qPCR Newsletter - April 2012 with focus on RNA integrity, RNA stability, an= d RNA decay ---------------------------------------------------------------------------= -- Dear researcher, dear Gene Quantification page reader, Our newsletter informs about the latest news in quantitative real-time PCR = (qPCR and RT-qPCR), which are compiled and summarised on the Gene Quantification = homepage. The focus of this newsletter http://qPCRnews.gene-quantification.info issu= e is: * RNA integrity, RNA stability, RNA decay - the page describes the importan= ce of RNA and DNA integrity on quantitative qPCR studies - http://RNA-integri= ty.gene-quantification.info * Follow ou new established "GeneQuan Daily NEWS" - a daily updated newslet= ter - http://Daily-News.gene-quantification.info * GenEx - a powerful tool For qPCR data analysis - download a free trial ve= rsion - http://GenEx.gene-quantification.info ---------------------------------------------------------------------------= -- RNA integrity - RNA stability - RNA decay mRNA and microRNA quality control for RT-qPCR analysis Becker C, Hammerle-Fickinger A, Riedmaier I, Pfaffl MW. Methods. 2010 50(4): 237-243 The importance of high quality sample material, i.e. non-degraded or fragme= nted RNA, for classical gene expression profiling is well documented. Hence, the anal= ysis of RNA quality is a valuable tool in the preparation of methods like RT-qPCR a= nd microarray analysis. For verification of RNA integrity, today the use of automated cap= illary electrophoresis is state of the art. Following the recently published MIQE = guidelines, these pre-PCR evaluations have to be clearly documented in scientific publi= cation to increase experimental transparency. RNA quality control may also be inte= grated in the routine analysis of new applications like the investigation of micro= RNA (miRNA) expression, as there is little known yet about factors compromising the miR= NA analysis. Agilent Technologies is offering a new lab-on-chip application for the 2100= Bioanalyzer making it possible to quantify miRNA in absolute amounts (pg) and as a perc= entage of small RNA (%). Recent results showed that this analysis method is strong= ly influenced by total RNA integrity. Ongoing RNA degradation is accompanied by the forma= tion of small RNA fragments leading to an overestimation of miRNA amount on the chi= p. Total RNA integrity is known to affect the performance of RT-qPCR as well as the = quantitative results in mRNA expression profiling. The actual study identified a compara= ble effect for miRNA gene expression profiling. Using a suitable normalization method = could partly reduce the impairing effect of total RNA integrity. You will find more publications on =3D> http://RNA-integrity.gene-quantific= ation.info ---------------------------------------------------------------------------= ----- RNA integrity - RNA stability - RNA decay Evaluation of a novel approach for the measurement of RNA quality. Wilkes TM, Devonshire AS, Ellison SL, Foy CA. BMC Res Notes. 2010 3:89. Combined expression of miR-122a, miR-1, and miR-200b can differentiate degr= aded RNA samples from liver, pancreas, and stomach. Kim J, Choi NE, Oh SJ, Park SJ, Kim HK. Pathol Int. 2011 Feb;61(2): 67-72 Evaluation of external RNA controls for the standardisation of gene express= ion biomarker measurements. Devonshire AS, Elaswarapu R, Foy CA. BMC Genomics. 2010 11:662. Effects of tissue handling on RNA integrity and microarray measurements fro= m resected breast cancers. Hatzis C, Sun H, Yao H, Hubbard RE, Meric-Bernstam F, Babiera GV, Wu Y, Pus= ztai L, Symmans WF. J Natl Cancer Inst. 2011 Dec 21;103(24):1871-83. Epub 2011 Oct 27. Implementation of a proficiency testing for the assessment of the preanalyt= ical phase of blood samples used for RNA based analysis. G=FCnther K, Malentacchi F, Verderio P, Pizzamiglio S, Ciniselli CM, Tichop= ad A, Kubista M, Wyrich R, Pazzagli M, Gelmini S. Clin Chim Acta. 2012 Apr 11;413(7-8): 779-86 A quantitative assay for measuring mRNA decapping by splinted ligation reve= rse transcription polymerase chain reaction: qSL-RT-PCR. Blewett N, Coller J, Goldstrohm A. RNA. 2011 Mar;17(3): 535-543 How the RNA isolation method can affect microRNA microarray results. Podolska A, Kaczkowski B, Litman T, Fredholm M, Cirera S. Acta Biochim Pol. 2011; 58(4): 535-540 RNA Stability in Human Liver: Comparison of Different Processing Times, Tem= peratures and Methods. Lee SM, Schelcher C, Gashi S, Schreiber S, Thasler RM, Jauch KW, Thasler WE= .. Mol Biotechnol. 2012 Jan 24 Maintaining Breast Cancer Specimen Integrity and Individual or Simultaneous= Extraction of Quality DNA, RNA, and Proteins from Allprotect-Stabilized and Nonstabili= zed Tissue Samples. Blanaid C. Mee, Paul Carroll, Simona Donatello, Elizabeth Connolly, Mairead= Griffin, Barbara Dunne, Louise Burke, Richard Flavin, Hala Rizkalla, Ciara Ryan, Bri= an Hayes, Charles D'Adhemar, Niamh Banville, Nazia Faheem, Cian Muldoon, and Eoin F. = Gaffney Biopreservation and Biobanking. December 2011, 9(4): 389-398 Comparison of RNA extraction methods from biofilm samples of Staphylococcus= epidermidis. Fran=E7a A, Melo LD, Cerca N. BMC Res Notes. 2011 4:572. Nucleic acids from long-term preserved FFPE tissues are suitable for downst= ream analyses. Ludyga N, Gr=FCnwald B, Azimzadeh O, Englert S, H=F6fler H, Tapio S, Aubele= M. Virchows Arch. 2012 Feb;460(2):131-40. Epub 2012 Jan 22. Systematic discovery of structural elements governing stability of mammalia= n messenger RNAs. Goodarzi H, Najafabadi HS, Oikonomou P, Greco TM, Fish L, Salavati R, Crist= ea IM, Tavazoie S. Nature. 2012 Apr 8 An improved method for isolation of RNA from bone. Carter LE, Kilroy G, Gimble JM, Floyd ZE. BMC Biotechnol. 2012 Jan 19;12:5. Determination of RNA degradation by capillary electrophoresis with cyan lig= ht-emitted diode-induced fluorescence. Yang TH, Chang PL J Chromatogr A. 2012 Mar 30 .... ... and much more publications on =3D> http://RNA-integrity.gene-quanti= fication.info ---------------------------------------------------------------------------= -- Follow our new established "GeneQuan Daily NEWS" A daily updated newsletter around Gene Quantification and qPCR - http://D= aily-News.gene-quantification.info ---------------------------------------------------------------------------= -- GenEx 5 - A Powerful Tool For qPCR Data Analysis Download a free trail version here =3D> http://GenEx.gene-quantification.in= fo GenEx is a popular software for qPCR data processing and analysis. Built in= a modular fashion GenEx provides a multitude of functionalities for the qPCR communit= y, ranging from basic data editing and management to advanced cutting-edge data analys= is. View our webpage =3D> http://GenEx.gene-quantification.info Basic data editing and management Arguably the most important part of qPCR experiments is to pre-process the = raw data into shape for subsequent statistical analyses. The pre-processing steps ne= ed to be performed consistently in correct order and with confidence. GenEx Stand= ard=92s streamlined and user-friendly interface ensures mistake-free data handling.= Intuitive and powerful presentation tools allow professional illustrations of even th= e most complex experimental designs. Advanced cutting-edge data analysis When you need more advanced analyses GenEx Enterprise is the product for yo= u. Powerful enough to demonstrate feasibility it often proves sufficient for most users= demands. Current features include parametric and non-parametric statistical tests, P= rincipal Component Analysis, and Artificial Neural Networks. New features are contin= uously added to GenEx with close attention to customers=92 needs. New features Sample handling and samples individual biology often contribute to confound= ing experimental variability. By using the new nested ANOVA feature in GenEx version 5 user = will be able to evaluate variance contributions from each step in the experimental = procedure. With a good knowledge of the variance contributions, an appropriate distrib= ution of experimental replicates can be selected to minimize confounding variance= and maximize the power of the experimental design! For experiments with complex features= , such as for example multifactorial diseases, analytical relationships and classi= fications may not readily be available. The support vector machine feature in the new= version of GenEx is so easy to use that it will make this advanced supervised class= ification method easily available to novice users, while providing access to advanced= parameters for experts. Download a free trail version here =3D> http://GenEx.gene-quantification.in= fo GenEx PDF user guides: NEW ! ! ! * GenEx user guide * GenEx user guide - Exiqon Wizard * GenEx user guide - Roche Wizard ---------------------------------------------------------------------------= -- Please forward this qPCR NEWS http://api.addthis.com/oexchange/0.8/forward= /email/offer?url=3Dhttp://qPCRnews.gene-quantification.info&title=3DJoin+ou= r+monthly+newsletter+on&username=3DqPCR-NEWS&email_template=3D&lng=3Den-us to further scientists and friends who are interested in qPCR ! Best regards, Michael W. Pfaffl responsible Editor of the Gene Quantification Pages If this newsletter is not displayed correctly by your email client, please = use following LINK http://qPCRnews.gene-quantification.info/ ---------------------------------------------------------------------------= -- The qPCR NEWS and the Gene Quantification Pages are educational sites with = the only purpose of facilitating access to qPCR related information on the internet.= The qPCR NEWS and the Gene Quantification Pages are edited by Michael W. Pfaffl. Copyright =A92005-2012 All rights reserved. Any unauthorized use, reproduct= ion, or transfer of this message or its contents, in any medium, is strictly prohib= ited. 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