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New RNA-seq, metabolomics protocol offers more efficient extraction that maintains data integrity

GRAND RAPIDS, Mich. (May 2, 2023)Van Andel Institute scientists have developed a new extraction protocol for RNA-seq and metabolomic analysis, offering a more complete picture of cellular activity than either technique on its own.

The protocol employs a streamlined extraction from a single sample, which reduces variation, improves efficiency, preserves data fidelity and maximizes use of precious biospecimens.

“Our new technique enables researchers to study metabolic phenotypes in a unique way while getting the most information we can out of single samples,” said Ryan Sheldon, Ph.D., director of VAI’s Mass Spectrometry Core. “The most important takeaway is there is no loss of information by using our new, more efficient protocol.”

Until now, scientists have had to use two sample extractions — one for RNA-seq and one for metabolomics. This approach requires multiple samples or a single sample divided into subsamples, which increases variation and has an unknown impact on data interpretation.

The current workflow also can make multi-omics approaches challenging, especially in rare sample types; the extraction process destroys the sample, precluding additional analysis.

To validate the protocol, the research team compared results from the standard extraction to results from the new approach. The findings clearly showed the new protocol preserved data quality while saving time and resources.

The new protocol is published in the journal RNA Biology. It was developed by scientists in VAI’s Core Technologies and Services and Department of Metabolism and Nutritional Programming. Core Technologies and Services provides state-of-the-art technologies and expertise to Institute scientists and collaborators.

“Our new strategy offers an important proof-of-concept for future efforts to incorporate additional-omics approaches, with the goal of creating a singular extraction pipeline for RNA-seq, metabolomics, proteomics, transcriptomics, and others,” Sheldon said. “This work would not have been possible without the exceptional Core Technologies and Services team here at VAI and the Institute’s commitment to collaboration and rigorous science.”

Authors include Zachary B. Madaj, M.S., Michael S. Dahabieh, Ph.D., Vijayvardhan Kamalumpundi, Brejnev Muhire, Ph.D., Dean J. Pettinga, Rebecca A. Siwicki, M.S., Abigail E. Ellis, Christine Isaguirre, Martha L. Escobar Galvis, Ph.D., Lisa DeCamp, Russell G. Jones, Ph.D., Scott A. Givan, Ph.D., Marie Adams, M.S., of VAI. The Institute’s Mass Spectrometry Core, Pathobiology and Biorepository Core, Bioinformatics and Biostatistics Core and Genomics Core played key roles in protocol development.

Research reported in this publication was supported by Van Andel Institute.

Banner image credit: Madaj ZB, Dahabieh MS, Kamalumpundi V, Muhire B, Pettinga J, Siwicki RA, Ellis AE, Isaguirre C, Escobar Galvis ML, DeCamp L, Jones RG, Givan SA, Adams M, Sheldon RD. 2023. Prior metabolite extraction fully preserves RNAseq quality and enables integrative multi-omics analysis of liver metabolic response to viral infection. RNA Biol 20(1).

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Van Andel Institute (VAI) is committed to improving the health and enhancing the lives of current and future generations through cutting-edge biomedical research and innovative educational offerings. Established in Grand Rapids, Michigan, in 1996 by the Van Andel family, VAI is now home to nearly 500 scientists, educators and support staff, who work with a growing number of national and international collaborators to foster discovery. The Institute’s scientists study the origins of cancer, Parkinson’s and other diseases and translate their findings into breakthrough prevention and treatment strategies. Our educators develop inquiry-based approaches for K-12 education to help students and teachers prepare the next generation of problem-solvers, while our Graduate School offers a rigorous, research-intensive Ph.D. program in molecular and cellular biology.