Novel Technology for RNA-Seq Extends to a Broad Range of Transcript Species

~Improved RNA-Seq data quality and lower sequencing costs enabled

SAN CARLOS, Calif.–()–NuGEN Technologies, Inc., a market leader in the development of sample preparation solutions for Next Generation Sequencing (NGS) applications, has developed a novel solution that enables more informative data to be generated from RNA-Seq studies performed with challenging samples, including model organisms. Human and non-human samples often have uninformative transcript species present in high abundance that can compromise data quality and cost-effectiveness of sequencing. NuGEN’s proprietary technology provides targeted depletion of a broad range of uninformative transcripts, a solution not addressed by standard library preparation methods for RNA-Seq.

“Further flexibility of this technology is demonstrated by NuGEN’s customers with the successful application to a broad range of model organisms.”

NuGEN’s novel method, Insert Dependent Adaptor Cleavage (InDA-C), employs primers during library creation to target specific transcripts for depletion in the final library and is the core technology employed in the Ovation Universal RNA-Seq Library System. Importantly, the method does not perturb the original total RNA input to the workflow. NuGEN provides a no-cost design service to assist researchers in choosing InDA-C primers, and primers can be designed for use with virtually any organism. The result is a significant reduction in sequencing reads derived from unwanted transcripts, including ribosomal RNA, globin and protein-coding RNAs, such as housekeeping genes. Unlike methods that use hybridization-mediated pull-down strategies to deplete unwanted RNA species, the InDA-C method avoids off-target mRNA cross-hybridization events that can potentially introduce bias.

“The InDA-C method is a unique and robust solution utilized previously in our Ovation Human Blood and FFPE RNA-Seq Systems for the removal of human reticulocyte globin and ribosomal RNA,” said Alan Dance, Vice President of Marketing at NuGEN. “Further flexibility of this technology is demonstrated by NuGEN’s customers with the successful application to a broad range of model organisms.”

Dr. Jason Wood, an Investigator at Brown University, commented, “We sequence Drosophila samples, and commercial library prep systems targeted at human/mouse rRNA depletion are ineffective, leaving about 70% of our total reads aligning to rRNA. With the InDA-C technology, using primers specifically targeting Drosophila rRNA, we were able to reduce this to 10-15% of total reads aligning to rRNA. This translates into far fewer reads being discarded, which drops our sequencing costs dramatically. We have been very satisfied with this technology in terms of performance, cost, workflow, and input requirements, and in fact have switched all of our RNA-Seq projects over to the NuGEN system.”

IGA Technology Services, an NGS service provider, has utilized the InDA-C technology for plant genome studies. Dr. Federica Cattonaro, NGS Lab Manager, stated, “We performed targeted depletion of rRNA in grape RNA-Seq libraries using InDA-C. The percentage of informative sequencing reads increased from 25% to about 56% with NuGEN’s InDA-C technology. This is a marked improvement that enables us to capture more meaningful data at a lower cost. We are now expanding the InDA-C primer design to target and deplete chloroplast RNA, another undesirable transcript species.”

The Ovation Universal RNA-Seq System is the core kit for the customizable InDA-C solution. Preconfigured modules will be available soon for Arabidopsis, Drosophila and Mouse. The InDA-C technology is also employed in both the Ovation Human FFPE RNA-Seq System and the Ovation Human Blood RNA-Seq Systems.

About NuGEN

NuGEN Technologies is a San Carlos, CA company focused on innovative sample preparation solutions for RNA and DNA that enable life scientists to do more with less. With reagent solutions that are quick, easy to use, and amenable to automation, NuGEN empowers researchers to prepare genomic samples of any size, from almost any source, regardless of the intended application or technology platform. For more information please visit

Ovation and NuGEN are registered trademarks of NuGEN Technologies, Inc.


NuGEN Technologies, Inc.
Carol Short, 650-590-3002
[email protected]