{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,4]],"date-time":"2026-03-04T10:12:04Z","timestamp":1772619124632,"version":"3.50.1"},"reference-count":59,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2021,4,14]],"date-time":"2021-04-14T00:00:00Z","timestamp":1618358400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Stoneygate Trust","award":["CARO\/SS\/2016\/CC1"],"award-info":[{"award-number":["CARO\/SS\/2016\/CC1"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Metabolites"],"abstract":"<jats:p>The integration of untargeted metabolomics and transcriptomics from the same population of cells or tissue enhances the confidence in the identified metabolic pathways and understanding of the enzyme\u2013metabolite relationship. Here, we optimised a simultaneous extraction method of metabolites\/lipids and RNA from ependymoma cells (BXD-1425). Relative to established RNA (mirVana kit) or metabolite (sequential solvent addition and shaking) single extraction methods, four dual-extraction techniques were evaluated and compared (methanol:water:chloroform ratios): cryomill\/mirVana (1:1:2); cryomill-wash\/Econospin (5:1:2); rotation\/phenol-chloroform (9:10:1); Sequential\/mirVana (1:1:3). All methods extracted the same metabolites, yet rotation\/phenol-chloroform did not extract lipids. Cryomill\/mirVana and sequential\/mirVana recovered the highest amounts of RNA, at 70 and 68% of that recovered with mirVana kit alone. sequential\/mirVana, involving RNA extraction from the interphase of our established sequential solvent addition and shaking metabolomics-lipidomics extraction method, was the most efficient approach overall. Sequential\/mirVana was applied to study a) the biological effect caused by acute serum starvation in BXD-1425 cells and b) primary ependymoma tumour tissue. We found (a) 64 differentially abundant metabolites and 28 differentially expressed metabolic genes, discovering four gene-metabolite interactions, and (b) all metabolites and 62% lipids were above the limit of detection, and RNA yield was sufficient for transcriptomics, in just 10 mg of tissue.<\/jats:p>","DOI":"10.3390\/metabo11040240","type":"journal-article","created":{"date-parts":[[2021,4,14]],"date-time":"2021-04-14T15:30:39Z","timestamp":1618414239000},"page":"240","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Integrated Metabolomics and Transcriptomics Using an Optimised Dual Extraction Process to Study Human Brain Cancer Cells and Tissues"],"prefix":"10.3390","volume":"11","author":[{"given":"Alison","family":"Woodward","sequence":"first","affiliation":[{"name":"Children\u2019s Brain Tumour Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alina","family":"Pandele","sequence":"additional","affiliation":[{"name":"Children\u2019s Brain Tumour Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Salah","family":"Abdelrazig","sequence":"additional","affiliation":[{"name":"Centre for Analytical Bioscience, Advanced Materials and Healthcare Division, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Catherine A.","family":"Ortori","sequence":"additional","affiliation":[{"name":"Centre for Analytical Bioscience, Advanced Materials and Healthcare Division, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Iqbal","family":"Khan","sequence":"additional","affiliation":[{"name":"National Arabidopsis Stock Centre, Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham NG7 2RD, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marcos Castellanos","family":"Uribe","sequence":"additional","affiliation":[{"name":"National Arabidopsis Stock Centre, Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham NG7 2RD, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5282-3250","authenticated-orcid":false,"given":"Sean","family":"May","sequence":"additional","affiliation":[{"name":"National Arabidopsis Stock Centre, Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham NG7 2RD, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David A.","family":"Barrett","sequence":"additional","affiliation":[{"name":"Centre for Analytical Bioscience, Advanced Materials and Healthcare Division, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard G.","family":"Grundy","sequence":"additional","affiliation":[{"name":"Children\u2019s Brain Tumour Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3689-2130","authenticated-orcid":false,"given":"Dong-Hyun","family":"Kim","sequence":"additional","affiliation":[{"name":"Centre for Analytical Bioscience, Advanced Materials and Healthcare Division, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6541-9983","authenticated-orcid":false,"given":"Ruman","family":"Rahman","sequence":"additional","affiliation":[{"name":"Children\u2019s Brain Tumour Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2021,4,14]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12931-017-0631-9","article-title":"Using omics approaches to understand pulmonary diseases","volume":"18","author":"Kan","year":"2017","journal-title":"Respir. 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