Nuclei Isolation from Embryonic Mouse Brain Tissue for Single Cell ATAC + Gene Expression Sequencing

Demonstrated Protocol, For use with tissues, Last Modified on September 9, 2020, Permalink


This protocol outlines how to isolate, wash, and count single nuclei from fresh, cryopreserved, and flash frozen embryonic mouse brain tissue samples for use with the Chromium Single Cell Multiome ATAC + Gene Expression solution. Tissue triturated into a nearly single cell suspension and subsequently frozen in media containing 10% DMSO produced metrics comparable to fresh tissue. High quality data can also be obtained using flash frozen tissue. Optimization of some protocol steps (e.g. homogenization, lysis reagent/time, centrifugation speed/time and filtration steps) may be needed when working with mouse brain tissues from different sources.

This protocol is only compatible with the Chromium Single Cell Multiome ATAC + Gene Expression reagent kits. Do not use with standalone Single Cell ATAC or SC3'v3.1 assays.