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Making and reading microarrays

Nature Genetics volume 21, pages 15–19 (1999)Cite this article

Abstract

There are a variety of options for making microarrays and obtaining microarray data. Here, we describe the building and use of two microarray facilities in academic settings. In addition to specifying technical detail, we comment on the advantages and disadvantages of components and approaches, and provide a protocol for hybridization. The fact that we are now making and using microarrays to answer biological questions demonstrates that the technology can be implemented in a university environment.

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Figure ig1: a, Penn microarray robot.
Figure ig2: a, Schematic representation of a 12 pen array.
Figure ig3: a, An hybridized microarray printed by the AECOM robot.

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References

  1. Schena, M., Shalon, D., Davis, R.W. & Brown, P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467–470 ( 1995).

    Article  CAS  Google Scholar 

  2. DeRisi, J. et al. Use of a cDNA microarray to analyze gene expression patterns in human cancer. Nature Genet. 14, 457– 460 (1997).

    Google Scholar 

  3. DeRisi, J.L., Iyer, V.R. & Brown, P.O. Exploring gene expression on a genomic scale. Science 278, 680–686 ( 1997).

    Article  CAS  Google Scholar 

  4. Southern, E. Mir, K. & Shchepinov, M. Molecular interactions on microarrays. Nature Genet. 21, 5–9 ( 1999).

    Article  CAS  Google Scholar 

  5. Cheung, V.G. et al. Linkage disequilibrium mapping without genotyping. Nature Genet. 18, 225–230 (1998).

    Article  CAS  Google Scholar 

  6. Duggan, D.J., Bittner, M., Chen, Y., Meltzer, P. & Trent, J. Expression profiling using cDNA microarrays. Nature Genet. 21, 10–14 (1999).

    Article  CAS  Google Scholar 

  7. Bowtell, D.L. Options available—from start to finish—for obtaining expression data by microarray. Nature Genet. 21, 25– 32 (1999).

    Article  CAS  Google Scholar 

  8. Church, G.M. & Gilbert, W. Genomic sequencing. Proc. Natl Acad. Sci. USA 81, 1991– 1995 (1983).

    Article  Google Scholar 

  9. Vollrath, D. & Davis, R.W. Resolution of DNA molecules greater than 5 megabases by contour–clamped homogeneous electric fields. Nucl. Acid Res. 15, 7865–7876 (1987).

    Article  CAS  Google Scholar 

  10. Sambrook, J., Fritsch, F. & Maniatis, T. Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Press, Cold Spring Harbor, New York, 1989).

    Google Scholar 

  11. Casey, J. & Davidson, N. Rates of formation and thermal stabilities of RNA:DNA and DNA:DNA duplexes at high concentrations of formamide. Nucl. Acid Res. 4, 1539– 1545 (1977).

    Article  CAS  Google Scholar 

  12. Boguski, M.S. & Schuler, G.D. ESTablishing a human transcript map. Nature Genet. 10, 369– 371 (1995).

    Article  CAS  Google Scholar 

  13. Schuler, G.D. et al. A gene map of the human genome. Science 274, 540–546 (1996).

    Article  CAS  Google Scholar 

  14. Ermoleava, O. et al. Data management and analysis for gene expression arrays. Nature Genet. 20, 19–23 (1998).

    Article  Google Scholar 

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Acknowledgements

The AECOM group is indebted to S. Kneitz, R. Yang, S. Chen and T. Harris for their strenuous efforts towards building our facility. We thank H. Hu, J. Gregg, M. Bittner and P. Brown for stimulating discussions and R. Spielman and A. Bruzel for comments on the manuscript. The work at AECOM was supported by the Human Genetics Program and the Comprehensive Cancer Center at AECOM (NIH CA 13330). Work at the University of Pennsylvania was supported by grants (to V.G.C.) from Merck Genome Research Institute and the NIH (DC00154).

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Authors and Affiliations

  1. Department of Pediatrics, University of Pennsylvania, Philadelphia, 19104, Pennsylvania, USA

    Vivian G. Cheung, Michael Morley & Francisco Aguilar

  2. Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, 10461, New York, USA

    Aldo Massimi, Raju Kucherlapati & Geoffrey Childs

Authors
  1. Vivian G. Cheung
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  2. Michael Morley
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  3. Francisco Aguilar
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  4. Aldo Massimi
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  5. Raju Kucherlapati
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  6. Geoffrey Childs
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Cheung, V., Morley, M., Aguilar, F. et al. Making and reading microarrays. Nat Genet 21 (Suppl 1), 15–19 (1999). https://doi.org/10.1038/4439

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