A novel integrated extraction protocol for multi-omic studies in heavily degraded samples
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ABSTRACT:
PROVIDER: PRJEB61253 | ENA |
REPOSITORIES: ENA
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Project description:The combination of multi-omic techniques, e.g. genomics, transcriptomics, proteomics, metabolomics and epigenomics has revolutionised studies in medical research. These are employed to support biomarker discovery, better understand molecular pathways and identify novel drug targets. Despite concerted efforts in integrating omic datasets, there is an absence for the integration of all four biomolecules in a single extraction protocol. Here, we demonstrate for the first time a novel, minimally destructive integrated protocol for the simultaneous extraction of artificially degraded DNA, proteins, lipids and metabolites from pig brain samples. We used an MTBE-based approach to separate lipids and metabolites, followed by subsequent isolation of DNA and proteins. We have validated this protocol against standalone extraction protocols and show comparable or higher yield of all four biomolecules. This integrated protocol is key towards facilitating preservation of irreplaceable samples while promoting downstream analyses and successful data integration by removing bias from univariate dataset noise and varied distribution characteristics. Keywords: deg
2024-08-09 | PXD047606 | Pride
Project description:The combination of multi-omic techniques, such as genomics, transcriptomics, proteomics, metabolomics and epigenomics, has revolutionised studies in medical research. These techniques are employed to support biomarker discovery, better understand molecular pathways and identify novel drug targets. Despite concerted efforts in integrating omic datasets, there is an absence of protocols that integrate all four biomolecules in a single extraction process. Here, we demonstrate for the first time a minimally destructive integrated protocol for the simultaneous extraction of artificially degraded DNA, proteins, lipids and metabolites from pig brain samples. We used an MTBE-based approach to separate lipids and metabolites, followed by subsequent isolation of DNA and proteins. We have validated this protocol against standalone extraction protocols and show comparable or higher yields of all four biomolecules. This integrated protocol is key to facilitating the preservation of irreplaceable samples while promoting downstream analyses and successful data integration by removing bias from univariate dataset noise and varied distribution characteristics.
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Project description:Archaeological materials are a finite resource, and efforts should be made to minimize destructive analyses. This can be achieved by using protocols combining extraction of several lines of evidence, which decreases the material needed for analyses while maximizing the information yield. Archaeological dental calculus is a source of several different types of biomolecules, as well as microfossils, and can tell us about the human host, microbiome, diet, and even occupational activities. Here, we present a unified protocol allowing for simultaneous extraction of DNA and proteins from archaeological dental calculus. We evaluate the protocol on dental calculus from a range of ages and estimated preservation states, and compare it against standard DNA-only and protein-only protocols. We find that most aspects of downstream analyses are unaffected by the unified protocol, although minor shifts in the recovered proteome can be detected. Protein recovery depends on both the amount of starting material and choice of extraction protocol, whereas DNA recovery is significantly lowered through the unified protocol. However, DNA recovery from dental calculus is generally very high, and we found no differences in DNA fragment characteristics or taxonomic profile. In conclusion, the unified protocol allows for simultaneous extraction of two complementary lines of evidence from archaeological dental calculus without compromising downstream analyses, thereby minimizing the need for destructive analysis of this finite resource.
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