authorNolin, Shellyen
dc.contributor.authorFloyd, Annaen
dc.contributor.authorMitchell, Thomasen
dc.contributor.authorGaladima, Nataliaen
dc.contributor.authorTucker, Saraen
dc.contributor.authorOrbach, Marcen
dc.contributor.authorPatel, Gayatrien
dc.contributor.authorFarman, Marken
dc.contributor.authorPampanwar, Vishalen
dc.contributor.authorSoderlund, Carien
dc.contributor.authorLee, Yong-Hwanen
dc.contributor.authorDean, Ralphen
dc.date.accessioned2016-05-20T08:59:17Z-
dc.date.available2016-05-20T08:59:17Z-
dc.date.issued2005en
dc.identifier.citationBMC Bioinformatics 2005, 6:94 doi:10.1186/1471-2105-6-94en
dc.identifier.doi10.1186/1471-2105-6-94en
dc.identifier.urihttp://hdl.handle.net/10150/610132-
dc.description.abstractBACKGROUND: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.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2105/6/94en
dc.rights© 2005 Donofrio et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)en
dc.title'PACLIMS': A component LIM system for high-throughput functional genomic analysisen
dc.typeArticleen
dc.identifier.eissn1471-2105en
dc.contributor.departmentDepartment of Plant Pathology, Fungal Genomics Laboratory, North Carolina State University, Raleigh, NC, USAen
dc.contributor.departmentDepartment of Plant Pathology, University of Arizona, Tucson, AZ, USAen
dc.contributor.departmentDepartment of Plant Pathology, Plant Sciences Building, 1405 Veteran's Drive, University of Kentucky, Lexington, KY, 40546, USAen
dc.contributor.departmentArizona Genomics Computational Laboratory, University of Arizona, Tucson, AZ, USAen
dc.contributor.departmentSchool of Agricultural Biotechnology, Seoul National University, Seoul, Koreaen
dc.identifier.journalBMC Bioinformaticsen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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