Researchers at the Van Andel Institute have created a new extraction protocol for RNA-seq and metabolomic analysis that provides a more comprehensive picture of cellular activity than either technique alone.
Image Credit: Madaj, Z., et al. (2023), RNA Biology.
The protocol uses a simplified extraction from a single sample, which lowers variation, improves efficiency, maintains data fidelity, and maximizes the utilization of valuable 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. The most important takeaway is there is no loss of information by using our new, more efficient protocol.”
Ryan Sheldon PhD, Director, Mass Spectrometry Core, Van Andel Institute
Till now, researchers had to use two different sample extraction methods: one for RNA-seq and another for metabolomics. This method necessitates the collection of many samples or the division of a single sample into subsamples, which increases variation and has an undetermined impact on data interpretation.
The existing workflow can also make multi-omics techniques difficult, particularly in unusual sample types; the extraction process destroys the sample, precluding further analysis.
To validate the protocol, the study team compared standard extraction findings to innovative approach outcomes. The results demonstrated that the new protocol kept data quality while saving time and resources.
The new protocol was published in RNA Biology. Scientists from VAI’s Core Technologies and Services and the Department of Metabolism and Nutritional Programming developed the protocol. Core Technologies and Services offers state-of-the-art technologies and expertise to Institute researchers and associates.
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. 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.”
Ryan Sheldon PhD, Director, Mass Spectrometry Core, Van Andel Institute
Source:
Journal reference:
Madaj, Z., et al. (2023). Prior metabolite extraction fully preserves RNAseq quality and enables integrative multi-‘omics analysis of the liver metabolic response to viral infection. RNA Biology. doi.org/10.1080/15476286.2023.2204586.
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