RNA-Seq for the Next Generation

RNA-Seq for the Next Generation

The RNA-Seq for the Next Generation site supports a three-year NSF-funded project to develop a sustainable infrastructure and training program to assist undergraduate faculty in integrating RNA-Seq next-generation sequence (NGS) analysis into course-based and independent student research.

In June 2014, several faculty participated in a Working Group Retreat at Cold Spring Harbor Laboratory. In Years 2 and 3, regional and virtual workshops were held for 80 faculty from diverse institutions and regions of the country. Project goals include instructing faculty teams to use the Green Line of DNA Subway, a bioinformatics RNA-Seq data analysis pipeline, and facilitating faculty collaboration to produce curricula and lesson plans.

Data analysis uses large-scale data storage, bioinformatics workflows, and high performance computing provided by the iPlant Collaborative now CyVerse, an NSF-supported cyberinfrastructure for biological research. Primary training will transition from in-person workshops to online webinars and self-paced learning via the RNA-Seq website, providing a sustainable method to introduce large numbers of faculty to NGS analysis.

NGS methods have dramatically decreased the cost of obtaining whole genome data on eukaryotic organisms, and data storage and analysis workflows are becoming freely available online. In particular, RNA-Seq can provide novel data on gene structure and function. This project is helping move undergraduate education into an age when students work with whole genome sequences as routinely as they work with PCR amplicons today. This project operates on the continuum of biology research and education. It recognizes that many college faculty would like to bring NGS to bear on a problem of their own interest – and invite students as co-investigators in class-based and independent projects. The program is preparing faculty to operate in a new, sequence-driven paradigm and empower them to guide students in novel genome explorations.

Free online tools have made sophisticated genome analysis available to anyone with an Internet connection. This project is further extending the egalitarian nature of genome research by providing an infrastructure for undergraduate faculty to generate and analyze their own genome-scale datasets. The project also provides faculty at predominately teaching institutions access to high performance computing through the NSF's Extreme Science and Engineering Discovery Environment (XSEDE). The Green Line of DNA Subway is an educational workflow specifically designed to support student analysis of RNA-Seq data sets. Advanced applications, including command line customization, are supported in the research-grade Discovery Environment. This infrastructure is making it possible to broadly disseminate on-demand experiments using RNA-Seq in undergraduate settings.

Visit the RNA-Seq for the Next Generation website for more information.