High throughput sequencing analysis of RNA libraries reveals the influences of initial library and PCR methods on SELEX efficiency.
High throughput sequencing analysis of RNA libraries reveals the influences of initial library and PCR methods on SELEX efficiency.
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DOI：
10.1038/srep33697
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发表时间：
2016-09-22
影响因子：
4.6
通讯作者：
Zhou J
中科院分区：
文献类型：
--
作者：
Takahashi M;Wu X;Ho M;Chomchan P;Rossi JJ;Burnett JC;Zhou J
The systemic evolution of ligands by exponential enrichment (SELEX) technique is a powerful and effective aptamer-selection procedure. However, modifications to the process can dramatically improve selection efficiency and aptamer performance. For example, droplet digital PCR (ddPCR) has been recently incorporated into SELEX selection protocols to putatively reduce the propagation of byproducts and avoid selection bias that result from differences in PCR efficiency of sequences within the random library. However, a detailed, parallel comparison of the efficacy of conventional solution PCR versus the ddPCR modification in the RNA aptamer-selection process is needed to understand effects on overall SELEX performance. In the present study, we took advantage of powerful high throughput sequencing technology and bioinformatics analysis coupled with SELEX (HT-SELEX) to thoroughly investigate the effects of initial library and PCR methods in the RNA aptamer identification. Our analysis revealed that distinct “biased sequences” and nucleotide composition existed in the initial, unselected libraries purchased from two different manufacturers and that the fate of the “biased sequences” was target-dependent during selection. Our comparison of solution PCR- and ddPCR-driven HT-SELEX demonstrated that PCR method affected not only the nucleotide composition of the enriched sequences, but also the overall SELEX efficiency and aptamer efficacy.
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影响因子：
3.7
作者：
Gold L;Ayers D;Bertino J;Bock C;Bock A;Brody EN;Carter J;Dalby AB;Eaton BE;Fitzwater T;Flather D;Forbes A;Foreman T;Fowler C;Gawande B;Goss M;Gunn M;Gupta S;Halladay D;Heil J;Heilig J;Hicke B;Husar G;Janjic N;Jarvis T;Jennings S;Katilius E;Keeney TR;Kim N;Koch TH;Kraemer S;Kroiss L;Le N;Levine D;Lindsey W;Lollo B;Mayfield W;Mehan M;Mehler R;Nelson SK;Nelson M;Nieuwlandt D;Nikrad M;Ochsner U;Ostroff RM;Otis M;Parker T;Pietrasiewicz S;Resnicow DI;Rohloff J;Sanders G;Sattin S;Schneider D;Singer B;Stanton M;Sterkel A;Stewart A;Stratford S;Vaught JD;Vrkljan M;Walker JJ;Watrobka M;Waugh S;Weiss A;Wilcox SK;Wolfson A;Wolk SK;Zhang C;Zichi D
通讯作者：
Zichi D
影响因子：
2.9
作者：
Schuetze, Tatjana;Rubelt, Florian;Gloekler, Joern
通讯作者：
Gloekler, Joern
影响因子：
14.9
作者：
Thiel KW;Hernandez LI;Dassie JP;Thiel WH;Liu X;Stockdale KR;Rothman AM;Hernandez FJ;McNamara JO 2nd;Giangrande PH
通讯作者：
Giangrande PH
影响因子：
4
作者：
Thiel, William H.;Bair, Thomas;Giangrande, Paloma H.
通讯作者：
Giangrande, Paloma H.
影响因子：
14.9
作者：
Hoinka J;Berezhnoy A;Dao P;Sauna ZE;Gilboa E;Przytycka TM
通讯作者：
Przytycka TM