Literature DB >> 24374352

Large-scale mapping of transposable element insertion sites using digital encoding of sample identity.

Daryl M Gohl1, Limor Freifeld, Marion Silies, Jennifer J Hwa, Mark Horowitz, Thomas R Clandinin.   

Abstract

Determining the genomic locations of transposable elements is a common experimental goal. When mapping large collections of transposon insertions, individualized amplification and sequencing is both time consuming and costly. We describe an approach in which large numbers of insertion lines can be simultaneously mapped in a single DNA sequencing reaction by using digital error-correcting codes to encode line identity in a unique set of barcoded pools.

Keywords:  Drosophila melanogaster; mapping; next-generation sequencing; transposable elements

Mesh：

Substances：

Year:  2013        PMID： 24374352      PMCID： PMC3948795          DOI： 10.1534/genetics.113.159483

Source DB:  PubMed          Journal:  Genetics        ISSN： 0016-6731            Impact factor:   4.562


  19 in total

1.  Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex.

Authors:  Micah Hamady; Jeffrey J Walker; J Kirk Harris; Nicholas J Gold; Rob Knight
Journal:  Nat Methods       Date:  2008-02-10       Impact factor: 28.547

2.  DNA Sudoku--harnessing high-throughput sequencing for multiplexed specimen analysis.

Authors:  Yaniv Erlich; Kenneth Chang; Assaf Gordon; Roy Ronen; Oron Navon; Michelle Rooks; Gregory J Hannon
Journal:  Genome Res       Date:  2009-05-15       Impact factor: 9.043

3.  Overlapping pools for high-throughput targeted resequencing.

Authors:  Snehit Prabhu; Itsik Pe'er
Journal:  Genome Res       Date:  2009-05-15       Impact factor: 9.043

4.  Genetic applications of an inverse polymerase chain reaction.

Authors:  H Ochman; A S Gerber; D L Hartl
Journal:  Genetics       Date:  1988-11       Impact factor: 4.562

5.  Splinkerettes--improved vectorettes for greater efficiency in PCR walking.

Authors:  R S Devon; D J Porteous; A J Brookes
Journal:  Nucleic Acids Res       Date:  1995-05-11       Impact factor: 16.971

6.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Authors:  Ben Langmead; Cole Trapnell; Mihai Pop; Steven L Salzberg
Journal:  Genome Biol       Date:  2009-03-04       Impact factor: 13.583

7.  Modular use of peripheral input channels tunes motion-detecting circuitry.

Authors:  Marion Silies; Daryl M Gohl; Yvette E Fisher; Limor Freifeld; Damon A Clark; Thomas R Clandinin
Journal:  Neuron       Date:  2013-07-10       Impact factor: 17.173

Review 8.  Signature-tagged mutagenesis: barcoding mutants for genome-wide screens.

Authors:  Piotr Mazurkiewicz; Christoph M Tang; Charles Boone; David W Holden
Journal:  Nat Rev Genet       Date:  2006-12       Impact factor: 53.242

9.  A high-throughput splinkerette-PCR method for the isolation and sequencing of retroviral insertion sites.

Authors:  Anthony G Uren; Harald Mikkers; Jaap Kool; Louise van der Weyden; Anders H Lund; Catherine H Wilson; Richard Rance; Jos Jonkers; Maarten van Lohuizen; Anton Berns; David J Adams
Journal:  Nat Protoc       Date:  2009-04-30       Impact factor: 13.491

10.  Accurate whole human genome sequencing using reversible terminator chemistry.

Authors:  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 M J 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 M D 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; T A 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; John Rogers; Maria C Rogert Bacigalupo; Nikolai Romanov; Anthony Romieu; Rithy K Roth; Natalie J Rourke; Silke T Ruediger; Eli Rusman; Raquel M Sanches-Kuiper; Martin R Schenker; Josefina M Seoane; Richard J Shaw; Mitch K Shiver; Steven W Short; Ning L Sizto; Johannes P Sluis; Melanie A Smith; Jean Ernest Sohna Sohna; Eric J Spence; Kim Stevens; Neil Sutton; Lukasz Szajkowski; Carolyn L Tregidgo; Gerardo Turcatti; Stephanie Vandevondele; Yuli Verhovsky; Selene M Virk; Suzanne Wakelin; Gregory C Walcott; Jingwen Wang; Graham J Worsley; Juying Yan; Ling Yau; Mike Zuerlein; Jane Rogers; James C Mullikin; Matthew E Hurles; Nick J McCooke; John S West; Frank L Oaks; Peter L Lundberg; David Klenerman; Richard Durbin; Anthony J Smith
Journal:  Nature       Date:  2008-11-06       Impact factor: 49.962
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  1 in total

1.  Comprehensive Functional Analysis of the Enterococcus faecalis Core Genome Using an Ordered, Sequence-Defined Collection of Insertional Mutations in Strain OG1RF.

Authors:  Jennifer L Dale; Kenneth B Beckman; Julia L E Willett; Jennifer L Nilson; Nagendra P Palani; Joshua A Baller; Adam Hauge; Daryl M Gohl; Raymond Erickson; Dawn A Manias; Michael J Sadowsky; Gary M Dunny
Journal:  mSystems       Date:  2018-09-11       Impact factor: 7.324
  1 in total

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