دورية أكاديمية
أعرض في EDS

A novel NGS library preparation method to characterize native termini of fragmented DNA.

التفاصيل البيبلوغرافية
العنوان: A novel NGS library preparation method to characterize native termini of fragmented DNA.
المؤلفون: Harkins KM; Claret Bioscience LLC, Santa Cruz, CA 95060, USA., Schaefer NK; Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA., Troll CJ; Claret Bioscience LLC, Santa Cruz, CA 95060, USA., Rao V; Claret Bioscience LLC, Santa Cruz, CA 95060, USA., Kapp J; Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA., Naughton C; Claret Bioscience LLC, Santa Cruz, CA 95060, USA., Shapiro B; Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA.; Howard Hughes Medical Institute, University of California, Santa Cruz, CA 95064, USA., Green RE; Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
المصدر: Nucleic acids research [Nucleic Acids Res] 2020 May 07; Vol. 48 (8), pp. e47.
نوع المنشور: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE
أسماء مطبوعة: Publication: 1992- : Oxford : Oxford University Press
Original Publication: London, Information Retrieval ltd.
مواضيع طبية MeSH: Gene Library*, High-Throughput Nucleotide Sequencing/*methods , Sequence Analysis, DNA/*methods, Cell-Free Nucleic Acids/blood ; DNA/chemistry ; Deoxyribonuclease I ; Humans ; Micrococcal Nuclease
مستخلص: Biological and chemical DNA fragmentation generates DNA molecules with a variety of termini, including blunt ends and single-stranded overhangs. We have developed a Next Generation Sequencing (NGS) assay, XACTLY, to interrogate the termini of fragmented DNA, information traditionally lost in standard NGS library preparation methods. Here we describe the XACTLY method, showcase its sensitivity and specificity, and demonstrate its utility in in vitro experiments. The XACTLY assay is able to report relative abundances of all lengths and types (5' and 3') of single-stranded overhangs, if present, on each DNA fragment with an overall accuracy between 80-90%. In addition, XACTLY retains the sequence of each native DNA molecule after fragmentation and can capture the genomic landscape of cleavage events at single nucleotide resolution. The XACTLY assay can be applied as a novel research and discovery tool for fragmentation analyses and in cell-free DNA.
(© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.)
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معلومات مُعتمدة: T32 HG008345 United States HG NHGRI NIH HHS; R43 CA232935 United States CA NCI NIH HHS
المشرفين على المادة: 0 (Cell-Free Nucleic Acids)
9007-49-2 (DNA)
EC 3.1.21.1 (Deoxyribonuclease I)
EC 3.1.31.1 (Micrococcal Nuclease)
تواريخ الأحداث: Date Created: 20200301 Date Completed: 20200727 Latest Revision: 20211001
رمز التحديث: 20221213
مُعرف محوري في PubMed: PMC7192605
DOI: 10.1093/nar/gkaa128
PMID: 32112100
قاعدة البيانات: MEDLINE
الوصف
تدمد:1362-4962
DOI:10.1093/nar/gkaa128