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dc.contributor.authorHOKAMP, KARSTENen
dc.date.accessioned2014-12-19T13:47:28Z
dc.date.available2014-12-19T13:47:28Z
dc.date.created2013en
dc.date.issued2013en
dc.date.submitted2013en
dc.identifier.citationNalpas, Nicolas C Park, Stephen DE Magee, David A Taraktsoglou, Maria Browne, John A Conlon, Kevin M Rue-Albrecht, Kévin Killick, Kate E Hokamp, Karsten Lohan, Amanda J, Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro, BMC genomics, 14, 1, 2013, 230 -en
dc.identifier.issn1471-2164en
dc.identifier.otherYen
dc.identifier.urihttp://hdl.handle.net/2262/72734
dc.descriptionPUBLISHEDen
dc.description.abstractBackground Mycobacterium bovis, the causative agent of bovine tuberculosis, is an intracellular pathogen that can persist inside host macrophages during infection via a diverse range of mechanisms that subvert the host immune response. In the current study, we have analysed and compared the transcriptomes of M. bovis-infected monocyte-derived macrophages (MDM) purified from six Holstein-Friesian females with the transcriptomes of non-infected control MDM from the same animals over a 24 h period using strand-specific RNA sequencing (RNA-seq). In addition, we compare gene expression profiles generated using RNA-seq with those previously generated by us using the high-density Affymetrix® GeneChip® Bovine Genome Array platform from the same MDM-extracted RNA. Results A mean of 7.2 million reads from each MDM sample mapped uniquely and unambiguously to single Bos taurus reference genome locations. Analysis of these mapped reads showed 2,584 genes (1,392 upregulated; 1,192 downregulated) and 757 putative natural antisense transcripts (558 upregulated; 119 downregulated) that were differentially expressed based on sense and antisense strand data, respectively (adjusted P-value ≤ 0.05). Of the differentially expressed genes, 694 were common to both the sense and antisense data sets, with the direction of expression (i.e. up- or downregulation) positively correlated for 693 genes and negatively correlated for the remaining gene. Gene ontology analysis of the differentially expressed genes revealed an enrichment of immune, apoptotic and cell signalling genes. Notably, the number of differentially expressed genes identified from RNA-seq sense strand analysis was greater than the number of differentially expressed genes detected from microarray analysis (2,584 genes versus 2,015 genes). Furthermore, our data reveal a greater dynamic range in the detection and quantification of gene transcripts for RNA-seq compared to microarray technology. Conclusions This study highlights the value of RNA-seq in identifying novel immunomodulatory mechanisms that underlie host-mycobacterial pathogen interactions during infection, including possible complex post-transcriptional regulation of host gene expression involving antisense RNA.en
dc.format.extent230en
dc.language.isoenen
dc.publisherBioMed Central Ltden
dc.relation.ispartofseriesBMC genomicsen
dc.relation.ispartofseries14en
dc.relation.ispartofseries1en
dc.rightsYen
dc.subjectBovine tuberculosisen
dc.subjectImmune responseen
dc.subjectMicroarrayen
dc.subjectMycobacterium bovisen
dc.subjectNatural antisense transcripten
dc.subjectRNA-sequencingen
dc.subjectTranscriptomeen
dc.titleWhole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitroen
dc.typeJournal Articleen
dc.type.supercollectionscholarly_publicationsen
dc.type.supercollectionrefereed_publicationsen
dc.identifier.peoplefinderurlhttp://people.tcd.ie/kahokampen
dc.identifier.rssinternalid98447en
dc.rights.ecaccessrightsopenAccess


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