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Gene Quantification Newsletter
April  2016

is sponsored by


Streamlined and automated NGS workflow 

  Dear researcher,
dear Gene Quantification page reader,

Our newsletter informs about the latest news in gene expression profiling using qPCR and related methods, which are compiled and summarised on www.Gene-Quantification.info
The focus of this qPCR NEWS issue is:


Streaming portal

Join the updated
eConferences streaming webportal
www.eConferences.de -- Amplify your knowledge in  qPCR, dPCR and NGS!
This streaming portal is dedicated to scientists from the community of qPCR, digital PCR, Next Generation Sequencing (NGS), MicroGenomics (MG) and Molecular Diagnostics (MDx). You’ll find here all the records of 280 presentations held at qPCR & NGS and MG Events in the past years – qPCR 2010 in Vienna  to qPCR & NGS 2015 in Freising-Weihenstephan.
We provide the presentations via movie streaming technology in high quality – high resolution and perfect sound quality in high speed – on any internet browser or mobile device.

A powerful tool

A powerful tool -- The inclusion of 'transcriptome anaylsis datasets' to the 'human protein atlas database'
Posted by RNA-Seq Blog -- from Health Canal

The Human Protein Atlas was launched in April 2016. The new version includes data from different sources, which makes comparisons between tissue profiles on both the mRNA and protein levels. =>  Visit your favorite gene to browse our new layout on the Tissue Atlas!
The Human Protein Atlas includes proteome analysis based on more than 25 000 antibodies targeting more than 17 000 unique proteins, combined with transcriptome analysis covering all 20 000 human protein coding genes. The new atlas also includes primary data from several sources, which allows for comparisons.

The new version of the Human Protein Atlas is significantly advancing in terms of mapping the transcriptome in different human tissues. These data have been the basis for much of the metabolic modelling we are doing here at Chalmers. I am therefore very excited about the progress, and the Human Protein Atlas will certainly be an important resources in our aims to advance towards better diagnostics and precision medicine, says Professor Jens Nielsen at the Department of Biology and Biological Engineering.

The launch is accompanied by an article in Molecular Systems Biology describing transcriptome resources with a focus on the comparison between the datasets generated from the Broad Institute, Boston, US (GTEx) and the Human Protein Atlas. The GTEx dataset includes more than 1600 samples from mostly overlapping, but in some cases unique, tissues compared to the Human Protein Atlas. RNA-seq data from 28 of the GTEx tissues with a corresponding tissue in Human Protein Atlas have been included to allow for direct comparisons between the Human Protein Atlas and GTEx data sets.

Transcriptomics resources of human tissues and organs
Mathias Uhlén, Björn M Hallström, Cecilia Lindskog, Adil Mardinoglu, Fredrik Pontén, Jens Nielsen
Molecular Systems Biology 12: 862 | 2016

Mammalian transcriptomic database

MTD -- A mammalian transcriptomic database to explore gene expression and regulation
Sheng X, Wu J, Sun Q, Li X, Xian F, Sun M, Fang W, Chen M, Yu J, Xiao J
Brief Bioinform. 2016 Jan 27. pii: bbv117

A systematic transcriptome survey is essential for the characterization and comprehension of the molecular basis underlying phenotypic variations. Recently developed RNA-seq methodology has facilitated efficient data acquisition and information mining of transcriptomes in multiple tissues. Current mammalian transcriptomic databases are either tissue specific or species specific, and they lack in-depth comparative features across tissues and species. Here, we present a MTD that is focused on mammalian transcriptomes with a current version that contains data from humans, mice, rats and pigs. Regarding the core features, the MTD browses genes based on their neighboring genomic coordinates or joint KEGG pathway and provides expression information on exons, transcripts, and genes by integrating them into a genome browser. We developed a novel nomenclature for each transcript that considers its genomic position and transcriptional features. The MTD allows a flexible search of genes or isoforms with user-defined transcriptional characteristics and provides both table-based descriptions and associated visualizations. To elucidate the dynamics of gene expression regulation, the MTD also enables comparative transcriptomic analysis in both intraspecies and interspecies manner. The MTD thus constitutes a valuable resource for transcriptomic and evolutionary studies.

The MTD is freely accessible at  http://mtd.cbi.ac.cn/
Further connected papers => http://bigd.big.ac.cn/publications

MIQE guidelines

MIQE Press Review -- Latest news about the MIQE guidelines => MIQE-press.Gene-Quantification.info

Find a summary of MIQE related key publications and more => MIQE.gene-quantification.info

MIQE is a set of guidelines that describe the minimum information necessary for evaluating qPCR experiments.
The goal is:

  • ... to provide guidelines for authors, reviewers and editors to measure the technical quality of submitted manuscripts
  • ... to establish a clear framework to conduct quantitative RT‑PCR experiments
  • ... to support experimental transparency
  • ... to increase reproducibility between laboratories worldwide
  • ... to promote more consistent, more comparable, and more reliable results
  • ... to standardize international qPCR nomenclature

 => To increase reliability of results to help to insure the integrity of scientific work, with major focus on biological relevance

MIQE translations:  English (original version)   Chinese   Japanese   Arabian


Call  for Papers in Special Issue
in Biomolecular Detection and Quantification
The new online, open access, peer-reviewed journal in molecular methodology applications.

Recent Advances in  MicroGenomics - Molecular Analysis at the Tissue-specific and Single Cell  Level
Second International Symposium on MicroGenomics 2016
Guest Editors:  Claudia Bevilacqua & Michael W. Pfaffl

Biomolecular Detection and Quantification (BDQ) is an open access, peer-reviewed international journal dedicated to championing excellence in molecular study design, measurement, data analysis and reporting. Its focus is on the application of qualitative and quantitative molecular methodologies to all areas of clinical and life sciences. Download the recent BDQ papers on Elsevier Science  Direct.

  BDQ is listed in PubMed Central (PMC) -- all papers free for download!

The journal has two main aims:

  • to provide a forum for discussion and recommendation of guidelines designed to improve the accuracy of molecular measurement, its data analysis and the transparency of its subsequent reporting;
  • to publish molecular biology based studies that adhere to best practice guidelines, both current and future.

We look forward to receiving your paper!

Kind regards,

The Editors
Stephen Bustin, Jim Huggett, Justin O'Grady, Michael W. Pfaffl, Carl Wittwer, Ron Cook

View full editorial board


GenEx 6.1

The most powerful tool for complex qPCR data analysis

Compliant with MIQE and CLSI guidelines

GenEx offers advanced methods to analyze real-time qPCR data with simple mouse clicks

Download a FREE GenEx 6.1 trial version => GenEx.Gene-Quantification.info
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. GenEx 6.1 – the software compliant with MIQE and CLSI guidelines

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, Hierarchical Cluster Analysis (HCA), Heatmap, Principal Component Analysis (PCA, 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 GenEx 6.1 trail version => http://GenEx.gene-quantification.info


Best regards,

Michael W. Pfaffl
responsible Editor of the Gene Quantification Pages



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