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Large-Scale Mapping of Transposable Element Insertion Sites Using Digital Encoding of Sample Identity

Daryl M. Gohl, Limor Freifeld, Marion Silies, Jennifer J. Hwa, Mark Horowitz and Thomas R. Clandinin
Genetics March 1, 2014 vol. 196 no. 3 615-623; https://doi.org/10.1534/genetics.113.159483
Daryl M. Gohl
Department of Neurobiology, Stanford University, Stanford, California 94305
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Limor Freifeld
Department of Electrical Engineering, Stanford University, Stanford, California 94305Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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Marion Silies
Department of Neurobiology, Stanford University, Stanford, California 94305
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Jennifer J. Hwa
Department of Neurobiology, Stanford University, Stanford, California 94305
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Mark Horowitz
Department of Electrical Engineering, Stanford University, Stanford, California 94305
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Thomas R. Clandinin
Department of Neurobiology, Stanford University, Stanford, California 94305
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  • For correspondence: trc@stanford.edu
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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.

  • transposable elements
  • mapping
  • next-generation sequencing
  • Drosophila melanogaster
  • Received November 8, 2013.
  • Accepted December 21, 2013.
  • Copyright © 2014 by the Genetics Society of America
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PUBLICATION INFORMATION

Volume 196 Issue 3, March 2014

Genetics: 196 (3)

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  • Methods, Technology, & Resources

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Methods, technology, and resources
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Large-Scale Mapping of Transposable Element Insertion Sites Using Digital Encoding of Sample Identity

Daryl M. Gohl, Limor Freifeld, Marion Silies, Jennifer J. Hwa, Mark Horowitz and Thomas R. Clandinin
Genetics March 1, 2014 vol. 196 no. 3 615-623; https://doi.org/10.1534/genetics.113.159483
Daryl M. Gohl
Department of Neurobiology, Stanford University, Stanford, California 94305
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Limor Freifeld
Department of Electrical Engineering, Stanford University, Stanford, California 94305Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Marion Silies
Department of Neurobiology, Stanford University, Stanford, California 94305
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jennifer J. Hwa
Department of Neurobiology, Stanford University, Stanford, California 94305
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Mark Horowitz
Department of Electrical Engineering, Stanford University, Stanford, California 94305
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Thomas R. Clandinin
Department of Neurobiology, Stanford University, Stanford, California 94305
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: trc@stanford.edu
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Citation

Large-Scale Mapping of Transposable Element Insertion Sites Using Digital Encoding of Sample Identity

Daryl M. Gohl, Limor Freifeld, Marion Silies, Jennifer J. Hwa, Mark Horowitz and Thomas R. Clandinin
Genetics March 1, 2014 vol. 196 no. 3 615-623; https://doi.org/10.1534/genetics.113.159483
Daryl M. Gohl
Department of Neurobiology, Stanford University, Stanford, California 94305
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Limor Freifeld
Department of Electrical Engineering, Stanford University, Stanford, California 94305Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Marion Silies
Department of Neurobiology, Stanford University, Stanford, California 94305
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jennifer J. Hwa
Department of Neurobiology, Stanford University, Stanford, California 94305
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Mark Horowitz
Department of Electrical Engineering, Stanford University, Stanford, California 94305
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Thomas R. Clandinin
Department of Neurobiology, Stanford University, Stanford, California 94305
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: trc@stanford.edu

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  • Mutational Pleiotropy and the Strength of Stabilizing Selection Within and Between Functional Modules of Gene Expression
  • Regulation of Glutamate Signaling in the Sensorimotor Circuit by CASY-1A/Calsyntenin in Caenorhabditis elegans
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  • Comparative Oligo-FISH Mapping: An Efficient and Powerful Methodology To Reveal Karyotypic and Chromosomal Evolution
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The Genetics Society of America (GSA), founded in 1931, is the professional membership organization for scientific researchers and educators in the field of genetics. Our members work to advance knowledge in the basic mechanisms of inheritance, from the molecular to the population level.

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