Accurate Adapter Information Is Crucial for Reproducibility and Reusability in Small RNA Seq Studies

Overview

Journal Noncoding RNA

Date 2019 Oct 31

PMID 31661777

Citations 5

Authors

Xiangfu Zhong

Fatima Heinicke

Benedicte A Lie

Simon Rayner

Affiliations

Soon will be listed here.

Abstract

A necessary pre-processing data analysis step is the removal of adapter sequences from the raw reads. While most adapter trimming tools require adapter sequence as an essential input, adapter information is often incomplete or missing. This can impact quantification of features, reproducibility of the study and might even lead to erroneous conclusions. Here, we provide examples to highlight the importance of specifying the adapter sequence by demonstrating the effect of using similar but different adapter sequences and identify additional potential sources of errors in the adapter trimming step. Finally, we propose solutions by which users can ensure their small RNA-seq data is fully annotated with adapter information.

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References

Seguin-Orlando A, Schubert M, Clary J, Stagegaard J, Alberdi M, Prado J . Ligation bias in illumina next-generation DNA libraries: implications for sequencing ancient genomes. PLoS One. 2013; 8(10):e78575. PMC: 3812280. DOI: 10.1371/journal.pone.0078575. View

Hafner M, Landgraf P, Ludwig J, Rice A, Ojo T, Lin C . Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing. Methods. 2007; 44(1):3-12. PMC: 2847350. DOI: 10.1016/j.ymeth.2007.09.009. View

Bolger A, Lohse M, Usadel B . Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15):2114-20. PMC: 4103590. DOI: 10.1093/bioinformatics/btu170. View

Sorefan K, Pais H, Hall A, Kozomara A, Griffiths-Jones S, Moulton V . Reducing ligation bias of small RNAs in libraries for next generation sequencing. Silence. 2012; 3(1):4. PMC: 3489589. DOI: 10.1186/1758-907X-3-4. View

Niu J, Meeus I, De Coninck D, Deforce D, Etebari K, Asgari S . Infections of virulent and avirulent viruses differentially influenced the expression of dicer-1, ago-1, and microRNAs in Bombus terrestris. Sci Rep. 2017; 7:45620. PMC: 5379481. DOI: 10.1038/srep45620. View

Tsuji J, Weng Z . DNApi: A De Novo Adapter Prediction Algorithm for Small RNA Sequencing Data. PLoS One. 2016; 11(10):e0164228. PMC: 5063419. DOI: 10.1371/journal.pone.0164228. View

Tian G, Yin X, Luo H, Xu X, Bolund L, Zhang X . Sequencing bias: comparison of different protocols of microRNA library construction. BMC Biotechnol. 2010; 10:64. PMC: 2946280. DOI: 10.1186/1472-6750-10-64. View

Dard-Dascot C, Naquin D, dAubenton-Carafa Y, Alix K, Thermes C, van Dijk E . Systematic comparison of small RNA library preparation protocols for next-generation sequencing. BMC Genomics. 2018; 19(1):118. PMC: 5799908. DOI: 10.1186/s12864-018-4491-6. View

Sansone S, McQuilton P, Rocca-Serra P, Gonzalez-Beltran A, Izzo M, Lister A . FAIRsharing as a community approach to standards, repositories and policies. Nat Biotechnol. 2019; 37(4):358-367. PMC: 6785156. DOI: 10.1038/s41587-019-0080-8. View

10.

Davis M, van Dongen S, Abreu-Goodger C, Bartonicek N, Enright A . Kraken: a set of tools for quality control and analysis of high-throughput sequence data. Methods. 2013; 63(1):41-9. PMC: 3991327. DOI: 10.1016/j.ymeth.2013.06.027. View

11.

Zhuang F, Fuchs R, Sun Z, Zheng Y, Robb G . Structural bias in T4 RNA ligase-mediated 3'-adapter ligation. Nucleic Acids Res. 2012; 40(7):e54. PMC: 3326334. DOI: 10.1093/nar/gkr1263. View

12.

Raabe C, Tang T, Brosius J, Rozhdestvensky T . Biases in small RNA deep sequencing data. Nucleic Acids Res. 2013; 42(3):1414-26. PMC: 3919602. DOI: 10.1093/nar/gkt1021. View

13.

Alon S, Vigneault F, Eminaga S, Christodoulou D, Seidman J, Church G . Barcoding bias in high-throughput multiplex sequencing of miRNA. Genome Res. 2011; 21(9):1506-11. PMC: 3166835. DOI: 10.1101/gr.121715.111. View

14.

Gumurdu A, Yildiz R, Eren E, Karakulah G, Unver T, Genc S . MicroRNA exocytosis by large dense-core vesicle fusion. Sci Rep. 2017; 7:45661. PMC: 5372467. DOI: 10.1038/srep45661. View

15.

Shore S, Henderson J, Lebedev A, Salcedo M, Zon G, McCaffrey A . Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation. PLoS One. 2016; 11(11):e0167009. PMC: 5119831. DOI: 10.1371/journal.pone.0167009. View

16.

Schubert M, Lindgreen S, Orlando L . AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res Notes. 2016; 9:88. PMC: 4751634. DOI: 10.1186/s13104-016-1900-2. View

17.

Niu J, Smagghe G, De Coninck D, Van Nieuwerburgh F, Deforce D, Meeus I . In vivo study of Dicer-2-mediated immune response of the small interfering RNA pathway upon systemic infections of virulent and avirulent viruses in Bombus terrestris. Insect Biochem Mol Biol. 2015; 70:127-37. DOI: 10.1016/j.ibmb.2015.12.006. View

18.

Lu C, Meyers B, Green P . Construction of small RNA cDNA libraries for deep sequencing. Methods. 2007; 43(2):110-7. DOI: 10.1016/j.ymeth.2007.05.002. View

19.

Corpas M, Kovalevskaya N, McMurray A, Nielsen F . A FAIR guide for data providers to maximise sharing of human genomic data. PLoS Comput Biol. 2018; 14(3):e1005873. PMC: 5854239. DOI: 10.1371/journal.pcbi.1005873. View

20.

Van Goethem A, Yigit N, Everaert C, Moreno-Smith M, Mus L, Barbieri E . Depletion of tRNA-halves enables effective small RNA sequencing of low-input murine serum samples. Sci Rep. 2016; 6:37876. PMC: 5129013. DOI: 10.1038/srep37876. View