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Volumn 2012, Issue , 2012, Pages

Technical considerations for reduced representation bisulfite sequencing with multiplexed libraries

Author keywords

[No Author keywords available]

Indexed keywords

BISULFITE; HYDROGEN SULFITE; SULFITE;

EID: 84869013266     PISSN: 11107243     EISSN: 11107251     Source Type: Journal    
DOI: 10.1155/2012/741542     Document Type: Article
Times cited : (64)

References (32)
  • 1
    • 77957279300 scopus 로고    scopus 로고
    • Next generation sequencing in functional genomics
    • 2-s2.0-77957279300 10.1093/bib/bbq018
    • Werner T., Next generation sequencing in functional genomics. Briefings in Bioinformatics 2010 11 5 499 511 2-s2.0-77957279300 10.1093/bib/bbq018
    • (2010) Briefings in Bioinformatics , vol.11 , Issue.5 , pp. 499-511
    • Werner, T.1
  • 2
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies the next generation
    • 2-s2.0-72849144434 10.1038/nrg2626
    • Metzker M. L., Sequencing technologies the next generation. Nature Reviews Genetics 2010 11 1 31 46 2-s2.0-72849144434 10.1038/nrg2626
    • (2010) Nature Reviews Genetics , vol.11 , Issue.1 , pp. 31-46
    • Metzker, M.L.1
  • 3
    • 64149123778 scopus 로고    scopus 로고
    • Next-generation sequencing: From basic research to diagnostics
    • 2-s2.0-64149123778 10.1373/clinchem.2008.112789
    • Voelkerding K. V., Dames S. A., Durtschi J. D., Next-generation sequencing: from basic research to diagnostics. Clinical Chemistry 2009 55 4 641 658 2-s2.0-64149123778 10.1373/clinchem.2008.112789
    • (2009) Clinical Chemistry , vol.55 , Issue.4 , pp. 641-658
    • Voelkerding, K.V.1    Dames, S.A.2    Durtschi, J.D.3
  • 4
    • 84858794353 scopus 로고    scopus 로고
    • Next generation sequencing in epigenetics: Insights and challenges
    • Meaburn E., Schulz R., Next generation sequencing in epigenetics: insights and challenges. Seminars in Cell & Developmental Biology 2011 23 2 192 199
    • (2011) Seminars in Cell & Developmental Biology , vol.23 , Issue.2 , pp. 192-199
    • Meaburn, E.1    Schulz, R.2
  • 5
    • 81055157018 scopus 로고    scopus 로고
    • Studying the epigenome using next generation sequencing
    • 2-s2.0-79961115155 10.1136/jmedgenet-2011-100242
    • Ku C. S., Naidoo N., Wu M., Soong R., Studying the epigenome using next generation sequencing. Journal of Medical Genetics 2011 48 721 730 2-s2.0-79961115155 10.1136/jmedgenet-2011-100242
    • (2011) Journal of Medical Genetics , vol.48 , pp. 721-730
    • Ku, C.S.1    Naidoo, N.2    Wu, M.3    Soong, R.4
  • 6
    • 0022540321 scopus 로고
    • CpG-rich islands and the function of DNA methylation
    • Bird A. P., CpG-rich islands and the function of DNA methylation. Nature 1986 321 6067 209 213 2-s2.0-0022540321 (Pubitemid 16016411)
    • (1986) Nature , vol.321 , Issue.6067 , pp. 209-213
    • Bird, A.P.1
  • 7
    • 0023701018 scopus 로고
    • Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells. The carboxyl-terminal domain of the mammalian enzymes is related to bacterial restriction methyltransferases
    • 2-s2.0-0023701018
    • Bestor T., Laudano A., Mattaliano R., Ingram V., Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells. The carboxyl-terminal domain of the mammalian enzymes is related to bacterial restriction methyltransferases. Journal of Molecular Biology 1988 203 4 971 983 2-s2.0-0023701018
    • (1988) Journal of Molecular Biology , vol.203 , Issue.4 , pp. 971-983
    • Bestor, T.1    Laudano, A.2    Mattaliano, R.3    Ingram, V.4
  • 8
    • 0026697174 scopus 로고
    • Activation of mammalian DNA methyltransferase by cleavage of a Zn binding regulatory domain
    • 2-s2.0-0026697174
    • Bestor T. H., Activation of mammalian DNA methyltransferase by cleavage of a Zn binding regulatory domain. The EMBO Journal 1992 11 7 2611 2617 2-s2.0-0026697174
    • (1992) The EMBO Journal , vol.11 , Issue.7 , pp. 2611-2617
    • Bestor, T.H.1
  • 9
    • 15244353967 scopus 로고    scopus 로고
    • X-inactivation profile reveals extensive variability in X-linked gene expression in females
    • DOI 10.1038/nature03479
    • Carrel L., Willard H. F., X-inactivation profile reveals extensive variability in X-linked gene expression in females. Nature 2005 434 7031 400 404 2-s2.0-15244353967 10.1038/nature03479 (Pubitemid 40469185)
    • (2005) Nature , vol.434 , Issue.7031 , pp. 400-404
    • Carrel, L.1    Willard, H.F.2
  • 10
    • 32044455298 scopus 로고    scopus 로고
    • Large-scale structure of genomic methylation patterns
    • DOI 10.1101/gr.4362006
    • Rollins R. A., Haghighi F., Edwards J. R., Das R., Zhang M. Q., Ju J., Bestor T. H., Large-scale structure of genomic methylation patterns. Genome Research 2006 16 2 157 163 2-s2.0-32044455298 10.1101/gr.4362006 (Pubitemid 43200263)
    • (2006) Genome Research , vol.16 , Issue.2 , pp. 157-163
    • Rollins, R.A.1    Haghighi, F.2    Edwards, J.R.3    Das, R.4    Zhang, M.Q.5    Ju, J.6    Bestor, T.H.7
  • 11
    • 43749098985 scopus 로고    scopus 로고
    • DNA methylation landscapes: Provocative insights from epigenomics
    • DOI 10.1038/nrg2341, PII NRG2341
    • Suzuki M. M., Bird A., DNA methylation landscapes: provocative insights from epigenomics. Nature Reviews Genetics 2008 9 6 465 476 2-s2.0-43749098985 10.1038/nrg2341 (Pubitemid 351693975)
    • (2008) Nature Reviews Genetics , vol.9 , Issue.6 , pp. 465-476
    • Suzuki, M.M.1    Bird, A.2
  • 13
    • 84868520898 scopus 로고    scopus 로고
    • Monozygotic twins: Genes are not the destiny?
    • Chatterjee A., Morison I. M., Monozygotic twins: genes are not the destiny? Bioinformation 2011 7 7 369 370
    • (2011) Bioinformation , vol.7 , Issue.7 , pp. 369-370
    • Chatterjee, A.1    Morison, I.M.2
  • 14
    • 0036561649 scopus 로고    scopus 로고
    • Altered methylation patterns in cancer cell genomes: Cause or consequence?
    • DOI 10.1016/S1535-6108(02)00061-2
    • Baylin S., Bestor T. H., Altered methylation patterns in cancer cell genomes: cause or consequence? Cancer Cell 2002 1 4 299 305 2-s2.0-0036561649 10.1016/S1535-6108(02)00061-2 (Pubitemid 41039130)
    • (2002) Cancer Cell , vol.1 , Issue.4 , pp. 299-305
    • Baylin, S.1    Bestor, T.H.2
  • 16
    • 84856568045 scopus 로고    scopus 로고
    • RRBSMAP: A fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing
    • Xi Y., Bock C., Muller F., RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing. Bioinformatics 2012 28 3 430 432
    • (2012) Bioinformatics , vol.28 , Issue.3 , pp. 430-432
    • Xi, Y.1    Bock, C.2    Muller, F.3
  • 19
    • 80052306947 scopus 로고    scopus 로고
    • Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation
    • e1002228
    • Gertz J., Varley K. E., Reddy T. E., Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. PLoS Genetics 2011 7 8 e1002228
    • (2011) PLoS Genetics , vol.7 , Issue.8
    • Gertz, J.1    Varley, K.E.2    Reddy, T.E.3
  • 20
    • 77449153454 scopus 로고    scopus 로고
    • Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution
    • 2-s2.0-77449153454 10.1038/nmeth.1414
    • Gu H., Bock C., Mikkelsen T. S., Jäger N., Smith Z. D., Tomazou E., Gnirke A., Lander E. S., Meissner A., Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nature Methods 2010 7 2 133 136 2-s2.0-77449153454 10.1038/nmeth.1414
    • (2010) Nature Methods , vol.7 , Issue.2 , pp. 133-136
    • Gu, H.1    Bock, C.2    Mikkelsen, T.S.3    Jäger, N.4    Smith, Z.D.5    Tomazou, E.6    Gnirke, A.7    Lander, E.S.8    Meissner, A.9
  • 23
    • 68949141599 scopus 로고    scopus 로고
    • BSMAP: Whole genome bisulfite sequence MAPping program
    • 2-s2.0-68949141599 10.1186/1471-2105-10-232article 232
    • Xi Y., Li W., BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics 2009 10, article 232 2-s2.0-68949141599 10.1186/1471-2105-10-232
    • (2009) BMC Bioinformatics , vol.10
    • Xi, Y.1    Li, W.2
  • 24
    • 84861563688 scopus 로고    scopus 로고
    • Comparison of alignment software for genome-wide bisulphite sequence data
    • Article E79
    • Chatterjee A., Stockwell P. A., Rodger E. J., Comparison of alignment software for genome-wide bisulphite sequence data. Nucleic Acids Research 2012 40 10, article e79
    • (2012) Nucleic Acids Research , vol.40 , Issue.10
    • Chatterjee, A.1    Stockwell, P.A.2    Rodger, E.J.3
  • 25
    • 79957868920 scopus 로고    scopus 로고
    • Bismark: A flexible aligner and methylation caller for Bisulfite-Seq applications
    • 2-s2.0-79957868920 10.1093/bioinformatics/btr167
    • Krueger F., Andrews S. R., Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 2011 27 11 1571 1572 2-s2.0-79957868920 10.1093/bioinformatics/btr167
    • (2011) Bioinformatics , vol.27 , Issue.11 , pp. 1571-1572
    • Krueger, F.1    Andrews, S.R.2
  • 26
    • 67649854923 scopus 로고    scopus 로고
    • High-throughput bisulfite sequencing in mammalian genomes
    • 2-s2.0-67649854923 10.1016/j.ymeth.2009.05.003
    • Smith Z. D., Gu H., Bock C., Gnirke A., Meissner A., High-throughput bisulfite sequencing in mammalian genomes. Methods 2009 48 3 226 232 2-s2.0-67649854923 10.1016/j.ymeth.2009.05.003
    • (2009) Methods , vol.48 , Issue.3 , pp. 226-232
    • Smith, Z.D.1    Gu, H.2    Bock, C.3    Gnirke, A.4    Meissner, A.5
  • 27
    • 79952788617 scopus 로고    scopus 로고
    • Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling
    • 2-s2.0-79952788617 10.1038/nprot.2010.190
    • Gu H., Smith Z. D., Bock C., Boyle P., Gnirke A., Meissner A., Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nature Protocols 2011 6 4 468 481 2-s2.0-79952788617 10.1038/nprot.2010.190
    • (2011) Nature Protocols , vol.6 , Issue.4 , pp. 468-481
    • Gu, H.1    Smith, Z.D.2    Bock, C.3    Boyle, P.4    Gnirke, A.5    Meissner, A.6
  • 28
    • 0036311202 scopus 로고    scopus 로고
    • Identification and resolution of artifacts in bisulfite sequencing
    • DOI 10.1016/S1046-2023(02)00060-9, PII S1046202302000609
    • Warnecke P. M., Stirzaker C., Song J., Grunau C., Melki J. R., Clark S. J., Identification and resolution of artifacts in bisulfite sequencing. Methods 2002 27 2 101 107 2-s2.0-0036311202 10.1016/S1046-2023(02)00060-9 (Pubitemid 34757119)
    • (2002) Methods , vol.27 , Issue.2 , pp. 101-107
    • Warnecke, P.M.1    Stirzaker, C.2    Song, J.3    Grunau, C.4    Melki, J.R.5    Clark, S.J.6
  • 30
    • 0014682668 scopus 로고
    • Structure of subtilisin B P N ′ at 2.5 Å resolution
    • 2-s2.0-0014682668 10.1038/221235a0
    • Wright C. S., Alden R. A., Kraut J., Structure of subtilisin B P N ′ at 2.5 Å resolution. Nature 1969 221 5177 235 242 2-s2.0-0014682668 10.1038/221235a0
    • (1969) Nature , vol.221 , Issue.5177 , pp. 235-242
    • Wright, C.S.1    Alden, R.A.2    Kraut, J.3
  • 31
    • 77951226627 scopus 로고    scopus 로고
    • The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
    • 2-s2.0-77951226627 10.1093/nar/gkp1137
    • Cock P. J. A., Fields C. J., Goto N., Heuer M. L., Rice P. M., The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Research 2009 38 6 1767 1771 2-s2.0-77951226627 10.1093/nar/gkp1137
    • (2009) Nucleic Acids Research , vol.38 , Issue.6 , pp. 1767-1771
    • Cock, P.J.A.1    Fields, C.J.2    Goto, N.3    Heuer, M.L.4    Rice, P.M.5
  • 32
    • 77957151956 scopus 로고    scopus 로고
    • SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data
    • 2-s2.0-77957151956 10.1186/1471-2105-11-485 article 485
    • Cox M. P., Peterson D. A., Biggs P. J., SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics 2010 11, article 485 2-s2.0-77957151956 10.1186/1471-2105-11-485
    • (2010) BMC Bioinformatics , vol.11
    • Cox, M.P.1    Peterson, D.A.2    Biggs, P.J.3


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