Chapter 4. High-Throughput and Industrial Methods for mRNA Expression Analysis

  1. Dr. Stefan Lorkowski41 and
  2. Dr. Paul Cullen42
  1. Dr. Paul Cullen42,*,
  2. Dr. Stefan Lorkowski41,*,
  3. Oliver Bauer1,
  4. Anna Guerasimova1,
  5. Hans Lehrach1,
  6. Michal Janitz1,
  7. Ralf Herwig1,
  8. Uwe Radelof2,
  9. Wanda Panter3,*,
  10. Jennifer Harrington3,
  11. Gerhard Lorkowski4,
  12. Alon Amit5,*,
  13. Ralf Bickel6,*,
  14. Annette Wagenhaus6,
  15. Eugen Ermantraut6,
  16. Gerd Wagner6,
  17. Ines Leube6,
  18. Jana Sachtschal6,
  19. Ralf Ehricht6,
  20. Thomas Ellinger6,
  21. Zhijian J. Chen7,
  22. Kenneth D. Tew7,*,
  23. Laurent Gate7,
  24. Warren Davis Jr.7,
  25. Hermann Lübbert8,
  26. Jeffrey S. Fisher9,
  27. Jamie Walden9,
  28. Jonathan Meade9,
  29. Peng Liang10,*,
  30. Zhen Guo9,
  31. Richard A. Shimkets11,
  32. Kousaku Okubo12,*,
  33. Shoko Kawamoto13,
  34. Jill M. Ray14,
  35. Michael C. MacLeod15,*,
  36. Brian S. Hilbush16,
  37. David Lo16,*,
  38. J. Gregor Sutcliffe17,
  39. Lianggui Chen16,
  40. Rick Woychik18,*,
  41. Glenn Albrecht18,
  42. Kevin Corcoran18,
  43. Norrie Russell18,
  44. Sydney Brenner18,
  45. Tim Burcham18,
  46. Vivian de Waard19,
  47. Anton-Jan van Zonneveld19,
  48. Hans Pannekoek20,*,
  49. Nicholas J. Beauchamp20,
  50. Nicole A. Datson22,*,
  51. Erno Vreugdenhil21,
  52. Jo-Ann L. Stanton23,
  53. David P. L. Green23,*,
  54. Jean-Marc Elalouf24,* and
  55. Dominic G. Spinella25

Published Online: 27 MAY 2004

DOI: 10.1002/352760149X.ch4

Analysing Gene Expression: A Handbook of Methods: Possibilities and Pitfalls

Analysing Gene Expression: A Handbook of Methods: Possibilities and Pitfalls

How to Cite

Cullen, P., Lorkowski, S., Bauer, O., Guerasimova, A., Lehrach, H., Janitz, M., Herwig, R., Radelof, U., Panter, W., Harrington, J., Lorkowski, G., Amit, A., Bickel, R., Wagenhaus, A., Ermantraut, E., Wagner, G., Leube, I., Sachtschal, J., Ehricht, R., Ellinger, T., Chen, Z. J., Tew, K. D., Gate, L., Davis, W., Lübbert, H., Fisher, J. S., Walden, J., Meade, J., Liang, P., Guo, Z., Shimkets, R. A., Okubo, K., Kawamoto, S., Ray, J. M., MacLeod, M. C., Hilbush, B. S., Lo, D., Sutcliffe, J. G., Chen, L., Woychik, R., Albrecht, G., Corcoran, K., Russell, N., Brenner, S., Burcham, T., de Waard, V., van Zonneveld, A.-J., Pannekoek, H., Beauchamp, N. J., Datson, N. A., Vreugdenhil, E., Stanton, J.-A. L., Green, D. P. L., Elalouf, J.-M. and Spinella, D. G. (2002) High-Throughput and Industrial Methods for mRNA Expression Analysis, in Analysing Gene Expression: A Handbook of Methods: Possibilities and Pitfalls (eds S. Lorkowski and P. Cullen), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, FRG. doi: 10.1002/352760149X.ch4

Editor Information

  1. 41

    Institute of Arteriosclerosis Research, University of Münster, Domagkstr. 3, 48149 Münster, Germany

  2. 42

    Ogham GmbH, Mendelstr. 11, 48149 Münster, Germany

Author Information

  1. 1

    Max Planck Institut für Molekulare Genetik, Berlin (Germany)

  2. 2

    Deutsches Ressourcenzentrum für Genomforschung GmbH, Berlin (Germany)

  3. 3

    R&D Systems, Inc., Minneapolis, MS (USA)

  4. 4

    Pharma Consulting, Münster (Germany)

  5. 5

    Compugen Ltd., Jamesburg (USA)

  6. 6

    Clondiag Chip Technologies GmbH, Jena (Germany)

  7. 7

    Fox Chase Cancer Center, Philadelphia (USA)

  8. 8

    Biofrontera Pharmaceuticals AG, Leverkusen (Germany)

  9. 9

    GenHunter Corporation, Nashville (USA)

  10. 10

    Vanderbilt University, Nashville (USA)

  11. 11

    CuraGen Corporation, Branford (USA)

  12. 12

    Kyushu University, Fukuoka (Japan)

  13. 13

    Medical Institute for Bioregulation, Fukuoka (Japan)

  14. 14

    Capital Genomix, Inc., Gaithersburg (USA)

  15. 15

    University of Texas, Smithville (USA)

  16. 16

    Digital Gene Technologies, Inc., La Jolla (USA)

  17. 17

    The Scripps Research Institute, La Jolla (USA)

  18. 18

    Lynx Therapeutics, Inc., Hayward (USA)

  19. 19

    Academic Medical Center, University of Amsterdam, Amsterdam (The Netherlands)

  20. 20

    University of Amsterdam, Amsterdam (The Netherlands)

  21. 21

    Leiden University Medical Centre, Leiden (The Netherlands)

  22. 22

    Leiden/Amsterdam Center for Drug Research, Leiden University Medical Centre, Leiden (The Netherlands)

  23. 23

    University of Otago, Dunedin (New Zealand)

  24. 24

    Commisariat á l'Ènergie Atomique (CEA) Saclay, Gif-sur-Yvette (France)

  25. 25

    Chugai Biopharmaceuticals, Inc., San Diego (USA)

  26. 41

    Institute of Arteriosclerosis Research, University of Münster, Domagkstr. 3, 48149 Münster, Germany

  27. 42

    Ogham GmbH, Mendelstr. 11, 48149 Münster, Germany

*Ogham GmbH, Mendelstr. 11, 48149 Münster, Germany

Publication History

  1. Published Online: 27 MAY 2004
  2. Published Print: 1 DEC 2002

ISBN Information

Print ISBN: 9783527304882

Online ISBN: 9783527601493

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Keywords:

  • mRNA expression analysis;
  • high-throughput and industrial methods;
  • hybridisation-based techniques;
  • DNA microarrays;
  • oligonucleotide fingerprinting;
  • nucleic acids labelling and detection;
  • PCR-based techniques;
  • sequencing-based techniques;
  • serial analysis

Summary

This chapter contains sections titled:

  • Introduction

  • Hybridisation-based techniques

    • DNA microarrays

    • OFP – Oligonucleotide fingerprinting

    • Quantikine® mRNA assay

  • PCR-based techniques

    • ADGE – Amplified differential gene expression

    • DEPD® – Digital expression pattern display

    • FDD – Automated fluorescent mRNA differential display

    • GeneCalling

    • iAFLP – Introduced amplified fragment length polymorphism

    • RAGE – Rapid analysis of gene expression

    • READSTM – Restriction enzyme analysis of differential sequences

    • TOGA – Total gene expression analysis

  • Sequencing-based techniques

    • MPSSTM – Massively parallel signature sequencing

    • SAGE – Serial analysis of gene expression

    • MicroSAGE

    • MiniSAGE

    • ORESTES – Open reading frame expressed sequence tags

    • PCR-SAGE and SAGE-Lite

    • SADE – SAGE adaption for downsized extracts

    • TALEST – Tandem arrayed ligation of expressed sequence tags

  • Summary

  • References