Inline index helped in cleaning up data contamination generated during library preparation and the subsequent steps
Background High-throughput sequencing involves library preparation and amplification steps, which may induce contamination across samples or between samples and the environment. Methods We tested the effect of applying an inline-index strategy, in which DNA indices of 6 bp were added to both ends of...
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| Veröffentlicht in: | Molecular biology reports 2022, Vol.49 (1), p.385-392 |
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| creator | Wang, Ying Yuan, Hao Huang, Junman Li, Chenhong |
| description | Background
High-throughput sequencing involves library preparation and amplification steps, which may induce contamination across samples or between samples and the environment.
Methods
We tested the effect of applying an inline-index strategy, in which DNA indices of 6 bp were added to both ends of the inserts at the ligation step of library prep for resolving the data contamination problem.
Results
Our results showed that the contamination ranged from 0.29 to 1.25% in one experiment and from 0.83 to 27.01% in the other. We also found that contamination could be environmental or from reagents besides cross-contamination between samples.
Conclusions
Inline-index method is a useful experimental design to clean up the data and address the contamination problem which has been plaguing high-throughput sequencing data in many applications. |
| doi_str_mv | 10.1007/s11033-021-06884-y |
| format | Article |
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High-throughput sequencing involves library preparation and amplification steps, which may induce contamination across samples or between samples and the environment.
Methods
We tested the effect of applying an inline-index strategy, in which DNA indices of 6 bp were added to both ends of the inserts at the ligation step of library prep for resolving the data contamination problem.
Results
Our results showed that the contamination ranged from 0.29 to 1.25% in one experiment and from 0.83 to 27.01% in the other. We also found that contamination could be environmental or from reagents besides cross-contamination between samples.
Conclusions
Inline-index method is a useful experimental design to clean up the data and address the contamination problem which has been plaguing high-throughput sequencing data in many applications.</description><identifier>ISSN: 0301-4851</identifier><identifier>EISSN: 1573-4978</identifier><identifier>DOI: 10.1007/s11033-021-06884-y</identifier><identifier>PMID: 34716505</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Animal Anatomy ; Animal Biochemistry ; Bar codes ; Biomedical and Life Sciences ; Contamination ; Histology ; Life Sciences ; Molecular biology ; Morphology ; Next-generation sequencing ; Original Article</subject><ispartof>Molecular biology reports, 2022, Vol.49 (1), p.385-392</ispartof><rights>The Author(s), under exclusive licence to Springer Nature B.V. 2021</rights><rights>2021. The Author(s), under exclusive licence to Springer Nature B.V.</rights><rights>The Author(s), under exclusive licence to Springer Nature B.V. 2021.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c419t-936420c694823648c71d02dd4bf6e84ff7d6af8c438b580cc1d6835eb3169c953</citedby><cites>FETCH-LOGICAL-c419t-936420c694823648c71d02dd4bf6e84ff7d6af8c438b580cc1d6835eb3169c953</cites><orcidid>0000-0003-3075-1756</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s11033-021-06884-y$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s11033-021-06884-y$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34716505$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wang, Ying</creatorcontrib><creatorcontrib>Yuan, Hao</creatorcontrib><creatorcontrib>Huang, Junman</creatorcontrib><creatorcontrib>Li, Chenhong</creatorcontrib><title>Inline index helped in cleaning up data contamination generated during library preparation and the subsequent steps</title><title>Molecular biology reports</title><addtitle>Mol Biol Rep</addtitle><addtitle>Mol Biol Rep</addtitle><description>Background
High-throughput sequencing involves library preparation and amplification steps, which may induce contamination across samples or between samples and the environment.
Methods
We tested the effect of applying an inline-index strategy, in which DNA indices of 6 bp were added to both ends of the inserts at the ligation step of library prep for resolving the data contamination problem.
Results
Our results showed that the contamination ranged from 0.29 to 1.25% in one experiment and from 0.83 to 27.01% in the other. We also found that contamination could be environmental or from reagents besides cross-contamination between samples.
Conclusions
Inline-index method is a useful experimental design to clean up the data and address the contamination problem which has been plaguing high-throughput sequencing data in many applications.</description><subject>Animal Anatomy</subject><subject>Animal Biochemistry</subject><subject>Bar codes</subject><subject>Biomedical and Life Sciences</subject><subject>Contamination</subject><subject>Histology</subject><subject>Life Sciences</subject><subject>Molecular biology</subject><subject>Morphology</subject><subject>Next-generation sequencing</subject><subject>Original Article</subject><issn>0301-4851</issn><issn>1573-4978</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9kUuLFTEQRoMoznX0D7iQgBs3rZVnJ0sZfAwMuNF1SCfVMz30TbdJGrz_3lx7VHDhKhU49VVSh5CXDN4ygP5dYQyE6ICzDrQxsjs9IgemetFJ25vH5AACWCeNYhfkWSn3ACBZr56SCyF7phWoAynXaZ4S0ilF_EHvcF4xtgsNM_o0pVu6rTT66mlYUvXHKfk6LYneYsLsa2Pjls_YPA3Z5xNdM64-75BPkdY7pGUbCn7fMFVaKq7lOXky-rngi4fzknz7-OHr1efu5sun66v3N12QzNbOCi05BG2l4a00oWcReIxyGDUaOY591H40QQozKAMhsKiNUDgIpm2wSlySN3vumpc2vlR3nErAefYJl604riyA4Vbphr7-B71ftpza6xzXzAjDe2kbxXcq5KWUjKNb83Rs33YM3FmJ25W4psT9UuJOrenVQ_Q2HDH-afntoAFiB8p6XiXmv7P_E_sThvWYQw</recordid><startdate>2022</startdate><enddate>2022</enddate><creator>Wang, Ying</creator><creator>Yuan, Hao</creator><creator>Huang, Junman</creator><creator>Li, Chenhong</creator><general>Springer Netherlands</general><general>Springer Nature B.V</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7TK</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0003-3075-1756</orcidid></search><sort><creationdate>2022</creationdate><title>Inline index helped in cleaning up data contamination generated during library preparation and the subsequent steps</title><author>Wang, Ying ; Yuan, Hao ; Huang, Junman ; Li, Chenhong</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c419t-936420c694823648c71d02dd4bf6e84ff7d6af8c438b580cc1d6835eb3169c953</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Animal Anatomy</topic><topic>Animal Biochemistry</topic><topic>Bar codes</topic><topic>Biomedical and Life Sciences</topic><topic>Contamination</topic><topic>Histology</topic><topic>Life Sciences</topic><topic>Molecular biology</topic><topic>Morphology</topic><topic>Next-generation sequencing</topic><topic>Original Article</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wang, Ying</creatorcontrib><creatorcontrib>Yuan, Hao</creatorcontrib><creatorcontrib>Huang, Junman</creatorcontrib><creatorcontrib>Li, Chenhong</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>ProQuest Central Basic</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Molecular biology reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wang, Ying</au><au>Yuan, Hao</au><au>Huang, Junman</au><au>Li, Chenhong</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Inline index helped in cleaning up data contamination generated during library preparation and the subsequent steps</atitle><jtitle>Molecular biology reports</jtitle><stitle>Mol Biol Rep</stitle><addtitle>Mol Biol Rep</addtitle><date>2022</date><risdate>2022</risdate><volume>49</volume><issue>1</issue><spage>385</spage><epage>392</epage><pages>385-392</pages><issn>0301-4851</issn><eissn>1573-4978</eissn><abstract>Background
High-throughput sequencing involves library preparation and amplification steps, which may induce contamination across samples or between samples and the environment.
Methods
We tested the effect of applying an inline-index strategy, in which DNA indices of 6 bp were added to both ends of the inserts at the ligation step of library prep for resolving the data contamination problem.
Results
Our results showed that the contamination ranged from 0.29 to 1.25% in one experiment and from 0.83 to 27.01% in the other. We also found that contamination could be environmental or from reagents besides cross-contamination between samples.
Conclusions
Inline-index method is a useful experimental design to clean up the data and address the contamination problem which has been plaguing high-throughput sequencing data in many applications.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><pmid>34716505</pmid><doi>10.1007/s11033-021-06884-y</doi><tpages>8</tpages><orcidid>https://orcid.org/0000-0003-3075-1756</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Animal Anatomy Animal Biochemistry Bar codes Biomedical and Life Sciences Contamination Histology Life Sciences Molecular biology Morphology Next-generation sequencing Original Article |
| title | Inline index helped in cleaning up data contamination generated during library preparation and the subsequent steps |
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