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Comparison between Normalised and Unnormalised 454-Sequencing Libraries for Small-Scale RNA-Seq Studies
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
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2012 (English)In: Comparative and functional genomics, ISSN 1531-6912, E-ISSN 1532-6268, Vol. 2012, 281693- p.Article in journal (Refereed) Published
Abstract [en]

Next-generation sequencing of transcriptomes (RNA-Seq) is being used increasingly in studies of nonmodel organisms. Here, we evaluate the effectiveness of normalising cDNA libraries prior to sequencing in a small-scale study of the zebra finch. We find that assemblies produced from normalised libraries had a larger number of contigs but used fewer reads compared to unnormalised libraries. Considerably more genes were also detected using the contigs produced from normalised cDNA, and microsatellite discovery was up to 73% more efficient in these. There was a positive correlation between the detected expression level of genes in normalised and unnormalised cDNA, and there was no difference in the number of genes identified as being differentially expressed between blood and spleen for the normalised and unnormalised libraries. We conclude that normalised cDNA libraries are preferable for many applications of RNA-Seq and that these can also be used in quantitative gene expression studies.

Place, publisher, year, edition, pages
2012. Vol. 2012, 281693- p.
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Genetics
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URN: urn:nbn:se:uu:diva-206868DOI: 10.1155/2012/281693OAI: oai:DiVA.org:uu-206868DiVA: diva2:645780
Available from: 2013-09-05 Created: 2013-09-05 Last updated: 2017-12-06Bibliographically approved

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