Institut Pasteur, Universite Paris Cite, INSERM U1224 1 article published in JoVE Biology High-Quality Brain and Bone Marrow Nuclei Preparation for Single Nuclei Multiome Assays Carolina Moraes Cabé1, Sophie Novault1, Ana Jeemin Choi2, Valerie Seffer1, Laura Barrio Cano1, Valentina Libri1,3, Milena Hasan1 1Cytometry and Biomarkers UTechS, C2RT, Institut Pasteur, Université Paris Cité, 2Microenvironment and Immunity Unit, Institut Pasteur, Université Paris Cité, INSERM U1224, 3Istituto Superiore di Sanità The success of single-cell/single-nuclei transcriptomics and multi-omics largely depends on the quality of cells/nuclei. Therefore, isolating cells/nuclei from tissue and their purification must be highly standardized. This protocol describes the preparation of nuclei from the brain and bone marrow for downstream single-nuclei multiome assay.