Project description:MicroRNAs are important negative regulators of protein coding gene expression, and have been studied intensively over the last few years. To this purpose, different measurement platforms to determine their RNA abundance levels in biological samples have been developed. In this study, we have systematically compared 12 commercially available microRNA expression platforms by measuring an identical set of 20 standardized positive and negative control samples, including human universal reference RNA, human brain RNA and titrations thereof, human serum samples, and synthetic spikes from homologous microRNA family members. We developed novel quality metrics in order to objectively assess platform performance of very different technologies such as small RNA sequencing, RT-qPCR and (microarray) hybridization. We assessed reproducibility, sensitivity, quantitative performance, and specificity. The results indicate that each method has its strengths and weaknesses, which helps guiding informed selection of a quantitative microRNA gene expression platform in function of particular study goals.
Project description:The simultaneous analysis of the proteome and metabolome in biological samples is essential for advancing systems biology, enabling a deeper understanding of molecular mechanisms governing diverse biological processes. This study compares three extraction methods: the Bligh and Dyer method, the Matyash method, and a simple methanol extraction technique. This study was conduct on lyophilized potato tuber powder, a complex matrix containing starches, proteins, and a variety of metabolites. With the use of high-resolution mass spectrometry (HRMS), specifically nanoLC-MS/MS and direct infusion Fourier transform ion cyclotron resonance mass spectrometry (DI-FT-ICR-MS), we aimed to select one of these extraction methods to understand the behaviours of several potato cultivar facing cold stress. Our findings indicate that the Matyash and methanol extraction methods provided superior performance and reproducibility for proteomic analysis, while all methods offered similar results in metabolomic profiling. Moreover, the dual-phase extraction from the Bligh and Dyer and Matyash methods revealed distinct and complementary datasets, emphasizing the importance of multi-phase approaches for comprehensive molecular characterization. Despite some redundancy observed between polar and apolar phases, the overall analysis highlights the necessity of optimal extraction techniques for future proteomic and metabolomic studies. These results enhance our understanding of the potato tuber’s biological landscape.
Project description:In order to determine whether dis-regulation of a genetic pathway could explain the increased apoptosis of parp-2-/- double positive thymocytes, the gene expression profiles in double positive thymocytes derived from wild-type and parp-2-/- mice were analysed using Affymetrix oligonucleotide chips (mouse genome 430 2.0).