{"database":"biostudies-literature","file_versions":[],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":52,"searchCount":0},"additional":{"submitter":["Van Nieuwerburgh F"],"funding":["NEI NIH HHS","PHS HHS"],"pagination":["e24"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC3273786"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["40(3)"],"pubmed_abstract":["Standard Illumina mate-paired libraries are constructed from 3- to 5-kb DNA fragments by a blunt-end circularization. Sequencing reads that pass through the junction of the two joined ends of a 3-5-kb DNA fragment are not easy to identify and pose problems during mapping and de novo assembly. Longer read lengths increase the possibility that a read will cross the junction. To solve this problem, we developed a mate-paired protocol for use with Illumina sequencing technology that uses Cre-Lox recombination instead of blunt end circularization. In this method, a LoxP sequence is incorporated at the junction site. This sequence allows screening reads for junctions without using a reference genome. Junction reads can be trimmed or split at the junction. Moreover, the location of the LoxP sequence in the reads distinguishes mate-paired reads from spurious paired-end reads. We tested this new method by preparing and sequencing a mate-paired library with an insert size of 3 kb from Saccharomyces cerevisiae. We present an analysis of the library quality statistics and a new bio-informatics tool called DeLoxer that can be used to analyze an IlluminaCre-Lox mate-paired data set. We also demonstrate how the resulting data significantly improves a de novo assembly of the S. cerevisiae genome."],"journal":["Nucleic acids research"],"pubmed_title":["Illumina mate-paired DNA sequencing-library preparation using Cre-Lox recombination."],"pmcid":["PMC3273786"],"funding_grant_id":["U19 A1063603-06","1RC2EY02678-01"],"pubmed_authors":["Ledesma J","Deforce D","Head SR","Ordoukhanian P","Gaasterland T","Van Nieuwerburgh F","Thompson RC"],"view_count":["52"],"additional_accession":[]},"is_claimable":false,"name":"Illumina mate-paired DNA sequencing-library preparation using Cre-Lox recombination.","description":"Standard Illumina mate-paired libraries are constructed from 3- to 5-kb DNA fragments by a blunt-end circularization. Sequencing reads that pass through the junction of the two joined ends of a 3-5-kb DNA fragment are not easy to identify and pose problems during mapping and de novo assembly. Longer read lengths increase the possibility that a read will cross the junction. To solve this problem, we developed a mate-paired protocol for use with Illumina sequencing technology that uses Cre-Lox recombination instead of blunt end circularization. In this method, a LoxP sequence is incorporated at the junction site. This sequence allows screening reads for junctions without using a reference genome. Junction reads can be trimmed or split at the junction. Moreover, the location of the LoxP sequence in the reads distinguishes mate-paired reads from spurious paired-end reads. We tested this new method by preparing and sequencing a mate-paired library with an insert size of 3 kb from Saccharomyces cerevisiae. We present an analysis of the library quality statistics and a new bio-informatics tool called DeLoxer that can be used to analyze an IlluminaCre-Lox mate-paired data set. We also demonstrate how the resulting data significantly improves a de novo assembly of the S. cerevisiae genome.","dates":{"release":"2012-01-01T00:00:00Z","publication":"2012 Feb","modification":"2021-03-18T08:06:55Z","creation":"2019-03-27T00:48:52Z"},"accession":"S-EPMC3273786","cross_references":{"pubmed":["22127871"],"doi":["10.1093/nar/gkr1000"]}}