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 How brains surrender to sleep
23.06.2017 | IMP - Forschungsinstitut für Molekulare Pathologie GmbH

nachricht A new technique isolates neuronal activity during memory consolidation
22.06.2017 | Spanish National Research Council (CSIC)

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Can we see monkeys from space? Emerging technologies to map biodiversity

An international team of scientists has proposed a new multi-disciplinary approach in which an array of new technologies will allow us to map biodiversity and the risks that wildlife is facing at the scale of whole landscapes. The findings are published in Nature Ecology and Evolution. This international research is led by the Kunming Institute of Zoology from China, University of East Anglia, University of Leicester and the Leibniz Institute for Zoo and Wildlife Research.

Using a combination of satellite and ground data, the team proposes that it is now possible to map biodiversity with an accuracy that has not been previously...

Im Focus: Climate satellite: Tracking methane with robust laser technology

Heatwaves in the Arctic, longer periods of vegetation in Europe, severe floods in West Africa – starting in 2021, scientists want to explore the emissions of the greenhouse gas methane with the German-French satellite MERLIN. This is made possible by a new robust laser system of the Fraunhofer Institute for Laser Technology ILT in Aachen, which achieves unprecedented measurement accuracy.

Methane is primarily the result of the decomposition of organic matter. The gas has a 25 times greater warming potential than carbon dioxide, but is not as...

Im Focus: How protons move through a fuel cell

Hydrogen is regarded as the energy source of the future: It is produced with solar power and can be used to generate heat and electricity in fuel cells. Empa researchers have now succeeded in decoding the movement of hydrogen ions in crystals – a key step towards more efficient energy conversion in the hydrogen industry of tomorrow.

As charge carriers, electrons and ions play the leading role in electrochemical energy storage devices and converters such as batteries and fuel cells. Proton...

Im Focus: A unique data centre for cosmological simulations

Scientists from the Excellence Cluster Universe at the Ludwig-Maximilians-Universität Munich have establised "Cosmowebportal", a unique data centre for cosmological simulations located at the Leibniz Supercomputing Centre (LRZ) of the Bavarian Academy of Sciences. The complete results of a series of large hydrodynamical cosmological simulations are available, with data volumes typically exceeding several hundred terabytes. Scientists worldwide can interactively explore these complex simulations via a web interface and directly access the results.

With current telescopes, scientists can observe our Universe’s galaxies and galaxy clusters and their distribution along an invisible cosmic web. From the...

Im Focus: Scientists develop molecular thermometer for contactless measurement using infrared light

Temperature measurements possible even on the smallest scale / Molecular ruby for use in material sciences, biology, and medicine

Chemists at Johannes Gutenberg University Mainz (JGU) in cooperation with researchers of the German Federal Institute for Materials Research and Testing (BAM)...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Plants are networkers

19.06.2017 | Event News

Digital Survival Training for Executives

13.06.2017 | Event News

Global Learning Council Summit 2017

13.06.2017 | Event News

 
Latest News

Quantum thermometer or optical refrigerator?

23.06.2017 | Physics and Astronomy

A 100-year-old physics problem has been solved at EPFL

23.06.2017 | Physics and Astronomy

Equipping form with function

23.06.2017 | Information Technology

VideoLinks
B2B-VideoLinks
More VideoLinks >>>