Chapter 3. Methods for Analysing mRNA Expression

  1. Dr. Stefan Lorkowski56 and
  2. Dr. Paul Cullen57
  1. Dr. Stefan Lorkowski56,*,
  2. Dr. Paul Cullen57,*,
  3. Sebastian Horstmann1,
  4. Beate Hess2,
  5. Claus Langer3,
  6. Udo Seedorf3,
  7. Rahul V. Gopalkrishnan4,
  8. Devanand Sarkar4,
  9. Dong-Chul Kang4,
  10. Frank Sivo4,
  11. Irina V. Lebedeva4,
  12. Magdalena Leszczyniecka5,
  13. Moira Sauane4,
  14. Neil I. Goldstein6,
  15. Paul B. Fisher4,*,
  16. Zao-Zhong Su4,
  17. Carsten Gerdemann7,
  18. Anne Sherwood8,
  19. Gobinda Sarkar9,*,
  20. Kunbo Zhang9,
  21. Mark E. Bolander9,
  22. Jian-Hua Luo10,*,
  23. Yan Ping Yu10,*,
  24. Katrin Stolle3,
  25. Zhou Wang11,*,
  26. Donald D. Brown13,
  27. Yuxun Wang12,
  28. Arthur J. Sytkowski14,*,
  29. David J. Volsky15,
  30. Hongping Jiang16,
  31. Lucas D. Bowler17,
  32. Annabelle Bouchardon18,
  33. Colette Dehay18,
  34. Daniel J. Lavery19,
  35. Karl J. Lackner20,
  36. Thomas Roeder21,*,
  37. Iris Bruchhaus22,
  38. Benoît Kornmann23,
  39. Daniele Rifat23,
  40. Nicolas Preitner23,
  41. Ueli Schibler23,*,
  42. Stephen A. Bustin24,
  43. Kim Theilgaard-Mönch25,*,
  44. Thomas Rasmussen26,
  45. Michael Schnoor3,
  46. Kikuya Kato27,
  47. Christian W. B. Bachem28,*,
  48. Asun Fernandes del Carmen28,
  49. Richard G. F. Visser28,
  50. Cruz A. Hinojos29,
  51. Peter A. Doris30,
  52. Sergey V. Shmelkov31,
  53. Alexander V. Belyavsky32,*,
  54. Michael P. Starkey33,
  55. Harin Mahadeva34,
  56. Sabine Bahn35,
  57. Chihiro Uematsu36,*,
  58. Fumihito Miura37,
  59. Hideki Kambara38,
  60. Junko Nishida38,
  61. Kazunori Okano38,
  62. Takashi Ito39,
  63. Yoshiyuki Sakaki40,
  64. Mikhail V. Matz41 and
  65. Sachihiko Watanabe42

Published Online: 27 MAY 2004

DOI: 10.1002/352760149X.ch3

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

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

How to Cite

Lorkowski, S., Cullen, P., Horstmann, S., Hess, B., Langer, C., Seedorf, U., Gopalkrishnan, R. V., Sarkar, D., Kang, D.-C., Sivo, F., Lebedeva, I. V., Leszczyniecka, M., Sauane, M., Goldstein, N. I., Fisher, P. B., Su, Z.-Z., Gerdemann, C., Sherwood, A., Sarkar, G., Zhang, K., Bolander, M. E., Luo, J.-H., Yu, Y. P., Stolle, K., Wang, Z., Brown, D. D., Wang, Y., Sytkowski, A. J., Volsky, D. J., Jiang, H., Bowler, L. D., Bouchardon, A., Dehay, C., Lavery, D. J., Lackner, K. J., Roeder, T., Bruchhaus, I., Kornmann, B., Rifat, D., Preitner, N., Schibler, U., Bustin, S. A., Theilgaard-Mönch, K., Rasmussen, T., Schnoor, M., Kato, K., Bachem, C. W. B., del Carmen, A. F., Visser, R. G. F., Hinojos, C. A., Doris, P. A., Shmelkov, S. V., Belyavsky, A. V., Starkey, M. P., Mahadeva, H., Bahn, S., Uematsu, C., Miura, F., Kambara, H., Nishida, J., Okano, K., Ito, T., Sakaki, Y., Matz, M. V. and Watanabe, S. (2002) Methods for Analysing mRNA Expression, 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.ch3

Editor Information

  1. 56

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

  2. 57

    Ogham GmbH, Mendelstr. 11, 48149 Münster, Germany

Author Information

  1. 1

    University of Cologne, Cologne (Germany)

  2. 2

    Würzburg (Germany)

  3. 3

    University of Münster, Münster (Germany)

  4. 4

    Columbia University, New York (USA)

  5. 5

    Novartis Pharmaceuticals, Summit (USA)

  6. 6

    DGI Biotechnologies, Inc., Edison (USA)

  7. 7

    Abbott GmbH, Wiesbaden (Germany)

  8. 8

    Inbios International, Inc., Seattle (USA)

  9. 9

    Mayo Clinic and Foundation, Rochester (USA)

  10. 10

    School of Medicine, University of Pittsburgh, Pittsburgh (USA)

  11. 11

    Feinberg School of Medicine, Northwestern University, Chicago (USA)

  12. 12

    Beth Israel Deaconess Medical Center, Harvard Medical School, Boston (USA)

  13. 13

    Carnegie Institution of Washington, Baltimore (USA)

  14. 14

    Harvard Medical School, Boston (USA)

  15. 15

    St. Luke's-Roosevelt Hospital Center, Columbia University, New York (USA)

  16. 16

    Medco Health Solutions, Inc., New Jersey (USA)

  17. 17

    Trafford Centre for Medical Research, Brighton (UK)

  18. 18

    INSERM U371 “Cerveau et Vision”, Bron (France)

  19. 19

    Purdue Pharma L.P., Cranbury (USA)

  20. 20

    University Hospital Mainz, Mainz (Germany)

  21. 21

    University of Würzburg, Würzburg (Germany)

  22. 22

    Bernhard-Nocht-Institut Für Tropenmedizin, Hamburg (Germany)

  23. 23

    University of Geneva, Geneva (Switzerland)

  24. 24

    Queen Mary's School of Medicine and Dentistry, Royal London Hospital, London (UK)

  25. 25

    Rigshospitalet, Copenhagen (Denmark)

  26. 26

    University of Copenhagen, Copenhagen (Denmark)

  27. 27

    Nara Institute of Science and Technology, Nara (Japan)

  28. 28

    Wageningen University and Research Centre (The Netherlands)

  29. 29

    University of Texas-Houston, Health Sciences Center, Houston (USA)

  30. 30

    Houston Health Sciences Center, Houston (USA)

  31. 31

    Weill Medical College of Cornell University, New York (USA)

  32. 32

    Engelhardt Institute of Molecular Biology, Moscow (Russia)

  33. 33

    Human Genome Mapping Project Resource Centre, Wellcome Trust Genome Campus, Hinxton (UK)

  34. 34

    University of Leicester, Leicester (UK)

  35. 35

    Babraham Institute, Cambridge (UK)

  36. 36

    Central Research Laboratory, Hitachi Ltd., Tokyo (Japan)

  37. 37

    Kanazawa University, Ishikawa (Japan)

  38. 38

    Hitachi Ltd., Tokyo (Japan)

  39. 39

    Cancer Research Institute, Kanazawa University, Ishikawa (Japan)

  40. 40

    University of Tokyo, Tokyo (Japan)

  41. 41

    University of Florida, St. Augustine (USA)

  42. 42

    Genomic Sciences Center, Yokohama Institute, Yokohama (Japan)

  43. 56

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

  44. 57

    Ogham GmbH, Mendelstr. 11, 48149 Münster, Germany

*Institute of Arteriosclerosis Research, University of Münster, Domagkstr. 3, 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;
  • methods;
  • hybridisation-based methods;
  • branched DNA assay;
  • Northern blot;
  • nuclear run-on assay;
  • subtractive hybridisation;
  • multiplexed analysis;
  • PCR-based methods;
  • restriction landmark cDNA scanning;
  • RNA patterns method

Summary

This chapter contains sections titled:

  • Introduction

  • Hybridisation-based methods

    • Branched DNA assay

    • Northern blot and related techniques

    • Nuclear run-on assay

    • Subtractive hybridisation

    • Multiplexed DNA and RNA analysis on fluorescent microbeads

    • RPA – Ribonuclease protection assay

    • Virtual Northern blot

  • PCR-based methods

    • ADDER – Amplification of double-stranded cDNA end restriction fragments

    • ATAC-PCR – Adapter-tagged competitive PCR

    • cDNA-AFLP – cDNA-based amplified-fragment length polymorphism fingerprinting

    • Competitive RT-PCR

    • GEF – Gene expression fingerprinting

    • IBDD – Indexing-based differential display

    • Molecular indexing of 3′-cDNA ends

    • MSP-PCR – Multiplex PCR using colour-tagged module-shuffling primers

    • ODD – Ordered differential display

    • PACS – Preferential amplification of coding sequences

    • RAP-PCR – RNA arbitrarily primed PCR fingerprinting

    • Real-time reverse transcription polymerase chain reaction

    • RD-PCR – Restriction display polymerase chain reaction

    • SIP RT-PCR

    • Targeted display

  • Further methods for analysing gene expression based on other principles

    • RLCS – Restriction landmark cDNA scanning

    • RNA patterns method

  • Summary and conclusions

  • References