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dc.contributor.authorHeyer, Erin E.
dc.contributor.authorOzadam, Hakan
dc.contributor.authorRicci, Emiliano P.
dc.contributor.authorCenik, Can
dc.contributor.authorMoore, Melissa J.
dc.date2022-08-11T08:08:55.000
dc.date.accessioned2022-08-23T16:12:18Z
dc.date.available2022-08-23T16:12:18Z
dc.date.issued2015-01-01
dc.date.submitted2015-08-13
dc.identifier.citationNucleic Acids Res. 2015 Jan;43(1):e2. doi: 10.1093/nar/gku1235. Epub 2014 Dec 12. <a href="http://dx.doi.org/10.1093/nar/gku1235">Link to article on publisher's site</a>
dc.identifier.issn0305-1048 (Linking)
dc.identifier.doi10.1093/nar/gku1235
dc.identifier.pmid25505164
dc.identifier.urihttp://hdl.handle.net/20.500.14038/33366
dc.description.abstractDeep sequencing of strand-specific cDNA libraries is now a ubiquitous tool for identifying and quantifying RNAs in diverse sample types. The accuracy of conclusions drawn from these analyses depends on precise and quantitative conversion of the RNA sample into a DNA library suitable for sequencing. Here, we describe an optimized method of preparing strand-specific RNA deep sequencing libraries from small RNAs and variably sized RNA fragments obtained from ribonucleoprotein particle footprinting experiments or fragmentation of long RNAs. Our approach works across a wide range of input amounts (400 pg to 200 ng), is easy to follow and produces a library in 2-3 days at relatively low reagent cost, all while giving the user complete control over every step. Because all enzymatic reactions were optimized and driven to apparent completion, sequence diversity and species abundance in the input sample are well preserved.
dc.language.isoen_US
dc.relation<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&list_uids=25505164&dopt=Abstract">Link to Article in PubMed</a>
dc.rightsCopyright The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<a href="http://creativecommons.org/licenses/by-nc/4.0/">http://creativecommons.org/licenses/by-nc/4.0/</a>), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/
dc.subjectDNA, Circular; DNA, Single-Stranded; Electrophoresis, Polyacrylamide Gel; *Gene Library; High-Throughput Nucleotide Sequencing; MicroRNAs; Reverse Transcriptase Polymerase Chain Reaction; Sequence Analysis, RNA
dc.subjectBiochemistry
dc.subjectBioinformatics
dc.subjectComputational Biology
dc.subjectGenetics and Genomics
dc.subjectNucleic Acids, Nucleotides, and Nucleosides
dc.titleAn optimized kit-free method for making strand-specific deep sequencing libraries from RNA fragments
dc.typeJournal Article
dc.source.journaltitleNucleic acids research
dc.source.volume43
dc.source.issue1
dc.identifier.legacyfulltexthttps://escholarship.umassmed.edu/cgi/viewcontent.cgi?article=2911&amp;context=gsbs_sp&amp;unstamped=1
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/gsbs_sp/1890
dc.identifier.contextkey7457245
refterms.dateFOA2022-08-23T16:12:18Z
html.description.abstract<p>Deep sequencing of strand-specific cDNA libraries is now a ubiquitous tool for identifying and quantifying RNAs in diverse sample types. The accuracy of conclusions drawn from these analyses depends on precise and quantitative conversion of the RNA sample into a DNA library suitable for sequencing. Here, we describe an optimized method of preparing strand-specific RNA deep sequencing libraries from small RNAs and variably sized RNA fragments obtained from ribonucleoprotein particle footprinting experiments or fragmentation of long RNAs. Our approach works across a wide range of input amounts (400 pg to 200 ng), is easy to follow and produces a library in 2-3 days at relatively low reagent cost, all while giving the user complete control over every step. Because all enzymatic reactions were optimized and driven to apparent completion, sequence diversity and species abundance in the input sample are well preserved.</p>
dc.identifier.submissionpathgsbs_sp/1890
dc.contributor.departmentRNA Therapeutics Institute
dc.contributor.departmentDepartment of Biochemistry and Molecular Pharmacology
dc.source.pagese2
dc.contributor.studentErin E. Heyer


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Copyright The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<a href="http://creativecommons.org/licenses/by-nc/4.0/">http://creativecommons.org/licenses/by-nc/4.0/</a>), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
Except where otherwise noted, this item's license is described as Copyright The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<a href="http://creativecommons.org/licenses/by-nc/4.0/">http://creativecommons.org/licenses/by-nc/4.0/</a>), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.