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Illumina MiSeq sequencing disfavours a sequence motif in the GFP reporter gene

Silvie Van den Hoecke (UGent) , Judith Verhelst (UGent) and Xavier Saelens (UGent)
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Abstract
Green fluorescent protein (GFP) is one of the most used reporter genes. We have used next-generation sequencing (NGS) to analyse the genetic diversity of a recombinant influenza A virus that expresses GFP and found a remarkable coverage dip in the GFP coding sequence. This coverage dip was present when virus-derived RT-PCR product or the parental plasmid DNA was used as starting material for NGS and regardless of whether Nextera XT transposase or Covaris shearing was used for DNA fragmentation. Therefore, the sequence coverage dip in the GFP coding sequence was not the result of emerging GFP mutant viruses or a bias introduced by Nextera XT fragmentation. Instead, we found that the Illumina MiSeq sequencing method disfavours the 'CCCGCC' motif in the GFP coding sequence.
Keywords
BIAS, INFECTION, CELLS, RATES, DNA, REPLICATION, RAPID GENERATION, IN-VIVO, INFLUENZA-A VIRUS, GREEN-FLUORESCENT PROTEIN

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Citation

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Chicago
Van den Hoecke, Silvie, Judith Verhelst, and Xavier Saelens. 2016. “Illumina MiSeq Sequencing Disfavours a Sequence Motif in the GFP Reporter Gene.” Scientific Reports 6.
APA
Van den Hoecke, Silvie, Verhelst, J., & Saelens, X. (2016). Illumina MiSeq sequencing disfavours a sequence motif in the GFP reporter gene. SCIENTIFIC REPORTS, 6.
Vancouver
1.
Van den Hoecke S, Verhelst J, Saelens X. Illumina MiSeq sequencing disfavours a sequence motif in the GFP reporter gene. SCIENTIFIC REPORTS. 2016;6.
MLA
Van den Hoecke, Silvie, Judith Verhelst, and Xavier Saelens. “Illumina MiSeq Sequencing Disfavours a Sequence Motif in the GFP Reporter Gene.” SCIENTIFIC REPORTS 6 (2016): n. pag. Print.
@article{8023609,
  abstract     = {Green fluorescent protein (GFP) is one of the most used reporter genes. We have used next-generation sequencing (NGS) to analyse the genetic diversity of a recombinant influenza A virus that expresses GFP and found a remarkable coverage dip in the GFP coding sequence. This coverage dip was present when virus-derived RT-PCR product or the parental plasmid DNA was used as starting material for NGS and regardless of whether Nextera XT transposase or Covaris shearing was used for DNA fragmentation. Therefore, the sequence coverage dip in the GFP coding sequence was not the result of emerging GFP mutant viruses or a bias introduced by Nextera XT fragmentation. Instead, we found that the Illumina MiSeq sequencing method disfavours the 'CCCGCC' motif in the GFP coding sequence.},
  articleno    = {26314},
  author       = {Van den Hoecke, Silvie and Verhelst, Judith and Saelens, Xavier},
  issn         = {2045-2322},
  journal      = {SCIENTIFIC REPORTS},
  keyword      = {BIAS,INFECTION,CELLS,RATES,DNA,REPLICATION,RAPID GENERATION,IN-VIVO,INFLUENZA-A VIRUS,GREEN-FLUORESCENT PROTEIN},
  language     = {eng},
  pages        = {8},
  title        = {Illumina MiSeq sequencing disfavours a sequence motif in the GFP reporter gene},
  url          = {http://dx.doi.org/10.1038/srep26314},
  volume       = {6},
  year         = {2016},
}

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