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Stacking the deck: double-tiled DNA microarrays

Nature Methods volume 3, pages 903907 (2006) | Download Citation



Microarrays—high-throughput platforms for analyzing the gene expression and features of total genomic DNA, among other applications—are gaining in popularity as researchers discover ever more uses for their unbiased and broad feature sets. At present, microarray analyses are limited by the number of individual features that can be placed on each array. Here we describe a double-tiling method that significantly increases the number of sequences present on an array, and we show that successful transcriptional profiling is possible and straightforward with such arrays. With this method, we and others can save money and precious samples by using fewer arrays to cover a region, or can carry out investigations at significantly higher resolution without incurring prohibitive costs or increasing the amount of sample required for the experiment.

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  1. 1.

    , & Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery. Chromosome Res. 13, 259–274 (2005).

  2. 2.

    et al. Global identification of human transcribed sequences with genome tiling arrays. Science 306, 2242–2246 (2004).

  3. 3.

    et al. Applications of DNA tiling arrays for whole-genome analysis. Genomics 85, 1–15 (2005).

  4. 4.

    et al. Experimental annotation of the human genome using microarray technology. Nature 409, 922–927 (2001).

  5. 5.

    et al. Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc. Natl. Acad. Sci. USA 94, 13057–13062 (1997).

  6. 6.

    Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3, 3 (2004).

  7. 7.

    et al. Multiple-laboratory comparison of microarray platforms. Nat. Methods 2, 345–350 (2005).

  8. 8.

    et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308, 1149–1154 (2005).

  9. 9.

    & Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol. 132, 365–386 (2000).

  10. 10.

    , , , & The transposon insertion site profiling chip (JJP-chip). Proc. Natl. Acad. Sci. USA (in press).

  11. 11.

    , & A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Res. 18, 3091–3092 (1990).

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We thank H. Zhu and J. Bader for helpful comments on the manuscript and B. Greenlee for help with the figures and the methods section. Supported by grants from the US National Institutes of Health.

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  1. The High Throughput Biology Center and Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, 733 North Broadway, BRB Suite 331 Baltimore, Maryland 21205, USA.

    • Sarah J Wheelan
    • , Francisco Martínez-Murillo
    •  & Jef D Boeke
  2. Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, E3132, Baltimore, Maryland 21205, USA.

    • Rafael A Irizarry


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S.J.W. designed arrays, executed one-color array experiments and prepared samples for two-color arrays, and analyzed data for one-color experiments; F.M.-M. executed two-color array experiments; R.A.I. analyzed data for two-color experiments; J.D.B. oversaw design, execution and analysis of all experiments.

Competing interests

The authors have filed a patent application covering the technology described in this article.

Corresponding authors

Correspondence to Rafael A Irizarry or Jef D Boeke.

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