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Stacking the deck: double-tiled DNA microarrays

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

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Abstract

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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Acknowledgements

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.

Author information

Affiliations

  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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Contributions

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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DOI

https://doi.org/10.1038/nmeth951