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New Tool (iSRAP) Developed for Rapid Profiling of Small RNA-Seq Data

A new open-access article, published online today (November 12, 2015) in the Journal of Extracellular Vesicles (JEV), describes the development of a one-touch, integrated small RNA analysis pipeline (iSRAP) research tool that is composed of widely used tools for rapid profiling of small RNAs. The authors say that their performance test of the new iSRAP tool, using publicly and in-house available data sets, demosntrates its ability at comprehensive profiling of small RNAs of various classes, and at analysis of differentially expressed small RNAs. They further assert the the iSRAP tool offers comprehensive analysis of small RNA sequencing data that leverage informed decisions on the downstream analyses of small RNA studies, including those of extracellular vesicles (EVs) such as exosomes. In their article summary, the authors state the new iSRAP tool “provides a flexible and integrated environment for small RNA expression analysis using a single command. The flexible and powerful features of iSRAP enable a comprehensive analysis of small RNAs, which covers from quality assessment of input data to differential expression analysis and visualization of results with the ease of use. iSRAP can potentially serve as a platform for rapid analysis of transcriptomic data so that a better-informed decision can be made on the downstream analyses.” In the background for their report, the authors note that “small non-coding RNAs have been significantly recognized as the key modulators in many biological processes, and are emerging as promising biomarkers for several diseases.” They say that “these RNA species are transcribed in cells and can be packaged in extracellular vesicles, which are small vesicles released from many biotypes, and are involved in intercellular communication.”

Currently, they note, “the advent of next-generation sequencing (NGS) technology for high-throughput profiling has further advanced the biological insights of non-coding RNA on a genome-wide scale and has become the preferred approach for the discovery and quantification of non-coding RNA species.”

However, they argue, “despite the routine practice of NGS, the processing of large data sets poses difficulty for analysis before conducting downstream experiments.”

“Often, the current analysis tools are designed for specific RNA species, such as microRNA, and are limited in flexibility for modifying parameters for optimization.”

“An analysis tool that allows for maximum control of different software is essential for drawing concrete conclusions for differentially expressed transcripts.”

In their new JEV article, the La Trobe University authors describe their development of just such an analysis tool: iSRAP.

The new JEV article is titled “iSRAP - A One-Touch Research Tool for Rapid Profiling of Small RNA-seq Data.”

The senior author of the article is Andrew F. Hill (photo), Ph.D., Head of the Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia. In 2010, Dr. Hill was awarded the the Merck Research Excellence Medal from the Australian Society for Biochemistry and Molecular Biology, has also received numerous other prestigious awards and prizes. Dr. Hill is currently also Executive Chair (Communications), the International Socieity for Extracellular Vesicles (ISEV).

Additional authors of the new JEV aricle are also from Australia's La Trobe University and much of the work was carried out at the University of Melbourne, where Dr. Hill had been prior to LaTrobe..

[Journal of Extracellular Vesicles article]