title: Deep-sequencing protocols influence the results obtained in small-RNA sequencing.
abstract: Second-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. 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 analysed and compared the expression of microRNAs, as well as populations of small RNAs derived from repetitive elements. 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 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.
authors.affiliation: Institut Curie, Paris, France.
authors.forename: Joern
authors.initials: J
authors.lastname: Toedling
authors.forename: Nicolas
authors.initials: N
authors.lastname: Servant
authors.forename: Constance
authors.initials: C
authors.lastname: Ciaudo
authors.forename: Laurent
authors.initials: L
authors.lastname: Farinelli
authors.forename: Olivier
authors.initials: O
authors.lastname: Voinnet
authors.forename: Edith
authors.initials: E
authors.lastname: Heard
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Barillot
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D053595:Embryonic Stem Cells / Q000166:cytology; D005260:Female; D020869:Gene Expression Profiling; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008297:Male; D051379:Mice; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D008957:Models, Genetic; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D035683:MicroRNAs; D012313:RNA