MSGID: 1:317/3 6451e35d   
   PID: hpt/lnx 1.9.0-cur 2019-01-08   
   TID: hpt/lnx 1.9.0-cur 2019-01-08   
    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   
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   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.   
      
      
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   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   
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   Link to news story:   
   https://www.sciencedaily.com/releases/2023/05/230502201354.htm   
      
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