Adapterama I: Universal Stubs and Primers for Thousands of Dual-Indexed Illumina Libraries (iTru & iNext)
作者： Romdhane Rekaya , Sandra Hoffberg , Jennifer K. Meece , Sammy Aggery , Brant C. Faircloth
DOI: 10.1101/049114
关键词:
摘要: Next-generation DNA sequencing (NGS) offers many benefits, but major factors limiting NGS include reducing the time and costs associated with: 1) start-up (i.e., doing for first time), 2) buy-in getting any data from a run), 3) sample preparation. Although researchers have focused on preparation costs, few addressed two problems. Here, we present iTru iNext, dual-indexing systems Illumina libraries that help address all three of these issues. By breaking library construction process into re-usable, combinatorial components, achieve low start-up, buy-in, per-sample while simultaneously increasing number samples can be combined within single run. We accomplish this by extending TruSeq approach 20 (8+12) indexed adapters produce 96 (8x12) unique combinations to 579 (192+387) primers 74,304 (192x387) combinations. synthesized 208 validation, 206 them passed our validation criteria (99% success). also used create hundreds in variety scenarios. Our reduces requiring only one universal adapter which works with PCR uniquely identify samples. because: relatively oligonucleotides are needed large libraries; possible allows use primer sets different projects, facilitates pooling during sequencing. methods highly customizable, resulting standard demultiplexed software packages, thereby minimizing instrument customization headaches. In subsequent Adapterama papers, same stubs construct double- quadruple-indexed amplicon double-digest restriction-site (RAD) libraries. For additional details updates, please see http://baddna.org.
sci-hub.st 参考文章(38)
Fraz Syed, Haiying Grunenwald, Nicholas Caruccio, Next-generation sequencing library preparation: simultaneous fragmentation and tagging using in vitro transposition Nature Methods. ,vol. 6, ,(2009) , 10.1038/NMETH.F.272
Salah M Aljanabi, Iciar Martinez, Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques Nucleic Acids Research. ,vol. 25, pp. 4692- 4693 ,(1997) , 10.1093/NAR/25.22.4692
John E. McCormack, Michael G. Harvey, Brant C. Faircloth, Nicholas G. Crawford, Travis C. Glenn, Robb T. Brumfield, A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing. PLOS ONE. ,vol. 8, ,(2013) , 10.1371/JOURNAL.PONE.0054848
David W Craig, John V Pearson, Szabolcs Szelinger, Aswin Sekar, Margot Redman, Jason J Corneveaux, Traci L Pawlowski, Trisha Laub, Gary Nunn, Dietrich A Stephan, Nils Homer, Matthew J Huentelman, None, Identification of genetic variants using bar-coded multiplexed sequencing Nature Methods. ,vol. 5, pp. 887- 893 ,(2008) , 10.1038/NMETH.1251
Brant C. Faircloth, Travis C. Glenn, Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels. PLOS ONE. ,vol. 7, ,(2012) , 10.1371/JOURNAL.PONE.0042543
David R Bentley, Shankar Balasubramanian, Harold P Swerdlow, Geoffrey P Smith, John Milton, Clive G Brown, Kevin P Hall, Dirk J Evers, Colin L Barnes, Helen R Bignell, Jonathan M Boutell, Jason Bryant, Richard J Carter, R Keira Cheetham, Anthony J Cox, Darren J Ellis, Michael R Flatbush, Niall A Gormley, Sean J Humphray, Leslie J Irving, Mirian S Karbelashvili, Scott M Kirk, Heng Li, Xiaohai Liu, Klaus S Maisinger, Lisa J Murray, Bojan Obradovic, Tobias Ost, Michael L Parkinson, Mark R Pratt, Isabelle MJ Rasolonjatovo, Mark T Reed, Roberto Rigatti, Chiara Rodighiero, Mark T Ross, Andrea Sabot, Subramanian V Sankar, Aylwyn Scally, Gary P Schroth, Mark E Smith, Vincent P Smith, Anastassia Spiridou, Peta E Torrance, Svilen S Tzonev, Eric H Vermaas, Klaudia Walter, Xiaolin Wu, Lu Zhang, Mohammed D Alam, Carole Anastasi, Ify C Aniebo, David MD Bailey, Iain R Bancarz, Saibal Banerjee, Selena G Barbour, Primo A Baybayan, Vincent A Benoit, Kevin F Benson, Claire Bevis, Phillip J Black, Asha Boodhun, Joe S Brennan, John A Bridgham, Rob C Brown, Andrew A Brown, Dale H Buermann, Abass A Bundu, James C Burrows, Nigel P Carter, Nestor Castillo, Maria Chiara E. Catenazzi, Simon Chang, R Neil Cooley, Natasha R Crake, Olubunmi O Dada, Konstantinos D Diakoumakos, Belen Dominguez-Fernandez, David J Earnshaw, Ugonna C Egbujor, David W Elmore, Sergey S Etchin, Mark R Ewan, Milan Fedurco, Louise J Fraser, Karin V Fuentes Fajardo, W Scott Furey, David George, Kimberley J Gietzen, Colin P Goddard, George S Golda, Philip A Granieri, David E Green, David L Gustafson, Nancy F Hansen, Kevin Harnish, Christian D Haudenschild, Narinder I Heyer, Matthew M Hims, Johnny T Ho, Adrian M Horgan, Katya Hoschler, Steve Hurwitz, Denis V Ivanov, Maria Q Johnson, Terena James, TA Huw Jones, Gyoung-Dong Kang, Tzvetana H Kerelska, Alan D Kersey, Irina Khrebtukova, Alex P Kindwall, Zoya Kingsbury, Paula I Kokko-Gonzales, Anil Kumar, Marc A Laurent, Cynthia T Lawley, Sarah E Lee, Xavier Lee, Arnold K Liao, Jennifer A Loch, Mitch Lok, Shujun Luo, Radhika M Mammen, John W Martin, Patrick G McCauley, Paul McNitt, Parul Mehta, Keith W Moon, Joe W Mullens, Taksina Newington, Zemin Ning, Bee Ling Ng, Sonia M Novo, Michael J O’Neill, Mark A Osborne, Andrew Osnowski, Omead Ostadan, Lambros L Paraschos, Lea Pickering, Andrew C Pike, Alger C Pike, D Chris Pinkard, Daniel P Pliskin, Joe Podhasky, Victor J Quijano, Come Raczy, Vicki H Rae, Stephen R Rawlings, Ana Chiva Rodriguez, Phyllida M Roe, None, Accurate whole human genome sequencing using reversible terminator chemistry Nature. ,vol. 456, pp. 53- 59 ,(2008) , 10.1038/NATURE07517
DIETHARD TAUTZ, HANS ELLEGREN, DETLEF WEIGEL, Next generation molecular ecology. Molecular Ecology. ,vol. 19, pp. 1- 3 ,(2010) , 10.1111/J.1365-294X.2009.04489.X
Miguel A Del Río-Portilla, Carmen E Vargas-Peralta, David A Paz-García, Fabiola Lafarga De La Cruz, Eduardo F Balart, Francisco J García-de-León, None, The complete mitochondrial DNA of endemic Eastern Pacific coral (Porites panamensis). Mitochondrial DNA. ,vol. 27, pp. 738- 739 ,(2016) , 10.3109/19401736.2014.913166
Carly F. Graham, Travis C. Glenn, Andrew G. McArthur, Douglas R. Boreham, Troy Kieran, Stacey Lance, Richard G. Manzon, Jessica A. Martino, Todd Pierson, Sean M. Rogers, Joanna Y. Wilson, Christopher M. Somers, Impacts of degraded DNA on restriction enzyme associated DNA sequencing (RADSeq). Molecular Ecology Resources. ,vol. 15, pp. 1304- 1315 ,(2015) , 10.1111/1755-0998.12404
Wilhelm J. Ansorge, Next-generation DNA sequencing techniques. New Biotechnology. ,vol. 25, pp. 195- 203 ,(2009) , 10.1016/J.NBT.2008.12.009