A High-Throughput Method for Illumina RNA-Seq Library Preparation
Identifieur interne : 000451 ( Pmc/Checkpoint ); précédent : 000450; suivant : 000452A High-Throughput Method for Illumina RNA-Seq Library Preparation
Auteurs : Ravi Kumar [États-Unis] ; Yasunori Ichihashi [États-Unis] ; Seisuke Kimura [États-Unis] ; Daniel H. Chitwood [États-Unis] ; Lauren R. Headland [États-Unis] ; Jie Peng [États-Unis] ; Julin N. Maloof [États-Unis] ; Neelima R. Sinha [États-Unis]Source :
- Frontiers in Plant Science [ 1664-462X ] ; 2012.
Abstract
With the introduction of cost effective, rapid, and superior quality next generation sequencing techniques, gene expression analysis has become viable for labs conducting small projects as well as large-scale gene expression analysis experiments. However, the available protocols for construction of RNA-sequencing (RNA-Seq) libraries are expensive and/or difficult to scale for high-throughput applications. Also, most protocols require isolated total RNA as a starting point. We provide a cost-effective RNA-Seq library synthesis protocol that is fast, starts with tissue, and is high-throughput from tissue to synthesized library. We have also designed and report a set of 96 unique barcodes for library adapters that are amenable to high-throughput sequencing by a large combination of multiplexing strategies. Our developed protocol has more power to detect differentially expressed genes when compared to the standard Illumina protocol, probably owing to less technical variation amongst replicates. We also address the problem of gene-length biases affecting differential gene expression calls and demonstrate that such biases can be efficiently minimized during mRNA isolation for library preparation.
Url:
DOI: 10.3389/fpls.2012.00202
PubMed: 22973283
PubMed Central: 3428589
Affiliations:
Links toward previous steps (curation, corpus...)
Links to Exploration step
PMC:3428589Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A High-Throughput Method for Illumina RNA-Seq Library Preparation</title>
<author><name sortKey="Kumar, Ravi" sort="Kumar, Ravi" uniqKey="Kumar R" first="Ravi" last="Kumar">Ravi Kumar</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Plant Biology, University of California</institution>
<country>Davis, CA, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea></wicri:regionArea>
<wicri:regionArea># see nlm:aff region in country</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Ichihashi, Yasunori" sort="Ichihashi, Yasunori" uniqKey="Ichihashi Y" first="Yasunori" last="Ichihashi">Yasunori Ichihashi</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Plant Biology, University of California</institution>
<country>Davis, CA, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea></wicri:regionArea>
<wicri:regionArea># see nlm:aff region in country</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Kimura, Seisuke" sort="Kimura, Seisuke" uniqKey="Kimura S" first="Seisuke" last="Kimura">Seisuke Kimura</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Plant Biology, University of California</institution>
<country>Davis, CA, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea></wicri:regionArea>
<wicri:regionArea># see nlm:aff region in country</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Chitwood, Daniel H" sort="Chitwood, Daniel H" uniqKey="Chitwood D" first="Daniel H." last="Chitwood">Daniel H. Chitwood</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Plant Biology, University of California</institution>
<country>Davis, CA, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea></wicri:regionArea>
<wicri:regionArea># see nlm:aff region in country</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Headland, Lauren R" sort="Headland, Lauren R" uniqKey="Headland L" first="Lauren R." last="Headland">Lauren R. Headland</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Plant Biology, University of California</institution>
<country>Davis, CA, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea></wicri:regionArea>
<wicri:regionArea># see nlm:aff region in country</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Peng, Jie" sort="Peng, Jie" uniqKey="Peng J" first="Jie" last="Peng">Jie Peng</name>
<affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Department of Statistics, University of California</institution>
<country>Davis, CA, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea></wicri:regionArea>
<wicri:regionArea># see nlm:aff region in country</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Maloof, Julin N" sort="Maloof, Julin N" uniqKey="Maloof J" first="Julin N." last="Maloof">Julin N. Maloof</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Plant Biology, University of California</institution>
<country>Davis, CA, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea></wicri:regionArea>
<wicri:regionArea># see nlm:aff region in country</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Sinha, Neelima R" sort="Sinha, Neelima R" uniqKey="Sinha N" first="Neelima R." last="Sinha">Neelima R. Sinha</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Plant Biology, University of California</institution>
<country>Davis, CA, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea></wicri:regionArea>
<wicri:regionArea># see nlm:aff region in country</wicri:regionArea>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">22973283</idno>
<idno type="pmc">3428589</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3428589</idno>
<idno type="RBID">PMC:3428589</idno>
<idno type="doi">10.3389/fpls.2012.00202</idno>
<date when="2012">2012</date>
<idno type="wicri:Area/Pmc/Corpus">000543</idno>
<idno type="wicri:Area/Pmc/Curation">000543</idno>
<idno type="wicri:Area/Pmc/Checkpoint">000451</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">A High-Throughput Method for Illumina RNA-Seq Library Preparation</title>
<author><name sortKey="Kumar, Ravi" sort="Kumar, Ravi" uniqKey="Kumar R" first="Ravi" last="Kumar">Ravi Kumar</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Plant Biology, University of California</institution>
<country>Davis, CA, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea></wicri:regionArea>
<wicri:regionArea># see nlm:aff region in country</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Ichihashi, Yasunori" sort="Ichihashi, Yasunori" uniqKey="Ichihashi Y" first="Yasunori" last="Ichihashi">Yasunori Ichihashi</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Plant Biology, University of California</institution>
<country>Davis, CA, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea></wicri:regionArea>
<wicri:regionArea># see nlm:aff region in country</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Kimura, Seisuke" sort="Kimura, Seisuke" uniqKey="Kimura S" first="Seisuke" last="Kimura">Seisuke Kimura</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Plant Biology, University of California</institution>
<country>Davis, CA, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea></wicri:regionArea>
<wicri:regionArea># see nlm:aff region in country</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Chitwood, Daniel H" sort="Chitwood, Daniel H" uniqKey="Chitwood D" first="Daniel H." last="Chitwood">Daniel H. Chitwood</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Plant Biology, University of California</institution>
<country>Davis, CA, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea></wicri:regionArea>
<wicri:regionArea># see nlm:aff region in country</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Headland, Lauren R" sort="Headland, Lauren R" uniqKey="Headland L" first="Lauren R." last="Headland">Lauren R. Headland</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Plant Biology, University of California</institution>
<country>Davis, CA, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea></wicri:regionArea>
<wicri:regionArea># see nlm:aff region in country</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Peng, Jie" sort="Peng, Jie" uniqKey="Peng J" first="Jie" last="Peng">Jie Peng</name>
<affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Department of Statistics, University of California</institution>
<country>Davis, CA, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea></wicri:regionArea>
<wicri:regionArea># see nlm:aff region in country</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Maloof, Julin N" sort="Maloof, Julin N" uniqKey="Maloof J" first="Julin N." last="Maloof">Julin N. Maloof</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Plant Biology, University of California</institution>
<country>Davis, CA, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea></wicri:regionArea>
<wicri:regionArea># see nlm:aff region in country</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Sinha, Neelima R" sort="Sinha, Neelima R" uniqKey="Sinha N" first="Neelima R." last="Sinha">Neelima R. Sinha</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Plant Biology, University of California</institution>
<country>Davis, CA, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea></wicri:regionArea>
<wicri:regionArea># see nlm:aff region in country</wicri:regionArea>
</affiliation>
</author>
</analytic>
<series><title level="j">Frontiers in Plant Science</title>
<idno type="eISSN">1664-462X</idno>
<imprint><date when="2012">2012</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p>With the introduction of cost effective, rapid, and superior quality next generation sequencing techniques, gene expression analysis has become viable for labs conducting small projects as well as large-scale gene expression analysis experiments. However, the available protocols for construction of RNA-sequencing (RNA-Seq) libraries are expensive and/or difficult to scale for high-throughput applications. Also, most protocols require isolated total RNA as a starting point. We provide a cost-effective RNA-Seq library synthesis protocol that is fast, starts with tissue, and is high-throughput from tissue to synthesized library. We have also designed and report a set of 96 unique barcodes for library adapters that are amenable to high-throughput sequencing by a large combination of multiplexing strategies. Our developed protocol has more power to detect differentially expressed genes when compared to the standard Illumina protocol, probably owing to less technical variation amongst replicates. We also address the problem of gene-length biases affecting differential gene expression calls and demonstrate that such biases can be efficiently minimized during mRNA isolation for library preparation.</p>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Benjamini, Y" uniqKey="Benjamini Y">Y. Benjamini</name>
</author>
<author><name sortKey="Hochberg, Y" uniqKey="Hochberg Y">Y. Hochberg</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Chen, H" uniqKey="Chen H">H. Chen</name>
</author>
<author><name sortKey="Boutros, P C" uniqKey="Boutros P">P. C. Boutros</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Craig, D W" uniqKey="Craig D">D. W. Craig</name>
</author>
<author><name sortKey="Pearson, J V" uniqKey="Pearson J">J. V. Pearson</name>
</author>
<author><name sortKey="Szelinger, S" uniqKey="Szelinger S">S. Szelinger</name>
</author>
<author><name sortKey="Sekar, A" uniqKey="Sekar A">A. Sekar</name>
</author>
<author><name sortKey="Redman, M" uniqKey="Redman M">M. Redman</name>
</author>
<author><name sortKey="Corneveaux, J J" uniqKey="Corneveaux J">J. J. Corneveaux</name>
</author>
<author><name sortKey="Pawlowski, T L" uniqKey="Pawlowski T">T. L. Pawlowski</name>
</author>
<author><name sortKey="Laub, T" uniqKey="Laub T">T. Laub</name>
</author>
<author><name sortKey="Nunn, G" uniqKey="Nunn G">G. Nunn</name>
</author>
<author><name sortKey="Stephan, D A" uniqKey="Stephan D">D. A. Stephan</name>
</author>
<author><name sortKey="Homer, N" uniqKey="Homer N">N. Homer</name>
</author>
<author><name sortKey="Huentelman, M J" uniqKey="Huentelman M">M. J. Huentelman</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Fisher, S" uniqKey="Fisher S">S. Fisher</name>
</author>
<author><name sortKey="Barry, A" uniqKey="Barry A">A. Barry</name>
</author>
<author><name sortKey="Abreu, J" uniqKey="Abreu J">J. Abreu</name>
</author>
<author><name sortKey="Minie, B" uniqKey="Minie B">B. Minie</name>
</author>
<author><name sortKey="Nolan, J" uniqKey="Nolan J">J. Nolan</name>
</author>
<author><name sortKey="Delorey, T M" uniqKey="Delorey T">T. M. Delorey</name>
</author>
<author><name sortKey="Young, G" uniqKey="Young G">G. Young</name>
</author>
<author><name sortKey="Fennell, T J" uniqKey="Fennell T">T. J. Fennell</name>
</author>
<author><name sortKey="Allen, A" uniqKey="Allen A">A. Allen</name>
</author>
<author><name sortKey="Ambrogio, L" uniqKey="Ambrogio L">L. Ambrogio</name>
</author>
<author><name sortKey="Berlin, A M" uniqKey="Berlin A">A. M. Berlin</name>
</author>
<author><name sortKey="Blumenstiel, B" uniqKey="Blumenstiel B">B. Blumenstiel</name>
</author>
<author><name sortKey="Cibulskis, K" uniqKey="Cibulskis K">K. Cibulskis</name>
</author>
<author><name sortKey="Friedrich, D" uniqKey="Friedrich D">D. Friedrich</name>
</author>
<author><name sortKey="Johnson, R" uniqKey="Johnson R">R. Johnson</name>
</author>
<author><name sortKey="Juhn, F" uniqKey="Juhn F">F. Juhn</name>
</author>
<author><name sortKey="Reilly, B" uniqKey="Reilly B">B. Reilly</name>
</author>
<author><name sortKey="Shammas, R" uniqKey="Shammas R">R. Shammas</name>
</author>
<author><name sortKey="Stalker, J" uniqKey="Stalker J">J. Stalker</name>
</author>
<author><name sortKey="Sykes, S M" uniqKey="Sykes S">S. M. Sykes</name>
</author>
<author><name sortKey="Thompson, J" uniqKey="Thompson J">J. Thompson</name>
</author>
<author><name sortKey="Walsh, J" uniqKey="Walsh J">J. Walsh</name>
</author>
<author><name sortKey="Zimmer, A" uniqKey="Zimmer A">A. Zimmer</name>
</author>
<author><name sortKey="Zwirko, Z" uniqKey="Zwirko Z">Z. Zwirko</name>
</author>
<author><name sortKey="Gabriel, S" uniqKey="Gabriel S">S. Gabriel</name>
</author>
<author><name sortKey="Nicol, R" uniqKey="Nicol R">R. Nicol</name>
</author>
<author><name sortKey="Nusbaum, C" uniqKey="Nusbaum C">C. Nusbaum</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Fox Walsh, K" uniqKey="Fox Walsh K">K. Fox-Walsh</name>
</author>
<author><name sortKey="Davis Turak, J" uniqKey="Davis Turak J">J. Davis-Turak</name>
</author>
<author><name sortKey="Zhou, Y" uniqKey="Zhou Y">Y. Zhou</name>
</author>
<author><name sortKey="Li, H" uniqKey="Li H">H. Li</name>
</author>
<author><name sortKey="Fu, X D" uniqKey="Fu X">X.-D. Fu</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>
<author><name sortKey="Matasci, N" uniqKey="Matasci N">N. Matasci</name>
</author>
<author><name sortKey="Wang, L" uniqKey="Wang L">L. Wang</name>
</author>
<author><name sortKey="Hanlon, M" uniqKey="Hanlon M">M. Hanlon</name>
</author>
<author><name sortKey="Lenards, A" uniqKey="Lenards A">A. Lenards</name>
</author>
<author><name sortKey="Muir, A" uniqKey="Muir A">A. Muir</name>
</author>
<author><name sortKey="Merchant, N" uniqKey="Merchant N">N. Merchant</name>
</author>
<author><name sortKey="Lowry, S" uniqKey="Lowry S">S. Lowry</name>
</author>
<author><name sortKey="Mock, S" uniqKey="Mock S">S. Mock</name>
</author>
<author><name sortKey="Helmke, M" uniqKey="Helmke M">M. Helmke</name>
</author>
<author><name sortKey="Kubach, A" uniqKey="Kubach A">A. Kubach</name>
</author>
<author><name sortKey="Narro, M" uniqKey="Narro M">M. Narro</name>
</author>
<author><name sortKey="Hopkins, N" uniqKey="Hopkins N">N. Hopkins</name>
</author>
<author><name sortKey="Micklos, D" uniqKey="Micklos D">D. Micklos</name>
</author>
<author><name sortKey="Hilgert, U" uniqKey="Hilgert U">U. Hilgert</name>
</author>
<author><name sortKey="Gonzales, M" uniqKey="Gonzales M">M. Gonzales</name>
</author>
<author><name sortKey="Jordan, C" uniqKey="Jordan C">C. Jordan</name>
</author>
<author><name sortKey="Skidmore, E" uniqKey="Skidmore E">E. Skidmore</name>
</author>
<author><name sortKey="Dooley, R" uniqKey="Dooley R">R. Dooley</name>
</author>
<author><name sortKey="Cazes, J" uniqKey="Cazes J">J. Cazes</name>
</author>
<author><name sortKey="Mclay, R" uniqKey="Mclay R">R. Mclay</name>
</author>
<author><name sortKey="Lu, Z" uniqKey="Lu Z">Z. Lu</name>
</author>
<author><name sortKey="Pasternak, S" uniqKey="Pasternak S">S. Pasternak</name>
</author>
<author><name sortKey="Koesterke, L" uniqKey="Koesterke L">L. Koesterke</name>
</author>
<author><name sortKey="Piel, W H" uniqKey="Piel W">W. H. Piel</name>
</author>
<author><name sortKey="Grene, R" uniqKey="Grene R">R. Grene</name>
</author>
<author><name sortKey="Noutsos, C" uniqKey="Noutsos C">C. Noutsos</name>
</author>
<author><name sortKey="Gendler, K" uniqKey="Gendler K">K. Gendler</name>
</author>
<author><name sortKey="Feng, X" uniqKey="Feng X">X. Feng</name>
</author>
<author><name sortKey="Tang, C" uniqKey="Tang C">C. Tang</name>
</author>
<author><name sortKey="Lent, M" uniqKey="Lent M">M. Lent</name>
</author>
<author><name sortKey="Kim, S J" uniqKey="Kim S">S.-J. Kim</name>
</author>
<author><name sortKey="Kvilekval, K" uniqKey="Kvilekval K">K. Kvilekval</name>
</author>
<author><name sortKey="Manjunath, B S" uniqKey="Manjunath B">B. S. Manjunath</name>
</author>
<author><name sortKey="Tannen, V" uniqKey="Tannen V">V. Tannen</name>
</author>
<author><name sortKey="Stamatakis, A" uniqKey="Stamatakis A">A. Stamatakis</name>
</author>
<author><name sortKey="Sanderson, M" uniqKey="Sanderson M">M. Sanderson</name>
</author>
<author><name sortKey="Welch, S M" uniqKey="Welch S">S. M. Welch</name>
</author>
<author><name sortKey="Cranston, K" uniqKey="Cranston K">K. Cranston</name>
</author>
<author><name sortKey="Soltis, P" uniqKey="Soltis P">P. Soltis</name>
</author>
<author><name sortKey="Soltis, D" uniqKey="Soltis D">D. Soltis</name>
</author>
<author><name sortKey="O Eara, B" uniqKey="O Eara B">B. O’meara</name>
</author>
<author><name sortKey="Ane, C" uniqKey="Ane C">C. Ane</name>
</author>
<author><name sortKey="Brutnell, T" uniqKey="Brutnell T">T. Brutnell</name>
</author>
<author><name sortKey="Kleibenstein, D J" uniqKey="Kleibenstein D">D. J. Kleibenstein</name>
</author>
<author><name sortKey="White, J W" uniqKey="White J">J. W. White</name>
</author>
<author><name sortKey="Leebens Mack, J" uniqKey="Leebens Mack J">J. Leebens-Mack</name>
</author>
<author><name sortKey="Donoghue, M J" uniqKey="Donoghue M">M. J. Donoghue</name>
</author>
<author><name sortKey="Spalding, E P" uniqKey="Spalding E">E. P. Spalding</name>
</author>
<author><name sortKey="Vision, T J" uniqKey="Vision T">T. J. Vision</name>
</author>
<author><name sortKey="Myers, C R" uniqKey="Myers C">C. R. Myers</name>
</author>
<author><name sortKey="Lowenthal, D" uniqKey="Lowenthal D">D. Lowenthal</name>
</author>
<author><name sortKey="Enquist, B J" uniqKey="Enquist B">B. J. Enquist</name>
</author>
<author><name sortKey="Boyle, B" uniqKey="Boyle B">B. Boyle</name>
</author>
<author><name sortKey="Akoglu, A" uniqKey="Akoglu A">A. Akoglu</name>
</author>
<author><name sortKey="Andrews, G" uniqKey="Andrews G">G. Andrews</name>
</author>
<author><name sortKey="Ram, S" uniqKey="Ram S">S. Ram</name>
</author>
<author><name sortKey="Ware, D" uniqKey="Ware D">D. Ware</name>
</author>
<author><name sortKey="Stein, L" uniqKey="Stein L">L. Stein</name>
</author>
<author><name sortKey="Stanzione, D" uniqKey="Stanzione D">D. Stanzione</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hansen, K D" uniqKey="Hansen K">K. D. Hansen</name>
</author>
<author><name sortKey="Brenner, S E" uniqKey="Brenner S">S. E. Brenner</name>
</author>
<author><name sortKey="Dudoit, S" uniqKey="Dudoit S">S. Dudoit</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hawkins, T L" uniqKey="Hawkins T">T. L. Hawkins</name>
</author>
<author><name sortKey="O Onnor Morin, T" uniqKey="O Onnor Morin T">T. O’Connor-Morin</name>
</author>
<author><name sortKey="Roy, A" uniqKey="Roy A">A. Roy</name>
</author>
<author><name sortKey="Santillan, C" uniqKey="Santillan C">C. Santillan</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" uniqKey="Salzberg S">S. Salzberg</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lennon, N J" uniqKey="Lennon N">N. J. Lennon</name>
</author>
<author><name sortKey="Lintner, R E" uniqKey="Lintner R">R. E. Lintner</name>
</author>
<author><name sortKey="Anderson, S" uniqKey="Anderson S">S. Anderson</name>
</author>
<author><name sortKey="Alvarez, P" uniqKey="Alvarez P">P. Alvarez</name>
</author>
<author><name sortKey="Barry, A" uniqKey="Barry A">A. Barry</name>
</author>
<author><name sortKey="Brockman, W" uniqKey="Brockman W">W. Brockman</name>
</author>
<author><name sortKey="Daza, R" uniqKey="Daza R">R. Daza</name>
</author>
<author><name sortKey="Erlich, R L" uniqKey="Erlich R">R. L. Erlich</name>
</author>
<author><name sortKey="Giannoukos, G" uniqKey="Giannoukos G">G. Giannoukos</name>
</author>
<author><name sortKey="Green, L" uniqKey="Green L">L. Green</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>
<author><name sortKey="Gnirke, A" uniqKey="Gnirke A">A. Gnirke</name>
</author>
<author><name sortKey="Regev, A" uniqKey="Regev A">A. Regev</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Mader, U" uniqKey="Mader U">U. Mader</name>
</author>
<author><name sortKey="Nicolas, P" uniqKey="Nicolas P">P. Nicolas</name>
</author>
<author><name sortKey="Richard, H" uniqKey="Richard H">H. Richard</name>
</author>
<author><name sortKey="Bessieres, P" uniqKey="Bessieres P">P. Bessieres</name>
</author>
<author><name sortKey="Aymerich, S" uniqKey="Aymerich S">S. Aymerich</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Marioni, J C" uniqKey="Marioni J">J. C. Marioni</name>
</author>
<author><name sortKey="Mason, C E" uniqKey="Mason C">C. E. Mason</name>
</author>
<author><name sortKey="Mane, S M" uniqKey="Mane S">S. M. Mane</name>
</author>
<author><name sortKey="Stephens, M" uniqKey="Stephens M">M. Stephens</name>
</author>
<author><name sortKey="Gilad, Y" uniqKey="Gilad Y">Y. Gilad</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="Nagalakshmi, U" uniqKey="Nagalakshmi U">U. Nagalakshmi</name>
</author>
<author><name sortKey="Waern, K" uniqKey="Waern K">K. Waern</name>
</author>
<author><name sortKey="Snyder, M" uniqKey="Snyder M">M. Snyder</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ozsolak, F" uniqKey="Ozsolak F">F. Ozsolak</name>
</author>
<author><name sortKey="Milos, P M" uniqKey="Milos P">P. M. Milos</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>
<author><name sortKey="Lehrach, H" uniqKey="Lehrach H">H. Lehrach</name>
</author>
<author><name sortKey="Soldatov, A" uniqKey="Soldatov A">A. Soldatov</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Quail, M A" uniqKey="Quail M">M. A. Quail</name>
</author>
<author><name sortKey="Kozarewa, I" uniqKey="Kozarewa I">I. Kozarewa</name>
</author>
<author><name sortKey="Smith, F" uniqKey="Smith F">F. Smith</name>
</author>
<author><name sortKey="Scally, A" uniqKey="Scally A">A. Scally</name>
</author>
<author><name sortKey="Stephens, P J" uniqKey="Stephens P">P. J. Stephens</name>
</author>
<author><name sortKey="Durbin, R" uniqKey="Durbin R">R. Durbin</name>
</author>
<author><name sortKey="Swerdlow, H" uniqKey="Swerdlow H">H. Swerdlow</name>
</author>
<author><name sortKey="Turner, D J" uniqKey="Turner D">D. J. Turner</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Robinson, M D" uniqKey="Robinson M">M. D. Robinson</name>
</author>
<author><name sortKey="Oshlack, A" uniqKey="Oshlack A">A. Oshlack</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wang, L" uniqKey="Wang L">L. Wang</name>
</author>
<author><name sortKey="Feng, Z" uniqKey="Feng Z">Z. Feng</name>
</author>
<author><name sortKey="Wang, X" uniqKey="Wang X">X. Wang</name>
</author>
<author><name sortKey="Zhang, X" uniqKey="Zhang X">X. Zhang</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="Wang, Y" uniqKey="Wang Y">Y. Wang</name>
</author>
<author><name sortKey="Ghaffari, N" uniqKey="Ghaffari N">N. Ghaffari</name>
</author>
<author><name sortKey="Johnson, C" uniqKey="Johnson C">C. Johnson</name>
</author>
<author><name sortKey="Braga Neto, U" uniqKey="Braga Neto U">U. Braga-Neto</name>
</author>
<author><name sortKey="Wang, H" uniqKey="Wang H">H. Wang</name>
</author>
<author><name sortKey="Chen, R" uniqKey="Chen R">R. Chen</name>
</author>
<author><name sortKey="Zhou, H" uniqKey="Zhou H">H. Zhou</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Weigel, D" uniqKey="Weigel D">D. Weigel</name>
</author>
<author><name sortKey="Mott, R" uniqKey="Mott R">R. Mott</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wickham, H" uniqKey="Wickham H">H. Wickham</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wilhelm, B T" uniqKey="Wilhelm B">B. T. Wilhelm</name>
</author>
<author><name sortKey="Marguerat, S" uniqKey="Marguerat S">S. Marguerat</name>
</author>
<author><name sortKey="Goodhead, I" uniqKey="Goodhead I">I. Goodhead</name>
</author>
<author><name sortKey="Bahler, J" uniqKey="Bahler J">J. Bahler</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zhong, S" uniqKey="Zhong S">S. Zhong</name>
</author>
<author><name sortKey="Joung, J G" uniqKey="Joung J">J. G. Joung</name>
</author>
<author><name sortKey="Zheng, Y" uniqKey="Zheng Y">Y. Zheng</name>
</author>
<author><name sortKey="Chen, Y R" uniqKey="Chen Y">Y. R. Chen</name>
</author>
<author><name sortKey="Liu, B" uniqKey="Liu B">B. Liu</name>
</author>
<author><name sortKey="Shao, Y" uniqKey="Shao Y">Y. Shao</name>
</author>
<author><name sortKey="Xiang, J Z" uniqKey="Xiang J">J. Z. Xiang</name>
</author>
<author><name sortKey="Fei, Z" uniqKey="Fei Z">Z. Fei</name>
</author>
<author><name sortKey="Giovannoni, J J" uniqKey="Giovannoni J">J. J. Giovannoni</name>
</author>
</analytic>
</biblStruct>
</listBibl>
</div1>
</back>
</TEI>
<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Front Plant Sci</journal-id>
<journal-id journal-id-type="iso-abbrev">Front Plant Sci</journal-id>
<journal-id journal-id-type="publisher-id">Front. Plant Sci.</journal-id>
<journal-title-group><journal-title>Frontiers in Plant Science</journal-title>
</journal-title-group>
<issn pub-type="epub">1664-462X</issn>
<publisher><publisher-name>Frontiers Research Foundation</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">22973283</article-id>
<article-id pub-id-type="pmc">3428589</article-id>
<article-id pub-id-type="doi">10.3389/fpls.2012.00202</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Plant Science</subject>
<subj-group><subject>Methods Article</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group><article-title>A High-Throughput Method for Illumina RNA-Seq Library Preparation</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Kumar</surname>
<given-names>Ravi</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="fn003"><sup>‡</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Ichihashi</surname>
<given-names>Yasunori</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="fn003"><sup>‡</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Kimura</surname>
<given-names>Seisuke</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="fn002"><sup>†</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Chitwood</surname>
<given-names>Daniel H.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Headland</surname>
<given-names>Lauren R.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Peng</surname>
<given-names>Jie</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Maloof</surname>
<given-names>Julin N.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Sinha</surname>
<given-names>Neelima R.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="fn001">*</xref>
</contrib>
</contrib-group>
<aff id="aff1"><sup>1</sup>
<institution>Department of Plant Biology, University of California</institution>
<country>Davis, CA, USA</country>
</aff>
<aff id="aff2"><sup>2</sup>
<institution>Department of Statistics, University of California</institution>
<country>Davis, CA, USA</country>
</aff>
<author-notes><fn fn-type="edited-by"><p>Edited by: Shawn Kaeppler, University of Wisconsin-Madison, USA</p>
</fn>
<fn fn-type="edited-by"><p>Reviewed by: Rajandeep Sekhon, University of Wisconsin-Madison, USA; Andrea L. Eveland, Cold Spring Harbor Laboratory, USA</p>
</fn>
<corresp id="fn001">*Correspondence: Neelima R. Sinha, Department of Plant Biology, 1002 Life Sciences, One Shields Avenue, Davis, CA, USA. e-mail: <email xlink:type="simple">nrsinha@ucdavis.edu</email>
</corresp>
<fn fn-type="present-address" id="fn002"><p><sup>†</sup>
Present address: Seisuke Kimura, Department of Bioresource and Environmental Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan.</p>
</fn>
<fn fn-type="other" id="fn003"><p><sup>‡</sup>
Ravi Kumar and Yasunori Ichihashi have contributed equally to this work.</p>
</fn>
<fn fn-type="other" id="fn004"><p>This article was submitted to Frontiers in Plant Genetics and Genomics, a specialty of Frontiers in Plant Science.</p>
</fn>
</author-notes>
<pub-date pub-type="epreprint"><day>01</day>
<month>6</month>
<year>2012</year>
</pub-date>
<pub-date pub-type="epub"><day>28</day>
<month>8</month>
<year>2012</year>
</pub-date>
<pub-date pub-type="collection"><year>2012</year>
</pub-date>
<volume>3</volume>
<elocation-id>202</elocation-id>
<history><date date-type="received"><day>03</day>
<month>5</month>
<year>2012</year>
</date>
<date date-type="accepted"><day>09</day>
<month>8</month>
<year>2012</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2012 Kumar, Ichihashi, Kimura, Chitwood, Headland, Peng, Maloof and Sinha.</copyright-statement>
<copyright-year>2012</copyright-year>
<license license-type="open-access" xlink:href="http://www.frontiersin.org/licenseagreement"><license-p>This is an open-access article distributed under the terms of the <uri xlink:type="simple" xlink:href="http://creativecommons.org/licenses/by/3.0/">Creative Commons Attribution License</uri>
, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc.</license-p>
</license>
</permissions>
<abstract><p>With the introduction of cost effective, rapid, and superior quality next generation sequencing techniques, gene expression analysis has become viable for labs conducting small projects as well as large-scale gene expression analysis experiments. However, the available protocols for construction of RNA-sequencing (RNA-Seq) libraries are expensive and/or difficult to scale for high-throughput applications. Also, most protocols require isolated total RNA as a starting point. We provide a cost-effective RNA-Seq library synthesis protocol that is fast, starts with tissue, and is high-throughput from tissue to synthesized library. We have also designed and report a set of 96 unique barcodes for library adapters that are amenable to high-throughput sequencing by a large combination of multiplexing strategies. Our developed protocol has more power to detect differentially expressed genes when compared to the standard Illumina protocol, probably owing to less technical variation amongst replicates. We also address the problem of gene-length biases affecting differential gene expression calls and demonstrate that such biases can be efficiently minimized during mRNA isolation for library preparation.</p>
</abstract>
<kwd-group><kwd>cDNA fragmentation</kwd>
<kwd>high-throughput</kwd>
<kwd>Illumina</kwd>
<kwd>mRNA isolation</kwd>
<kwd>multiplexing</kwd>
<kwd>RNA-Seq</kwd>
<kwd>sequencing</kwd>
</kwd-group>
<counts><fig-count count="4"></fig-count>
<table-count count="0"></table-count>
<equation-count count="0"></equation-count>
<ref-count count="28"></ref-count>
<page-count count="10"></page-count>
<word-count count="6783"></word-count>
</counts>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>États-Unis</li>
</country>
</list>
<tree><country name="États-Unis"><noRegion><name sortKey="Kumar, Ravi" sort="Kumar, Ravi" uniqKey="Kumar R" first="Ravi" last="Kumar">Ravi Kumar</name>
</noRegion>
<name sortKey="Chitwood, Daniel H" sort="Chitwood, Daniel H" uniqKey="Chitwood D" first="Daniel H." last="Chitwood">Daniel H. Chitwood</name>
<name sortKey="Headland, Lauren R" sort="Headland, Lauren R" uniqKey="Headland L" first="Lauren R." last="Headland">Lauren R. Headland</name>
<name sortKey="Ichihashi, Yasunori" sort="Ichihashi, Yasunori" uniqKey="Ichihashi Y" first="Yasunori" last="Ichihashi">Yasunori Ichihashi</name>
<name sortKey="Kimura, Seisuke" sort="Kimura, Seisuke" uniqKey="Kimura S" first="Seisuke" last="Kimura">Seisuke Kimura</name>
<name sortKey="Maloof, Julin N" sort="Maloof, Julin N" uniqKey="Maloof J" first="Julin N." last="Maloof">Julin N. Maloof</name>
<name sortKey="Peng, Jie" sort="Peng, Jie" uniqKey="Peng J" first="Jie" last="Peng">Jie Peng</name>
<name sortKey="Sinha, Neelima R" sort="Sinha, Neelima R" uniqKey="Sinha N" first="Neelima R." last="Sinha">Neelima R. Sinha</name>
</country>
</tree>
</affiliations>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Ticri/CIDE/explor/CyberinfraV1/Data/Pmc/Checkpoint
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000451 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Pmc/Checkpoint/biblio.hfd -nk 000451 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Ticri/CIDE |area= CyberinfraV1 |flux= Pmc |étape= Checkpoint |type= RBID |clé= PMC:3428589 |texte= A High-Throughput Method for Illumina RNA-Seq Library Preparation }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Pmc/Checkpoint/RBID.i -Sk "pubmed:22973283" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Pmc/Checkpoint/biblio.hfd \ | NlmPubMed2Wicri -a CyberinfraV1
![]() | This area was generated with Dilib version V0.6.25. | ![]() |