Question: Which nuclei isolation protocol should I use for the Single Cell Multiome ATAC + Gene Expression assay?
Answer: The following flow chart has our recommended starting points for isolating nuclei from different sample types:
The protocols are linked here:
- Chromium Nuclei Isolation Kit Sample Prep User Guide (CG000505) and Chromium Nuclei Isolation Kit Tested Tissues
- Nuclei Isolation from Complex Tissues for Single Cell Multiome ATAC + Gene Expression Sequencing (CG000375)
- Nuclei Isolation from Embryonic Mouse Brain Tissue for Single Cell Multiome ATAC + Gene Expression Sequencing (CG000366)
- Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing (CG000365)
Additional optimization may be required to obtain high quality nuclei. We expect that the Chromium Nuclei Isolation Kit will require less optimization than the other Demonstrated Protocols for which we recommend lysis timelines and rigorous assessment of nuclei under high magnification brightfield microscopy to determine the most appropriate lysis time (see How can I assess the quality of my nuclei for Single Cell ATAC or Single Cell Multiome ATAC+GEX Sequencing?).
We have not tested and do not support enrichment of nuclei subpopulations, for example in samples containing nuclear fluorescent proteins, however CG000375 includes FACS purification of nuclei which could potentially be adapted to this application. Please note that 7-AAD is the only recommended nuclear dye as alternatives may impact ATAC data quality (see Can I sort nuclei for Single Cell ATAC sequencing or Single Cell Multiome ATAC + GEX?).
Products: Single Cell Multiome ATAC+GEX