BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction
Identifieur interne : 000644 ( Ncbi/Checkpoint ); précédent : 000643; suivant : 000645BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction
Auteurs : Brad T. Townsley ; Michael F. Covington ; Yasunori Ichihashi ; Kristina Zumstein ; Neelima R. SinhaSource :
- Frontiers in Plant Science [ 1664-462X ] ; 2015.
Abstract
Next Generation Sequencing (NGS) is driving rapid advancement in biological understanding and RNA-sequencing (RNA-seq) has become an indispensable tool for biology and medicine. There is a growing need for access to these technologies although preparation of NGS libraries remains a bottleneck to wider adoption. Here we report a novel method for the production of strand specific RNA-seq libraries utilizing the terminal breathing of double-stranded cDNA to capture and incorporate a sequencing adapter. Breath Adapter Directional sequencing (BrAD-seq) reduces sample handling and requires far fewer enzymatic steps than most available methods to produce high quality strand-specific RNA-seq libraries. The method we present is optimized for 3-prime Digital Gene Expression (DGE) libraries and can easily extend to full transcript coverage shotgun (SHO) type strand-specific libraries and is modularized to accommodate a diversity of RNA and DNA input materials. BrAD-seq offers a highly streamlined and inexpensive option for RNA-seq libraries.
Url:
DOI: 10.3389/fpls.2015.00366
PubMed: 26052336
PubMed Central: 4441129
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000058
- to stream Pmc, to step Curation: 000058
- to stream Pmc, to step Checkpoint: 000130
- to stream Ncbi, to step Merge: 000644
- to stream Ncbi, to step Curation: 000644
Links to Exploration step
PMC:4441129Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction</title><author><name sortKey="Townsley, Brad T" sort="Townsley, Brad T" uniqKey="Townsley B" first="Brad T." last="Townsley">Brad T. Townsley</name></author><author><name sortKey="Covington, Michael F" sort="Covington, Michael F" uniqKey="Covington M" first="Michael F." last="Covington">Michael F. Covington</name></author><author><name sortKey="Ichihashi, Yasunori" sort="Ichihashi, Yasunori" uniqKey="Ichihashi Y" first="Yasunori" last="Ichihashi">Yasunori Ichihashi</name></author><author><name sortKey="Zumstein, Kristina" sort="Zumstein, Kristina" uniqKey="Zumstein K" first="Kristina" last="Zumstein">Kristina Zumstein</name></author><author><name sortKey="Sinha, Neelima R" sort="Sinha, Neelima R" uniqKey="Sinha N" first="Neelima R." last="Sinha">Neelima R. Sinha</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26052336</idno><idno type="pmc">4441129</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4441129</idno><idno type="RBID">PMC:4441129</idno><idno type="doi">10.3389/fpls.2015.00366</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000058</idno><idno type="wicri:Area/Pmc/Curation">000058</idno><idno type="wicri:Area/Pmc/Checkpoint">000130</idno><idno type="wicri:Area/Ncbi/Merge">000644</idno><idno type="wicri:Area/Ncbi/Curation">000644</idno><idno type="wicri:Area/Ncbi/Checkpoint">000644</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction</title><author><name sortKey="Townsley, Brad T" sort="Townsley, Brad T" uniqKey="Townsley B" first="Brad T." last="Townsley">Brad T. Townsley</name></author><author><name sortKey="Covington, Michael F" sort="Covington, Michael F" uniqKey="Covington M" first="Michael F." last="Covington">Michael F. Covington</name></author><author><name sortKey="Ichihashi, Yasunori" sort="Ichihashi, Yasunori" uniqKey="Ichihashi Y" first="Yasunori" last="Ichihashi">Yasunori Ichihashi</name></author><author><name sortKey="Zumstein, Kristina" sort="Zumstein, Kristina" uniqKey="Zumstein K" first="Kristina" last="Zumstein">Kristina Zumstein</name></author><author><name sortKey="Sinha, Neelima R" sort="Sinha, Neelima R" uniqKey="Sinha N" first="Neelima R." last="Sinha">Neelima R. Sinha</name></author></analytic><series><title level="j">Frontiers in Plant Science</title><idno type="eISSN">1664-462X</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Next Generation Sequencing (NGS) is driving rapid advancement in biological understanding and RNA-sequencing (RNA-seq) has become an indispensable tool for biology and medicine. There is a growing need for access to these technologies although preparation of NGS libraries remains a bottleneck to wider adoption. Here we report a novel method for the production of strand specific RNA-seq libraries utilizing the terminal breathing of double-stranded cDNA to capture and incorporate a sequencing adapter. Breath Adapter Directional sequencing (BrAD-seq) reduces sample handling and requires far fewer enzymatic steps than most available methods to produce high quality strand-specific RNA-seq libraries. The method we present is optimized for 3-prime Digital Gene Expression (DGE) libraries and can easily extend to full transcript coverage shotgun (SHO) type strand-specific libraries and is modularized to accommodate a diversity of RNA and DNA input materials. BrAD-seq offers a highly streamlined and inexpensive option for RNA-seq libraries.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Armour, C D" uniqKey="Armour C">C. D. Armour</name></author><author><name sortKey="Castle, J C" uniqKey="Castle J">J. C. Castle</name></author><author><name sortKey="Chen, R" uniqKey="Chen R">R. Chen</name></author><author><name sortKey="Babak, T" uniqKey="Babak T">T. Babak</name></author><author><name sortKey="Loerch, P" uniqKey="Loerch P">P. Loerch</name></author><author><name sortKey="Jackson, S" uniqKey="Jackson S">S. Jackson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Goff, S A" uniqKey="Goff S">S. A. Goff</name></author><author><name sortKey="Vaughn, M" uniqKey="Vaughn M">M. Vaughn</name></author><author><name sortKey="Mckay, S" uniqKey="Mckay S">S. Mckay</name></author><author><name sortKey="Lyons, E" uniqKey="Lyons E">E. Lyons</name></author><author><name sortKey="Stapleton, A E" uniqKey="Stapleton A">A. E. Stapleton</name></author><author><name sortKey="Gessler, D" uniqKey="Gessler D">D. Gessler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hsu, P Y" uniqKey="Hsu P">P. Y. Hsu</name></author><author><name sortKey="Devisetty, U K" uniqKey="Devisetty U">U. K. Devisetty</name></author><author><name sortKey="Harmer, S L" uniqKey="Harmer S">S. L. Harmer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Koboldt, D C" uniqKey="Koboldt D">D. C. Koboldt</name></author><author><name sortKey="Steinberg, K M" uniqKey="Steinberg K">K. M. Steinberg</name></author><author><name sortKey="Larson, D E" uniqKey="Larson D">D. E. Larson</name></author><author><name sortKey="Wilson, R K" uniqKey="Wilson R">R. K. Wilson</name></author><author><name sortKey="Mardis, E R" uniqKey="Mardis E">E. R. Mardis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kumar, R" uniqKey="Kumar R">R. Kumar</name></author><author><name sortKey="Ichihashi, Y" uniqKey="Ichihashi Y">Y. Ichihashi</name></author><author><name sortKey="Kimura, S" uniqKey="Kimura S">S. Kimura</name></author><author><name sortKey="Chitwood, D H" uniqKey="Chitwood D">D. H. Chitwood</name></author><author><name sortKey="Headland, L R" uniqKey="Headland L">L. R. Headland</name></author><author><name sortKey="Peng, J" uniqKey="Peng J">J. Peng</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Langmead, B" uniqKey="Langmead B">B. Langmead</name></author><author><name sortKey="Trapnell, C" uniqKey="Trapnell C">C. Trapnell</name></author><author><name sortKey="Pop, M" uniqKey="Pop M">M. Pop</name></author><author><name sortKey="Salzberg, S L" uniqKey="Salzberg S">S. L. Salzberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Levin, J Z" uniqKey="Levin J">J. Z. Levin</name></author><author><name sortKey="Yassour, M" uniqKey="Yassour M">M. Yassour</name></author><author><name sortKey="Adiconis, X" uniqKey="Adiconis X">X. Adiconis</name></author><author><name sortKey="Nusbaum, C" uniqKey="Nusbaum C">C. Nusbaum</name></author><author><name sortKey="Thompson, D A" uniqKey="Thompson D">D. A. Thompson</name></author><author><name sortKey="Friedman, N" uniqKey="Friedman N">N. Friedman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lister, R" uniqKey="Lister R">R. Lister</name></author><author><name sortKey="O Malley, R C" uniqKey="O Malley R">R. C. O'malley</name></author><author><name sortKey="Tonti Filippini, J" uniqKey="Tonti Filippini J">J. Tonti-Filippini</name></author><author><name sortKey="Gregory, B D" uniqKey="Gregory B">B. D. Gregory</name></author><author><name sortKey="Berry, C C" uniqKey="Berry C">C. C. Berry</name></author><author><name sortKey="Millar, A H" uniqKey="Millar A">A. H. Millar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Meyer, M" uniqKey="Meyer M">M. Meyer</name></author><author><name sortKey="Kircher, M" uniqKey="Kircher M">M. Kircher</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mignone, F" uniqKey="Mignone F">F. Mignone</name></author><author><name sortKey="Gissi, C" uniqKey="Gissi C">C. Gissi</name></author><author><name sortKey="Liuni, S" uniqKey="Liuni S">S. Liuni</name></author><author><name sortKey="Pesole, G" uniqKey="Pesole G">G. Pesole</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Parkhomchuk, D" uniqKey="Parkhomchuk D">D. Parkhomchuk</name></author><author><name sortKey="Borodina, T" uniqKey="Borodina T">T. Borodina</name></author><author><name sortKey="Amstislavskiy, V" uniqKey="Amstislavskiy V">V. Amstislavskiy</name></author><author><name sortKey="Banaru, M" uniqKey="Banaru M">M. Banaru</name></author><author><name sortKey="Hallen, L" uniqKey="Hallen L">L. Hallen</name></author><author><name sortKey="Krobitsch, S" uniqKey="Krobitsch S">S. Krobitsch</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Semon, S P A M" uniqKey="Semon S">S. P. A. M. Sémon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tang, F" uniqKey="Tang F">F. Tang</name></author><author><name sortKey="Barbacioru, C" uniqKey="Barbacioru C">C. Barbacioru</name></author><author><name sortKey="Nordman, E" uniqKey="Nordman E">E. Nordman</name></author><author><name sortKey="Li, B" uniqKey="Li B">B. Li</name></author><author><name sortKey="Xu, N" uniqKey="Xu N">N. Xu</name></author><author><name sortKey="Bashkirov, V I" uniqKey="Bashkirov V">V. I. Bashkirov</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Von Hippel, P H" uniqKey="Von Hippel P">P. H. von Hippel</name></author><author><name sortKey="Johnson, N P" uniqKey="Johnson N">N. P. Johnson</name></author><author><name sortKey="Marcus, A H" uniqKey="Marcus A">A. H. Marcus</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, L" uniqKey="Wang L">L. Wang</name></author><author><name sortKey="Si, Y" uniqKey="Si Y">Y. Si</name></author><author><name sortKey="Dedow, L K" uniqKey="Dedow L">L. K. Dedow</name></author><author><name sortKey="Shao, Y" uniqKey="Shao Y">Y. Shao</name></author><author><name sortKey="Liu, P" uniqKey="Liu P">P. Liu</name></author><author><name sortKey="Brutnell, T P" uniqKey="Brutnell T">T. P. Brutnell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhu, Y Y" uniqKey="Zhu Y">Y. Y. Zhu</name></author><author><name sortKey="Machleder, E M" uniqKey="Machleder E">E. M. Machleder</name></author><author><name sortKey="Chenchik, A" uniqKey="Chenchik A">A. Chenchik</name></author><author><name sortKey="Li, R" uniqKey="Li R">R. Li</name></author><author><name sortKey="Siebert, P D" uniqKey="Siebert P">P. D. Siebert</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list></list><tree><noCountry><name sortKey="Covington, Michael F" sort="Covington, Michael F" uniqKey="Covington M" first="Michael F." last="Covington">Michael F. Covington</name><name sortKey="Ichihashi, Yasunori" sort="Ichihashi, Yasunori" uniqKey="Ichihashi Y" first="Yasunori" last="Ichihashi">Yasunori Ichihashi</name><name sortKey="Sinha, Neelima R" sort="Sinha, Neelima R" uniqKey="Sinha N" first="Neelima R." last="Sinha">Neelima R. Sinha</name><name sortKey="Townsley, Brad T" sort="Townsley, Brad T" uniqKey="Townsley B" first="Brad T." last="Townsley">Brad T. Townsley</name><name sortKey="Zumstein, Kristina" sort="Zumstein, Kristina" uniqKey="Zumstein K" first="Kristina" last="Zumstein">Kristina Zumstein</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Ticri/CIDE/explor/CyberinfraV1/Data/Ncbi/Checkpoint
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000644 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Ncbi/Checkpoint/biblio.hfd -nk 000644 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Ticri/CIDE
|area= CyberinfraV1
|flux= Ncbi
|étape= Checkpoint
|type= RBID
|clé= PMC:4441129
|texte= BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Checkpoint/RBID.i -Sk "pubmed:26052336" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Checkpoint/biblio.hfd \
| NlmPubMed2Wicri -a CyberinfraV1
| This area was generated with Dilib version V0.6.25. |  |