Abstract
Large insert mate pair reads have been used in de novo assembly and discovery of structural variants. We developed a new approach, Cre-LoxP inverse PCR paired end (CLIP-PE), which exploits the advantages of (1) Cre-LoxP recombination system to efficiently circularize large DNA fragments, (2) inverse PCR to enrich for the desired products that contain both ends of the large DNA fragments, and (3) use of restriction enzymes to introduce a recognizable junction site between ligated fragment ends. We have successfully created CLIP-PE libraries of up to 22 kb jumping pairs and demonstrated their ability to improve genome assemblies. The CLIP-PE methodology can be implemented with existing and future next-generation sequencing platforms.
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Acknowledgement
The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231.
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Peng, Z., Nath, N., Zhao, Z., Froula, J.L., Cheng, JF., Chen, F. (2017). Preparing Mate-Paired Illumina Libraries Using Cre Recombinase. In: Eroshenko, N. (eds) Site-Specific Recombinases. Methods in Molecular Biology, vol 1642. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7169-5_16
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DOI: https://doi.org/10.1007/978-1-4939-7169-5_16
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