Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Reliable RNA analysis now easier with NIST 'dashboard' tool

04.12.2014

A new, innovative "dashboard" from the National Institute of Standards and Technology (NIST) won't help you drive your car, but it will help enable reproducible research in biology.

In a recent paper in the journal Nature Communications,* an international multi-laboratory team demonstrates a new software tool, the "erccdashboard," to evaluate the performance of experimental methods used to study gene expression. The analysis tool is designed for use with RNA spike-in controls developed by the NIST-hosted External RNA Controls Consortium (ERCC**). These ERCC controls are produced from the DNA Sequence Library for External RNA Controls (Standard Reference Material 2374) that was issued by the agency in 2013.


This is an artist's conception of an RNA polymerase (globular molecule) creating strands of RNA (exiting the polymerase on the right) from a DNA template (entering the polymerase on the left). Known as RNA transcription, the process is the first step in gene expression, the carrying out of biological functions as directed by DNA. Researchers studying gene expression can use a new NIST software tool to evaluate the performance of their experimental methods and be confident that the results are valid.

Credit: © 2014 John Liebler, www.ArtoftheCell.com

"In gene expression experiments, scientists try to understand how a cell's biological activities arise from the genetic information contained in its genome by simultaneously quantifying the thousands of RNA molecules expressed by that genome," says Sarah Munro, lead author on the Nature Communications paper.

Munro says that the validation provided by the erccdashboard is essential to ensure that these complex experiments are reproducible. "The results of gene expression experiments are often used in making medical decisions such as identifying which drug is best for a particular patient," she explains. "Our new software tool gives researchers the ability to gauge the performance of their methods for any experiment, evaluate repeatability and reproducibility of experiments over time and between laboratories, and provide confidence that the results can be trusted."

The erccdashboard provides the first standardized approach for any lab to evaluate the quality of its gene expression analyses. The ERCC spike-in control materials are derived from NIST SRM 2374, which consists of 96 different DNA molecules, each with a specific certified gene sequence. The distinct RNA molecules produced from this DNA can be mixed together in a "cocktail" of defined proportions and then used to "spike" biological samples of RNA molecules.

The RNA "spike-in" molecules act as controls to check the technical performance of the experiment. To avoid interfering with the measurements made of the sample RNA molecules, the ERCC control RNA sequences are designed to be different from the RNA sequences found in the types of mammalian cells that many researchers study, such as human or mouse cells.

Previously, Munro says, there was no standard, technology-independent approach for analyzing the data obtained from gene expression experiments. "The ERCC control materials made the development of our new method validation tool, the erccdashboard, possible," she explains.

The new NIST software, Munro says, provides a simple 'turnkey' mechanism for biologists to assess any gene expression experiment. "Its performance metrics are designed to be independent of the type of measurement technology used for an experiment, so results can be compared as technologies improve over time," she says. "Using the dashboard will enable reproducible research and prevent researchers from drawing erroneous conclusions from low-quality experimental data."

Munro says that the next goal for the NIST team that developed the dashboard is to apply the software to analyze a new suite of RNA control molecules that the ERCC is currently developing. Eventually, the team plans to extend the tool for use with protein measurements.

Free of charge to users, the erccdashboard software is an open source code written in the R statistical language. It can be downloaded from the Bioconductor repository and is easily incorporated into other analysis software packages.

* S.A. Munro, S.P. Lund, P.S. Pine, H. Binder, D-A. Clevert, A. Conesa, J. Dopazo, M. Fasold, S. Hochreiter, H. Hong, N. Jafari, D.P. Kreil, P.P. Labaj, S. Li, Y. Liao, S.M. Lin, J. Meehan, C.E. Mason, J. Santoyo-Lopez, R.A. Setterquist, L. Shi, W. Shi, G.K. Smyth, N. Stralis-Pavese, Z. Su, W. Tong, C. Wang, J. Wang, J. Xu, Z. Ye, Y. Yang, Y. Yu and M. Salit. Assessing Technical Performance in Differential Gene Expression Experiments with External Spike-in RNA Control Ratio Mixtures. Nature Communications 5, 2014, DOI: 10.1038/ncomms6125.

**ERCC, which stands for the External RNA Controls Consortium, is an industry-initiated, NIST-hosted consortium with members from more than 90 international pharmaceutical, diagnostic, biotechnology, academic, clinical and government organizations. The ERCC is charged with developing commonly agreed-upon and tested RNA controls for use in gene expression assays.

Michael E. Newman | EurekAlert!
Further information:
http://www.nist.gov

More articles from Life Sciences:

nachricht New risk factors for anxiety disorders
24.02.2017 | Julius-Maximilians-Universität Würzburg

nachricht Stingless bees have their nests protected by soldiers
24.02.2017 | Johannes Gutenberg-Universität Mainz

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Breakthrough with a chain of gold atoms

In the field of nanoscience, an international team of physicists with participants from Konstanz has achieved a breakthrough in understanding heat transport

In the field of nanoscience, an international team of physicists with participants from Konstanz has achieved a breakthrough in understanding heat transport

Im Focus: DNA repair: a new letter in the cell alphabet

Results reveal how discoveries may be hidden in scientific “blind spots”

Cells need to repair damaged DNA in our genes to prevent the development of cancer and other diseases. Our cells therefore activate and send “repair-proteins”...

Im Focus: Dresdner scientists print tomorrow’s world

The Fraunhofer IWS Dresden and Technische Universität Dresden inaugurated their jointly operated Center for Additive Manufacturing Dresden (AMCD) with a festive ceremony on February 7, 2017. Scientists from various disciplines perform research on materials, additive manufacturing processes and innovative technologies, which build up components in a layer by layer process. This technology opens up new horizons for component design and combinations of functions. For example during fabrication, electrical conductors and sensors are already able to be additively manufactured into components. They provide information about stress conditions of a product during operation.

The 3D-printing technology, or additive manufacturing as it is often called, has long made the step out of scientific research laboratories into industrial...

Im Focus: Mimicking nature's cellular architectures via 3-D printing

Research offers new level of control over the structure of 3-D printed materials

Nature does amazing things with limited design materials. Grass, for example, can support its own weight, resist strong wind loads, and recover after being...

Im Focus: Three Magnetic States for Each Hole

Nanometer-scale magnetic perforated grids could create new possibilities for computing. Together with international colleagues, scientists from the Helmholtz Zentrum Dresden-Rossendorf (HZDR) have shown how a cobalt grid can be reliably programmed at room temperature. In addition they discovered that for every hole ("antidot") three magnetic states can be configured. The results have been published in the journal "Scientific Reports".

Physicist Dr. Rantej Bali from the HZDR, together with scientists from Singapore and Australia, designed a special grid structure in a thin layer of cobalt in...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Booth and panel discussion – The Lindau Nobel Laureate Meetings at the AAAS 2017 Annual Meeting

13.02.2017 | Event News

Complex Loading versus Hidden Reserves

10.02.2017 | Event News

International Conference on Crystal Growth in Freiburg

09.02.2017 | Event News

 
Latest News

Stingless bees have their nests protected by soldiers

24.02.2017 | Life Sciences

New risk factors for anxiety disorders

24.02.2017 | Life Sciences

MWC 2017: 5G Capital Berlin

24.02.2017 | Trade Fair News

VideoLinks
B2B-VideoLinks
More VideoLinks >>>