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Volumn 8, Issue 1, 2013, Pages

RNaseIII and T4 Polynucleotide Kinase sequence biases and solutions during RNA-seq library construction

Author keywords

Heat fragmentation; OptiKinase; RNA seq; RNaseIII; Sequence bias; T4PNK

Indexed keywords

POLYNUCLEOTIDE 5' HYDROXYL KINASE; RIBONUCLEASE III; TRANSCRIPTOME;

EID: 84879826996     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/1745-6150-8-16     Document Type: Article
Times cited : (12)

References (27)
  • 1
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: discovering splice junctions with RNA-Seq
    • 10.1093/bioinformatics/btp120, 2672628, 19289445
    • Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25(9):1105-1111. 10.1093/bioinformatics/btp120, 2672628, 19289445.
    • (2009) Bioinformatics , vol.25 , Issue.9 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 2
    • 78650970907 scopus 로고    scopus 로고
    • SNP discovery in the bovine milk transcriptome using RNA-Seq technology
    • 3002166, 21057797
    • Canovas A, Rincon G, Islas-Trejo A, Wickramasinghe S, Medrano JF. SNP discovery in the bovine milk transcriptome using RNA-Seq technology. Mamm Genome 2010, 21(11-12):592-598. 3002166, 21057797.
    • (2010) Mamm Genome , vol.21 , Issue.11-12 , pp. 592-598
    • Canovas, A.1    Rincon, G.2    Islas-Trejo, A.3    Wickramasinghe, S.4    Medrano, J.F.5
  • 4
    • 0020164793 scopus 로고
    • The effect of acceptor oligoribonucleotide sequence on the T4 RNA ligase reaction
    • 10.1111/j.1432-1033.1982.tb06730.x, 7117259
    • Romaniuk E, McLaughlin LW, Neilson T, Romaniuk PJ. The effect of acceptor oligoribonucleotide sequence on the T4 RNA ligase reaction. Eur J Biochem 1982, 125(3):639-643. 10.1111/j.1432-1033.1982.tb06730.x, 7117259.
    • (1982) Eur J Biochem , vol.125 , Issue.3 , pp. 639-643
    • Romaniuk, E.1    McLaughlin, L.W.2    Neilson, T.3    Romaniuk, P.J.4
  • 5
    • 77955883388 scopus 로고    scopus 로고
    • Biases in Illumina transcriptome sequencing caused by random hexamer priming
    • 10.1093/nar/gkq224, 2896536, 20395217
    • Hansen KD, Brenner SE, Dudoit S. Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res 2010, 38(12):e131. 10.1093/nar/gkq224, 2896536, 20395217.
    • (2010) Nucleic Acids Res , vol.38 , Issue.12
    • Hansen, K.D.1    Brenner, S.E.2    Dudoit, S.3
  • 6
    • 78149456704 scopus 로고    scopus 로고
    • Development of a low bias method for characterizing viral populations using next generation sequencing technology
    • 10.1371/journal.pone.0013564, 2962647, 21042592
    • Willerth SM, Pedro HA, Pachter L, Humeau LM, Arkin AP, Schaffer DV. Development of a low bias method for characterizing viral populations using next generation sequencing technology. PLoS One 2010, 5(10):e13564. 10.1371/journal.pone.0013564, 2962647, 21042592.
    • (2010) PLoS One , vol.5 , Issue.10
    • Willerth, S.M.1    Pedro, H.A.2    Pachter, L.3    Humeau, L.M.4    Arkin, A.P.5    Schaffer, D.V.6
  • 7
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies - the next generation
    • 10.1038/nrg2626, 19997069
    • Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010, 11(1):31-46. 10.1038/nrg2626, 19997069.
    • (2010) Nat Rev Genet , vol.11 , Issue.1 , pp. 31-46
    • Metzker, M.L.1
  • 9
    • 66349122954 scopus 로고    scopus 로고
    • Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing
    • 10.1126/science.1170995, 19478186
    • Li JB, Levanon EY, Yoon JK, Aach J, Xie B, Leproust E, Zhang K, Gao Y, Church GM. Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science 2009, 324(5931):1210-1213. 10.1126/science.1170995, 19478186.
    • (2009) Science , vol.324 , Issue.5931 , pp. 1210-1213
    • Li, J.B.1    Levanon, E.Y.2    Yoon, J.K.3    Aach, J.4    Xie, B.5    Leproust, E.6    Zhang, K.7    Gao, Y.8    Church, G.M.9
  • 10
    • 77952727403 scopus 로고    scopus 로고
    • Noncanonical transcript forms in yeast and their regulation during environmental stress
    • 10.1261/rna.2038810, 2874177, 20421314
    • Yoon OK, Brem RB. Noncanonical transcript forms in yeast and their regulation during environmental stress. RNA 2010, 16(6):1256-1267. 10.1261/rna.2038810, 2874177, 20421314.
    • (2010) RNA , vol.16 , Issue.6 , pp. 1256-1267
    • Yoon, O.K.1    Brem, R.B.2
  • 12
    • 78649510146 scopus 로고    scopus 로고
    • Intron 4 containing novel GABAB1 isoforms impair GABAB receptor function
    • 10.1371/journal.pone.0014044, 2987798, 21124972
    • Lee C, Mayfield RD, Harris RA. Intron 4 containing novel GABAB1 isoforms impair GABAB receptor function. PLoS One 2010, 5(11):e14044. 10.1371/journal.pone.0014044, 2987798, 21124972.
    • (2010) PLoS One , vol.5 , Issue.11
    • Lee, C.1    Mayfield, R.D.2    Harris, R.A.3
  • 14
    • 0029919935 scopus 로고    scopus 로고
    • RNase III cleaves eukaryotic preribosomal RNA at a U3 snoRNP-dependent site
    • 10.1016/S0092-8674(00)81087-9, 8620530
    • Elela SA, Igel H, Ares M. RNase III cleaves eukaryotic preribosomal RNA at a U3 snoRNP-dependent site. Cell 1996, 85(1):115-124. 10.1016/S0092-8674(00)81087-9, 8620530.
    • (1996) Cell , vol.85 , Issue.1 , pp. 115-124
    • Elela, S.A.1    Igel, H.2    Ares, M.3
  • 15
    • 0035155389 scopus 로고    scopus 로고
    • The RNase III family: a conserved structure and expanding functions in eukaryotic dsRNA metabolism
    • Lamontagne B, Larose S, Boulanger J, Elela SA. The RNase III family: a conserved structure and expanding functions in eukaryotic dsRNA metabolism. Curr Issues Mol Biol 2001, 3(4):71-78.
    • (2001) Curr Issues Mol Biol , vol.3 , Issue.4 , pp. 71-78
    • Lamontagne, B.1    Larose, S.2    Boulanger, J.3    Elela, S.A.4
  • 17
    • 21844477027 scopus 로고    scopus 로고
    • Human microRNA prediction through a probabilistic co-learning model of sequence and structure
    • 10.1093/nar/gki668, 1159118, 15987789
    • Nam JW, Shin KR, Han J, Lee Y, Kim VN, Zhang BT. Human microRNA prediction through a probabilistic co-learning model of sequence and structure. Nucleic Acids Res 2005, 33(11):3570-3581. 10.1093/nar/gki668, 1159118, 15987789.
    • (2005) Nucleic Acids Res , vol.33 , Issue.11 , pp. 3570-3581
    • Nam, J.W.1    Shin, K.R.2    Han, J.3    Lee, Y.4    Kim, V.N.5    Zhang, B.T.6
  • 18
    • 79960185923 scopus 로고    scopus 로고
    • Dicer recognizes the 5' end of RNA for efficient and accurate processing
    • 10.1038/nature10198, 21753850
    • Park JE, Heo I, Tian Y, Simanshu DK, Chang H, Jee D, Patel DJ, Kim VN. Dicer recognizes the 5' end of RNA for efficient and accurate processing. Nature 2011, 475(7355):201-205. 10.1038/nature10198, 21753850.
    • (2011) Nature , vol.475 , Issue.7355 , pp. 201-205
    • Park, J.E.1    Heo, I.2    Tian, Y.3    Simanshu, D.K.4    Chang, H.5    Jee, D.6    Patel, D.J.7    Kim, V.N.8
  • 20
    • 84880333381 scopus 로고    scopus 로고
    • Primer3 http://frodo.wi.mit.edu/primer3/.
    • Primer3
  • 21
    • 84880329101 scopus 로고    scopus 로고
    • fq_all2std.pl http://maq.sourceforge.net/fq_all2std.pl.
    • fq_all2std.pl
  • 22
    • 84880331873 scopus 로고    scopus 로고
    • Igvtools http://www.broadinstitute.org/software/igv/download.
    • Igvtools
  • 24
    • 2142738304 scopus 로고    scopus 로고
    • WebLogo: a sequence logo generator
    • 10.1101/gr.849004, 419797, 15173120
    • Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Res 2004, 14(6):1188-1190. 10.1101/gr.849004, 419797, 15173120.
    • (2004) Genome Res , vol.14 , Issue.6 , pp. 1188-1190
    • Crooks, G.E.1    Hon, G.2    Chandonia, J.M.3    Brenner, S.E.4
  • 25
    • 84880325586 scopus 로고    scopus 로고
    • WebLogo http://WebLogo.berkeley.edu.
    • WebLogo


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.