An alternative method to amplify RNA without loss of signal conservation for expression analysis with a proteinase DNA microarray in the Array Tube® format

BMC Genomics

Volumn 7, Issue , 2006, Pages

  Schüler, Susann ^a   Wenz, Ingrid ^a   Wiederanders, B ^a   Slickers, Piet ^b   Ehricht, Ralf ^b  

^a JENA UNIVERSITY HOSPITAL   (Germany)

^b Clondiag Chip Technologies GmbH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; OLIGOMER; PROTEINASE; RNA;

ARTICLE; CELL FUNCTION; COMPUTER PROGRAM; CONSERVATION GENETICS; CONTROLLED STUDY; DIAGNOSTIC PROCEDURE; DNA MICROARRAY; ECONOMIC ASPECT; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; GENETIC TRANSCRIPTION; GENOME; HUMAN; HUMAN CELL; INTERMETHOD COMPARISON; LABORATORY APPARATUS, EQUIPMENT AND SUPPLIES; MOLECULAR GENETICS; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA HYBRIDIZATION; TUMOR BIOPSY;

CELLS, CULTURED; COMPUTER SYSTEMS; DNA PRIMERS; DNA PROBES; GENE EXPRESSION PROFILING; HUMANS; MICROARRAY ANALYSIS; NUCLEIC ACID AMPLIFICATION TECHNIQUES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PEPTIDE HYDROLASES; POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; STAINING AND LABELING;

EID: 33746593686     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-7-144     Document Type: Article

References (30)

1. Sternlicht MD, Werb Z: How matrix metalloproteinases regulate cell behavior. Annu Rev Cell Dev Biol 2001, 17:463-516.
2. John A, Tuszynski G: The role of matrix metalloproteinases in tumor angiogenesis and tumor metastasis. Pathol Oncol Res 2001, 7(1):14-23.
3. Mignatti P, Rifkin DB: Biology and biochemistry of proteinases in tumor invasion. Physiol Rev 1993, 73(1):161-195.
4. Ala-Aho R, Kahari VM: Collagenases in cancer. Biochimie 2005, 87(3-4):273-286.
5. Duffy MJ: Cellular oncogenes and suppressor genes as prognostic markers in cancer. Clin Biochem 1993, 26(6):439-447.
6. Fuchs T, Allgayer H: Transcriptional regulation of the urokinase receptor (u-PAR) - a central molecule of invasion and metastasis. Biol Chem 2003, 384(5):755-761.
7. Werle B, Kotzsch M, Lah TT, Kos J, Gabrijelcic-Geiger D, Spiess E, Schirren J, Ebert W, Fiehn W, Luther T, Magdolen V, Schmitt M, Harbeck N: Cathepsin B, plasminogenactivator-inhibitor (PAI-1) and plasminogenactivator-receptor (uPAR) are prognostic factors for patients with non-small cell lung cancer. Anticancer Res 2004, 24(6):4147-4161.
8. Jedeszko C, Sloane BF: Cysteine cathepsins in human cancer. Biol Chem 2004, 385(11):1017-1027.
9. Smolen JS, Steiner G: Therapeutic strategies for rheumatoid arthritis. Nat Rev Drug Discov 2003, 2(6):473-488.
10. Heller MJ: DNA microarray technology: devices, systems, and applications. Annu Rev Biomed Eng 2002, 4:129-153.
11. Sachse K, Hotzel H, Slickers P, Ellinger T, Ehricht R: DNA microarray-based detection and identification of Chlamydia and Chlamydophila spp. Mol Cell Probes 2005, 19(1):41-50.
12. Korczak B, Frey J, Schrenzel J, Pluschke G, Pfister R, Ehricht R, Kuhnert P: Use of diagnostic microarrays for determination of virulence gene patterns of Escherichia coli K1, a major cause of neonatal meningitis. J Clin Microbiol 2005, 43(3):1024-1031.
13. Perreten V, Vorlet-Fawer L, Slickers P, Ehricht R, Kuhnert P, Frey J: Microarray-based detection of 90 antibiotic resistance genes of gram-positive bacteria. J Clin Microbiol 2005, 43(5):2291-2302.
14. Monecke S ER: Rapid genotyping of methicillin resistant Staphylococcus aureus isolates using miniaturised oligonucleotide arrays. Clin Microbiol Infect 2005, 11:825-33.
15. Overall CM, Tam EM, Kappelhoff R, Connor A, Ewart T, Morrison CJ, Puente X, Lopez-Otin C, Seth A: Protease degradomics: mass spectrometry discovery of protease substrates and the CLIP-CHIP, a dedicated DNA microarray of all human proteases and inhibitors. Biol Chem 2004, 385(6):493-504.
16. Smith L, Underhill P, Pritchard C, Tymowska-Lalanne Z, Abdul-Hussein S, Hilton H, Winchester L, Williams D, Freeman T, Webb S, Greenfield A: Single primer amplification (SPA) of cDNA for microarray expression analysis. Nucleic Acids Res 2003, 31(3):e9.
17. Karsten SL, Van Deerlin VM, Sabatti C, Gill LH, Geschwind DH: An evaluation of tyramide signal amplification and archived fixed and frozen tissue in microarray gene expression analysis. Nucleic Acids Res 2002, 30(2):E4.
18. Cox WG, Singer VL: Fluorescent DNA hybridization probe preparation using amine modification and reactive dye coupling. Biotechniques 2004, 36(1):114-122.
19. Van Gelder RN, von Zastrow ME, Yool A, Dement WC, Barchas JD, Eberwine JH: Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc Natl Acad Sci U S A 1990, 87(5):1663-1667.
20. Petalidis L, Bhattacharyya S, Morris GA, Collins VP, Freeman TC, Lyons PA: Global amplification of mRNA by template-switching PCR: linearity and application to microarray analysis. Nucleic Acids Res 2003, 31(22):e142.
21. Singh R, Maganti RJ, Jabba SV, Wang M, Deng G, Heath JD, Kurn N, Wangemann P: Microarray based comparison of three amplification methods for nanogram amounts of total RNA. Am J Physiol Cell Physiol 2005, 288:C1179-89.
22. Che S, Ginsberg SD: Amplification of RNA transcripts using terminal continuation. Lab Invest 2004, 84(1):131-137.
23. Dozmorov I, Knowlton N, Tang Y, Centola M: Statistical monitoring of weak spots for improvement of normalization and ratio estimates in microarrays. BMC Bioinformatics 2004, 5(1):53.
24. Park PJ, Cao YA, Lee SY, Kim JW, Chang MS, Hart R, Choi S: Current issues for DNA microarrays: platform comparison, double linear amplification, and universal RNA reference. J Biotechnol 2004, 112(3):225-245.
25. Benes V, Muckenthaler M: Standardization of protocols in cDNA microarray analysis. Trends Biochem Sci 2003, 28(5):244-249.
26. Yu J, Othman MI, Farjo R, Zareparsi S, MacNee SP, Yoshida S, Swaroop A: Evaluation and optimization of procedures for target labeling and hybridization of cDNA microarrays. Mol Vis 2002, 8:130-137.
27. Wilson CL, Pepper SD, Hey Y, Miller CJ: Amplification protocols introduce systematic but reproducible errors into gene expression studies. Biotechniques 2004, 36(3):498-506.
28. Livesey FJ: Strategies for microarray analysis of limiting amounts of RNA. Brief Funct Genomic Proteomic 2003, 2(1):31-36.
29. Vecsey-Semjen B, Becker KF, Sinski A, Blennow E, Vietor I, Zatloukal K, Beug H, Wagner E, Huber LA: Novel colon cancer cell lines leading to better understanding of the diversity of respective primary cancers. Oncogene 2002, 21(30):4646-4662.
30. PUBMED Database [http://www.ncbi.nlm.nih.gov/BLAST/]