Metabolomic and Transcriptomic data - in vitro ependymoma +/- serum starvation

Abstract

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–metabolite relationship. Here, we optimised a simultaneous extraction method of me-tabolites/lipids and RNA from ependymoma cells (BXD-1425). Two existing single extraction and four dual extraction protocols were critically assessed based on their practical reproducibility, the suitability of the metabolite extraction protocol to human cancer cells and their RNA recovery. The effectiveness of the optimised method was verified by testing the sensitivity to a) discriminate both subtle and profound altera-tions in transcription and metabolism in an acute serum starvation period in a human ependymoma cell line;