Nucleic Acids Research, 1994, Vol. 22, No. 25 5640-5648
© 1994
Articles |
Identifying differences in mRNA expression by representational difference analysis of cDNA
Section of Immunobiology, Howard Hughes Medical Institute, Yale University School of Medicine 310 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA
*To whom correspondence should be addressed
Received September 2, 1994. Revised November 12, 1994. Accepted November 12, 1994.
Detection of differentially regulated genes has been severely hampered by technical limitations. In an effort to overcome these problems, the PCR-coupled subtractlve process of representational difference analysis (RDA) [Lisitsyn,N. et al. (1993) Science 259, 946-951] has been adapted for use with cDNA. In a model system, RAG-1 and RAG-2, the genes responsible for activating V(D)J recombination, were identified in a genomic transfectant by cDNA RDA In a small fraction of the time taken by conventional means. The system was also modified to eliminate expected difference products to facilitate the identification of novel genes. Additional alterations to the conditions allowed isolation of differentially expressed fragments. Several caffeine up-regulated clones were obtained from the pre-B cell line 1-8, Including IGF-1B, and a predicted homologue of the natural killer cell antigen, NKR-P1. The approach was found to be fast, extremely sensitive, reproducible, and predominantly lacked false positives. cDNA RDA has the capacity and adaptability to be applied to a wide range of biological problems, including the study of single gene disorders, characterization of mutant and complemented cell types, developmental or post-event expression time courses, and examination of pathogen - host interactions.
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R. HUANG, T. WU, L. XU, A. LIU, Y. JI, and G. HU Upstream binding factor up-regulated in hepatocellular carcinoma is related to the survival and cisplatin-sensitivity of cancer cells FASEB J, March 1, 2002; 16(3): 293 - 301. [Abstract] [Full Text] [PDF]
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J. Y. Choi, C. D. Sifri, B. C. Goumnerov, L. G. Rahme, F. M. Ausubel, and S. B. Calderwood Identification of Virulence Genes in a Pathogenic Strain of Pseudomonas aeruginosa by Representational Difference Analysis J. Bacteriol., February 15, 2002; 184(4): 952 - 961. [Abstract] [Full Text] [PDF]
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I. R. Adams and A. McLaren Sexually dimorphic development of mouse primordial germ cells: switching from oogenesis to spermatogenesis Development, January 3, 2002; 129(5): 1155 - 1164. [Abstract] [Full Text] [PDF]
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 G. A. Boorman, S. P. Anderson, W. M. Casey, R. H. Brown, L. M. Crosby, K. Gottschalk, M. Easton, Hong Ni, and K. T. Morgan Toxicogenomics, Drug Discovery, and the Pathologist Toxicol Pathol, January 1, 2002; 30(1): 15 - 27. [Abstract] [PDF]
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R. A. Sturm, K. Satyamoorthy, F. Meier, B. B. Gardiner, D. J. Smit, B. Vaidya, and M. Herlyn Osteonectin/SPARC Induction by Ectopic {beta}3 Integrin in Human Radial Growth Phase Primary Melanoma Cells Cancer Res., January 1, 2002; 62(1): 226 - 232. [Abstract] [Full Text] [PDF]
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 D. Haase, M. H. Lehmann, M. M. Korner, R. Korfer, H. H. Sigusch, and H. R. Figulla Identification and validation of selective upregulation of ventricular myosin light chain type 2 mRNA in idiopathic dilated cardiomyopathy Eur J Heart Fail, January 1, 2002; 4(1): 23 - 31. [Abstract] [Full Text] [PDF]
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J. E. Prescott, R. C. Osthus, L. A. Lee, B. C. Lewis, H. Shim, J. F. Barrett, Q. Guo, A. L. Hawkins, C. A. Griffin, and C. V. Dang A Novel c-Myc-responsive Gene, JPO1, Participates in Neoplastic Transformation J. Biol. Chem., December 14, 2001; 276(51): 48276 - 48284. [Abstract] [Full Text] [PDF]
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 M. Pontoglio, M. Pausa, A. Doyen, B. Viollet, M. Yaniv, and F. Tedesco Hepatocyte Nuclear Factor 1{alpha} Controls the Expression of Terminal Complement Genes J. Exp. Med., December 3, 2001; 194(11): 1683 - 1690. [Abstract] [Full Text] [PDF]
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J. W. Rooney and K. L. Calame TIF1beta functions as a coactivator for C/EBPbeta and is required for induced differentiation in the myelomonocytic cell line U937 Genes & Dev., November 15, 2001; 15(22): 3023 - 3038. [Abstract] [Full Text] [PDF]
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S. M. Tanner, J. L. Austin, G. Leone, L. J. Rush, C. Plass, K. Heinonen, K. Mrozek, H. Sill, S. Knuutila, J. E. Kolitz, et al. BAALC, the human member of a novel mammalian neuroectoderm gene lineage, is implicated in hematopoiesis and acute leukemia PNAS, November 9, 2001; (2001) 241525498. [Abstract] [Full Text] [PDF]
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A. M. Owyang, J. R. Tumang, B. R. Schram, C. Y. Hsia, T. W. Behrens, T. L. Rothstein, and H.-C. Liou c-Rel Is Required for the Protection of B Cells from Antigen Receptor-Mediated, But Not Fas-Mediated, Apoptosis J. Immunol., November 1, 2001; 167(9): 4948 - 4956. [Abstract] [Full Text] [PDF]
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I. Caminschi, K. M. Lucas, M. A. O'Keeffe, H. Hochrein, Y. Laabi, F. Kontgen, A. M. Lew, K. Shortman, and M. D. Wright Molecular Cloning of F4/80-Like-Receptor, a Seven-Span Membrane Protein Expressed Differentially by Dendritic Cell and Monocyte-Macrophage Subpopulations J. Immunol., October 1, 2001; 167(7): 3570 - 3576. [Abstract] [Full Text] [PDF]
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K.-K. Hwang, J. C. Eissenberg, and H. J. Worman Transcriptional repression of euchromatic genes by Drosophila heterochromatin protein 1 and histone modifiers PNAS, September 13, 2001; (2001) 211303598. [Abstract] [Full Text] [PDF]
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J. Dang, T. Inukai, H. Kurosawa, K. Goi, T. Inaba, N. T. Lenny, J. R. Downing, S. Stifani, and A. T. Look The E2A-HLF Oncoprotein Activates Groucho-Related Genes and Suppresses Runx1 Mol. Cell. Biol., September 1, 2001; 21(17): 5935 - 5945. [Abstract] [Full Text] [PDF]
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 M.-S. Li, I. M. Monahan, S. J. Waddell, J. A. Mangan, S. L. Martin, M. J. Everett, and P. D. Butcher cDNA-RNA subtractive hybridization reveals increased expression of mycocerosic acid synthase in intracellular Mycobacterium bovis BCG Microbiology, August 1, 2001; 147(8): 2293 - 2305. [Abstract] [Full Text] [PDF]
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 P. Becker, W. Hufnagle, G. Peters, and M. Herrmann Detection of Differential Gene Expression in Biofilm-Forming versus Planktonic Populations of Staphylococcus aureus Using Micro-Representational-Difference Analysis Appl. Envir. Microbiol., July 1, 2001; 67(7): 2958 - 2965. [Abstract] [Full Text] [PDF]
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Y. Zhang, B. D. Price, S. Tetradis, S. Chakrabarti, G. Maulik, and G. M. Makrigiorgos Reproducible and inexpensive probe preparation for oligonucleotide arrays Nucleic Acids Res., July 1, 2001; 29(13): e66 - e66. [Abstract] [Full Text] [PDF]
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S. Hayashida-Hibino, H. Watanabe, K. Nishida, M. Tsujikawa, T. Tanaka, Y. Hori, Y. Saishin, and Y. Tano The Effect of TGF-{beta}1 on Differential Gene Expression Profiles in Human Corneal Epithelium Studied by cDNA Expression Array Invest. Ophthalmol. Vis. Sci., July 1, 2001; 42(8): 1691 - 1697. [Abstract] [Full Text] [PDF]
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 I. Morlais and D. W. Severson Identification of a Polymorphic Mucin-like Gene Expressed in the Midgut of the Mosquito, Aedes aegypti, Using an Integrated Bulked Segregant and Differential Display Analysis Genetics, July 1, 2001; 158(3): 1125 - 1136. [Abstract] [Full Text] [PDF]
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L. M. Johansen, A. Iwama, T. A. Lodie, K. Sasaki, D. W. Felsher, T. R. Golub, and D. G. Tenen c-Myc Is a Critical Target for C/EBP{alpha} in Granulopoiesis Mol. Cell. Biol., June 1, 2001; 21(11): 3789 - 3806. [Abstract] [Full Text]
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S. Nishizuka, H. Tsujimoto, and E. J. Stanbridge Detection of Differentially Expressed Genes in HeLa Fibroblast Hybrids Using Subtractive Suppression Hybridization Cancer Res., June 1, 2001; 61(11): 4536 - 4540. [Abstract] [Full Text] [PDF]
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Z. J. Chen, H. Shen, and K. D. Tew Gene expression profiling using a novel method: amplified differential gene expression (ADGE) Nucleic Acids Res., May 15, 2001; 29(10): e46 - e46. [Abstract] [Full Text] [PDF]
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G. Schaefer, C. Venkataraman, and U. Schindler Cutting Edge: FISP (IL-4-Induced Secreted Protein), a Novel Cytokine-Like Molecule Secreted by Th2 Cells J. Immunol., May 15, 2001; 166(10): 5859 - 5863. [Abstract] [Full Text] [PDF]
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 A. G. DiLella, T. J. Toner, C. P. Austin, and B. M. Connolly Identification of Genes Differentially Expressed in Benign Prostatic Hyperplasia J. Histochem. Cytochem., May 1, 2001; 49(5): 669 - 670. [Abstract] [Full Text]
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 M. Frohme, A. A. Camargo, C. Czink, A. Y. Matsukuma, A. J.G. Simpson, J. D. Hoheisel, and S. Verjovski-Almeida Directed Gap Closure in Large-Scale Sequencing Projects Genome Res., May 1, 2001; 11(5): 901 - 903. [Abstract] [Full Text]
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 S Shinozaki, T Nakamura, M Iimura, Y Kato, B Iizuka, M Kobayashi, and N Hayashi Upregulation of Reg 1{alpha} and GW112 in the epithelium of inflamed colonic mucosa Gut, May 1, 2001; 48(5): 623 - 629. [Abstract] [Full Text] [PDF]
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 R. Wu and Y. Chen Fishing for inflammatory cytokine-inducible genes with an old trick Am J Physiol Lung Cell Mol Physiol, May 1, 2001; 280(5): L839 - L840. [Full Text] [PDF]
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P. Cooper, S. Potter, B. Mueck, S. Yousefi, and G. Jarai Identification of genes induced by inflammatory cytokines in airway epithelium Am J Physiol Lung Cell Mol Physiol, May 1, 2001; 280(5): L841 - L852. [Abstract] [Full Text] [PDF]
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F. Diehl, S. Grahlmann, M. Beier, and J. D. Hoheisel Manufacturing DNA microarrays of high spot homogeneity and reduced background signal Nucleic Acids Res., April 1, 2001; 29(7): e38 - e38. [Abstract] [Full Text] [PDF]
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