{"data":{"id":"10.6084/m9.figshare.1494592","type":"dois","attributes":{"doi":"10.6084/m9.figshare.1494592","prefix":"10.6084","suffix":"m9.figshare.1494592","identifiers":[],"alternateIdentifiers":[],"creators":[{"name":"Kangli Wang","affiliation":[],"nameIdentifiers":[]},{"name":"Xianfeng Li","affiliation":[],"nameIdentifiers":[]},{"name":"Shanshan Dong","affiliation":[],"nameIdentifiers":[]},{"name":"Jialong Liang","affiliation":[],"nameIdentifiers":[]},{"name":"Fengbiao Mao","affiliation":[],"nameIdentifiers":[]},{"name":"Zeng, Cheng","nameType":"Personal","givenName":"Cheng","familyName":"Zeng","affiliation":[],"nameIdentifiers":[]},{"name":"Honghu Wu","affiliation":[],"nameIdentifiers":[]},{"name":"Wu, Jinyu","nameType":"Personal","givenName":"Jinyu","familyName":"Wu","affiliation":[],"nameIdentifiers":[]},{"name":"Wanshi Cai","affiliation":[],"nameIdentifiers":[]},{"name":"Sun, Zhong Sheng","nameType":"Personal","givenName":"Zhong Sheng","familyName":"Sun","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"Q-RRBS: a quantitative reduced representation bisulfite sequencing method for single-cell methylome analyses"}],"publisher":"Taylor \u0026 Francis","container":{},"publicationYear":2015,"subjects":[{"subject":"Biochemistry"},{"subject":"Space Science"},{"subject":"Cell Biology"},{"subject":"Genetics"},{"subject":"FOS: Biological sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Biological sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Molecular Biology"},{"subject":"Pharmacology"},{"subject":"19999 Mathematical Sciences not elsewhere classified","subjectScheme":"FOR"},{"subject":"FOS: Mathematics","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Mathematics","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Plant Biology"}],"contributors":[],"dates":[{"date":"2015-07-25","dateType":"Created"},{"date":"2016-03-11","dateType":"Updated"},{"date":"2015","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[{"relationType":"IsSupplementTo","relatedIdentifier":"10.1080/15592294.2015.1075690","relatedIdentifierType":"DOI"}],"relatedItems":[],"sizes":["893961 Bytes"],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[{"description":"Reduced representation bisulfite sequencing (RRBS) is a powerful method of DNA methylome profiling that can be applied to single cells. However, no previous report has described how PCR-based duplication-induced artifacts affect the accuracy of this method when measuring DNA methylation levels. For quantifying the effects of duplication-induced artifacts on methylome profiling when using ultra-trace amounts of starting material, we developed a novel method, namely quantitative RRBS (Q-RRBS), in which PCR-induced duplication is excluded through the use of unique molecular identifiers (UMIs). By performing Q-RRBS on varying amounts of starting material, we determined that duplication-induced artifacts were more severe when small quantities of the starting material were used. However, through using the UMIs, we successfully eliminated these artifacts. In addition, Q-RRBS could accurately detect allele-specific methylation in absence of allele-specific genetic variants. Our results demonstrate that Q-RRBS is an optimal strategy for DNA methylation profiling of single cells or samples containing ultra-trace amounts of cells.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"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","url":"https://tandf.figshare.com/articles/dataset/Q_RRBS_a_quantitative_reduced_representation_bisulfite_s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