Nucleic Acids Research, 2003, Vol. 31, No. 24 e154
© 2003 Oxford University Press
Article |
A PCR primer bank for quantitative gene expression analysis
Department of Molecular Biology, Massachusetts General Hospital, 50 Blossom Street, Boston, MA 02114, USA
*To whom correspondence should be addressed. Tel: +1 617 726 5975; Fax: +1 617 726 5962; Email: seed{at}molbio.mgh.harvard.edu
Although gene expression profiling by microarray analysis is a useful tool for assessing global levels of transcriptional activity, variability associated with the data sets usually requires that observed differences be validated by some other method, such as real-time quantitative polymerase chain reaction (real-time PCR). However, non-specific amplification of non-target genes is frequently observed in the latter, confounding the analysis in 
40% of real-time PCR attempts when primer-specific labels are not used. Here we present an experimentally validated algorithm for the identification of transcript-specific PCR primers on a genomic scale that can be applied to real-time PCR with sequence-independent detection methods. An online database, PrimerBank, has been created for researchers to retrieve primer information for their genes of interest. PrimerBank currently contains 147 404 primers encompassing most known human and mouse genes. The primer design algorithm has been tested by conventional and real-time PCR for a subset of 112 primer pairs with a success rate of 98.2%.
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T. Morrison, J. Hurley, J. Garcia, K. Yoder, A. Katz, D. Roberts, J. Cho, T. Kanigan, S. E. Ilyin, D. Horowitz, et al. Nanoliter high throughput quantitative PCR Nucleic Acids Res., October 6, 2006; 34(18): e123 - e123. [Abstract] [Full Text] [PDF]
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D. Lewandowski, M. Marquis, F. Aumont, A.-C. Lussier-Morin, M. Raymond, S. Senechal, Z. Hanna, P. Jolicoeur, and L. de Repentigny Altered CD4+ T Cell Phenotype and Function Determine the Susceptibility to Mucosal Candidiasis in Transgenic Mice Expressing HIV-1 J. Immunol., July 1, 2006; 177(1): 479 - 491. [Abstract] [Full Text] [PDF]
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S. Peddada, D. H. Yasui, and J. M. LaSalle Inhibitors of differentiation (ID1, ID2, ID3 and ID4) genes are neuronal targets of MeCP2 that are elevated in Rett syndrome Hum. Mol. Genet., June 15, 2006; 15(12): 2003 - 2014. [Abstract] [Full Text] [PDF]
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S. C. Martinez, C. Cras-Meneur, E. Bernal-Mizrachi, and M. A. Permutt Glucose Regulates Foxo1 Through Insulin Receptor Signaling in the Pancreatic Islet {beta}-cell Diabetes, June 1, 2006; 55(6): 1581 - 1591. [Abstract] [Full Text] [PDF]
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A. Bosco, K. L. McKenna, C. J. Devitt, M. J. Firth, P. D. Sly, and P. G. Holt Identification of novel th2-associated genes in T memory responses to allergens. J. Immunol., April 15, 2006; 176(8): 4766 - 4777. [Abstract] [Full Text] [PDF]
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L. Lin and S. L. Peng Coordination of NF-{kappa}B and NFAT Antagonism by the Forkhead Transcription Factor Foxd1. J. Immunol., April 15, 2006; 176(8): 4793 - 4803. [Abstract] [Full Text] [PDF]
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K.-H. Chung, C. C. Hart, S. Al-Bassam, A. Avery, J. Taylor, P. D. Patel, A. B. Vojtek, and D. L. Turner Polycistronic RNA polymerase II expression vectors for RNA interference based on BIC/miR-155 Nucleic Acids Res., April 13, 2006; 34(7): e53 - e53. [Abstract] [Full Text] [PDF]
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X. Wang and X. Wang Systematic identification of microRNA functions by combining target prediction and expression profiling Nucleic Acids Res., March 20, 2006; 34(5): 1646 - 1652. [Abstract] [Full Text] [PDF]
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X. Tang, A. Guilherme, A. Chakladar, A. M. Powelka, S. Konda, J. V. Virbasius, S. M. C. Nicoloro, J. Straubhaar, and M. P. Czech An RNA interference-based screen identifies MAP4K4/NIK as a negative regulator of PPAR{gamma}, adipogenesis, and insulin-responsive hexose transport PNAS, February 14, 2006; 103(7): 2087 - 2092. [Abstract] [Full Text] [PDF]
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D. Floryk and E. Huberman Differentiation of Androgen-Independent Prostate Cancer PC-3 Cells Is Associated with Increased Nuclear Factor-{kappa}B Activity Cancer Res., December 15, 2005; 65(24): 11588 - 11596. [Abstract] [Full Text] [PDF]
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A.-M. Lemay and C. K. Haston Bleomycin-induced pulmonary fibrosis susceptibility genes in AcB/BcA recombinant congenic mice Physiol Genomics, September 21, 2005; 23(1): 54 - 61. [Abstract] [Full Text] [PDF]
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D. S. Currle, X. Cheng, C.-m. Hsu, and E. S. Monuki Direct and indirect roles of CNS dorsal midline cells in choroid plexus epithelia formation Development, August 1, 2005; 132(15): 3549 - 3559. [Abstract] [Full Text] [PDF]
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H. Bjorkbacka, K. A. Fitzgerald, F. Huet, X. Li, J. A. Gregory, M. A. Lee, C. M. Ordija, N. E. Dowley, D. T. Golenbock, and M. W. Freeman The induction of macrophage gene expression by LPS predominantly utilizes Myd88-independent signaling cascades Physiol Genomics, February 7, 2005; 19(3): 319 - 330. [Abstract] [Full Text] [PDF]
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