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 The birth of a new protein
20.10.2017 | University of Arizona

nachricht Building New Moss Factories
20.10.2017 | Albert-Ludwigs-Universität Freiburg im Breisgau

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Neutron star merger directly observed for the first time

University of Maryland researchers contribute to historic detection of gravitational waves and light created by event

On August 17, 2017, at 12:41:04 UTC, scientists made the first direct observation of a merger between two neutron stars--the dense, collapsed cores that remain...

Im Focus: Breaking: the first light from two neutron stars merging

Seven new papers describe the first-ever detection of light from a gravitational wave source. The event, caused by two neutron stars colliding and merging together, was dubbed GW170817 because it sent ripples through space-time that reached Earth on 2017 August 17. Around the world, hundreds of excited astronomers mobilized quickly and were able to observe the event using numerous telescopes, providing a wealth of new data.

Previous detections of gravitational waves have all involved the merger of two black holes, a feat that won the 2017 Nobel Prize in Physics earlier this month....

Im Focus: Smart sensors for efficient processes

Material defects in end products can quickly result in failures in many areas of industry, and have a massive impact on the safe use of their products. This is why, in the field of quality assurance, intelligent, nondestructive sensor systems play a key role. They allow testing components and parts in a rapid and cost-efficient manner without destroying the actual product or changing its surface. Experts from the Fraunhofer IZFP in Saarbrücken will be presenting two exhibits at the Blechexpo in Stuttgart from 7–10 November 2017 that allow fast, reliable, and automated characterization of materials and detection of defects (Hall 5, Booth 5306).

When quality testing uses time-consuming destructive test methods, it can result in enormous costs due to damaging or destroying the products. And given that...

Im Focus: Cold molecules on collision course

Using a new cooling technique MPQ scientists succeed at observing collisions in a dense beam of cold and slow dipolar molecules.

How do chemical reactions proceed at extremely low temperatures? The answer requires the investigation of molecular samples that are cold, dense, and slow at...

Im Focus: Shrinking the proton again!

Scientists from the Max Planck Institute of Quantum Optics, using high precision laser spectroscopy of atomic hydrogen, confirm the surprisingly small value of the proton radius determined from muonic hydrogen.

It was one of the breakthroughs of the year 2010: Laser spectroscopy of muonic hydrogen resulted in a value for the proton charge radius that was significantly...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

ASEAN Member States discuss the future role of renewable energy

17.10.2017 | Event News

World Health Summit 2017: International experts set the course for the future of Global Health

10.10.2017 | Event News

Climate Engineering Conference 2017 Opens in Berlin

10.10.2017 | Event News

 
Latest News

NRL clarifies valley polarization for electronic and optoelectronic technologies

20.10.2017 | Interdisciplinary Research

Metallic nanoparticles will help to determine the percentage of volatile compounds

20.10.2017 | Materials Sciences

Shallow soils promote savannas in South America

20.10.2017 | Earth Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>