Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation
For most sample types, the automation of RNA and DNA sample preparation workflows enables high throughput next-generation sequencing (NGS) library preparation. Greater adoption of small RNA (sRNA) sequencing has been hindered by high sample input requirements and inherent ligation side products form...
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| Veröffentlicht in: | PloS one 2016-11, Vol.11 (11), p.e0167009-e0167009 |
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| creator | Shore, Sabrina Henderson, Jordana M Lebedev, Alexandre Salcedo, Michelle P Zon, Gerald McCaffrey, Anton P Paul, Natasha Hogrefe, Richard I |
| description | For most sample types, the automation of RNA and DNA sample preparation workflows enables high throughput next-generation sequencing (NGS) library preparation. Greater adoption of small RNA (sRNA) sequencing has been hindered by high sample input requirements and inherent ligation side products formed during library preparation. These side products, known as adapter dimer, are very similar in size to the tagged library. Most sRNA library preparation strategies thus employ a gel purification step to isolate tagged library from adapter dimer contaminants. At very low sample inputs, adapter dimer side products dominate the reaction and limit the sensitivity of this technique. Here we address the need for improved specificity of sRNA library preparation workflows with a novel library preparation approach that uses modified adapters to suppress adapter dimer formation. This workflow allows for lower sample inputs and elimination of the gel purification step, which in turn allows for an automatable sRNA library preparation protocol. |
| doi_str_mv | 10.1371/journal.pone.0167009 |
| format | Article |
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Greater adoption of small RNA (sRNA) sequencing has been hindered by high sample input requirements and inherent ligation side products formed during library preparation. These side products, known as adapter dimer, are very similar in size to the tagged library. Most sRNA library preparation strategies thus employ a gel purification step to isolate tagged library from adapter dimer contaminants. At very low sample inputs, adapter dimer side products dominate the reaction and limit the sensitivity of this technique. Here we address the need for improved specificity of sRNA library preparation workflows with a novel library preparation approach that uses modified adapters to suppress adapter dimer formation. This workflow allows for lower sample inputs and elimination of the gel purification step, which in turn allows for an automatable sRNA library preparation protocol.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0167009</identifier><identifier>PMID: 27875576</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Acids ; Adapters ; Aptamers, Nucleotide ; Automation ; Bioinformatics ; Biology and life sciences ; Biomarkers ; Breast cancer ; Contaminants ; Deoxyribonucleic acid ; DNA ; DNA sequencing ; Gene Library ; Gene sequencing ; Genomics ; High-Throughput Nucleotide Sequencing ; Libraries ; Methods ; MicroRNAs ; Molecular biology ; Purification ; R&D ; Research & development ; Research and analysis methods ; Ribonucleic acid ; RNA ; RNA, Small Untranslated - chemistry ; RNA, Small Untranslated - genetics ; Sample preparation ; Technology application ; Workflow</subject><ispartof>PloS one, 2016-11, Vol.11 (11), p.e0167009-e0167009</ispartof><rights>COPYRIGHT 2016 Public Library of Science</rights><rights>2016 Shore et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2016 Shore et al 2016 Shore et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c791t-f2c82eccda59b681012c801f328d6b75ffd2eddcff6129c7774a4372050b10723</citedby><cites>FETCH-LOGICAL-c791t-f2c82eccda59b681012c801f328d6b75ffd2eddcff6129c7774a4372050b10723</cites><orcidid>0000-0002-6848-1088</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5119831/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5119831/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79343,79344</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27875576$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Mahalingam, Ramamurthy</contributor><creatorcontrib>Shore, Sabrina</creatorcontrib><creatorcontrib>Henderson, Jordana M</creatorcontrib><creatorcontrib>Lebedev, Alexandre</creatorcontrib><creatorcontrib>Salcedo, Michelle P</creatorcontrib><creatorcontrib>Zon, Gerald</creatorcontrib><creatorcontrib>McCaffrey, Anton P</creatorcontrib><creatorcontrib>Paul, Natasha</creatorcontrib><creatorcontrib>Hogrefe, Richard I</creatorcontrib><title>Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>For most sample types, the automation of RNA and DNA sample preparation workflows enables high throughput next-generation sequencing (NGS) library preparation. Greater adoption of small RNA (sRNA) sequencing has been hindered by high sample input requirements and inherent ligation side products formed during library preparation. These side products, known as adapter dimer, are very similar in size to the tagged library. Most sRNA library preparation strategies thus employ a gel purification step to isolate tagged library from adapter dimer contaminants. At very low sample inputs, adapter dimer side products dominate the reaction and limit the sensitivity of this technique. Here we address the need for improved specificity of sRNA library preparation workflows with a novel library preparation approach that uses modified adapters to suppress adapter dimer formation. This workflow allows for lower sample inputs and elimination of the gel purification step, which in turn allows for an automatable sRNA library preparation protocol.</description><subject>Acids</subject><subject>Adapters</subject><subject>Aptamers, Nucleotide</subject><subject>Automation</subject><subject>Bioinformatics</subject><subject>Biology and life sciences</subject><subject>Biomarkers</subject><subject>Breast cancer</subject><subject>Contaminants</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA sequencing</subject><subject>Gene Library</subject><subject>Gene sequencing</subject><subject>Genomics</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Libraries</subject><subject>Methods</subject><subject>MicroRNAs</subject><subject>Molecular biology</subject><subject>Purification</subject><subject>R&D</subject><subject>Research & development</subject><subject>Research and analysis methods</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA, Small Untranslated - 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| subjects | Acids Adapters Aptamers, Nucleotide Automation Bioinformatics Biology and life sciences Biomarkers Breast cancer Contaminants Deoxyribonucleic acid DNA DNA sequencing Gene Library Gene sequencing Genomics High-Throughput Nucleotide Sequencing Libraries Methods MicroRNAs Molecular biology Purification R&D Research & development Research and analysis methods Ribonucleic acid RNA RNA, Small Untranslated - chemistry RNA, Small Untranslated - genetics Sample preparation Technology application Workflow |
| title | Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation |
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