Optimized protocol for linear RNA amplification and application to gene expression profiling of human renal biopsies

BioTechniques

Volumn 34, Issue 3, 2003, Pages 546-556

  Scherer, A ^a,d   Krause, A ^a   Walker, J R ^b   Sutton, S E ^b   Seron D ^c   Raulf, F ^a   Cooke, M P ^b  

^a NOVARTIS PHARMA AG   (Switzerland)

^b GENOMICS INSTITUTE OF THE NOVARTIS RESEARCH FOUNDATION   (United States)

^c HOSPITAL UNIVERSITARI DE BELLVITGE   (Spain)

^d Transplantation Research   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

AMPLIFICATION; BIOLOGICAL ORGANS; BIOPSY; HISTOLOGY; RNA;

TRANSCRIPTOMICS;

GENETIC ENGINEERING;

FRUCTOSE BISPHOSPHATASE; POLYADENYLATED RNA; RNA;

ARTICLE; CHRONIC KIDNEY DISEASE; DNA MICROARRAY; GENE AMPLIFICATION; GENE EXPRESSION; GENETIC TRANSCRIPTION; GRAFT REJECTION; HUMAN; HUMAN CELL; HUMAN TISSUE; KIDNEY ALLOGRAFT; KIDNEY BIOPSY; RNA HYBRIDIZATION; TECHNIQUE;

EID: 0037337914     PISSN: 07366205     EISSN: None     Source Type: Journal    
DOI: 10.2144/03343rr01     Document Type: Article

References (22)

1. Lockhart, D.J. and E.A. Winzeler. 2000. Genomics, gene expression and DNA arrays. Nature 405:827-833.
2. Eberwine, J.H., H. Yeh, K. Miyashiro, Y. Cao, S. Nair, R. Finnell, M. Zettel, and P. Coleman. 1992. Analysis of gene expression in single live neurons. Proc. Natl. Acad. Sci. USA 89:3010-3014.
3. Eberwine, J.H., J.E. Kacharmina, C. Andrews, K. Miyashiro, T. McIntosh, K. Becker, T. Barrett, D. Hinkle, et al. 2001. mRNA expression analysis of tissue sections and single cells. J. Neurosci. 21:8310-8314.
4. Welsh, J.B., L.M. Sapinoso, A.I. Su, S.G. Kern, J. Wang-Rodriguez, C.A. Moskaluk, H.F. Frierson, Jr., and G.M. Hampton. 2001. Analysis of gene expression identifies candidate markers and pharmacological targets in prostate cancer. Cancer Res. 61:5974-5978.
5. Luo, L., R.C. Salunga, H. Guo, A. Bittner, K.C. Joy, J.E. Galindo, H. Xiao, K.E. Rogers, et al. 1999. Gene expression profiles of laser-captured adjacent neuronal subtypes. Nat. Med. 5:117-122.
6. Mariani, T.J., J.J. Reed, and S.D. Shapiro. 2002. Expression profiling of the developing mouse lung: insights into the establishment of the extracellular matrix. Am. J. Respir. Cell Mol. Biol. 26:541-548.
7. Panda, S., J.B. Hogenesch, and S.A. Kay. 2002. Circadian rhythm from flies to human. Nature 417:329-335.
8. Meltzer, P.S. 2001. Spotting the target: microarrays for disease gene discovery. Curr. Opin. Gen. Dev. 11:258-263.
9. Orr, M.S. and U. Scherf. 2002. Large-scale gene expression analysis in molecular target discovery. Leukemia 16:473-477.
10. Affymetrix. 2001. Affymetrix GeneChip® Expression Analysis Technical Protocol. Affymetrix, Palo Alto, CA.
11. Kacharmina, J.E., P.B. Crino, and L.H. Eberwine. 1999. Preparation of cDNA from single cells and subcellular regions. Methods Enzymol. 303:3-18.
12. Saiki, R., T. Bugawan, G. Horn, K. Mullis, and H. Erlich. 1986. Analysis of enzymatically amplified β-globin and HLA-DQ α DNA with allele-specific oligonucleotide probes. Nature 324:163.
13. Van Gelder, R.N., M.E. von Zastrow, A. Yool, W.C. Dement, J.D. Barchas, and J.H. Eberwine. 1990. Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc. Natl. Acad. Sci. USA 87:1663-1667.
14. Jeffreys, A., V. Wilson, R. Neumann, and J. Keyte. 1988. Amplification of human minisatellites by the polymerase chain reaction: towards DNA fingerprinting of single cells. Nucleic Acids Res. 16:10953-10971.
15. Baugh, L.R., E.L. Hill, and C.P. Hunter. 2001. Quantitative analysis of mRNA amplification by in vitro transcription. Nucleic Acids Res. 29:e29.
16. Wang, E., L.D. Miller, G.A. Ohnmacht, E.T. Liu, and F.M. Marincola. 2000. High-fidelity mRNA amplification for gene profiling. Nat. Biotechnol. 18:457-459.
17. Pabón, C., Z. Modrusan, M.V. Ruvolo, I.M. Coleman, S. Daniel, H. Yoe, L.J. Arnold, Jr., and M.A. Reynolds. 2001. Optimized T7 amplification system for microarray analysis. BioTechniques 31:874-879.
18. Serón, D., F. Moreso, J. Bover, E. Condom, S. Gil-Vernet, C. Canas, X. Fulladosa, J. Torras, et al. 1997. Early protocol allograft biopsies and graft outcome. Kidney Int. 51:310-317.
19. Racusen, L.C., K. Solez, R.B. Colvin, S.M. Bonsib, M.C. Castro, T. Cavallo, B.P. Croker, A.J. Demetris, et al. 1999. The BANFF 97 working classification of renal allograft pathology. Kidney Int. 55:713-723.
20. Jindal, R.M. and S. Hariharan. 1999. Chronic rejection in kidney transplants: an indepth review. Nephron 83:13-24.
21. Affymetrix. 2001. Affymetrix Technical Note: Array Design for the GeneChip® Human Genome U133 Set. Affymetrix, Palo Alto, CA.
22. Kinoshita, T. 1991. Biology of complement: the overture. Immunol. Today 12:291-295.