mRNA Applications

  • Fatih Ozsolak
  • Veronica Luzzi
  • Mark A. Watson
Part of the Principles and Practice book series (PRINCIPLES)


Laser Capture Microdissection FFPE Tissue Fresh Freeze Tissue Label cRNA Human Clinical Specimen 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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  1. Alevizos I, Mahadevappa M, Zhang X, Ohyama H, Kohno Y, Posner M, Gallagher GT, Varvares M, Cohen D, Kim D, Kent R, Donoff RB, Todd R, Yung CM, Warrington JA, Wong DT (2001) Oral cancer in vivo gene expression profiling assisted by laser capture microdissection and microarray analysis. Oncogene 20:6196–6204CrossRefPubMedGoogle Scholar
  2. Bustin SA (2002) Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems. J Mol Endocrinol 29:23–39CrossRefPubMedGoogle Scholar
  3. Chiang MK, Melton DA (2003) Single-cell transcript analysis of pancreas development. Dev Cell 4:383–393CrossRefPubMedGoogle Scholar
  4. Coombs NJ, Gough AC, Primrose JN (1999) Optimisation of DNA and RNA extraction from archival formalin-fixed tissue. Nucleic Acids Res 27:e12CrossRefPubMedGoogle Scholar
  5. Godfrey TE, Kim SH, Chavira M, Ruff DW, Warren RS, Gray JW, Jensen RH (2000) Quantitative mRNA expression analysis from formalin-fixed, paraffin-embedded tissues using 5′ nuclease quantitative reverse transcription-polymerase chain reaction. J Mol Diagn 2:84–91PubMedGoogle Scholar
  6. Hamalainen HK, Tubman JC, Vikman S, Kyrola T, Ylikoski E, Warrington JA, Lahesmaa R (2001) Identification and validation of endogenous reference genes for expression profiling of T helper cell differentiation by quantitative real-time RT-PCR. Anal Biochem 299:63–70CrossRefPubMedGoogle Scholar
  7. Huang E, Cheng SH, Dressman H, Pittman J, Tsou MH, Horng CF, Bild A, Iversen ES, Liao M, Chen CM, West M, Nevins JR, Huang AT (2003) Gene expression predictors of breast cancer outcomes. Lancet 361:1590–1596CrossRefPubMedGoogle Scholar
  8. Huang LE, Luzzi V, Ehrig T, Holtschlag V, Watson MA (2002) Optimized tissue processing and staining for laser capture microdissection and nucleic acid retrieval. Methods Enzymol 356:49–62PubMedGoogle Scholar
  9. Iscove NN, Barbara M, Gu M, Gibson M, Modi C, Winegarden N (2002) Representation is faithfully preserved in global cDNA amplified exponentially from sub-pi-cogram quantities of mRNA. Nat Biotechnol 20:940–943CrossRefPubMedGoogle Scholar
  10. Kabbarah O, Pinto K, Mutch DG, Goodfellow PJ (2003) Expression profiling of mouse endometrial cancers microdissected from ethanol-fixed, paraffin-embedded tissues. Am J Pathol 162:755–762PubMedGoogle Scholar
  11. Karsten SL, Van Deerlin VM, Sabatti C, Gill LH, Geschwind DH (2002) An evaluation of tyramide signal amplification and archived fixed and frozen tissue in microarray gene expression analysis. Nucleic Acids Res 30:E4CrossRefPubMedGoogle Scholar
  12. Korbler T, Grskovic M, Dominis M, Antica M (2003) A simple method for RNA isolation from formalin-fixed and paraffin-embedded lymphatic tissues. Exp Mol Pathol 74:336–340CrossRefPubMedGoogle Scholar
  13. Krafft AE, Duncan BW, Bijwaard KE, Taubenberger JK, Lichy JH (1997) Optimization of the isolation and amplification of RNA from formalin-fixed, paraffin-embedded tissue: the Armed Forces Institute of Pathology Experience and Literature Review. Mol Diagn 2:217–230PubMedGoogle Scholar
  14. Leethanakul C, Patel V, Gillespie J, Pallente M, Ensley JF, Koontongkaew S, Liotta LA, Emmert-Buck M, Gutkind JS (2000) Distinct pattern of expression of differentiation and growth-related genes in squamous cell carcinomas of the head and neck revealed by the use of laser capture microdissection and cDNA arrays. Oncogene 19:3220–3224CrossRefPubMedGoogle Scholar
  15. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 25:402–408CrossRefPubMedGoogle Scholar
  16. Luzzi V, Holtschlag V, Watson MA (2001) Expression profiling of ductal carcinoma in situ by laser capture microdissection and high-density oligonucleotide arrays. Am J Pathol 158:2005–2010PubMedGoogle Scholar
  17. Luzzi V, Mahadevappa M, Raja R, Warrington JA, Watson MA (2003) Accurate and reproducible gene expression profiles from laser capture microdissection, transcript amplification, and high density oligonucleotide microarray analysis. J Mol Diagn 5:9–14PubMedGoogle Scholar
  18. Ma XJ, Salunga R, Tuggle JT, Gaudet J, Enright E, McQuary P, Payette T, Pistone M, Stecker K, Zhang BM, Zhou YX, Varnholt H, Smith B, Gadd M, Chatfield E, Kessler J, Baer TM, Erlander MG, Sgroi DC (2003) Gene expression profiles of human breast cancer progression. Proc Natl Acad Sci USA 100:5974–5979PubMedGoogle Scholar
  19. Macabeo-Ong M, Ginzinger DG, Dekker N, McMillan A, Regezi JA, Wong DT, Jordan RC ((2002) Effect of duration of fixation on quantitative reverse transcription polymerase chain reaction analyses. Mod Pathol 15:979–987CrossRefPubMedGoogle Scholar
  20. Masuda N, Ohnishi T, Kawamoto S, Monden M, Okubo K (1999) Analysis of chemical modification of RNA from formalin-fixed samples and optimization of molecular biology applications for such samples. Nucleic Acids Res 27:4436–4443CrossRefPubMedGoogle Scholar
  21. Morrison TB, Weis JJ, Wittwer CT (1998) Quantification of low-copy transcripts by continuous SYBR Green I monitoring during amplification. Biotechniques 24:954–958PubMedGoogle Scholar
  22. Specht K, Richter T, Muller U, Walch A, Werner M, Hofler H (2001) Quantitative gene expression analysis in microdissected archival formalin-fixed and paraffin-embedded tumor tissue. Am J Pathol 158:419–429PubMedGoogle Scholar
  23. Stuart JM, Segal E, Roller D, Kim SK (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science 302:249–255CrossRefPubMedGoogle Scholar
  24. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3:RE-SEARCH0034Google Scholar
  25. Van Gelder RN, von Zastrow ME, Yool A, Dement WC, Barchas JD, Eberwine JH (1990) Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc Natl Acad Sci USA 87:1663–1667PubMedGoogle Scholar

Copyright information

© Springer Berlin Heidelberg 2005

Authors and Affiliations

  • Fatih Ozsolak
  • Veronica Luzzi
  • Mark A. Watson

There are no affiliations available

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