Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures.

Autor: Munro SA; 1] National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, USA [2] Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, California 94305, USA., Lund SP; National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, USA., Pine PS; 1] National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, USA [2] Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, California 94305, USA., Binder H; Interdisciplinary Centre for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, 04107 Leipzig, Germany., Clevert DA; Institute of Bioinformatics, Johannes Kepler University, Altenberger Str. 69, 4040 Linz, Austria., Conesa A; Computational Genomics Program, Principe Felipe Research Center, Avd Eduardo Primo Yúfera 3, 46012 Valencia, Spain., Dopazo J; 1] Computational Genomics Program, Principe Felipe Research Center, Avd Eduardo Primo Yúfera 3, 46012 Valencia, Spain [2] CIBER de Enfermedades Raras (CIBERER) and Functional Genomics Node, INB., Valencia, Spain., Fasold M; ecSeq Bioinformatics, Brandvorwerkstrasse 43, 04275 Leipzig, Germany., Hochreiter S; Institute of Bioinformatics, Johannes Kepler University, Altenberger Str. 69, 4040 Linz, Austria., Hong H; National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, Arkansas 72079, USA., Jafari N; Genomics Core Facility, Feinberg School of Medicine, Northwestern University, Tarry building 2-757, 300 E. Superior St. Chicago, Illinois 60611, USA., Kreil DP; 1] Chair of Bioinformatics, Boku University Vienna, Muthgasse 18, Vienna 1190, Austria [2] University of Warwick, Coventry CV4 7AL, UK., Łabaj PP; Chair of Bioinformatics, Boku University Vienna, Muthgasse 18, Vienna 1190, Austria., Li S; Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medical College, 1305 York Avenue, Room Y13-04, Box 140, New York, New York 10021, USA., Liao Y; 1] Division of Bioinformatics, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia [2] Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia., Lin SM; Nationwide Children's Hospital, Columbus, Ohio 43205, USA., Meehan J; National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, Arkansas 72079, USA., Mason CE; Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medical College, 1305 York Avenue, Room Y13-04, Box 140, New York, New York 10021, USA., Santoyo-Lopez J; 1] CIBER de Enfermedades Raras (CIBERER) and Functional Genomics Node, INB., Valencia, Spain [2] Medical Genome Project, Genomics and Bioinformatics Platform of Andalusia, c/ Albert Einstein s/n, 41092 Sevilla, Spain., Setterquist RA; Thermo Fisher Scientific, Research &Development, 2170 Woodward Street, Austin, Texas 78744, USA., Shi L; State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University, Shanghai 201203, China., Shi W; 1] Division of Bioinformatics, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia [2] Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria 3010, Australia., Smyth GK; 1] Division of Bioinformatics, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia [2] Department of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria 3010, Australia., Stralis-Pavese N; Chair of Bioinformatics, Boku University Vienna, Muthgasse 18, Vienna 1190, Austria., Su Z; National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, Arkansas 72079, USA., Tong W; National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, Arkansas 72079, USA., Wang C; Division of Microbiology and Molecular Genetics, Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, California 92350, USA., Wang J; Research Informatics, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, USA., Xu J; National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, Arkansas 72079, USA., Ye Z; Biomedical Informatics Research Center, Marshfield Clinic Research Foundation, 1000 N Oak Avenue, Marshfield, Wisconsin 54449, USA., Yang Y; Research Informatics, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, USA., Yu Y; State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University, Shanghai 201203, China., Salit M; 1] National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, USA [2] Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, California 94305, USA.

Publikováno v: Nature communications [Nat Commun] 2014 Sep 25; Vol. 5, pp. 5125. Date of Electronic Publication: 2014 Sep 25.

Improved microarray gene expression profiling of virus-infected cells after removal of viral RNA.

Autor: Raaben M; Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands. m.raaben@uu.nl, Whitley P, Bouwmeester D, Setterquist RA, Rottier PJ, de Haan CA

Publikováno v: BMC genomics [BMC Genomics] 2008 May 14; Vol. 9, pp. 221. Date of Electronic Publication: 2008 May 14.

Using RNA sample titrations to assess microarray platform performance and normalization techniques.

Autor: Shippy R; GE Healthcare, 7700 S. River Pkwy., Suite #2603, Tempe, Arizona 85284, USA. richard.shippy@ge.com, Fulmer-Smentek S, Jensen RV, Jones WD, Wolber PK, Johnson CD, Pine PS, Boysen C, Guo X, Chudin E, Sun YA, Willey JC, Thierry-Mieg J, Thierry-Mieg D, Setterquist RA, Wilson M, Lucas AB, Novoradovskaya N, Papallo A, Turpaz Y, Baker SC, Warrington JA, Shi L, Herman D

Publikováno v: Nature biotechnology [Nat Biotechnol] 2006 Sep; Vol. 24 (9), pp. 1123-31.

Small RNA sequences are readily stabilized by inclusion in a carrier rRNA.

Autor: D'Souza LM; Department of Biology and Biochemistry, University of Houston, 4800 Calhoun Road, Houston, Texas 77204-5513, USA., Larios-Sanz M, Setterquist RA, Willson RC, Fox GE

Publikováno v: Biotechnology progress [Biotechnol Prog] 2003 May-Jun; Vol. 19 (3), pp. 734-8.

Diagnostic probes targeting the major sperm protein gene that may be useful in the molecular identification of nematodes.

Autor: Setterquist RA; Department of Biochemical and Biophysical Sciences, University of Houston, TX 77204-5934, USA., Smith GK, Jones R, Fox GE

Publikováno v: Journal of nematology [J Nematol] 1996 Dec; Vol. 28 (4 Suppl), pp. 414-21.