qPCR Newsletter - April 2012 with focus on RNA integrity

Editor www.Gene-Quantification.info via methods%40net.bio.net (by editor from gene-quantification.info)
Sun Apr 29 03:00:30 EST 2012


qPCR Newsletter - April 2012 with focus on RNA integrity
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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

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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


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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


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Follow our new established "GeneQuan Daily NEWS"
A daily updated newsletter around Gene Quantification and qPCR  -  http://D=
aily-News.gene-quantification.info


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y, ranging
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is. View
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Best regards,
Michael W. Pfaffl
responsible Editor of the Gene Quantification Pages

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