Characterization of the effect of sample quality on high density oligonucleotide microarray data using progressively degraded rat liver RNA

[1]  A. Kohlmann,et al.  Intraplatform reproducibility and technical precision of gene expression profiling in 4 laboratories investigating 160 leukemia samples: the DACH study. , 2008, Clinical chemistry.

[2]  D. K. Willis,et al.  Evaluation of isolation methods and RNA integrity for bacterial RNA quantitation. , 2008, Journal of microbiological methods.

[3]  S. Weis,et al.  Quality control for microarray analysis of human brain samples: The impact of postmortem factors, RNA characteristics, and histopathology , 2007, Journal of Neuroscience Methods.

[4]  M. Fernö,et al.  An improved genetic system for detection and analysis of protein nuclear import signals. , 2007 .

[5]  P. Mazière,et al.  Impact of RNA degradation on gene expression profiles: assessment of different methods to reliably determine RNA quality. , 2007, Journal of biotechnology.

[6]  T Haferlach,et al.  Consensus guidelines for microarray gene expression analyses in leukemia from three European leukemia networks , 2006, Leukemia.

[7]  James M. Olson,et al.  Assessment of the relationship between pre-chip and post-chip quality measures for Affymetrix GeneChip expression data , 2006, BMC Bioinformatics.

[8]  Chris T. A. Evelo,et al.  Biologically relevant effects of mRNA amplification on gene expression profiles , 2006, BMC Bioinformatics.

[9]  Michael W Pfaffl,et al.  RNA integrity and the effect on the real-time qRT-PCR performance. , 2006, Molecular aspects of medicine.

[10]  Rafael A Irizarry,et al.  Analysis of Affymetrix GeneChip data using amplified RNA. , 2006, BioTechniques.

[11]  Thomas Ragg,et al.  The RIN: an RNA integrity number for assigning integrity values to RNA measurements , 2006, BMC Molecular Biology.

[12]  James C. Fuscoe,et al.  Use of a mixed tissue RNA design for performance assessments on multiple microarray formats , 2005, Nucleic acids research.

[13]  Kellie J Archer,et al.  Assessing quality of hybridized RNA in Affymetrix GeneChip experiments using mixed-effects models. , 2005, Biostatistics.

[14]  E. Wang.  RNA amplification for successful gene profiling analysis , 2005, Journal of Translational Medicine.

[15]  Frank Speleman,et al.  Impact of RNA quality on reference gene expression stability. , 2005, BioTechniques.

[16]  Juan F Medrano,et al.  Real-time PCR for mRNA quantitation. , 2005, BioTechniques.

[17]  S A Bustin,et al.  Quantitative real-time RT-PCR--a perspective. , 2005, Journal of molecular endocrinology.

[18]  D. Finkelstein,et al.  Trends in the quality of data from 5168 oligonucleotide microarrays from a single facility. , 2005, Journal of biomolecular techniques : JBT.

[19]  Charles Auffray,et al.  Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces , 2005, Nucleic acids research.

[20]  H. Ikeda,et al.  Differential modulation of gene expression among rat tissues with warm ischemia. , 2004, Experimental and molecular pathology.

[21]  Kellie J Archer,et al.  Evaluation of quality-control criteria for microarray gene expression analysis. , 2004, Clinical chemistry.

[22]  Tania Nolan,et al.  Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction. , 2004, Journal of biomolecular techniques : JBT.

[23]  G. Karypis,et al.  Expression levels for many genes in human peripheral blood cells are highly sensitive to ex vivo incubation , 2004, Genes and Immunity.

[24]  M. Hellmich,et al.  Comparison of different isolation techniques prior gene expression profiling of blood derived cells: impact on physiological responses, on overall expression and the role of different cell types , 2004, The Pharmacogenomics Journal.

[25]  R. Yolken,et al.  Evaluating RNA status for RT-PCR in extracts of postmortem human brain tissue. , 2004, BioTechniques.

[26]  Andrea Didier,et al.  Inhibition of Real-time Rt –pcr Quantification Due to Tissue-specific Contaminants , 2003 .

[27]  Hans-Georg Rammensee,et al.  Moderate degradation does not preclude microarray analysis of small amounts of RNA. , 2003, BioTechniques.

[28]  M. Pfaffl,et al.  Standardized determination of real-time PCR efficiency from a single reaction set-up. , 2003, Nucleic acids research.

[29]  Tzachi Bar,et al.  Kinetic Outlier Detection (KOD) in real-time PCR. , 2003, Nucleic acids research.

[30]  Brad T. Sherman,et al.  DAVID: Database for Annotation, Visualization, and Integrated Discovery , 2003, Genome Biology.

[31]  Karl Kornacker,et al.  Chipping away at the chip bias: RNA degradation in microarray analysis , 2003, Nature Genetics.

[32]  J. Warrington,et al.  Accurate and reproducible gene expression profiles from laser capture microdissection, transcript amplification, and high density oligonucleotide microarray analysis. , 2003, The Journal of molecular diagnostics : JMD.

[33]  J. McClintick,et al.  Reproducibility of oligonucleotide arrays using small samples , 2003, BMC Genomics.

[34]  A. Kimura,et al.  Degradation profile of mRNA in a dead rat body: basic semi-quantification study. , 2002, Forensic science international.

[35]  Michael W. Pfaffl,et al.  Improving quantitative real-time RT-PCR reproducibility by boosting primer-linked amplification efficiency , 2002, Biotechnology Letters.

[36]  Wei-Min Liu,et al.  Analysis of high density expression microarrays with signed-rank call algorithms , 2002, Bioinform..

[37]  H Phillip Koeffler,et al.  Myelodysplastic Bone Marrow Cells from Normal and + Characterization of Gene Expression of Cd34 , 2002 .

[38]  Ronglai Shen,et al.  Changes in differential gene expression because of warm ischemia time of radical prostatectomy specimens. , 2002, The American journal of pathology.

[39]  S A Bustin,et al.  Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems. , 2002, Journal of molecular endocrinology.

[40]  Thomas D. Schmittgen,et al.  Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. , 2001, Methods.

[41]  M. Pfaffl,et al.  A new mathematical model for relative quantification in real-time RT-PCR. , 2001, Nucleic acids research.

[42]  S. Peltz,et al.  The cap-to-tail guide to mRNA turnover , 2001, Nature Reviews Molecular Cell Biology.

[43]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[44]  Nigel Mackman,et al.  Egr-1, a master switch coordinating upregulation of divergent gene families underlying ischemic stress , 2000, Nature Medicine.

[45]  J. Geiger,et al.  Recovery of high-integrity mRNA from brains of rats killed by high-energy focused microwave irradiation. , 1999, Brain research. Brain research protocols.

[46]  M. Brown,et al.  mRNA quantification by real time TaqMan polymerase chain reaction: validation and comparison with RNase protection. , 1999, Analytical biochemistry.

[47]  V. Singer,et al.  RNA quantitation by fluorescence-based solution assay: RiboGreen reagent characterization. , 1998, Analytical biochemistry.

[48]  Z. Kote-Jarai,et al.  Ribonucleases from rat and bovine liver: purification, specificity and structural characterization. , 1998, Biochimica et biophysica acta.

[49]  I G Wilson,et al.  Inhibition and facilitation of nucleic acid amplification , 1997, Applied and environmental microbiology.

[50]  K. Manchester.  Use of UV methods for measurement of protein and nucleic acid concentrations. , 1996, BioTechniques.

[51]  C. Y. Chen,et al.  AU-rich elements: characterization and importance in mRNA degradation. , 1995, Trends in biochemical sciences.

[52]  A. Nylander,et al.  RNA extraction from gastrointestinal tract and pancreas by a modified Chomczynski and Sacchi method. , 1995, BioTechniques.

[53]  L. Raeymaekers,et al.  Quantitative PCR: theoretical considerations with practical implications. , 1993, Analytical biochemistry.

[54]  K. Holmstrøm,et al.  Inhibition of PCR by components of food samples, microbial diagnostic assays and DNA-extraction solutions. , 1992, International journal of food microbiology.

[55]  J. Eberwine,et al.  Amplified RNA synthesized from limited quantities of heterogeneous cDNA. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[56]  I. Purvis,et al.  The relationship between mRNA stability and length in Saccharomyces cerevisiae. , 1986, Nucleic acids research.

[57]  A. Wollenberger,et al.  Improvements in the ethidium bromide method for direct fluorometric estimation of DNA and RNA in cell and tissue homogenates. , 1977, Analytical biochemistry.

[58]  C. Paoletti,et al.  A new fluorometric method for RNA and DNA determination. , 1966, Analytical biochemistry.

[59]  M. Pfaffl.  NUCLEIC ACIDS | mRNA Identification and Quantification , 2005 .

[60]  G. Schroth,et al.  The whole story of quantitative PCR – from Tissue Preparation to BioInformatics , 2005 .

[61]  O. Mueller,et al.  RNA Integrity Number ( RIN ) – Standardization of RNA Quality Control Application , 2004 .

[62]  V. Marx.  RNA Quality : Defining the Good , the Bad , & the Ugly by Vivien Marx , 2004 .

[63]  Guidel Ines,et al.  Expression profiling — best practices for data generation and interpretation in clinical trials , 2004, Nature Reviews Genetics.

[64]  Array Design and Performance of the GeneChip ® Rat Expression Set 230 , 2003 .

[65]  S. Lightfoot,et al.  Quantitation comparison of total RNA using the Agilent , 2002 .

[66]  D. Ilsley,et al.  A microfluidic system for high‐speed reproducible DNA sizing and quantitation , 2000, Electrophoresis.