Skip to main content
SpringerLink
Log in

Evaluation of hybridization conditions for spotted oligonucleotide-based DNA microarrays

  • Hints And Tips
  • Published:
Molecular Biotechnology Aims and scope Submit manuscript

Abstract

We compared different hybridization conditions of oligonucleotide-based DNA microarray to acquire optimized and reliable microarray data. Several parameters were evaluated at different hybridization conditions, including signal-to-background (S:B) ratios, signal dynamic range, usable spots, and reproducibility. Statistical analysis showed that better results were obtained when spotted, presynthesized long oligonucleotide arrays were blocked with succinic anhydride and hybridized at 42°C in the presence of 50% formamide.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Duggan, D. J., Bittner, M., Chen, Y., et al. (1999) Expression profiling using cDNA microarrays. Nat Genet. 21(1 Suppl), 10–14.

    Article  PubMed  CAS  Google Scholar 

  2. Brown, P. O. and Botstein, D. (1999) Exploring the new world of the genome with DNA microarrays. Nat Genet. 21(1 Suppl), 33–37.

    Article  PubMed  CAS  Google Scholar 

  3. Schena, M., et al. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467–470.

    Article  PubMed  CAS  Google Scholar 

  4. Okamoto, T., Suzuki, T., and Yamamoto, N. (2000) Microarray fabrication with covalent attachment of DNA using bubble jet technology. Nat Biotechnol. 18, 438–441.

    Article  PubMed  CAS  Google Scholar 

  5. Chuang, Y. Y., Chen, Y., Gadisetti, Chandramouli V. R., et al. (2002) Gene expression after treatment with hydrogen peroxide, menadione, or t-butyl hydroperoxide in breast cancer cells. Cancer Res. 62, 6246–6254.

    PubMed  CAS  Google Scholar 

  6. Belosludtsev, Y., Belosludtsev, I., Iverson, B., et al. (2001) DNA microarrays based on noncovalent oligonucleotide attachment and hybridization in two dimensions. Anal Biochem. 292, 250–256.

    Article  PubMed  CAS  Google Scholar 

  7. Eisen, M. B. and Brown, P. O. (1999) DNA arrays for analysis of gene expression. Methods Enzymol. 303, 179–205.

    Article  PubMed  CAS  Google Scholar 

  8. Yang, Y. H., Dudoit, S., Luu, P., et al. (2002) Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30, e15.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Radiation Oncology Sciences Program, Radiation Oncology Branch, Radiation Biology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 8717 Grovemont Cr., Room 109J, 20878, Gaithersburg, MD

    Mong-Hsun Tsai, Hailing Yan, Xi Chen, G. V. R. Chandramouli, Shuping Zhao, Deborah Coffin, C. Norman Coleman, James B. Mitchell & Eric Y. Chuang

Authors
  1. Mong-Hsun Tsai
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hailing Yan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Xi Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. G. V. R. Chandramouli
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Shuping Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Deborah Coffin
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. C. Norman Coleman
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. James B. Mitchell
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Eric Y. Chuang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Eric Y. Chuang.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Tsai, MH., Yan, H., Chen, X. et al. Evaluation of hybridization conditions for spotted oligonucleotide-based DNA microarrays. Mol Biotechnol 29, 221–224 (2005). https://doi.org/10.1385/MB:29:3:221

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1385/MB:29:3:221

Index Entries

Search

Navigation