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dc.contributor.authorLyne, Rachelen
dc.contributor.authorBurns, Gen
dc.contributor.authorMata, Juanen
dc.contributor.authorPenkett, CJen
dc.contributor.authorRustici, Gen
dc.contributor.authorChen, DRen
dc.contributor.authorLangford, Cen
dc.contributor.authorVetrie, Den
dc.contributor.authorBahler, Jen
dc.date.accessioned2011-06-14T16:17:29Z
dc.date.available2011-06-14T16:17:29Z
dc.date.issued2003-07-10en
dc.identifier.citationBMC Genomics 2003, 4:27
dc.identifier.issn1471-2164
dc.identifier.urihttp://www.dspace.cam.ac.uk/handle/1810/237736
dc.description.abstractAbstract Background The genome of the fission yeast Schizosaccharomyces pombe has recently been sequenced, setting the stage for the post-genomic era of this increasingly popular model organism. We have built fission yeast microarrays, optimised protocols to improve array performance, and carried out experiments to assess various characteristics of microarrays. Results We designed PCR primers to amplify specific probes (180–500 bp) for all known and predicted fission yeast genes, which are printed in duplicate onto separate regions of glass slides together with control elements (~13,000 spots/slide). Fluorescence signal intensities depended on the size and intragenic position of the array elements, whereas the signal ratios were largely independent of element properties. Only the coding strand is covalently linked to the slides, and our array elements can discriminate transcriptional direction. The microarrays can distinguish sequences with up to 70% identity, above which cross-hybridisation contributes to the signal intensity. We tested the accuracy of signal ratios and measured the reproducibility of array data caused by biological and technical factors. Because the technical variability is lower, it is best to use samples prepared from independent biological experiments to obtain repeated measurements with swapping of fluorochromes to prevent dye bias. We also developed a script that discards unreliable data and performs a normalization to correct spatial artefacts. Conclusions This paper provides data for several microarray properties that are rarely measured. The results define critical parameters for microarray design and experiments and provide a framework to optimise and interpret array data. Our arrays give reproducible and accurate expression ratios with high sensitivity. The scripts for primer design and initial data processing as well as primer sequences and detailed protocols are available from our website.
dc.language.isoen
dc.subjectGENE-EXPRESSIONen
dc.subjectPROTEINSen
dc.subjecthybridizationen
dc.subjectMODULESen
dc.subjectSCHIZOSACCHAROMYCES-POMBEen
dc.subjectvectorsen
dc.subjectDNA microarrayen
dc.subjectnormalizationen
dc.subjectMEIOSISen
dc.titleWhole-genome microarrays of fission yeast: characteristics, accuracy, reproducibility, and processing of array dataen
dc.typeArticle
dc.date.updated2011-06-14T16:17:29Z
dc.rights.holderLyne et al.; licensee BioMed Central Ltd.
prism.number27en
prism.publicationDate2003en
prism.publicationNameBMC GENOMICSen
prism.volume4en
dcterms.dateAccepted2003-07-10en
rioxxterms.versionofrecord10.1186/1471-2164-4-27en
rioxxterms.licenseref.urihttp://www.rioxx.net/licenses/all-rights-reserveden
rioxxterms.licenseref.startdate2003-07-10en
dc.contributor.orcidLyne, Rachel [0000-0001-8050-402X]
dc.contributor.orcidMata, Juan [0000-0002-5514-3653]
dc.identifier.eissn1471-2164
rioxxterms.typeJournal Article/Reviewen


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