Important facilities and tools used within RIMLS-Science include next generation sequencing, mass spectrometry, single cell (multi-omics) analysis and computational analysis and method development. To perform state-of-the-art research, RIMLS operates its own wet-lab and computational facilities.
The sequencing facility is a dedicated research infrastructure that provides support for Next Generation Sequencing (NGS) based projects for research groups in and outside Nijmegen. The aim is to stimulate research and innovation by sharing expertise, providing access to NGS technologies, and increasing knowledge transfer. This enables stronger interaction and collaborations between different research teams, further stimulated through the embedding of the facility within an active research department.
The institute operates a state-of-the-art single cell RNA-sequencing infrastructure. It encompasses CEL-seq2 in 384-well format, including in-house cell sorting (BD FACSMelody) and automated nanolitre dispensing (GC Biotech Nanodrop II) for cDNA generation, as well as the commercial 10X genomics and Dolomite Nadia (Drop-seq) platforms.
The main focus of the research is on protein interactions with either other proteins or nucleic acids. In addition, (phospho)proteomes are analysed to study changes in protein (expression) levels upon differentiation or during disease. Several affinity purification methods such as GFP pull-down (or other epitope tag), DNA pull-down, peptide pull-down, proximity ligation, as well as whole (phospho)proteome analysis are applied. Different (semi)quantitative methods, such as label-free quantification, dimethyl labelling, SILAC, and TMT labelling, all having their own advantages and disadvantages, are used. For protein analysis, a Thermo Scientific Orbitrap Fusion tribrid and a Thermo Scientific Orbitrap Exploris 480 mass spectrometer are operated, the latter with or without the FAIMS module.