PXD047606-2
PXD047606 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | A novel integrated extraction protocol for multi-omic studies in heavily degraded samples |
| 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 |
| HostingRepository | PRIDE |
| AnnounceDate | 2024-10-22 |
| AnnouncementXML | Submission_2024-10-22_06:53:44.817.xml |
| DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD047606 |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Supported dataset by repository |
| PrimarySubmitter | Konstantina Drosou |
| SpeciesList | scientific name: Sus scrofa domesticus (domestic pig); NCBI TaxID: 9825; |
| ModificationList | acetylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue |
| Instrument | Orbitrap Exploris 480 |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2023-12-07 03:12:42 | ID requested | |
| 1 | 2024-08-09 03:00:37 | announced | |
| ⏵ 2 | 2024-10-22 06:53:49 | announced | 2024-10-22: Updated project metadata. |
Publication List
| 10.1038/s41598-024-67104-8; |
| 10.6019/PXD047606; |
| Boggi B, Sharpen JDA, Taylor G, Drosou K, A novel integrated extraction protocol for multi-omic studies in heavily degraded samples. Sci Rep, 14(1):17477(2024) [pubmed] |
Keyword List
| submitter keyword: integrated protocol, multi-omics, ancient DNA, extraction protocol,pig brain, degraded omics |
Contact List
| Konstantina Drosou | |
|---|---|
| contact affiliation | Division of Cell Matrix Biology & Regenerative Medicine and KNH Centre for Biomedical Egyptology Faculty of Biology, Medicine and Health University of Manchester United Kingdom |
| contact email | konstantina.drosou@manchester.ac.uk |
| lab head | |
| Konstantina Drosou | |
| contact affiliation | University of Manchester |
| contact email | konstantina.drosou@manchester.ac.uk |
| dataset submitter | |
Full Dataset Link List
| Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/08/PXD047606 |
| PRIDE project URI |
Repository Record List
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