comparison between normalised and unnormalised 454-sequencing libraries for small-scale rna-seq studies比较正常和unnormalised 454 -测序小规模rna-seq研究图书馆.pdfVIP

Hindawi Publishing Corporation Comparative and Functional Genomics Volume 2012, Article ID 281693, 8 pages doi:10.1155/2012/281693 Research Article Comparison between Normalised and Unnormalised 454-Sequencing Libraries for Small-Scale RNA-Seq Studies Robert Ekblom,1, 2 Jon Slate,2 Gavin J. Horsburgh,2 Tim Birkhead,2 and Terry Burke2 1 Department of Ecology and Genetics, Uppsala University, Norbyvagen 18 D, 75236 Uppsala, Sweden ¨ 2 Department of Animal and Plant Sciences, University of Sheffi eld, Sheffi eld S10 2TN, UK Correspondence should be addressed to Robert Ekblom, robert.ekblom@ebc.uu.se Received 15 September 2011; Accepted 25 October 2011 Academic Editor: Giulia Piaggio Copyright © 2012 Robert Ekblom et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 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 nor