DNA immunoprecipitation semiconductor sequencing (DIP-SC-seq) as a rapid method to generate genome wide epigenetic signatures View Full Text


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Article Info

DATE

2015-09

AUTHORS

John P. Thomson, Angie Fawkes, Raffaele Ottaviano, Jennifer M. Hunter, Ruchi Shukla, Heidi K. Mjoseng, Richard Clark, Audrey Coutts, Lee Murphy, Richard R. Meehan

ABSTRACT

Modification of DNA resulting in 5-methylcytosine (5 mC) or 5-hydroxymethylcytosine (5hmC) has been shown to influence the local chromatin environment and affect transcription. Although recent advances in next generation sequencing technology allow researchers to map epigenetic modifications across the genome, such experiments are often time-consuming and cost prohibitive. Here we present a rapid and cost effective method of generating genome wide DNA modification maps utilising commercially available semiconductor based technology (DNA immunoprecipitation semiconductor sequencing; "DIP-SC-seq") on the Ion Proton sequencer. Focussing on the 5hmC mark we demonstrate, by directly comparing with alternative sequencing strategies, that this platform can successfully generate genome wide 5hmC patterns from as little as 500 ng of genomic DNA in less than 4 days. Such a method can therefore facilitate the rapid generation of multiple genome wide epigenetic datasets. More... »

PAGES

9778

References to SciGraph publications

  • 2012-10. The anti-CMS technique for genome-wide mapping of 5-hydroxymethylcytosine in NATURE PROTOCOLS
  • 2014. Hydroxymethylated DNA Immunoprecipitation (hmeDIP) in FUNCTIONAL ANALYSIS OF DNA AND CHROMATIN
  • 2012-10. The GLIB technique for genome-wide mapping of 5-hydroxymethylcytosine in NATURE PROTOCOLS
  • 2013-06. Subtelomeric hotspots of aberrant 5-hydroxymethylcytosine-mediated epigenetic modifications during reprogramming to pluripotency in NATURE CELL BIOLOGY
  • 2012-11. Mapping recently identified nucleotide variants in the genome and transcriptome in NATURE BIOTECHNOLOGY
  • 2010-04-15. CpG islands influence chromatin structure via the CpG-binding protein Cfp1 in NATURE
  • 2012. Balance of DNA methylation and demethylation in cancer development. in GENOME BIOLOGY
  • 2011-07. An integrated semiconductor device enabling non-optical genome sequencing in NATURE
  • 2011-01. Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine in NATURE BIOTECHNOLOGY
  • 2002-12. Microarray data normalization and transformation in NATURE GENETICS
  • 2011-09. Sequencing: Speed-reading DNA in the dark in NATURE METHODS
  • 2014. Investigating 5-Hydroxymethylcytosine (5hmC): The State of the Art in FUNCTIONAL ANALYSIS OF DNA AND CHROMATIN
  • 2011-05. Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation in NATURE
  • 2012-09. Genomics: ENCODE explained in NATURE
  • 2013-12. Semiconductor-based DNA sequencing of histone modification states in NATURE COMMUNICATIONS
  • 2012-10. Non-genotoxic carcinogen exposure induces defined changes in the 5-hydroxymethylome in GENOME BIOLOGY
  • 2013-08. Genome-wide analysis identifies a functional association of Tet1 and Polycomb repressive complex 2 in mouse embryonic stem cells in GENOME BIOLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/srep09778

    DOI

    http://dx.doi.org/10.1038/srep09778

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1008799336

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/25985418


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    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/srep09778'

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

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/srep09778'


     

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