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

Date:
May 2, 2023
Source:
Van Andel Research Institute
Summary:
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.


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FULL STORY ==========================================================================
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'sMass Spectrometry Core,Pathobiology and Biorepository Core,Bioinformatics and Biostatistics CoreandGenomics Coreplayed key
roles in protocol development.

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

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========================================================================== Story Source: Materials provided by Van_Andel_Research_Institute. Note:
Content may be edited for style and length.


========================================================================== Journal Reference:
1. Zachary B Madaj, Michael S. Dahabieh, Vijayvardhan Kamalumpundi,
Brejnev
Muhire, J. Pettinga, Rebecca A. Siwicki, Abigail E. Ellis,
Christine Isaguirre, Martha L. Escobar Galvis, Lisa DeCamp, Russell
G. Jones, Scott A. Givan, Marie Adams, Ryan D. Sheldon. Prior
metabolite extraction fully preserves RNAseq quality and
enables integrative multi-`omics analysis of the liver metabolic
response to viral infection. RNA Biology, 2023; 20 (1): 186 DOI:
10.1080/15476286.2023.2204586 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2023/05/230502201354.htm

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