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Food and Drug Administration1, GE Healthcare2, Thermo Fisher Scientific3, Illumina4, Agilent Technologies5, National Institutes of Health6, Applied Biosystems7, University of Toledo8, Stratagene9, United States Environmental Protection Agency10, University of Massachusetts Boston11, Clinical Data, Inc12, University of California, Los Angeles13, SAS Institute14, Biogen Idec15, Yale University16, Cold Spring Harbor Laboratory17, Discovery Institute18, Stanford University19, Harvard University20, Vanderbilt University21, University of Texas at Dallas22, University of Oslo23, Novartis24, University of Texas MD Anderson Cancer Center25, Luminex Corporation26, Wake Forest University27, University of Illinois at Urbana–Champaign28
TL;DR: This study describes the experimental design and probe mapping efforts behind the MicroArray Quality Control project and shows intraplatform consistency across test sites as well as a high level of interplatform concordance in terms of genes identified as differentially expressed.
Abstract: Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, has raised concerns about the reliability of this technology. The MicroArray Quality Control (MAQC) project was initiated to address these concerns, as well as other performance and data analysis issues. Expression data on four titration pools from two distinct reference RNA samples were generated at multiple test sites using a variety of microarray-based and alternative technology platforms. Here we describe the experimental design and probe mapping efforts behind the MAQC project. We show intraplatform consistency across test sites as well as a high level of interplatform concordance in terms of genes identified as differentially expressed. This study provides a resource that represents an important first step toward establishing a framework for the use of microarrays in clinical and regulatory settings.
1,987 citations
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TL;DR: A novel bacteriophage lambda vector system was used to express in Escherichia coli a combinatorial library of Fab fragments of the mouse antibody repertoire, which allows rapid and easy identification of monoclonal Fab fragments in a form suitable for genetic manipulation.
Abstract: A novel bacteriophage lambda vector system was used to express in Escherichia coli a combinatorial library of Fab fragments of the mouse antibody repertoire. The system allows rapid and easy identification of monoclonal Fab fragments in a form suitable for genetic manipulation. It was possible to generate, in 2 weeks, large numbers of monoclonal Fab fragments against a transition state analog hapten. The methods described may supersede present-day hybridoma technology and facilitate the production of catalytic and other antibodies.
1,816 citations
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TL;DR: A lambda insertion type cDNA cloning vector, Lambda ZAP, has been constructed in this article, which eliminates the need to subclone DNA inserts from the lambda phage into a plasmid by restriction digestion and ligation.
Abstract: A lambda insertion type cDNA cloning vector, Lambda ZAP, has been constructed. In E. coli a phagemid, pBluescript SK(-), contained within the vector, can be excised by f1 or M13 helper phage. The excision process eliminates the need to subclone DNA inserts from the lambda phage into a plasmid by restriction digestion and ligation. This is possible because Lambda ZAP incorporates the signals for both initiation and termination of DNA synthesis from the f1 bacteriophage origin of replication (1). Six of 21 restriction sites in the excised pBluescript SK polylinker, contained within the NH2-portion of the lacZ gene, are unique in lambda ZAP. Coding sequences inserted into these restriction sites, in the appropriate reading frame, can be expressed from the lacZ promoter as fusion proteins. The features of this vector significantly increase the rate at which clones can be isolated and analyzed. The lambda ZAP vector was tested by the preparation of a chicken liver cDNA library and the isolation of actin clones by screening with oligonucleotide probes. Putative actin clones were excised from the lambda vector and identified by DNA sequencing. The ability of lambda ZAP to serve as a vector for the construction of cDNA expression libraries was determined by detecting fusion proteins from clones containing glucocerbrosidase cDNA's using rabbit IgG anti-glucocerbrosidase antibodies.
1,321 citations
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TL;DR: An increase in error rate with pH has also been noted for the exonuclease-deficient DNA polymerases Taq and exo- Klenow, suggesting that the parameters which influence replication error rates may be similar in pol l- and alpha-like polymerases.
Abstract: The replication fidelities of Pfu, Taq, Vent, Deep Vent and UlTma DNA polymerases were compared using a PCR-based forward mutation assay. Average error rates (mutation frequency/bp/duplication) increased as follows: Pfu (1.3 · 10 ‐6 ) < Deep Vent (2.7 · 10 ‐6 ) < Vent (2.8 · 10 ‐6 ) < Taq (8.0 · 10 ‐6 ) << exo ‐ Pfu and UlTma (~5 · 10 ‐5 ). Buffer optimization experiments indicated that Pfu fidelity was highest in the presence of 2‐3 mM MgSO4 and 100‐300 μM each dNTP and at pH 8.5‐9.1. Under these conditions, the error rate of exo ‐ Pfu was ~40-fold higher (5 · 10 ‐5 ) than the error rate of Pfu. As the reaction pH was raised from pH 8 to 9, the error rate of Pfu decreased ~2-fold, while the error rate of exo ‐ Pfu increased ~9-fold. An increase in error rate with pH has also been noted for the exonucleasedeficient DNA polymerases Taq and exo ‐ Klenow, suggesting that the parameters which influence replication error rates may be similar in pol I- and α-like polymerases. Finally, the fidelity of ‘long PCR’ DNA polymerase mixtures was examined. The error rates of a Taq/Pfu DNA polymerase mixture and a Klentaq/Pfu DNA polymerase mixture were found to be less than the error rate of Taq DNA polymerase, but ~3‐4-fold higher than the error rate of Pfu DNA polymerase.
780 citations
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TL;DR: These studies demonstrate that the error rate per nucleotide induced in the 182 known detectable sites of the lacI gene was 1.6 x 10(-6) for Pfu DNA polymerase, a greater than tenfold improvement over the 2.0 x 10 (-5) error rate for Taq DNA polymerases.
685 citations
Authors
Showing all 161 results
Name | H-index | Papers | Citations |
---|---|---|---|
Ronald W. Davis | 155 | 644 | 151276 |
Michael Wigler | 113 | 298 | 63159 |
Michael McClelland | 79 | 372 | 27627 |
Jay M. Short | 41 | 66 | 13812 |
Joseph A. Sorge | 29 | 85 | 3981 |
Michael P. Weiner | 28 | 51 | 14127 |
Quinn Lu | 21 | 43 | 1955 |
John Welsh | 20 | 27 | 8075 |
Joseph A. Sorge | 15 | 36 | 2593 |
Bahram Arezi | 12 | 18 | 561 |
Eric J. Mathur | 12 | 59 | 1023 |
Natalia Novoradovskaya | 10 | 24 | 2527 |
Holly H. Hogrefe | 10 | 15 | 525 |
Jeffrey C. Braman | 10 | 16 | 1084 |
Patricia L. Kretz | 8 | 11 | 1155 |