Next-generation analysis of deep sequencing data: Bringing light into the black box of SELEX experiments

Methods in Molecular Biology

Volumn 1380, Issue , 2016, Pages 85-95

  Blank, Michael ^a  

^a NONE

Author keywords

Bioinformatics; In silico analysis; Next generation sequencing; NGS; SELEX

Indexed keywords

ANALYTIC METHOD; BIOINFORMATICS; COMBINATORIAL LIBRARY; COMPAS SOFTWARE; COMPUTER MODEL; COMPUTER PROGRAM; DATA ANALYSIS; GENE TECHNOLOGY; IN VITRO SELECTION; NEXT GENERATION SEQUENCING; QUALITY CONTROL; SELEX PROCEDURE; BIOLOGY; DNA SEQUENCE; GENE LIBRARY; HIGH THROUGHPUT SEQUENCING; HUMAN; PROCEDURES; STANDARDS; SYSTEMATIC EVOLUTION OF LIGANDS BY EXPONENTIAL ENRICHMENT APTAMER TECHNIQUE;

APTAMER;

APTAMERS, NUCLEOTIDE; COMPUTATIONAL BIOLOGY; GENE LIBRARY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; SELEX APTAMER TECHNIQUE; SEQUENCE ANALYSIS, DNA;

EID: 84946888242     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-3197-2_7     Document Type: Chapter

References (16)

1. Kahvejian A, Quackenbush J, Thompson JF (2008) What would you do if you could sequence everything? Nat Biotechnol 26:1125-1133
2. Blind M, Blank M (2015) Aptamer selection technology and recent advances. Mol Ther Nucleic Acids 4:e223
3. Ditzler MA, Lange MJ, Bose D, Bottoms CA, Virkler KF, Sawyer AW et al (2013) Highthroughput sequence analysis reveals structural diversity and improved potency among RNA inhibitors of HIV reverse transcriptase. Nucleic Acids Res 41:1873-1884
4. Cho M, Soh HT (2010) Quantitative selection of DNA aptamers through microfluidic selection and high-throughput sequencing. Proc Natl Acad Sci U S A 107:15373-15378
5. Kupakuwana GV, Crill JE, McPike MP, Borer PN (2011) Acyclic identification of aptamers for human alpha-thrombin using overrepresented libraries and deep sequencing. PLoS One 6, e19395
6. Schütze T, Wilhelm B, Greiner N, Braun H, Peter F, Mörl M et al (2011) Probing the SELEX process with next-generation sequencing. PLoS One 6:e29604
7. Hoon S, Zhou B, Janda K, Brenner S, Scolnick J (2011) Aptamer selection by high- throughput sequencing and informatic analysis. Biotechniques 51:413-416
8. Thiel KW, Hernandez LI, Dassie JP, Thiel WH, Liu X, Stockdale KR et al (2012) Delivery of chemo-sensitizing siRNAs to HER2+-breast cancer cells using RNA aptamers. Nucleic Acids Res 40:6319-6337
9. Berezhnoy A, Stewart CA, Mcnamara JO II, Thiel W, Giangrande P, Trinchieri G et al (2009) Isolation and optimization of murine IL-10 receptor blocking oligonucleotide aptamers using high-throughput sequencing. Mol Ther 20:1242-1250
10. Hoinka J, Berezhnoy A, Dao P, Sauna ZE, Gilboa E, Przytycka TM (2015) Large scale analysis of mutational landscape in HT-SELEX improves aptamer discovery. Nucleic Acids Res. doi: 10.1093/nar/gkv308
11. Alam KK, Chang JL, Burke DH (2015) FASTaptamer: a bioinformatic toolkit for highthroughput sequence analysis of combinatorial selections. Mol Ther Nucleic Acids 4:e230
12. Levay A, Brennemann R, Hoinka J, Sant D, Cardone M, Trinchieri G et al (2015) Nucleic Acids Res. doi: 10.1093/nar/gkv534. Epub 2015 May 24
13. Dias-Neto E, Nunes DN, Giordano RJ, Sun J, Botz GH, Yang K et al (2009) Next-generation phage display: integrating and comparing available molecular tools to enable cost-effective high-throughput analysis. PLoS One 4:e8338
14. Ravn U, Gueneau F, Baerlocher L, Osteras M, Desmurs M, Malinge P et al (2010) By-passing in vitro screening-next generation sequencing technologies applied to antibody display and in silico candidate selection. Nucleic Acids Res 38:e193
15. 't Hoen PA, Jirka SM, Ten Broeke BR, Schultes EA, Aguilera B, Pang KH et al (2012) Phage display screening without repetitious selection rounds. Anal Biochem 421:622-631
16. Mannocci L, Zhang Y, Scheuermann J, Leimbacher M, De Bellis G, Rizzi E et al (2008) High-throughput sequencing allows the identification of binding molecules isolated from DNA-encoded chemical libraries. Proc Natl Acad Sci U S A 105:17670-17675