@article{RN39,
   author = {Ji, L. and Sasaki, T. and Sun, X. and Ma, P. and Lewis, Z. A. and Schmitz, R. J.},
   title = {Methylated DNA is over-represented in whole-genome bisulfite sequencing data},
   journal = {Front Genet},
   volume = {5},
   pages = {341},
   note = {1664-8021
Ji, Lexiang
Sasaki, Takahiko
Sun, Xiaoxiao
Ma, Ping
Lewis, Zachary A
Schmitz, Robert J
R00 GM100000/GM/NIGMS NIH HHS/United States
Journal Article
Switzerland
2014/11/07
Front Genet. 2014 Oct 21;5:341. doi: 10.3389/fgene.2014.00341. eCollection 2014.},
   abstract = {The development of whole-genome bisulfite sequencing (WGBS) has resulted in a number of exciting discoveries about the role of DNA methylation leading to a plethora of novel testable hypotheses. Methods for constructing sodium bisulfite-converted and amplified libraries have recently advanced to the point that the bottleneck for experiments that use WGBS has shifted to data analysis and interpretation. Here we present empirical evidence for an over-representation of reads from methylated DNA in WGBS. This enrichment for methylated DNA is exacerbated by higher cycles of PCR and is influenced by the type of uracil-insensitive DNA polymerase used for amplifying the sequencing library. Future efforts to computationally correct for this enrichment bias will be essential to increasing the accuracy of determining methylation levels for individual cytosines. It is especially critical for studies that seek to accurately quantify DNA methylation levels in populations that may segregate for allelic DNA methylation states.},
   keywords = {DNA methylation
Epigenomics
PCR bias
epigenetics
whole genome bisulfite sequencing},
   ISSN = {1664-8021 (Print)
1664-8021},
   DOI = {10.3389/fgene.2014.00341},
   year = {2014},
   type = {Journal Article}
}

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J."],"bibdata":{"bibtype":"article","type":"Journal Article","author":[{"propositions":[],"lastnames":["Ji"],"firstnames":["L."],"suffixes":[]},{"propositions":[],"lastnames":["Sasaki"],"firstnames":["T."],"suffixes":[]},{"propositions":[],"lastnames":["Sun"],"firstnames":["X."],"suffixes":[]},{"propositions":[],"lastnames":["Ma"],"firstnames":["P."],"suffixes":[]},{"propositions":[],"lastnames":["Lewis"],"firstnames":["Z.","A."],"suffixes":[]},{"propositions":[],"lastnames":["Schmitz"],"firstnames":["R.","J."],"suffixes":[]}],"title":"Methylated DNA is over-represented in whole-genome bisulfite sequencing data","journal":"Front Genet","volume":"5","pages":"341","note":"1664-8021 Ji, Lexiang Sasaki, Takahiko Sun, Xiaoxiao Ma, Ping Lewis, Zachary A Schmitz, Robert J R00 GM100000/GM/NIGMS NIH HHS/United States Journal Article Switzerland 2014/11/07 Front Genet. 2014 Oct 21;5:341. doi: 10.3389/fgene.2014.00341. eCollection 2014.","abstract":"The development of whole-genome bisulfite sequencing (WGBS) has resulted in a number of exciting discoveries about the role of DNA methylation leading to a plethora of novel testable hypotheses. Methods for constructing sodium bisulfite-converted and amplified libraries have recently advanced to the point that the bottleneck for experiments that use WGBS has shifted to data analysis and interpretation. Here we present empirical evidence for an over-representation of reads from methylated DNA in WGBS. This enrichment for methylated DNA is exacerbated by higher cycles of PCR and is influenced by the type of uracil-insensitive DNA polymerase used for amplifying the sequencing library. Future efforts to computationally correct for this enrichment bias will be essential to increasing the accuracy of determining methylation levels for individual cytosines. It is especially critical for studies that seek to accurately quantify DNA methylation levels in populations that may segregate for allelic DNA methylation states.","keywords":"DNA methylation Epigenomics PCR bias epigenetics whole genome bisulfite sequencing","issn":"1664-8021 (Print) 1664-8021","doi":"10.3389/fgene.2014.00341","year":"2014","bibtex":"@article{RN39,\r\n author = {Ji, L. and Sasaki, T. and Sun, X. and Ma, P. and Lewis, Z. A. and Schmitz, R. J.},\r\n title = {Methylated DNA is over-represented in whole-genome bisulfite sequencing data},\r\n journal = {Front Genet},\r\n volume = {5},\r\n pages = {341},\r\n note = {1664-8021\r\nJi, Lexiang\r\nSasaki, Takahiko\r\nSun, Xiaoxiao\r\nMa, Ping\r\nLewis, Zachary A\r\nSchmitz, Robert J\r\nR00 GM100000/GM/NIGMS NIH HHS/United States\r\nJournal Article\r\nSwitzerland\r\n2014/11/07\r\nFront Genet. 2014 Oct 21;5:341. doi: 10.3389/fgene.2014.00341. eCollection 2014.},\r\n abstract = {The development of whole-genome bisulfite sequencing (WGBS) has resulted in a number of exciting discoveries about the role of DNA methylation leading to a plethora of novel testable hypotheses. Methods for constructing sodium bisulfite-converted and amplified libraries have recently advanced to the point that the bottleneck for experiments that use WGBS has shifted to data analysis and interpretation. Here we present empirical evidence for an over-representation of reads from methylated DNA in WGBS. This enrichment for methylated DNA is exacerbated by higher cycles of PCR and is influenced by the type of uracil-insensitive DNA polymerase used for amplifying the sequencing library. Future efforts to computationally correct for this enrichment bias will be essential to increasing the accuracy of determining methylation levels for individual cytosines. It is especially critical for studies that seek to accurately quantify DNA methylation levels in populations that may segregate for allelic DNA methylation states.},\r\n keywords = {DNA methylation\r\nEpigenomics\r\nPCR bias\r\nepigenetics\r\nwhole genome bisulfite sequencing},\r\n ISSN = {1664-8021 (Print)\r\n1664-8021},\r\n DOI = {10.3389/fgene.2014.00341},\r\n year = {2014},\r\n type = {Journal Article}\r\n}\r\n\r\n","author_short":["Ji, L.","Sasaki, T.","Sun, X.","Ma, P.","Lewis, Z. A.","Schmitz, R. 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