Does anyone know the maker of a heating unit that is
somewhat similar to a thermal cycler, except was not made
for cycling (PCR), but holding for one or more temperature
incubations?  I remember reading about one about a year
ago, but cannot remember the maker.  Since it doesn't
cycle, it is much cheaper than a standard PCR machine.
  Thank you for all your help!

Linda

This may be from Taiwan, but I don't know if it is commercialized. 
www.genomeweb.com/​pcrsample-prep/​taiwanese...based-pcr-potential-mdx-use-d\
eveloping-world 
http://www.biotechniques.com/BiotechniquesJournal/2011/January/Rapid-DNA-amplifi\
cation-in-a-capillary-tube-by-natural-convection-with-a-single-isothermal-heater\
/biotechniques-307538.html

-----Original Message-----
From: Forum: microarray and related technologies
[mailto:GENE-ARRAYS@...] On Behalf Of Linda Ta
Sent: Friday, August 12, 2011 4:50 PM
To: GENE-ARRAYS@...
Subject: Non-cycling thermal 'cycler'

Does anyone know the maker of a heating unit that is somewhat similar to a
thermal cycler, except was not made for cycling (PCR), but holding for one or
more temperature incubations?  I remember reading about one about a year ago,
but cannot remember the maker.  Since it doesn't cycle, it is much cheaper than
a standard PCR machine.
  Thank you for all your help!

Linda

A later Biotechniques article gives the Taiwanese group current research to
detect changes perhaps by eye or imaging from a cell phone.  There are some
accessories to allow cell phones to act as microscopes. You should contact
the authors for their latest efforts.
http://www.biotechniques.com/news/The-ups-and-downs-of-convection-PCR/biotec
hniques-307800.html

Walt Schick

-----Original Message-----
From: Forum: microarray and related technologies
[mailto:GENE-ARRAYS@...] On Behalf Of Linda Ta
Sent: Friday, August 12, 2011 4:50 PM
To: GENE-ARRAYS@...
Subject: Non-cycling thermal 'cycler'

Does anyone know the maker of a heating unit that is somewhat similar to a
thermal cycler, except was not made for cycling (PCR), but holding for one
or more temperature incubations?  I remember reading about one about a year
ago, but cannot remember the maker.  Since it doesn't cycle, it is much
cheaper than a standard PCR machine.
  Thank you for all your help!

Linda

Hi Linda,

We carry one model (follow the link below) should work for you.

http://www.wisbiomed.com/ec/index.php?main_page=product_info&cPath=12&produc
ts_id=1166
ThermoCube500 Programmable Heat-Cool Block
ThermoCube500 Cooling & Heating Blocks provide temperature control and a
convenient means to incubate samples. This unit employs Peltier effect heat
exchange technology to provide accurate, stable temperature control. It can
be used with a selection of interchangeable blocks for plates and tubes.
Programmable for up to 5 sequential steps of different temperature and
duration.
Large LCD display and simple controls make an easy-to-use interface for
programming. Displays set temperature, actual temperature, running time and
time remaining simultaneously.
Automatic stabilizing (PID) control to maintain set temperature.
Wide Temperature Setting Range
Sample blocks are easily removed for cleaning or replacement.
Five interchangeable sample blocks are available to accommodate different
sized sample containers.
Optional water bath block provides added application flexibility.

Martin



-----Original Message-----
From: Forum: microarray and related technologies
[mailto:GENE-ARRAYS@...] On Behalf Of Linda Ta
Sent: Friday, August 12, 2011 4:50 PM
To: GENE-ARRAYS@...
Subject: Non-cycling thermal 'cycler'

Does anyone know the maker of a heating unit that is
somewhat similar to a thermal cycler, except was not made
for cycling (PCR), but holding for one or more temperature
incubations?  I remember reading about one about a year
ago, but cannot remember the maker.  Since it doesn't
cycle, it is much cheaper than a standard PCR machine.
  Thank you for all your help!

Linda

We have been using an incubator of this series;
http://e-taitec.com/products/products-detail-en.php?machine_name=CTU-Mini
  nando nakazawa

2011/8/13 Linda Ta <lta@...>

> Does anyone know the maker of a heating unit that is somewhat similar to a
> thermal cycler, except was not made for cycling (PCR), but holding for one
> or more temperature incubations?  I remember reading about one about a year
> ago, but cannot remember the maker.  Since it doesn't cycle, it is much
> cheaper than a standard PCR machine. Thank you for all your help!
>  Linda
>


[Non-text portions of this message have been removed]

how about a simple heating block unit, with the aluminum block milled to the
appropriate size? As I recall, the interchangeable blocks I have used came
in 1.5 ml eppy, 0.5 ml eppy, and a few larger glass tube sizes. For highish
temperatures, mineral oil can be used to fill the block wells, for more
uniform heating of the tube. I remember using a lead brick to weigh down the
lids of eppys at 95 degrees C. Sand baths can be used for over 100 degrees
C. Check your used equipment exchange at the uni. Fisher and similar
suppliers carried the units.

Your uni. electronics shop repairperson may know of a used PCR cycler with
burned-out electronics, not considered worth repairing. I had one that
maintained high temperature well but didn't cycle to cooler temperature, and
it was repurposed as a heating block.

On Fri, Aug 12, 2011 at 6:50 PM, Linda Ta <lta@...> wrote:

> Does anyone know the maker of a heating unit that is somewhat similar to a
> thermal cycler, except was not made for cycling (PCR), but holding for one
> or more temperature incubations?  I remember reading about one about a year
> ago, but cannot remember the maker.  Since it doesn't cycle, it is much
> cheaper than a standard PCR machine. Thank you for all your help!
>  Linda
>


[Non-text portions of this message have been removed]

Eppendorf has a product called the Thermomixer R which does what you wish. It
has a shaking function and you can program 2 steps.

I think most real-time instruments have isothermal capabilities fwiw

Austin

Dear Colleague,

HTStec (www.htstec.com) is conducting a survey to understand your current
interest in pathway analysis (signal transduction), as part of our tracking of
emerging life science marketplaces.

If you are an end user involved in pathway analysis assays we would greatly
appreciate it if you could fill out an online survey to share some of your
views. We estimate the survey will take about 15-20 minutes of your time to
complete. There are 29 mainly simple multi-choice questions and all results will
be viewed and analyzed in aggregate form only.

Please click or paste the following link to access the survey:
http://www.selectbiosciences.com/redirect.aspx?cid=128656&uid=340904&link=http:/\
/www.surveymonkey.com/s/GJVHBJP

To thank you for your time and effort all validated* respondents that complete
the survey will be eligible to receive our full survey REPORT afterwards, so you
can benchmark your views on pathway analysis with the industry average.

The survey will close on Friday 26 August 2011 or earlier if sufficient
responses are received.

We are very grateful for your time in completing this survey and thank you for
your valuable feedback.

Sincerely,

Dr John Comley
HTStec Limited

* PLEASE NOTE responses from CONSULTANTS, ANALYSTS or any VENDORS active in any
aspect of pathway analysis (signal transduction) will NOT be accepted.


This email was sent from Select Biosciences Ltd on behalf of HTStec Ltd. If you
received this email in error, please forward it to the appropriate department at
your company.
To unsubscribe from future emails, please use this link -
http://www.selectbiosciences.com/unsubscribeo.aspx?nid=20

Select Biosciences Ltd, Woodview, Bull Lane, Sudbury, CO10 0BD, United Kingdom

[Non-text portions of this message have been removed]

Hello everyone –

I am looking for some microarray researchers to test a new Ingenuity product
offering between now and September 30th, 2011. Some of you may be familiar with
Ingenuity's IPA product. We have been working on a new solution designed for
bench scientists, lower cost, more streamlined, and easier to learn.

We have started an Early Access program and I am looking for researchers that:

  - Are bench scientist or biologists with a
    specific area of research focus.
  - Have a mammalian microarray experiment
    to analyze.
  - Can spend about 2 hours reviewing this new
    product between now and Sept 30th.

We currently support Affymetrix, Agilent, Illumina and Nimblegen platforms;
others will need to be mapped (we can help). RNASeq is in the works as well. You
can use a public dataset instead of your own if you like, however it should be
from an area of expertise where you can evaluate the biological analysis of the
dataset.

Participation is this Early Access Program is free but we have limited testing
spots open. We will run your dataset through the new system and give you access
to the results over the web, usually within 24 hours. There are a couple of
surveys to fill out plus we'd like to follow up over the phone to discuss your
findings and experience with the new product.

If you are interested, please drop me a line at felciano (at) ingenuity.com.

Also, please pass this on to any colleagues that you think might benefit from a
free, professional analysis of their microarray data.

Thanks,

Ramon

The `NGS data analysis workshop' is a 4 day comprehensive workshop
with interactive speaker sessions and hands on data analysis. The workshop is
designed to provide in-depth hands-on NGS data analysis experience in data QC,
genome assembly, SNP detection, Transcriptome analysis and ChIPSeq analysis. Top
scientists from academia and from all the sequencing technology providers such
as Illumina, Roche 454, SOLiD, Ion Torrent and Pacific biosciences will share
their experience and expertise with the participants.

Visit http://labindia-gpod.blogspot.com for more info or write
uddeshpande@... for registration

Important: Eligible young researchers shall be given 50% rebate in the fees and
additionally they will be provided free accommodation in the campus guest house.
Please send your CV and letter of interest to attend the workshop to
uday@... at the earliest.


A comprehensive hands-on NGS data analysis workshop organized jointly by
Persistent Systems Ltd. and Rajiv Gandhi Institute of Information Technology and
Biotechnology, Bharati Vidyapeeth University to provide hands-on NGS data
analysis training to students and young researchers.This workshop is suitable
for biologists, bioinformaticians and software developers who are completely new
to- or have some experience with NGS data analysis.The aim of the workshop is to
familiarize participants with characteristics of data generated by different
platforms and analysis workflows in the varied areas of NGS technology
applications.

The workshop will include a series of talks by eminent scientists from academia
as well as industry and hands-on data analysis sessions.
Day 1 --Introduction to NGS Data: This session is aimed at providing information
about data output
from different platforms and basic quality control using FASTQC.

Day 2 --Genome Assembly: In this session participants will perform assembly and
annotation of a
bacterial genome using open source tools.
ChIP-Seq Analysis: This data analysis session will involve basic analysis (Motif
enrichment and identification) of a small ChIP-Seq dataset.

Day 3 -- RNA-Seq Analysis: This data analysis session is aimed at performing
alignment, quantification
and differential expression in a small RNA-Seq dataset.

Day 4 -- Genetic Variation Analysis: This analysis session is aimed at
performing alignment, SNP and
detection and visualization in a small DNA-Seq data.

Registration:

The cost of the workshop is Rs. 30000/- per participant. The cost includes
course material, food and transportation between the two workshop venues.
The workshop is limited to 20 participants. Participants can register for the
workshop at http://biocrats.co.in/biocrat_portal/.

Venue
Persistent Systems Ltd, Dewang Mehta Hall, Bhageerath, SenapatiBapat Road, Pune.
Rajiv Gandhi Institute of Information technology and Biotechnology (RGIITBT),
Pune Satara Road, Katraj-Dhankawadi, Pune – 411 046

qPCR NEWS - October 2011 - focus on MIQE and RefGenes
-------------------------------------------------------------------------------



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 issue is:

* MIQE Guidelines are entering "high impact" journals!  - 
http://MIQE-press.gene-quantification.info
* RefGenes - a unique tool to find suitable reference genes  - 
http://normalisation.gene-quantification.info
* MIQE qPCR APP for iPhone, iPad and iPod -  new updated version available - 
http://MIQE.gene-quantification.info
* Join the qPCR 2011 US - http://www.qPCRsymposium.com


-----------------------------------------------------------------------------
If this newsletter is not displayed correctly by your email client, please use
following http://qPCRnews.gene-quantification.info
-----------------------------------------------------------------------------


MIQE Guidelines are entering "high impact" journals!
http://MIQE-press.gene-quantification.info

LIFE SCIENCE TECHNOLOGIES - qPCR Innovations and Blueprints
Science,  7. October 2011  by Chris Tachibana
http://www.sciencemag.org/site/products/lst_20111007.xhtml

Quantitative PCR users can rapidly generate large amounts of high-quality data
with new instruments and products made possible by microfluidics and
miniaturization technology. These platforms are the tools for developing
techniques that require extremely high throughput and sensitivity such as
digital PCR and single-cell analysis. Researchers are adopting these methods to
ask sophisticated questions about genetics and cancer biology as well as to
develop novel research and diagnostic assays. As qPCR innovators explore new
frontiers and everyday users venture into more complicated workflows,
international groups of industry and academic partners are keeping us on the
path of best practices. Two consortia (MIQE & SPIDIA) are generating guidelines
on the qPCR process - from experimental design and pre-analysis sample
collection, to processing data and publishing results. The guidelines are
blueprints that ensure reproducibility, validity, and transparency.

Routine lab method's accuracy called into question
Nature Medicine Vol 16, page 349 (2010)  by  Catherine Shaffer  in  Nature
Medicine
http://www.nature.com/nm/journal/v16/n4/full/nm0410-349.html

In 2002, four years after first sparking public controversy over whether the
measles, mumps and rubella vaccine causes autism, Andrew Wakefield reported a
possible molecular mechanism for the connection. He claimed that a form of
irritable bowel disease, which he called autistic enterocolitis, was triggered
by the measles virus (Molec. Pathol. 55, 84–90, 2002). That finding, however,
was based on a "defective experimental technique," Stephen Bustin, a molecular
biologist at Barts and the London School of Medicine and Dentistry, told a US
federal court in 2007. The problem: Wakefield had incorrectly applied the common
laboratory protocol known as quantitative real-time polymerase chain reaction
(qPCR) to come to his conclusions.
Bustin says this faulty lab work is a problem shared by many researchers around
the world who have turned to qPCR to measure gene expression. Unlike standard
PCR, which can only crudely quantify levels of DNA, the chemistry behind qPCR
allows researchers to assess such levels more precisely by comparing sequences
of interest against a known reference added to the test tube mix as a control.
But the reference genes used in qPCR can vary between experiments and
laboratories, which can give misleading results or make it difficult to compare
one study to another. As a result of this and other variables in the technique,
a majority of scientific papers involving qPCR include flawed methods, say a
team of leading qPCR experts. Most qPCR methods, as reported in the literature,
are improperly validated and irreproducible, Bustin claims.
Last year, he and 11 colleagues published a set of more than 60 individual
standards - collectively called the Minimum Information for Publication of
Quantitative Real-Time PCR Experiments (MIQE) to address this problem ( Clin.
Chem. 55, 611–622, 2009 ). "If you look at the literature, you find again and
again and again the appalling quality of qPCR protocols," says Bustin, who this
month repeated his call for the scientific community to adopt the MIQE
guidelines (Methods 50, 217–226, 2010). "There's no excuse for anyone either not
reporting or not doing experiments properly."
The consequence of poor methodology is that many published papers contain
erroneous conclusions, says Mikael Kubista, a coauthor of the MIQE guidelines
and chief executive of the TATAA Biocenter in Göteborg, Sweden. "The problem is
that the technique itself seems so simple and so easy to do, (but) in real life
you're analyzing biological samples with complexity."


-----------------------------------------------------------------------------

RefGenes - a unique tool to find suitable reference genes
http://www.refgenes.org

General problem
The choice of suitable reference genes is absolutely crucial in RT-qPCR gene
expression analysis. Often, genes from commercial panels don't work well for
one's own biological context. Ideally, the expression of reference genes should
remain unchanged across samples within the context under study.

Solution
RefGenes is an online app from Genevestigator that allows users to search for
genes that are most stable across a chosen set of samples based on microarray
data. This set of samples can be chosen according to experimental conditions or
tissue types. For example, if you are performing a RT-qPCR experiment on mouse
liver samples, you can use RefGenes to identify the set of genes that are most
stable across all microarrays done on mouse liver in Genevestigator. This method
offers two major improvements over existing methods because a) it does not
narrow down from a small set of genes (e.g. commercial housekeeping gene
panels), but looks for novel candidates from a genome-wide set of genes b) it is
based on condition-specific stability. The below schema shows how RefGenes can
be used in combination with existing approaches to yield valuable reference
genes for specific experimental conditions.

RefGenes: identification of reliable and condition specific reference genes for
RT-qPCR data normalization.
Hruz T, Wyss M, Docquier M, Pfaffl MW, Masanetz S, Borghi L, Verbrugge P,
Kalaydjieva L, Bleuler S, Laule O, Descombes P, Gruissem W and P Zimmermann
BMC Genomics 2011, 12: 156


-----------------------------------------------------------------------------

MIQE_qPCR APP for iPhone, iPad and iPod - iOS Universal
new version available!

Get help from a special team of experts in qPCR while on the move. MIQE - qPCR
helps you in reviewing scientific works and checking your own experiments, when
qPCR is involved. Check your project's compliance to MIQE in minutes, have all
required references to hand, and follow qPCR events and news.....
http://www.gene-quantification.de/miqe-qpcr-app-slide-show.pdf
Over 2,000 downloads up to now!

http://itunes.apple.com/app/miqe-qpcr/id423650002?mt=8


-----------------------------------------------------------------------------

qPCR 2011 US - http://www.qPCRsymposium.com

Mission Center Ballroom, Santa Clara Convention Center, 5001 Great America
Parkway, Santa Clara, CA 95054

Symposium Focus

* Preanalytics, Standardization and quality control
* High throughput expression profiling – digital PCR
* Epigenetics, mutation analysis and copy number variation
* Molecular diagnostics of complex diseases – detection and profiling of tumor
cells
* Single-cell and subcellular expression profiling
* Non coding RNAs
* qPCR in Forensics and AgriBio
* Next Generation Sequencing (NGS)
* qPCR & NGS experimental design and data mining
* Clinical applications of qPCR and NGS

Follow the symposium agenda!  
http://www.qpcrsymposium.com/default.asp?pagecat=C


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ail_template=&lng=en-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/


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SUBSCRIBE mailto:newsletter@...?subject=SUBSCRIBE

Dear microarray technology users,

If you live nearby New York City or will be visiting the big Apple
during the 4th week of October, I would recommend to attend the
symposium of the Systems Biology Discussion Group at the New York
Academy of Sciences, on the subject of `The Reactivity of the
Cellular Transcriptome to Xenobiotic Compound Perturbation'.

More information, including a link to the registration site, is
available through the event website at www.nyas.org/transcriptomics
<http://www.nyas.org/transcriptomics>

This event will present outstanding new developments with respect to DNA
microarray data applied to drug discovery.

Best Regards,

Manuel

Manuel X. Duval, PhD

Network Therapeutics Foundation Inc.

Groton, CT 06340

http://www.networktherapeutics.org/
<http://www.networktherapeutics.org/>

Office:     860 405 9124



[Non-text portions of this message have been removed]

Dear colleagues,

I would like to ask about the realiability &repetability related with microarray
data maching inter-platform (Agilent, Affy, others)? Thank you --ramona

Hi everyone... my samples are preimplantation mouse embryos. I pooled embryos
more than 20 to extract the RNA. My extraction using Trizol is more than 40ng/ul
I got even reached 100++ ng/ul for 40 embryos. I have tried also extract
Trizol+RNeasy mini kit, the concentration drop more than 50% from concentration
with trizol but the purity 260/280 not achieved 1.8 and 260/230 also not achieve
0.5. Why its so? anyone could help me to increase putiry when extracting RNA
from Trizol with RNeasy.or i need to buy RNEasy cleanup kit?

Hello,
We are trying to isolate RNA from sorted cells that will be used to run
microarrays. We have used both Micro & Mini prep kits from Agilent. I have
noticed one big difference is the use of pre-spin filter cup in Mini kit. My
question is how essential is that step, considering it is not used in microprep
kit and even the Miniprep manual says in case of low cell numbers reduce the
duration.
Reason for the query is due to very low cell counts we have and our previous
attempt to isolate RNA using Mini kit with pre-filter step was a disaster. Our
typical cell cout is less than 200K. Any help will be appreciated.
Thanks,
- Soumyaroop

Hi folks,

I'm new on Microarrays. I have to develop a project for my Data Mining course.

I would appreciate if you can share with me any document about how are
microaarrays?  algorithms used? work areas where it is used? etc

Any help would be greatly appreciated.

My email is jon.salas@...

Regards,
Jonathan

Dear Soumyaroop,

The Mini-kit filter has lower cut-off value in order to recover smaller
RNAs such as microRNA and siRNA therefore it is necessary to pre-filtering
to prevent the clogging of the filter by cell debris. As I remember the
recommended cell count is 1 million so you've used one/firth of the
required. Probably most of your RNA has been absorbed by the pre-filter.
You may skip pre-filtering or use micro-kit.  But the best option is to get
proper amount of cells, you may also try pooling 4 or 5 replicates if you
can't increase input sample.

Good Luck,
Ibrahim

2011/11/10 Soumyaroop <soumyaroopbhatt@...>

> **
>
>
> Hello,
> We are trying to isolate RNA from sorted cells that will be used to run
> microarrays. We have used both Micro & Mini prep kits from Agilent. I have
> noticed one big difference is the use of pre-spin filter cup in Mini kit.
> My question is how essential is that step, considering it is not used in
> microprep kit and even the Miniprep manual says in case of low cell numbers
> reduce the duration.
> Reason for the query is due to very low cell counts we have and our
> previous attempt to isolate RNA using Mini kit with pre-filter step was a
> disaster. Our typical cell cout is less than 200K. Any help will be
> appreciated.
> Thanks,
> - Soumyaroop
>
>
>


[Non-text portions of this message have been removed]

Dear colleagues,

I'm encountering troubles with my first self-spotted microarray analysis: a
high green background, even after I've set the channel ratio at ~1. The
bizarre thing is new slides, just out of a just openend package, give an
identical uniform green background when scanned. I tested a new pack of
slides from a colleague, and a new pack of slides (a different manufacturer)
from another colleague: all a high green background. A regular miroscopical
slides gives an even higher green background, but that may be normal (I
don't know!). But they all should be almost black isn't it?

Does blocking and washing normally reduce this green background (then its a
buffer problem), do i have a scanner problem (Genepix 4100a) -maybe some
stupid settings -or a slide problem (buy new slides)? Currently the scanner
seems the most probable suspect to me.

I can do three things:

1) buy new slides of the best quality
2) renew all my buffer and stock solutions (although i do'nt think this is
the problem)
3) scan them on another scanner (then i should find one first!).

Some advice is much appreciated!

Kind regards,

Yves
---
Yves Verhaegen
Chemical Monitoring and Production Technology group
Department of Fisheries
Institute for Agricultural and Fisheries Research (ILVO)
Ankerstraat 1, B-8400 Oostende, Belgium
Tel.   +3259569864
Fax.  +3259330629
yves.verhaegen@... [mailto:yves.verhaegen@...]
www.ilvo.vlaanderen.be [http://www.ilvo.vlaanderen.be/]

[Non-text portions of this message have been removed]

Dear Yves,

Background auto-fluorescence in the "Cy3" channel (532nm) is nothing unusual and
nothing you shouldn't be able to get rid easily, i.e. by using suitable slide
processing protocols. However, in order to give you any tips on this I would
need to know what slides are you using (aldehye, amino, poly-l-lysine, epoxy,
....). It is also so that there are differences in slides quality - some just
have higher background auto-fluorescence: It is always a question of finding the
suitable compromise between slide quality/price and the needs of your
experiments.

Hope this helps a bit, and if you have any further questions I would be happy to
try and help.

Best regards
Tanja

P.S. we have been working with GenPix scanners since 10y and are extremely happy
with them

TANJA KOSTIC, PhD
Health & Environment Department
Bioresources

AIT Austrian Institute of Technology GmbH
Konrad Lorenz Strasse 24
A - 3430 Tulln an der Donau | Austria
M +43(0) 664 8251134 | T +43(0) 50550 3635 | F +43(0) 50550-3666
tanja.kostic@...<mailto:iris.hagenauer@...>  | 
http://www.ait.ac.at<http://www.ait.ac.at/>

FN: 115980 i HG Wien  |  UID: ATU14703506
This email and any attachments thereto, is intended only for use by the
addressee(s) named herein and may contain legally privileged and/or confidential
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return e-mail or by telephone and delete this message from your system and any
printout thereof. Any unauthorized use, reproduction, or dissemination of this
message is strictly prohibited. Please note that e-mails are susceptible to
change. AIT Austrian Institute of Technology GmbH shall not be liable for the
improper or incomplete transmission of the information contained in this
communication, nor shall it be liable for any delay in its receipt.


________________________________
From: microarray@yahoogroups.com [microarray@yahoogroups.com] On Behalf Of Yves
Verhaegen [Yves.Verhaegen@...]
Sent: Thursday, November 17, 2011 2:27 PM
To: microarray@yahoogroups.com
Subject: [microarray-group] Green background on new unused microarray slides



Dear colleagues,

I'm encountering troubles with my first self-spotted microarray analysis: a
high green background, even after I've set the channel ratio at ~1. The
bizarre thing is new slides, just out of a just openend package, give an
identical uniform green background when scanned. I tested a new pack of
slides from a colleague, and a new pack of slides (a different manufacturer)
from another colleague: all a high green background. A regular miroscopical
slides gives an even higher green background, but that may be normal (I
don't know!). But they all should be almost black isn't it?

Does blocking and washing normally reduce this green background (then its a
buffer problem), do i have a scanner problem (Genepix 4100a) -maybe some
stupid settings -or a slide problem (buy new slides)? Currently the scanner
seems the most probable suspect to me.

I can do three things:

1) buy new slides of the best quality
2) renew all my buffer and stock solutions (although i do'nt think this is
the problem)
3) scan them on another scanner (then i should find one first!).

Some advice is much appreciated!

Kind regards,

Yves
---
Yves Verhaegen
Chemical Monitoring and Production Technology group
Department of Fisheries
Institute for Agricultural and Fisheries Research (ILVO)
Ankerstraat 1, B-8400 Oostende, Belgium
Tel. +3259569864
Fax. +3259330629
yves.verhaegen@...<mailto:yves.verhaegen%40ilvo.vlaanderen.be>
[mailto:yves.verhaegen@...<mailto:yves.verhaegen%40ilvo.vlaandere\
n.be>]
www.ilvo.vlaanderen.be [http://www.ilvo.vlaanderen.be/]

[Non-text portions of this message have been removed]





[Non-text portions of this message have been removed]

RNA-Seq Data Analysis Online Course

Making Sense of RNA-Seq Data
RNA-Seq is sequencing of steady state RNA in a given sample.RNA-Seq is used for
1. identifying allele specific gene expression 2. finding novel transcripts and
isoforms and 3. differential gene expression. This training programme exposes
participants to the available public domain tools and techniques for the
analysis of RNA-Seq data and addresses complete analysis pipeline from mapping
reads to differential expression and systems biology. Course delivery includes
prerecorded webinars and the exercise labs.

Course Duration

Course will run for four weeks from  02.01.2012 to 29.01.2012.
Course Material
Course material will be delivered online for each week at the start of the week.
Register at http://www.labindia-gpod.com or write to uday@...
Registration
Send a copy of your biodata along with DD of Rs 5000/-  in the name of Labindia
Instruments Pvt. Ltd. payable at Thane to Co-ordinator, Labindia-GPOD, Swnand,
Jivan Vihar Housing Society, SB Road, Pune or make online payment with
debit/credit card using payment gateway.
  1. Tools for mapping reads to reference genome or transcriptome

A. Webinar : Overview of available tools and techniques for mapping  reads to
reference genome
B. Lab Exercises: Mapping reads to reference genome using Bowtie
2. De novo assembly of Transcriptome
A. Webinar : Tools and algorithms for De novo transcriptome assembly
B. Lab exercise : Using MIRA for De novo assembly

3. Finding isoforms and novel transcripts
A. Webinar : Overview of tools available for finding novel transcripts and
isoforms
B. Lab exercises: Use of TopHat and Cufflink for finding isoforms and novel
transcripts
4. Summarising mapped reads
A. Webinar : Review of tools for summarising mapped data and performing QC
B. Lab exercises : R Bioconductor tools for summarising mapped reads and QC
5.Normalization and Differential Expression
A. Webinar : Review of tools and method for normalising and analysis of
differential expression of RNA-Seq data
B. R and Bioconductor tools for differential expression analysis prefernce will
be given to DESeq package.
6. Gene set and pathway enrichment
A. Webinar : Overview of tools for gene set and pathways enrichment
B. Lab exercises : Goseq, Gostat and DAVID tools for enrichment analysis of
differentially expressed genes.

Look up a paper published several years ago in NAR by Martinez et al (I'm on it 
-Werner-Washburne). We gave several methods for removing this, if it is the same
reagent.  Maggie WW
On Nov 19, 2011, at 6:09 AM, Kostic Tanja wrote:

> Dear Yves,
>
> Background auto-fluorescence in the "Cy3" channel (532nm) is nothing unusual
and nothing you shouldn't be able to get rid easily, i.e. by using suitable
slide processing protocols. However, in order to give you any tips on this I
would need to know what slides are you using (aldehye, amino, poly-l-lysine,
epoxy, ....). It is also so that there are differences in slides quality - some
just have higher background auto-fluorescence: It is always a question of
finding the suitable compromise between slide quality/price and the needs of
your experiments.
>
> Hope this helps a bit, and if you have any further questions I would be happy
to try and help.
>
> Best regards
> Tanja
>
> P.S. we have been working with GenPix scanners since 10y and are extremely
happy with them
>
> TANJA KOSTIC, PhD
> Health & Environment Department
> Bioresources
>
> AIT Austrian Institute of Technology GmbH
> Konrad Lorenz Strasse 24
> A - 3430 Tulln an der Donau | Austria
> M +43(0) 664 8251134 | T +43(0) 50550 3635 | F +43(0) 50550-3666
> tanja.kostic@...<mailto:iris.hagenauer@...> |
http://www.ait.ac.at<http://www.ait.ac.at/>
>
> FN: 115980 i HG Wien | UID: ATU14703506
> This email and any attachments thereto, is intended only for use by the
addressee(s) named herein and may contain legally privileged and/or confidential
information. If you are not the intended recipient, please notify the sender by
return e-mail or by telephone and delete this message from your system and any
printout thereof. Any unauthorized use, reproduction, or dissemination of this
message is strictly prohibited. Please note that e-mails are susceptible to
change. AIT Austrian Institute of Technology GmbH shall not be liable for the
improper or incomplete transmission of the information contained in this
communication, nor shall it be liable for any delay in its receipt.
>
> ________________________________
> From: microarray@yahoogroups.com [microarray@yahoogroups.com] On Behalf Of
Yves Verhaegen [Yves.Verhaegen@...]
> Sent: Thursday, November 17, 2011 2:27 PM
> To: microarray@yahoogroups.com
> Subject: [microarray-group] Green background on new unused microarray slides
>
> Dear colleagues,
>
> I'm encountering troubles with my first self-spotted microarray analysis: a
> high green background, even after I've set the channel ratio at ~1. The
> bizarre thing is new slides, just out of a just openend package, give an
> identical uniform green background when scanned. I tested a new pack of
> slides from a colleague, and a new pack of slides (a different manufacturer)
> from another colleague: all a high green background. A regular miroscopical
> slides gives an even higher green background, but that may be normal (I
> don't know!). But they all should be almost black isn't it?
>
> Does blocking and washing normally reduce this green background (then its a
> buffer problem), do i have a scanner problem (Genepix 4100a) -maybe some
> stupid settings -or a slide problem (buy new slides)? Currently the scanner
> seems the most probable suspect to me.
>
> I can do three things:
>
> 1) buy new slides of the best quality
> 2) renew all my buffer and stock solutions (although i do'nt think this is
> the problem)
> 3) scan them on another scanner (then i should find one first!).
>
> Some advice is much appreciated!
>
> Kind regards,
>
> Yves
> ---
> Yves Verhaegen
> Chemical Monitoring and Production Technology group
> Department of Fisheries
> Institute for Agricultural and Fisheries Research (ILVO)
> Ankerstraat 1, B-8400 Oostende, Belgium
> Tel. +3259569864
> Fax. +3259330629
> yves.verhaegen@...<mailto:yves.verhaegen%40ilvo.vlaanderen.be>
[mailto:yves.verhaegen@...<mailto:yves.verhaegen%40ilvo.vlaandere\
n.be>]
> www.ilvo.vlaanderen.be [http://www.ilvo.vlaanderen.be/]
>
> [Non-text portions of this message have been removed]
>
> [Non-text portions of this message have been removed]
>
>

Maggie Werner-Washburne
Regents' Professor
Biology - University of New Mexico

http://biology.unm.edu/biology/maggieww/Public_Html/Maggieww.html






[Non-text portions of this message have been removed]

Hi Yves,

There is a good article on sources of contaminating fluorescence:

MJ Martinez, et al, "Identification and removal of contaminating fluorescence
from
commercial and in-house printed DNA microarrays", Nucleic Acids Research, 31(4),
e18
(2003)
DOI: 10.1093/nar/gng018

-Peter Wentzell

On 17 Nov 2011 at 14:27, Yves Verhaegen wrote:

>
>
> Dear colleagues,
>
> I'm encountering troubles with my first self-spotted microarray analysis: a
> high green background, even after I've set the channel ratio at ~1. The
> bizarre thing is new slides, just out of a just openend package, give an
> identical uniform green background when scanned. I tested a new pack of
> slides from a colleague, and a new pack of slides (a different manufacturer)
> from another colleague: all a high green background. A regular miroscopical
> slides gives an even higher green background, but that may be normal (I
> don't know!). But they all should be almost black isn't it?
>
> Does blocking and washing normally reduce this green background (then its a
> buffer problem), do i have a scanner problem (Genepix 4100a) -maybe some
> stupid settings -or a slide problem (buy new slides)? Currently the scanner
> seems the most probable suspect to me.
>
> I can do three things:
>
> 1) buy new slides of the best quality
> 2) renew all my buffer and stock solutions (although i do'nt think this is
> the problem)
> 3) scan them on another scanner (then i should find one first!).
>
> Some advice is much appreciated!
>
> Kind regards,
>
> Yves
> ---
> Yves Verhaegen
> Chemical Monitoring and Production Technology group
> Department of Fisheries
> Institute for Agricultural and Fisheries Research (ILVO)
> Ankerstraat 1, B-8400 Oostende, Belgium
> Tel. +3259569864
> Fax. +3259330629
> yves.verhaegen@... [mailto:yves.verhaegen@...]
> www.ilvo.vlaanderen.be [http://www.ilvo.vlaanderen.be/]
>
> [Non-text portions of this message have been removed]
>
>
>


  ================================================
Peter Wentzell                           Ph. 902-494-3708 or 3305
Professor                                   Fax 902-494-1310
Department of Chemistry           e-mail: Peter.Wentzell@...
Dalhousie University                  http://myweb.dal.ca/pdwentze/index.html
Halifax, NS  B3H 4R2
Canada
================================================


[Non-text portions of this message have been removed]

Hi Yevs,

I remember reading the answer to a similar question on one of discussion group.
As far as I remember Agilent knows about this problem and they even have a name
for it - "Green Monster". So you may contact them. If your arrays are from
Agilent they will probably send you new ones.

Good luck.

Oleg Suslov
University of Florida

--- In microarray@yahoogroups.com, "Yves Verhaegen" <Yves.Verhaegen@...> wrote:
>
> Dear colleagues,
>
> I'm encountering troubles with my first self-spotted microarray analysis: a
> high green background, even after I've set the channel ratio at ~1. The
> bizarre thing is new slides, just out of a just openend package, give an
> identical uniform green background when scanned. I tested a new pack of
> slides from a colleague, and a new pack of slides (a different manufacturer)
> from another colleague: all a high green background. A regular miroscopical
> slides gives an even higher green background, but that may be normal (I
> don't know!). But they all should be almost black isn't it?
>
> Does blocking and washing normally reduce this green background (then its a
> buffer problem), do i have a scanner problem (Genepix 4100a) -maybe some
> stupid settings -or a slide problem (buy new slides)? Currently the scanner
> seems the most probable suspect to me.
>
> I can do three things:
>
> 1) buy new slides of the best quality
> 2) renew all my buffer and stock solutions (although i do'nt think this is
> the problem)
> 3) scan them on another scanner (then i should find one first!).
>
> Some advice is much appreciated!
>
> Kind regards,
>
> Yves
> ---
> Yves Verhaegen
> Chemical Monitoring and Production Technology group
> Department of Fisheries
> Institute for Agricultural and Fisheries Research (ILVO)
> Ankerstraat 1, B-8400 Oostende, Belgium
> Tel.   +3259569864
> Fax.  +3259330629
> yves.verhaegen@... [mailto:yves.verhaegen@...]
> www.ilvo.vlaanderen.be [http://www.ilvo.vlaanderen.be/]
>
> [Non-text portions of this message have been removed]
>

qPCR NEWS - November 2011 - focus on mirtrons
---------------------------------------------------------------



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 issue is:

* Introducing the mirtron - http://mirtron.gene-quantification.info
* MIQE qPCR APP for IOS and Android is available -
http://MIQE.gene-quantification.info
* MIQE guidelines - online translation service to CHINESE,  JAPANESE,  KOREAN
and RUSSIAN


If this newsletter is not displayed correctly by your email client, please use
following  http://qPCRnews.gene-quantification.info
-----------------------------------------------------------------------------

Mirtrons were first identified in Drosophila melanogaster and Caenorhabditis
elegans and are a type of microRNA that are located in the introns of the mRNA
encoding genes. Mirtrons are alternative precursors for microRNA biogenesis. The
short hairpin introns use splicing to bypass DROSHA cleavage, which is otherwise
essential for the generation of canonical animal microRNAs. Mirtrons arise from
the spliced-out introns and are known to function like classical microRNAs
(miRs) and regulate gene expression, by either mRNA destabilisation, inhibition
of the translation or target mRNA cleavage.
=> http://mirtron.gene-quantification.info

selected mirtron papers:

MicroRNA - Introducing the mirtron
Patrick Goymer, Nature Reviews Molecular Cell Biology 2007 (8): 597

And Now Introducing Mammalian Mirtrons
Shih-Peng Chan and Frank J. Slack
Department of Molecular, Cellular and Developmental Biology, Yale University,
USA, Developmental Cell 13 (2007): 605-607

Mammalian mirtron genes
Berezikov E, Chung WJ, Willis J, Cuppen E, Lai EC., Hubrecht Institute, Utrecht,
The Netherlands, Mol Cell. 2007 28(2): 328-336.

Mirtrons - microRNA biogenesis via splicing
Jakub O. Westholm, Eric C. Lai Corresponding Author Contact Information, E-mail
The Corresponding Author
Department of Developmental Biology, Sloan-Kettering Institute, 1275 York Ave,
Box 252, NY 10065, USA, Biochimie 93(11): 1897-1904

Intronic microRNA precursors that bypass Drosha processing
J. Graham Ruby, Calvin H. Jan, & David P. Bartel
Nature Letters Vol 448:5 2007

The biogenesis and characterization of mammalian microRNAs of mirtron origin
Sibley CR, Seow Y, Saayman S, Dijkstra KK, El Andaloussi S, Weinberg MS, Wood
MJ.
Nucleic Acids Res. 2011

Computational and experimental identification of mirtrons in Drosophila
melanogaster and Caenorhabditis elegans
Chung WJ, Agius P, Westholm JO, Chen M, Okamura K, Robine N, Leslie CS, Lai EC.
Department of Developmental Biology, Sloan-Kettering Institute, Rockefeller
Research Laboratories, New York, USA, Genome Res. 2011 21(2): 286-300

miRNAs in human cancer
Farazi TA, Spitzer JI, Morozov P, Tuschl T.
Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology,
Rockefeller University, New York, NY 10065, USA, J Pathol. 2011 223(2): 102-115

The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila
Okamura K, Hagen JW, Duan H, Tyler DM, Lai EC.
Memorial Sloan-Kettering Cancer Center, Department of Developmental Biology, New
York, USA, Cell. 2007 130(1): 89-100

MicroRNA biogenesis via splicing and exosome-mediated trimming in Drosophila
Flynt AS, Greimann JC, Chung WJ, Lima CD, Lai EC.
Developmental Biology Program, Sloan-Kettering Institute, 1275 York Avenue, Box
252, New York, NY 10065, USA, Mol Cell. 2010 38(6): 900-907

Intronic noncoding RNAs and splicing
Brown JW, Marshall DF, Echeverria M.
Plant Sciences Division, University of Dundee at the Scottish Crop Research
Institute (SCRI), Invergowrie, Dundee, DD2 5DA, UK, Trends Plant Sci. 2008
13(7): 335-342

and much more papers are available here =>
http://mirtron.gene-quantification.info


-----------------------------------------------------------------------------

MIQE_qPCR APP for - iOS Universal & Android version

Get help from a special team of experts in qPCR while on the move. MIQE - qPCR
helps you in reviewing scientific works and checking your own experiments, when
qPCR is involved. Check your project's compliance to MIQE in minutes, have all
required references to hand, and follow qPCR events and news.....
http://www.gene-quantification.de/miqe-qpcr-app-slide-show.pdf
Over 2,400 downloads
=> http://itunes.apple.com/app/miqe-qpcr/id423650002?mt=8

MIQE_qPCR Android version - Now available in Nov 2011
=> https://market.android.com/details?id=com.biorad.miqeqPCR


-----------------------------------------------------------------------------

Please forward this qPCR NEWS 
http://api.addthis.com/oexchange/0.8/forward/email/offer?url=http://qPCRnews.gen\
e-quantification.info&title=Join+our+monthly+newsletter+on&username=qPCR-NEWS&em\
ail_template=&lng=en-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 © 2005 - 2011 All rights reserved. Any unauthorized use, reproduction,
or transfer of this message or its contents, in any medium, is strictly
prohibited. Disclaimer & Copyrights are displayed on the homepage
http://www.gene-quantification.info
To subscribe or change your e-mail address in qPCR NEWS, and if you would like
to receive future issues FREE of charge, please send an e-mail with the subject
SUBSCRIBE mailto:newsletter@...?subject=SUBSCRIBE

I'm not sure anyone is still interested in printing arrays, but if you are, we
have a deRisi style Linear Servo Arrayer with a full set of telechem pins and a
positive-pressure enclosure we are selling for cheap!  Here are a few pictures
and details:

https://docs.google.com/present/edit?id=0AZrVnDjCnEvIZGd2ZmNiOV8wY3NjNmhwZnY

Please contact me if interested.

Seth Crosby

scrosby at wustl dot edu

314.286.1256

__________________________________________
Seth D. Crosby, MD
Director, Alliances and Partnerships
Department of Genetics
Washington University School of Medicine

This years event will be held in Edinburgh, Scotland.

28 - 29 March 2012

The conference will discuss,

     * Advances in DNA Arrays

     * Advances in Protein and Antibody Arrays

     * Advances in Lipid and Tissue Arrays

     * Biomarker Validation

     * Bioinformatics for Microarrays

     * Molecular Diagnostics
     * Emerging Technologies
The conference will be co-located with Lab-on-a-Chip
<http://www.selectbiosciences.com/conferences/LOACEC2012> , Single Cell
Analysis Europe <http://www.selectbiosciences.com/conferences/SCAE2012>
and Advances in Biodetection & Biosensors
<http://www.selectbiosciences.com/conferences/ABB2012> . Registered
delegates will have access to all four meetings ensuring a very
cost-effective trip.

For more information on Advances in Microarray Technology conference,
click here <http://www.selectbiosciences.com/conferences/AMT2012/>  .





[Non-text portions of this message have been removed]

The new methods for transcriptomics are bringing new challenges in
bioinformatics. This online course from The University of Manchester,
UK, covers microarray data analysis in depth, and also introduces the
areas where new work is needed for next generation sequence (RNA-seq)
analysis.

http://octette.cs.man.ac.uk/bioinformatics/modules/transcriptomics.html
<http://octette.cs.man.ac.uk/bioinformatics/modules/transcriptomics.html\
>

Course details:

Week 1                     Introduction and software setup
Weeks 2 and 3          Microarrays and experimental design
Weeks 4 and 5          Data capture and preliminary checks
Weeks 6 and 7          Data analysis
Weeks 8 and 9          Other methods for transcriptome analysis
Weeks 10 and 11      Independent research and work on the first
assessment
Weeks 12 and 13      Gene Class Tests
Weeks 14 to 16         Independent research and work on the second
assessment

This is just one of our Masters-level courses in Digital Biology.  You
will find information on all our courses, including fees and a link to
the enquiry form, here :
http://octette.cs.man.ac.uk/bioinformatics/index.html
<http://octette.cs.man.ac.uk/bioinformatics/index.html>  If you need
further information, or would like to book a place on a course, please
contact our office for Advanced Professional Education (ape@...
<mailto:ape@...> ).


[Non-text portions of this message have been removed]

qPCR NEWS - December 2011 - focus on qPCR efficiency
------------------------------------------------------------------------




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 issue is:

* qPCR efficiency calculation  -  sub-domain updated  - 
http://Efficiency.gene-quantification.info
* real-time PCR Cycler  -  sub-domain updated  - 
http://CYCLERS.gene-quantification.info
* GenEx version 5  - download a free trial version  - 
http://GenEx.gene-quantification.info
* MIQE qPCR APP for IOS and Android is available -
http://MIQE.gene-quantification.info

If this newsletter is not displayed correctly by your email client, please use
following Link
http://qPCRnews.gene-quantification.info

-----------------------------------------------------------------------------

Determination of real-time PCR amplification efficiency

Individual samples generate different and individual fluorescence histories in
real-time PCR. The shapes of amplification curves differ in the steepness of any
fluorescence increase and in the absolute fluorescence levels at plateau
depending on background fluorescence levels. The PCR efficiency has 'the 'major
impact' on the fluorescence history and the accuracy of the calculated
expression result and is critically influenced by PCR reaction components. The
efficiency evaluation is an essential marker in gene quantification procedure
and one of the important characteristicum of the MIQE guidelines. Constant
amplification efficiency in all compared samples is one important criterion for
reliable comparison between samples. This becomes crucially important when
analyzing the relationship between an unknown sequence versus a standard
sequence, which is performed in all relative quantification models. In
experimental designs employing standardization with reference genes, the demand
for invariable amplification efficiency between target and standard is often
ignored, despite the fact that corrections have been suggested. A correction for
efficiency, as performed in efficiency corrected mathematically models, is
strongly recommended and results in a more reliable estimation of the `real
expression ratio' compared to NO efficiency correction. Small efficiency
differences between target and reference gene generate false expression ratio,
and the researcher over- or under-estimates the `real' initial mRNA amount.

Find the latest literature about real-time PCR efficiency determination:

Efficiency of the Polymerase Chain Reaction.
Booth CS, Pienaar E, Termaat JR, Whitney SE, Louw TM, Viljoen HJ.
Chem Eng Sci. 2010 65(17): 4996-5006.

pcrEfficiency: a Web tool for PCR amplification efficiency prediction.
Mallona I, Weiss J, Marcos EC.
BMC Bioinformatics. 2011 12: 404

Experimental Validation of a Fundamental Model for PCR Efficiency.
Louw TM, Booth CS, Pienaar E, Termaat JR, Whitney SE, Viljoen HJ.
Chem Eng Sci. 2011 Apr 15;66(8): 1783-1789.

Enhanced analysis of real-time PCR data by using a variable efficiency model:
FPK-PCR.
Lievens A, Van Aelst S, Van den Bulcke M, Goetghebeur E.
Nucleic Acids Res. 2011 Nov 18.

Validation of kinetics similarity in qPCR.
Bar T, Kubista M, Tichopad A.
Nucleic Acids Res. 2011 Oct 19.

A mechanistic model of PCR for accurate quantification of quantitative PCR data.
Boggy GJ, Woolf PJ.
Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan,
United States of America.
PLoS One. 2010 5(8): e12355.

Shape based kinetic outlier detection in real-time PCR.
Sisti D, Guescini M, Rocchi MB, Tibollo P, D'Atri M, Stocchi V.
BMC Bioinformatics. 2010 12;11: 186

Quality control for quantitative PCR based on amplification compatibility test.
Tichopad A, Bar T, Pecen L, Kitchen RR, Kubista M, Pfaffl MW.
Methods. 2010 50(4): 308-312

Efficiency clustering for low-density microarrays and its application to qPCR
Eric F Lock, Ryan Ziemiecke, J. S. Marron and Dirk P Dittmer
BMC Bioinformatics 2010, 11

Assessing the performance capabilities of LRE-based assays for absolute
quantitative real-time PCR.
Rutledge RG, Stewart D.
PLoS One. 2010 5(3): e9731.

Bias in the Cq value observed with hydrolysis probe based quantitative PCR can
be corrected with the estimated PCR efficiency value.
Tuomi JM, Voorbraak F, Jones DL, Ruijter JM.
Methods. 2010 50(4): 313-22

... ... and more =>  http://Efficiency.gene-quantification.info

-----------------------------------------------------------------------------

UPDATE - real-time PCR Cycler

On http://CYCLERS.gene-quantification.info the most prominent real-time PCR
cycler are described.
In the cycler descriptions the specifications and the advantages of the
displayed systems are shown. Which real-time platform meets your requirements
best, depends on your research application. Some of the systems are designed for
research with low capacities and others are for high-throughput applications,
most in combination with pipetting robots. Most of them use solid-block for
thermal cycling, other use hot- and cooled-air. Most differences are obviously
in the application software, especially in the way of data analysis and how the
derived crossing points or threshold levels are computed. Each of these systems
employs either one of several general types of fluorescent probes for detection.
There are also big differences how data are displayed. Some of the limitations
of end-point detection in (RT-) PCR have been assuaged in real-time PCR systems,
a number of which are now on the market. These systems offer many general
technical advantages, including reduced probabilities of variability and
contamination, as well as online monitoring and the lack of need for post
reaction analyses. Further, some of these systems were developed with
contemporary applications such as quantitative PCR, multiplexing, and
high-throughput analysis in mind. Initial template levels can be calculated by
analysing the shape of the curve or by determining when the signal rises above
some threshold value.

A hopefully complete list of the commercially available real-time PCR systems
are overviewed on this page and summarized here =>
http://CYCLERS.gene-quantification.info


-----------------------------------------------------------------------------

GenEx 5 -  A Powerful Tool For qPCR Data Analysis

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://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
need to be performed consistently in correct order and with confidence. GenEx
Standard's 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://GenEx.gene-quantification.info


-----------------------------------------------------------------------------

MIQE_qPCR APP for - iOS Universal & Android version

Get help from a special team of experts in qPCR while on the move. MIQE - qPCR
helps you in reviewing scientific works and checking your own experiments, when
qPCR is involved. Check your project's compliance to MIQE in minutes, have all
required references to hand, and follow qPCR events and news.....
http://www.gene-quantification.de/miqe-qpcr-app-slide-show.pdf

Over 2,500 iOS versions downloaded on
http://itunes.apple.com/app/miqe-qpcr/id423650002?mt=8

MIQE_qPCR Android version - Now available since Nov 2011

https://market.android.com/details?id=com.biorad.miqeqPCR


-----------------------------------------------------------------------------

Please forward this qPCR NEWS 
http://api.addthis.com/oexchange/0.8/forward/email/offer?url=http://qPCRnews.gen\
e-quantification.info&title=Join+our+monthly+newsletter+on&username=qPCR-NEWS&em\
ail_template=&lng=en-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


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Hello,

I am seeking a "Calibration block for Molecular Devices Vmax Microplate Reader".
The Vmax we have in our lab still works and we would like to know if there are
any available calibration blocks for sale.

RB
CTgen