Parallel tagged sequencing on the 454 platform
Parallel tagged sequencing (PTS) is a molecular barcoding method designed to adapt the recently developed high-throughput 454 parallel sequencing technology for use with multiple samples. Unlike other barcoding methods, PTS can be applied to any type of double-stranded DNA (dsDNA) sample, including...
Gespeichert in:
| Veröffentlicht in: | Nature protocols 2008-02, Vol.3 (2), p.267-278 |
|---|---|
| Hauptverfasser: | , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 278 |
|---|---|
| container_issue | 2 |
| container_start_page | 267 |
| container_title | Nature protocols |
| container_volume | 3 |
| creator | Meyer, Matthias Stenzel, Udo Hofreiter, Michael |
| description | Parallel tagged sequencing (PTS) is a molecular barcoding method designed to adapt the recently developed high-throughput 454 parallel sequencing technology for use with multiple samples. Unlike other barcoding methods, PTS can be applied to any type of double-stranded DNA (dsDNA) sample, including shotgun DNA libraries and pools of PCR products, and requires no amplification or gel purification steps. The method relies on attaching sample-specific barcoding adapters, which include sequence tags and a restriction site, to blunt-end repaired DNA samples by ligation and strand-displacement. After pooling multiple barcoded samples, molecules without sequence tags are effectively excluded from sequencing by dephosphorylation and restriction digestion, and using the tag sequences, the source of each DNA sequence can be traced. This protocol allows for sequencing 300 or more complete mitochondrial genomes on a single 454 GS FLX run, or twenty-five 6-kb plasmid sequences on only one 16th plate region. Most of the reactions can be performed in a multichannel setup on 96-well reaction plates, allowing for processing up to several hundreds of samples in a few days. |
| doi_str_mv | 10.1038/nprot.2007.520 |
| format | Article |
| fullrecord | <record><control><sourceid>gale_proqu</sourceid><recordid>TN_cdi_proquest_miscellaneous_70292682</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A186854605</galeid><sourcerecordid>A186854605</sourcerecordid><originalsourceid>FETCH-LOGICAL-c529t-b701ad9b3b9dc194fda3ca1e566d696bdfb9efe0ca2de03a7d4dac28923acc5e3</originalsourceid><addsrcrecordid>eNqFkt1rFDEUxYMotlZffZQBQRCZaZLJx-RxWaoWihWt-BgyyZ1xykxmm2TA_vdm24W6slLykHDzu4d7Dweh1wRXBNfNqd-EOVUUY1lxip-gYyI5LqlU6undm5WUNOoIvYjxGmMmayGfoyPSUMk4Vceo-mqCGUcYi2T6HlwR4WYBbwffF7Mv0i8oGGfFZjSpm8P0Ej3rzBjh1e4-QT8-nl2tP5cXl5_O16uL0mbVVLYSE-NUW7fKWaJY50xtDQEuhBNKtK5rFXSAraEOcG2kY85Y2ihaG2s51Cfo3b1uXi_PE5OehmhhHI2HeYlaYqqoaOijIMW8EZxvwbf_gNfzEnxeQhPMCKXZQ_xA9WYEPfhuTsHYraRekUY0nAnMM1UdoPJxMA129tANub7X8H6vITMJfqfeLDHq8-_f9tkP_2dXVz_XXw6OYsMcY4BOb8IwmXCbt9LbhOi7hOhtQnROSG54s_NhaSdwD_guEhk4vQdi_vI9hL-NOij5Bz6TwtY</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1041222000</pqid></control><display><type>article</type><title>Parallel tagged sequencing on the 454 platform</title><source>MEDLINE</source><source>Nature Journals Online</source><source>SpringerLink Journals - AutoHoldings</source><creator>Meyer, Matthias ; Stenzel, Udo ; Hofreiter, Michael</creator><creatorcontrib>Meyer, Matthias ; Stenzel, Udo ; Hofreiter, Michael</creatorcontrib><description>Parallel tagged sequencing (PTS) is a molecular barcoding method designed to adapt the recently developed high-throughput 454 parallel sequencing technology for use with multiple samples. Unlike other barcoding methods, PTS can be applied to any type of double-stranded DNA (dsDNA) sample, including shotgun DNA libraries and pools of PCR products, and requires no amplification or gel purification steps. The method relies on attaching sample-specific barcoding adapters, which include sequence tags and a restriction site, to blunt-end repaired DNA samples by ligation and strand-displacement. After pooling multiple barcoded samples, molecules without sequence tags are effectively excluded from sequencing by dephosphorylation and restriction digestion, and using the tag sequences, the source of each DNA sequence can be traced. This protocol allows for sequencing 300 or more complete mitochondrial genomes on a single 454 GS FLX run, or twenty-five 6-kb plasmid sequences on only one 16th plate region. Most of the reactions can be performed in a multichannel setup on 96-well reaction plates, allowing for processing up to several hundreds of samples in a few days.</description><identifier>ISSN: 1754-2189</identifier><identifier>EISSN: 1750-2799</identifier><identifier>DOI: 10.1038/nprot.2007.520</identifier><identifier>PMID: 18274529</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>Analysis ; Analytical Chemistry ; Applications software ; Bar codes ; Biological Techniques ; Biomedical and Life Sciences ; Computational Biology/Bioinformatics ; Deoxyribonucleic acid ; DNA ; DNA sequencing ; DNA, Mitochondrial - chemistry ; Enzymes ; Genetic testing ; Genome, Mitochondrial - genetics ; Genomes ; Humans ; Life Sciences ; Methods ; Microarrays ; Mitochondrial DNA ; Nucleotide sequencing ; Organic Chemistry ; Physiological aspects ; Plasmids ; Plasmids - chemistry ; Protocol ; Sequence Analysis, DNA - methods ; Sequence Tagged Sites</subject><ispartof>Nature protocols, 2008-02, Vol.3 (2), p.267-278</ispartof><rights>Springer Nature Limited 2008</rights><rights>COPYRIGHT 2008 Nature Publishing Group</rights><rights>Copyright Nature Publishing Group Feb 2008</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c529t-b701ad9b3b9dc194fda3ca1e566d696bdfb9efe0ca2de03a7d4dac28923acc5e3</citedby><cites>FETCH-LOGICAL-c529t-b701ad9b3b9dc194fda3ca1e566d696bdfb9efe0ca2de03a7d4dac28923acc5e3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1038/nprot.2007.520$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1038/nprot.2007.520$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,777,781,27905,27906,41469,42538,51300</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/18274529$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Meyer, Matthias</creatorcontrib><creatorcontrib>Stenzel, Udo</creatorcontrib><creatorcontrib>Hofreiter, Michael</creatorcontrib><title>Parallel tagged sequencing on the 454 platform</title><title>Nature protocols</title><addtitle>Nat Protoc</addtitle><addtitle>Nat Protoc</addtitle><description>Parallel tagged sequencing (PTS) is a molecular barcoding method designed to adapt the recently developed high-throughput 454 parallel sequencing technology for use with multiple samples. Unlike other barcoding methods, PTS can be applied to any type of double-stranded DNA (dsDNA) sample, including shotgun DNA libraries and pools of PCR products, and requires no amplification or gel purification steps. The method relies on attaching sample-specific barcoding adapters, which include sequence tags and a restriction site, to blunt-end repaired DNA samples by ligation and strand-displacement. After pooling multiple barcoded samples, molecules without sequence tags are effectively excluded from sequencing by dephosphorylation and restriction digestion, and using the tag sequences, the source of each DNA sequence can be traced. This protocol allows for sequencing 300 or more complete mitochondrial genomes on a single 454 GS FLX run, or twenty-five 6-kb plasmid sequences on only one 16th plate region. Most of the reactions can be performed in a multichannel setup on 96-well reaction plates, allowing for processing up to several hundreds of samples in a few days.</description><subject>Analysis</subject><subject>Analytical Chemistry</subject><subject>Applications software</subject><subject>Bar codes</subject><subject>Biological Techniques</subject><subject>Biomedical and Life Sciences</subject><subject>Computational Biology/Bioinformatics</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA sequencing</subject><subject>DNA, Mitochondrial - chemistry</subject><subject>Enzymes</subject><subject>Genetic testing</subject><subject>Genome, Mitochondrial - genetics</subject><subject>Genomes</subject><subject>Humans</subject><subject>Life Sciences</subject><subject>Methods</subject><subject>Microarrays</subject><subject>Mitochondrial DNA</subject><subject>Nucleotide sequencing</subject><subject>Organic Chemistry</subject><subject>Physiological aspects</subject><subject>Plasmids</subject><subject>Plasmids - chemistry</subject><subject>Protocol</subject><subject>Sequence Analysis, DNA - methods</subject><subject>Sequence Tagged Sites</subject><issn>1754-2189</issn><issn>1750-2799</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2008</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqFkt1rFDEUxYMotlZffZQBQRCZaZLJx-RxWaoWihWt-BgyyZ1xykxmm2TA_vdm24W6slLykHDzu4d7Dweh1wRXBNfNqd-EOVUUY1lxip-gYyI5LqlU6undm5WUNOoIvYjxGmMmayGfoyPSUMk4Vceo-mqCGUcYi2T6HlwR4WYBbwffF7Mv0i8oGGfFZjSpm8P0Ej3rzBjh1e4-QT8-nl2tP5cXl5_O16uL0mbVVLYSE-NUW7fKWaJY50xtDQEuhBNKtK5rFXSAraEOcG2kY85Y2ihaG2s51Cfo3b1uXi_PE5OehmhhHI2HeYlaYqqoaOijIMW8EZxvwbf_gNfzEnxeQhPMCKXZQ_xA9WYEPfhuTsHYraRekUY0nAnMM1UdoPJxMA129tANub7X8H6vITMJfqfeLDHq8-_f9tkP_2dXVz_XXw6OYsMcY4BOb8IwmXCbt9LbhOi7hOhtQnROSG54s_NhaSdwD_guEhk4vQdi_vI9hL-NOij5Bz6TwtY</recordid><startdate>200802</startdate><enddate>200802</enddate><creator>Meyer, Matthias</creator><creator>Stenzel, Udo</creator><creator>Hofreiter, Michael</creator><general>Nature Publishing Group UK</general><general>Nature Publishing Group</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>ATWCN</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7T5</scope><scope>7T7</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PATMY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>200802</creationdate><title>Parallel tagged sequencing on the 454 platform</title><author>Meyer, Matthias ; Stenzel, Udo ; Hofreiter, Michael</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c529t-b701ad9b3b9dc194fda3ca1e566d696bdfb9efe0ca2de03a7d4dac28923acc5e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2008</creationdate><topic>Analysis</topic><topic>Analytical Chemistry</topic><topic>Applications software</topic><topic>Bar codes</topic><topic>Biological Techniques</topic><topic>Biomedical and Life Sciences</topic><topic>Computational Biology/Bioinformatics</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA sequencing</topic><topic>DNA, Mitochondrial - chemistry</topic><topic>Enzymes</topic><topic>Genetic testing</topic><topic>Genome, Mitochondrial - genetics</topic><topic>Genomes</topic><topic>Humans</topic><topic>Life Sciences</topic><topic>Methods</topic><topic>Microarrays</topic><topic>Mitochondrial DNA</topic><topic>Nucleotide sequencing</topic><topic>Organic Chemistry</topic><topic>Physiological aspects</topic><topic>Plasmids</topic><topic>Plasmids - chemistry</topic><topic>Protocol</topic><topic>Sequence Analysis, DNA - methods</topic><topic>Sequence Tagged Sites</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Meyer, Matthias</creatorcontrib><creatorcontrib>Stenzel, Udo</creatorcontrib><creatorcontrib>Hofreiter, Michael</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Middle School</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Immunology Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Nucleic Acids Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</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 One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</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>AIDS and Cancer Research Abstracts</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>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Nature protocols</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Meyer, Matthias</au><au>Stenzel, Udo</au><au>Hofreiter, Michael</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Parallel tagged sequencing on the 454 platform</atitle><jtitle>Nature protocols</jtitle><stitle>Nat Protoc</stitle><addtitle>Nat Protoc</addtitle><date>2008-02</date><risdate>2008</risdate><volume>3</volume><issue>2</issue><spage>267</spage><epage>278</epage><pages>267-278</pages><issn>1754-2189</issn><eissn>1750-2799</eissn><abstract>Parallel tagged sequencing (PTS) is a molecular barcoding method designed to adapt the recently developed high-throughput 454 parallel sequencing technology for use with multiple samples. Unlike other barcoding methods, PTS can be applied to any type of double-stranded DNA (dsDNA) sample, including shotgun DNA libraries and pools of PCR products, and requires no amplification or gel purification steps. The method relies on attaching sample-specific barcoding adapters, which include sequence tags and a restriction site, to blunt-end repaired DNA samples by ligation and strand-displacement. After pooling multiple barcoded samples, molecules without sequence tags are effectively excluded from sequencing by dephosphorylation and restriction digestion, and using the tag sequences, the source of each DNA sequence can be traced. This protocol allows for sequencing 300 or more complete mitochondrial genomes on a single 454 GS FLX run, or twenty-five 6-kb plasmid sequences on only one 16th plate region. Most of the reactions can be performed in a multichannel setup on 96-well reaction plates, allowing for processing up to several hundreds of samples in a few days.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>18274529</pmid><doi>10.1038/nprot.2007.520</doi><tpages>12</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1754-2189 |
| ispartof | Nature protocols, 2008-02, Vol.3 (2), p.267-278 |
| issn | 1754-2189 1750-2799 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_70292682 |
| source | MEDLINE; Nature Journals Online; SpringerLink Journals - AutoHoldings |
| subjects | Analysis Analytical Chemistry Applications software Bar codes Biological Techniques Biomedical and Life Sciences Computational Biology/Bioinformatics Deoxyribonucleic acid DNA DNA sequencing DNA, Mitochondrial - chemistry Enzymes Genetic testing Genome, Mitochondrial - genetics Genomes Humans Life Sciences Methods Microarrays Mitochondrial DNA Nucleotide sequencing Organic Chemistry Physiological aspects Plasmids Plasmids - chemistry Protocol Sequence Analysis, DNA - methods Sequence Tagged Sites |
| title | Parallel tagged sequencing on the 454 platform |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-19T11%3A51%3A03IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_proqu&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Parallel%20tagged%20sequencing%20on%20the%20454%20platform&rft.jtitle=Nature%20protocols&rft.au=Meyer,%20Matthias&rft.date=2008-02&rft.volume=3&rft.issue=2&rft.spage=267&rft.epage=278&rft.pages=267-278&rft.issn=1754-2189&rft.eissn=1750-2799&rft_id=info:doi/10.1038/nprot.2007.520&rft_dat=%3Cgale_proqu%3EA186854605%3C/gale_proqu%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1041222000&rft_id=info:pmid/18274529&rft_galeid=A186854605&rfr_iscdi=true |