The Chromium Nuclei Isolation Kit offers a highly optimized protocol for isolating nuclei from frozen tissue samples for use in 10x Genomics Single Cell assays. The comprehensive kit streamlines the nuclei isolation process into a single, reproducible workflow. This Technical Note compares gene expression and chromatin accessibility data derived from nuclei isolated using the Chromium Nuclei Isolation Kit versus three alternative nuclei isolation methods in human jejunum, human kidney cancer, adult mouse kidney, and adult mouse brain tissue samples run on the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression assay.