Skip to main content

DNA Microarrays for Gene Expression Analysis in Brain Tissue and Cell Lines

  • Protocol
  • First Online:
Expression Profiling in Neuroscience

Part of the book series: Neuromethods ((NM,volume 64))

Abstract

Microarray expression profiling of the nervous system provides a powerful approach to ascribe activities to genes involved in distinct phases of neural development and function. Expression profiling of neural tissues and cell lines requires isolation of high-quality RNA, amplification of the isolated RNA, and hybridization to DNA microarrays. In this chapter, theoretical background for expression profiling as well as protocols for reproducible microarray experiments from brain tissue and cell lines derived from brain tissue will be presented in the context of neural proliferation and tumorigenesis in the cerebellum.

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

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Wechsler-Reya, R. J., and Scott, M. P. (1999) Control of neuronal precursor proliferation in the cerebellum by Sonic Hedgehog, Neuron 22, 103–114.

    Article  PubMed  CAS  Google Scholar 

  2. Kenney, A. M., Cole, M. D., and Rowitch, D. H. (2003) Nmyc upregulation by sonic hedgehog signaling promotes proliferation in developing cerebellar granule neuron precursors, Development (Cambridge, England) 130, 15–28.

    Google Scholar 

  3. Knoepfler, P. S., Cheng, P. F., and Eisenman, R. N. (2002) N-myc is essential during neurogenesis for the rapid expansion of progenitor cell populations and the inhibition of neuronal differentiation, Genes & development 16, 2699–2712.

    Article  CAS  Google Scholar 

  4. Oliver, T. G., Grasfeder, L. L., Carroll, A. L., Kaiser, C., Gillingham, C. L., Lin, S. M., Wickramasinghe, R., Scott, M. P., and Wechsler-Reya, R. J. (2003) Transcriptional profiling of the Sonic hedgehog response: a critical role for N-myc in proliferation of neuronal precursors, Proceedings of the National Academy of Sciences of the United States of America 100, 7331–7336.

    Article  PubMed  CAS  Google Scholar 

  5. Ingham, P. W., and McMahon, A. P. (2001) Hedgehog signaling in animal development: paradigms and principles, Genes & development 15, 3059–3087.

    Article  CAS  Google Scholar 

  6. McNeil, D. E., Coté, T. R., Clegg, L., and Rorke, L. B. (2002) Incidence and trends in pediatric malignancies medulloblastoma/primitive neuroectodermal tumor: A SEER update, 39, 190–194.

    Google Scholar 

  7. Wechsler-Reya, R., and Scott, M. P. (2001) The developmental biology of brain tumors, Annual review of neuroscience 24, 385–428.

    Article  PubMed  CAS  Google Scholar 

  8. Brian, R. R., Tobey, J. M., and Roger, J. P. (2004) Current treatment of medulloblastoma: Recent advances and future challenges, Seminars in oncology 31, 666–675.

    Article  Google Scholar 

  9. Yun, J. S., Rust, J. M., Ishimaru, T., and Diaz, E. (2007) A novel role of the Mad family member Mad3 in cerebellar granule neuron precursor proliferation, Mol Cell Biol. 27, 8178–89

    Article  PubMed  CAS  Google Scholar 

  10. Hurlin, P. J., Queva, C., Koskinen, P. J., Steing-rimsson, E., Ayer, D. E., Copeland, N. G., Jenkins, N. A., and Eisenman, R. N. (1995) Mad3 and Mad4: novel Max-interacting transcriptional repressors that suppress c-myc dependent transformation and are expressed during neural and epidermal differentiation, The EMBO journal 14, 5646–5659.

    PubMed  CAS  Google Scholar 

  11. Goodrich, L. V., Milenkovic, L., Higgins, K. M., and Scott, M. P. (1997) Altered neural cell fates and medulloblastoma in mouse patched mutants, Science (New York, N.Y 277, 1109–1113.

    Google Scholar 

  12. Barisone, G. A., Yun, J. S., and Diaz, E. (2008) From cerebellar proliferation to tumorigenesis: new insights into the role of Mad3, Cell cycle (Georgetown, Tex 7, 423–427.

    Google Scholar 

  13. Van Gelder, R. N., von Zastrow, M. E., Yool, A., Dement, W. C., Barchas, J. D., and Eberwine, J. H. (1990) Amplified RNA synthesized from limited quantities of heterogeneous cDNA, Proceedings of the National Academy of Sciences of the United States of America 87, 1663–1667.

    Article  PubMed  Google Scholar 

Download references

Acknowledgments

This work was supported by grants to E. D. from the Alfred P. Sloan Research Foundation, the James S. McDonnell Foundation Twenty-first Century Award Program, the UC Davis Health System Research Award Program, an individual allocation of the UC Davis Institutional Research Grant from the American Cancer Society, a Career Development Award from the UCSF Brain Tumor SPORE Program, and a NIH Director’s New Innovator Award. G. A. B. was supported in part by a postdoctoral fellowship from the California Institute of Regenerative Medicine.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Elva Díaz .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Barisone, G.A., Díaz, E. (2012). DNA Microarrays for Gene Expression Analysis in Brain Tissue and Cell Lines. In: Karamanos, Y. (eds) Expression Profiling in Neuroscience. Neuromethods, vol 64. Humana Press. https://doi.org/10.1007/978-1-61779-448-3_1

Download citation

  • DOI: https://doi.org/10.1007/978-1-61779-448-3_1

  • Published:

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-447-6

  • Online ISBN: 978-1-61779-448-3

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics