Quantitative analysis of mRNA amplification by in vitro transcription

Nucleic Acids Research

Volumn 29, Issue 5, 2021, Pages

  Baugh, L R ^a   Hill, A A ^b   Brown, E L ^b   Hunter, Craig P ^a  

^a HARVARD UNIVERSITY   (United States)

^b PFIZER INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; COMPLEMENTARY DNA;

ARTICLE; CAENORHABDITIS ELEGANS; CONTROLLED STUDY; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA SYNTHESIS; FLUORESCENCE; FLUOROMETRY; GEL ELECTROPHORESIS; GENE AMPLIFICATION; HYBRIDIZATION; IN VITRO STUDY; MICROARRAY HYBRIDIZATION; MOLECULAR WEIGHT; NATIVE POLYACRYLAMIDE GEL ELECTROPHORESIS; NONHUMAN; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; RNA TRANSCRIPTION; ANIMAL; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

ANIMALS; CAENORHABDITIS ELEGANS; DNA, COMPLEMENTARY; GENE EXPRESSION PROFILING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; TRANSCRIPTION, GENETIC;

MLCS; MLOWN;

EID: 0035293021     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/29.5.e29     Document Type: Article

References (29)

1. De Risi, J.L., Iyer, V.R. and Brown, P.O. (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science, 278, 680-686.
2. Chu, S., De Risi, J., Eisen, M.B., Mulholland, J., Botstein, D., Brown, P.O. and Herskowitz, I. (1998) The transcriptional program of sporulation in budding yeast. Science, 282, 699-705.
3. Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botstein, D. and Futcher, B. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.Mol. Biol. Cell, 9, 3272-3297.
4. Heller, R.A., Schena, M., Chai, A., Shalon, D., Bedilion, T., Gilmore, J., Wooley, D.E. and Davis, R.W. (1997) Discovery and analysis of inflammatory disease-related genes using cDNA microarrays. Proc. Natl Acad. Sci. USA, 94, 2150-2155.
5. Iyer, V.R., Eisen, M.B., Ross, D.T., Schuler, G., Moore, T., Lee, J.C.F., Trent, J.M., Staudt, L.M., Hudson, J., Boguski, M.S. et al. (1999) The transcriptional program in the response of human fibroblasts to serum. Science, 283, 83-87.
6. Roberts, C.J., Nelson, B., Marton, M.J., Stoughton, R., Meyer, M.R., Bennett, H.A., He, Y.D., Dai, H., Walker, W.L., Hughes, T.R. et al. (2000) Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science, 287, 873-880.
7. Hughes, T.R., Marton, M.J., Jones, A.R., Roberts, C.J., Stoughton, R., Armour, C.D., Bennet, H.A., Coffey, E., Dai, H., He, Y.D. et al. (2000) Functional discovery via a compendium of expression profiles. Cell, 102, 109-126.
8. St. Croix, B., Rago, C., Velculesco, V., Traverso, G., Romans, K.E., Montgomery, E., Lal, A., Riggins, G.J., Lengauer, C., Vogelstein, B. and Kinzler, K.W. (2000) Genes expressed in human tumor endothelium. Science, 289, 1197-1202.
9. Young, R.A. (2000) Biomedical discovery with DNA arrays. Cell, 102, 9-15.
10. Lockhart, D.J. and Winzeler, E.A. (2000) Genomics, gene expression and DNA arrays. Nature, 405, 827-836.
11. Wetmur, J.G. and Davidson, N. (1968) Kinetics of renaturation of DNA. J. Mol. Biol., 31, 349-370.
12. Peccoud, J. and Jacob, C. (1996) Theoretical uncertainty of measurements using quantitative polymerase chain reaction. Biophys. J., 71, 101-108.
13. Van Gelder, R.N., von Zastrow, M.E., Yool, A., Dement, W.C., Barchas, J.D. and Eberwine, J.H. (1990) Amplified RNA synthesized from limited quantities of heterogeneous c DNA. Proc. Natl Acad. Sci. USA, 87, 1663-1667.
14. Lockhart, D.J., Dong, H., Byrne, M.C., Follettie, M.T., Gallo, M.V., Chee, M.S., Mittmann, M., Wang, C., Kobayashi, M., Horton, H. and Brown, E.L. (1996) Expression monitoring by hybridization to highdensity oligonucleotide arrays. Nat. Biotechnol., 14, 1675-1680.
15. Mahadevappa, M. and Warrington, J.A. (1999) A high-density probe array sample preparation method using 10-to 100-fold fewer cells. Nat. Biotechnol., 17, 1134-1136.
16. Luo, L., Salunga, R.C., Guo, H., Bittner, A., Joy, K.C., Galindo, J.E., Xiao, H., Rogers, K.E., Wan, J.S., Jackson,.M.R. and Erlander, M.G. (1999) Gene expression profiles of laser-captured adjacent neuronal subtypes. Nature Med., 5, 117-122.
17. Wang, E., Miller, L.D., Ohnmacht, G.A., Liu, E.T. and Marincola, F.M. (2000) High-fidelity mRNA amplification for gene profiling. Nat. Biotechnol., 18, 457-459.
18. Hill, A.A., Hunter, C.P., Tsung, B.T., Tucker-Kellog, G. and Brown, E.L. (2000) Genomic analysis of gene expression in C. elegans. Science, 290, 809-812.
19. Chomczynski, P. and Sacchi, N. (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal. Biochem., 162, 156-159.
20. Gubler, U. and Hoffman, B. (1983) A simple and very efficient method for generating cDNA libraries. Gene, 25, 263-269.
21. De Angelis, M.M., Wang, D.G. and Hawkins, T.L. (1995) Solid-phase reversible immobilization for the isolation of PCR products. Nucleic Acids Res., 22, 4742-4743.
22. Box, G.E.P., Hunter, W.G. and Hunter, J.S. (1978) Statistics for Experimenters. Wiley, New York, NY.
23. Kacharmina, J.E., Crino, P.B. and Eberwine, J. (1999) Preparation of cDNA from single cells and subcellular regions. Methods Enzymol., 303, 3-18.
24. Eberwine, J. (1996) Amplification of mRNA populations using aRNA generated from immobilized oligo(dT)-T7 primed c DNA. Biotechniques, 20, 584-591.
25. Madison, R.D. and Robinson, G.A. (1998) λRNA internal standards quantify sensitivity and amplification efficiency of mammalian gene expression profiling. Biotechniques, 25, 504-514.
26. Rapley, R. (1994) Enhancing PCR amplification and sequencing using DNA-binding proteins. Mol. Biotechnol., 2, 295-298.
27. Ji, X., Klarmann, G.J. and Preston, B.D. (1996) Effect of human immunodeficiency virus type 1 (HIV-1) nucleocapsid protein on HIV-1 reverse transcriptase activity in vitro. Biochemistry, 35, 132-143.
28. Biebricher, C.K. and Luce, R. (1996) Template-free generation of RNA species that replicate with bacteriophage T7 RNA polymerase. EMBO J., 15, 3458-3465.
29. Arnaud-Barbe, N., Cheynet-Sauvion, V., Oriol, G., Mandrand, B. and Mallet, F. (1998) Transcription of RNA templates by T7 RNA polymerase. Nucleic Acids Res., 26, 3550-3554.