qPCR Newsletter - April 2012 with focus on RNA integrity, RNA stability, and RNA decay 
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 qPCR Newsletter - April 2012 with focus on RNA integrity, RNA stability, and RNA decay

qPCR Newsletter - April 2012 with focus on RNA integrity, RNA stability, and 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://www.***.com/  issue is:

* RNA integrity, RNA stability, RNA decay - the page describes the importance of
  RNA and DNA integrity on quantitative qPCR studies  -   http://www.***.com/
* Follow ou new established "GeneQuan Daily NEWS" - a daily updated newsletter  -
* GenEx - a powerful tool For qPCR data analysis - download a free trial version
  - http://www.***.com/


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 fragmented RNA,
for classical gene expression profiling is well documented. Hence, the analysis of
RNA quality is a valuable tool in the preparation of methods like RT-qPCR and microarray
analysis. For verification of RNA integrity, today the use of automated capillary
electrophoresis is state of the art. Following the recently published MIQE guidelines,
these pre-PCR evaluations have to be clearly documented in scientific publication
to increase experimental transparency. RNA quality control may also be integrated
in the routine analysis of new applications like the investigation of microRNA (miRNA)
expression, as there is little known yet about factors compromising the miRNA 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 percentage
of small RNA (%). Recent results showed that this analysis method is strongly influenced
by total RNA integrity. Ongoing RNA degradation is accompanied by the formation of
small RNA fragments leading to an overestimation of miRNA amount on the chip. 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 comparable 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 => http://www.***.com/


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 degraded 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 expression biomarker
Devonshire AS, Elaswarapu R, Foy CA.
BMC Genomics. 2010 11:662.

Effects of tissue handling on RNA integrity and microarray measurements from resected
{*filter*} cancers.
Hatzis C, Sun H, Yao H, Hubbard RE, Meric-Bernstam F, Babiera GV, Wu Y, Pusztai 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 preanalytical phase
of {*filter*} samples used for RNA based analysis.
Gnther K, Malentacchi F, Verderio P, Pizzamiglio S, Ciniselli CM, Tichopad 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 reverse 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, Temperatures
and Methods.
Lee SM, Schelcher C, Gashi S, Schreiber S, Thasler RM, Jauch KW, Thasler WE.
Mol Biotechnol. 2012 Jan 24

Maintaining {*filter*} Cancer Specimen Integrity and Individual or Simultaneous Extraction
of Quality DNA, RNA, and Proteins from Allprotect-Stabilized and Nonstabilized Tissue
Blanaid C. Mee, Paul Carroll, Simona Donatello, Elizabeth Connolly, Mairead Griffin,
Barbara Dunne, Louise Burke, Richard Flavin, Hala Rizkalla, Ciara Ryan, Brian 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?a A, Melo LD, Cerca N.
BMC Res Notes. 2011 4:572.

Nucleic acids from long-term preserved FFPE tissues are suitable for downstream analyses.
Ludyga N, Grnwald B, Azimzadeh O, Englert S, H?fler 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 mammalian messenger
Goodarzi H, Najafabadi HS, Oikonomou P, Greco TM, Fish L, Salavati R, Cristea 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 light-emitted
diode-induced fluorescence.
Yang TH, Chang PL
J Chromatogr A. 2012 Mar 30

... ... and much more publications on => http://www.***.com/


Follow our new established "GeneQuan Daily NEWS"
A daily updated newsletter around Gene Quantification and qPCR  -   http://www.***.com/


GenEx 5 -  A Powerful Tool For qPCR Data Analysis
Download a free trail version here => http://www.***.com/

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 community, ranging
from basic data editing and management to advanced cutting-edge data analysis. View
our webpage => http://www.***.com/

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 need to
be performed consistently in correct order and with confidence. GenEx Standards
streamlined and user-friendly interface ensures mistake-free data handling. Intuitive
and powerful presentation tools allow professional illustrations of even the most
complex experimental designs.

Advanced cutting-edge data analysis
When you need more advanced analyses GenEx Enterprise is the product for you. Powerful
enough to demonstrate feasibility it often proves sufficient for most users demands.
Current features include parametric and non-parametric statistical tests, Principal
Component Analysis, and Artificial Neural Networks. New features are continuously
added to GenEx with close attention to customers needs.

New features
Sample handling and samples individual biology often contribute to confounding 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 distribution
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 classifications
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 classification
method easily available to novice users, while providing access to advanced parameters
for experts.

Download a free trail version here => http://www.***.com/

GenEx PDF user guides:     NEW ! ! !

* GenEx user guide
* GenEx user guide - Exiqon Wizard
* GenEx user guide - Roche Wizard


Please forward this qPCR NEWS   http://www.***.com/ ://q...
to further scientists and friends who are interested in qPCR !

Best regards,
Michael W. Pfaffl
responsible Editor of the Gene Quantification Pages

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