Nuclei Isolation from Adult Mouse Brain Tissue for Single Cell RNA Sequencing

Demonstrated Protocol, Last Modified on March 31, 2021, Permalink


This protocol outlines how to isolate, wash, and count single nuclei from adult neural tissue for use with 10x Genomics Single Cell RNA protocol. The protocols described here are expected to be compatible with many tissue types. Additional optimization may be required when working with new sample types.

This protocol is only compatible with the Chromium Single Cell Gene Expression reagent kits. Do not use with Multiome ATAC + Gene Expression or Single Cell ATAC assays.
This demonstrated protocol is optimized for counting nuclei in the range of 700-1200 nuclei/µl. If using the Single Cell 3' LT v3.1 (low throughput) application, ensure cells are counted as indicated in this protocol and then diluted to the LT specific optimal loading concentration of 100-600 nuclei/µl using the Cell Dilution Overview in the LT User Guide.