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Assessing the hodgepodge of non-mapped reads in bacterial transcriptomes: real or artifactual RNA chimeras?

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dc.contributor.author Lloréns Rico, Verónica, 1989-
dc.contributor.author Serrano Pubull, Luis, 1982-
dc.contributor.author Lluch-Senar, Maria 1982-
dc.date.accessioned 2016-04-14T13:23:48Z
dc.date.available 2016-04-14T13:23:48Z
dc.date.issued 2014
dc.identifier.citation Lloréns-Rico V, Serrano L, Lluch-Senar M. Assessing the hodgepodge of non-mapped reads in bacterial transcriptomes: real or artifactual RNA chimeras? BMC Genomics. 2014; 15: 633. DOI 10.1186/1471-2164-15-633
dc.identifier.issn 1471-2164
dc.identifier.uri http://hdl.handle.net/10230/26096
dc.description.abstract Background: RNA sequencing methods have already altered our view of the extent and complexity of bacterial and eukaryotic transcriptomes, revealing rare transcript isoforms (circular RNAs, RNA chimeras) that could play an important role in their biology./nResults: We performed an analysis of chimera formation by four different computational approaches, including a custom designed pipeline, to study the transcriptomes of M. pneumoniae and P. aeruginosa, as well as mixtures of both. We found that rare transcript isoforms detected by conventional pipelines of analysis could be artifacts of the experimental procedure used in the library preparation, and that they are protocol-dependent. Conclusion: By using a customized pipeline we show that optimal library preparation protocol and the pipeline to analyze the results are crucial to identify real chimeric RNAs. Keywords: Chimeric RNAs, Fusion transcripts, RNA-seq, Library preparation protocols
dc.description.sponsorship The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013), through the European Research Council, under grant agreement Nr. 232913, the Fundación Botín, the Spanish Ministry of Economy and Competitiveness (BIO2007-61762), the National Plan of R + D + i, the ISCIII -Subdirección General de Evaluación y/nFomento de la Investigación- (PI10/01702), and the European Regional Development Fund (ERDF) to the ICREA Research Professor LS. We acknowledge support from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013-2017’ (SEV-2012-0208)
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher BioMed Central
dc.relation.ispartof BMC Genomics. 2014; 15: 633
dc.rights © 2014 Lloréns-Rico 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/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
dc.rights.uri http://creativecommons.org/licenses/by/4.0
dc.subject.other Genètica bacteriana
dc.subject.other RNA
dc.title Assessing the hodgepodge of non-mapped reads in bacterial transcriptomes: real or artifactual RNA chimeras?
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1186/1471-2164-15-633
dc.subject.keyword Chimeric RNAs
dc.subject.keyword Fusion transcripts
dc.subject.keyword RNA-seq
dc.subject.keyword Library preparation protocols
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/232913
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/232913
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/SEV-2012-0208
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PN/BIO2007-61762
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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