Comprehensive multi-center assessment of small RNA-seq methods for quantitative miRNA profiling
| Autor: | Giraldez, Maria D, Spengler, Ryan M, Etheridge, Alton, Godoy, Paula M, Barczak, Andrea J, Srinivasan, Srimeenakshi, De Hoff, Peter L, Tanriverdi, Kahraman, Courtright, Amanda, Lu, Shulin, Khoory, Joseph, Rubio, Renee, Baxter, David, Driedonks, Tom A P, Buermans, Henk P J, Nolte-'t Hoen, Esther N M, Jiang, Hui, Wang, Kai, Ghiran, Ionita, Wang, Yaoyu E, Van Keuren-Jensen, Kendall, Freedman, Jane E, Woodruff, Prescott G, Laurent, Louise C, Erle, David J, Galas, David J, Tewari, Muneesh, LS Celbiologie-Algemeen, dB&C I&I |
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| Přispěvatelé: | LS Celbiologie-Algemeen, dB&C I&I |
| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Small RNA Adenosine Sequence analysis Computer science Absolute quantification Biomedical Engineering Bioengineering Computational biology Applied Microbiology and Biotechnology 03 medical and health sciences MD Multidisciplinary microRNA Mirna profiling Humans Small nucleolar RNA RNA Reproducibility of Results Reference Standards Inosine MicroRNAs 030104 developmental biology RNA editing Molecular Medicine RNA Editing Sequence Analysis Biotechnology |
| Zdroj: | Nature biotechnology, vol 36, iss 8 Nature Biotechnology, 36(8), 746. Nature Publishing Group Giraldez, Maria D; Spengler, Ryan M; Etheridge, Alton; Godoy, Paula M; Barczak, Andrea J; Srinivasan, Srimeenakshi; et al.(2018). Comprehensive multi-center assessment of small RNA-seq methods for quantitative miRNA profiling.. Nature biotechnology, 36(8), 746-757. doi: 10.1038/nbt.4183. UC San Diego: Retrieved from: http://www.escholarship.org/uc/item/2671613v |
| ISSN: | 1087-0156 |
| Popis: | RNA-seq is increasingly used for quantitative profiling of small RNAs (for example, microRNAs, piRNAs and snoRNAs) in diverse sample types, including isolated cells, tissues and cell-free biofluids. The accuracy and reproducibility of the currently used small RNA-seq library preparation methods have not been systematically tested. Here we report results obtained by a consortium of nine labs that independently sequenced reference, 'ground truth' samples of synthetic small RNAs and human plasma-derived RNA. We assessed three commercially available library preparation methods that use adapters of defined sequence and six methods using adapters with degenerate bases. Both protocol- and sequence-specific biases were identified, including biases that reduced the ability of small RNA-seq to accurately measure adenosine-to-inosine editing in microRNAs. We found that these biases were mitigated by library preparation methods that incorporate adapters with degenerate bases. MicroRNA relative quantification between samples using small RNA-seq was accurate and reproducible across laboratories and methods. |
| Databáze: | OpenAIRE |
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