Linear amplification for deep sequencing View Full Text


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Article Info

DATE

2011-07

AUTHORS

Wieteke A M Hoeijmakers, Richárd Bártfai, Kees-Jan Françoijs, Hendrik G Stunnenberg

ABSTRACT

Linear amplification for deep sequencing (LADS) is an amplification method that produces representative libraries for Illumina next-generation sequencing within 2 d. The method relies on attaching two different sequencing adapters to blunt-end repaired and A-tailed DNA fragments, wherein one of the adapters is extended with the sequence for the T7 RNA polymerase promoter. Ligated and size-selected DNA fragments are transcribed in vitro with high RNA yields. Subsequent cDNA synthesis is initiated from a primer complementary to the first adapter, ensuring that the library will only contain full-length fragments with two distinct adapters. Contrary to the severely biased representation of AT- or GC-rich fragments in standard PCR-amplified libraries, the sequence coverage in T7-amplified libraries is indistinguishable from that of nonamplified libraries. Moreover, in contrast to amplification-free methods, LADS can generate sequencing libraries from a few nanograms of DNA, which is essential for all applications in which the starting material is limited. More... »

PAGES

1026

References to SciGraph publications

  • 2010-02. Defining transcribed regions using RNA-seq in NATURE PROTOCOLS
  • 2009-01. RNA-Seq: a revolutionary tool for transcriptomics in NATURE REVIEWS GENETICS
  • 2010-01. Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA in NATURE METHODS
  • 2002-10. Genome sequence of the human malaria parasite Plasmodium falciparum in NATURE
  • 2008-07. Stem cell transcriptome profiling via massive-scale mRNA sequencing in NATURE METHODS
  • 2009-04. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes in NATURE METHODS
  • 2002-07. Sequence and analysis of chromosome 2 of Dictyostelium discoideum in NATURE
  • 2008-07. Mapping and quantifying mammalian transcriptomes by RNA-Seq in NATURE METHODS
  • 2008-02. Whole-genome sequencing and variant discovery in C. elegans in NATURE METHODS
  • 2010-12. Whole genome sequencing of enriched chloroplast DNA using the Illumina GAII platform in PLANT METHODS
  • 2008-12. A large genome center's improvements to the Illumina sequencing system in NATURE METHODS
  • 2003-12. Development and validation of a T7 based linear amplification for genomic DNA in BMC GENOMICS
  • 2010-02. FRT-seq: amplification-free, strand-specific transcriptome sequencing in NATURE METHODS
  • 2009-09. Digital transcriptome profiling using selective hexamer priming for cDNA synthesis in NATURE METHODS
  • 2010-10. Quantitative comparison of genome-wide DNA methylation mapping technologies in NATURE BIOTECHNOLOGY
  • 1998-06. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence in NATURE
  • 2010-03. RNA-Seq analysis to capture the transcriptome landscape of a single cell in NATURE PROTOCOLS
  • 2008-11. Accurate whole human genome sequencing using reversible terminator chemistry in NATURE
  • 2009-10. ChIP–seq: advantages and challenges of a maturing technology in NATURE REVIEWS GENETICS
  • 2010-01. Sequencing technologies — the next generation in NATURE REVIEWS GENETICS
  • 2008-02. Parallel tagged sequencing on the 454 platform in NATURE PROTOCOLS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nprot.2011.345

    DOI

    http://dx.doi.org/10.1038/nprot.2011.345

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1018492224

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/21720315


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    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/nprot.2011.345'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/nprot.2011.345'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nprot.2011.345'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nprot.2011.345'


     

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