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Analysis of Small RNA Populations Using Hybridization to DNA Tiling Arrays

  • Martine BoccaraEmail author
  • Alexis Sarazin
  • Bernard Billoud
  • Agnes Bulski
  • Louise Chapell
  • David Baulcombe
  • Vincent Colot
Protocol
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Part of the Methods in Molecular Biology™ book series (MIMB, volume 631)

Abstract

Small RNA (sRNA) populations extracted from Arabidopsis plants submitted or not to biotic stress, were reverse-transcribed into cDNAs, and these were subsequently hybridized after labelling to a custom-made DNA tiling array covering Arabidopsis chromosome 4. We first designed a control experiment with eight cDNA clones corresponding to sequences located on chromosome 4 and obtained robust and specific hybridization signals. Furthermore, hybridization signals along chromosome 4 were in good agreement with sRNA abundance as previously determined by Massive Parallel Sequence Signature (MPSS) in the case of untreated plants, but differed substantially after stress treatment. These results demonstrate the utility of hybridization to DNA tiling arrays to detect major changes in small RNA populations.

Key words

Small RNA cDNA libraries cy-dye indirect labelling Hypersensitive response Microarray Harpin 

Notes

Acknowledgments

MB was supported by a Visiting Scientist Fellowship from INRA. VC and DB are members of the European Union Network of Excellence “The Epigenome”.

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Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Martine Boccara
    • 1
    Email author
  • Alexis Sarazin
    • 2
  • Bernard Billoud
    • 3
  • Agnes Bulski
    • 4
  • Louise Chapell
    • 5
  • David Baulcombe
    • 5
  • Vincent Colot
    • 1
  1. 1.Unité de Recherche en Génomique Végétale (URGV), INRA/CNRS/UEVEEvry cedexFrance
  2. 2.CNRS UMR8186, Département de biologieEcole Normale SupérieureParis cedex 05France
  3. 3.Atelier de bioinformatique, Université Pierre et Marie CurieParisFrance
  4. 4.CNRS UMR8186, Département de biologieEcole Normale SupérieureParis cedexFrance
  5. 5.The Sainsbury Laboratory, John Innes CentreNorwichUK

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