The web supplement to
Toedling, Servant, Ciaudo et al. 2011
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| Sequencing platform and protocol influence the results obtained in small- RNA sequencing |
| Joern Toedling*1,2,3,4,5, Nicolas Servant*1,2,3 , Constance Ciaudo*1,4,5,6, Lauren Farinelli8, Olivier Voinnet6,7 , Edith Heard#1,4,5 and Emmanuel Barillot#1,2,3 |
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1Institut Curie, 26 rue d'Ulm, Paris, F-75248 France. 2INSERM U900, Paris, F-75248 France. 3Mines ParisTech, Fontainebleau, F-77300 France. 4CNRS UMR3215, Paris, F-75248 France. 5 INSERM U934, Paris, F-75248 France. 6Swiss Federal Institute of Technology Zurich, Department of Biology, Chair of RNA biology, CH- 8092 Zurich, Switzerland. 7Institut de Biologie Moléculaire des Plantes, CNRS UPR2357 - Université Louis Pasteur, Strasbourg, France. 8Fasteris, Ch. du Pont-du-Centenaire 109, Case postale 28, CH-1228 Plan-les-Ouates, Switzerland *, # These authors contributed equally to this work. |
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Abstract Background Next-generation sequencing is a powerful method for identifying and quantifying small-RNA components of cells. However, little attention has been paid to the effects of the choice of sequencing platform and library preparation protocol on the results obtained. Results We present a thorough comparison of small-RNA sequencing libraries generated from the same embryonic stem cell lines, using different sequencing platforms, which represent the three major second-generation sequencing technologies, and protocols. We have analyzed and compared the expression of microRNAs, as well as populations of small RNAs derived from repetitive elements. Conclusions Despite the fact that different libraries display a good correlation between sequencing platforms, qualitative and quantitative variations in the results were found, depending on the protocol and the sequencing platform used. Thus, when comparing libraries from different biological samples, it is strongly recommended to use the same sequencing platform and protocol in order to ensure the biological relevance of the comparisons. |
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