Scientists at the Van Andel Institute have developed a new extraction protocol for RNA-seq and metabolomic analysis, which offers a more complete picture of cell activity than either technique alone.
The protocol employs simplified single-sample extraction, which reduces variation, improves efficiency, preserves data fidelity, and maximizes the use of valuable biological samples.
“Our new technique allows researchers to study metabolic phenotypes in a unique way and obtain as much information as possible from individual samples,” said Ryan Sheldon, Ph.D., director of VAI’s Mass Spectrometry Core. “Most importantly, no information is lost when 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.
Today’s workflow can also make multi-omics approaches challenging, especially on infrequent sample types; the extraction process destroys the sample, preventing further analysis.
To validate the protocol, the research team compared the results of the standard extraction with the results of the new approach. The findings clearly showed that 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 from Core Technologies and Services and VAI’s 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 unique 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, MS, Michael S. Dahabieh, Ph.D., Vijayvardhan Kamalumpundi, Brejnev Muhire, Ph.D., Dean J. Pettinga, Rebecca A. Siwicki, MS, 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, MS, of VAI. from high school mass spectrometry core, Pathobiology and Biorepository Nucleus, Bioinformatics and Biostatistics Nucleus and genomics core played a key role in the development of the protocol.
The research reported in this publication was supported by the Van Andel Institute.
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