Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing

Demonstrated Protocol, For use with cell lines and PBMCs, Last Modified on March 9, 2022, Permalink


This protocol outlines how to isolate, wash, and count nuclei suspensions for use with the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (GEX) protocol (CG000338). Cryopreserved primary cells (PBMCs) and cell lines (GM12878 cells; 3T3 cells) were used to develop this protocol. PBMCs were cryopreserved in IMDM + 40% FBS + 15% DMSO. Cell lines were cryopreserved in RPMI + 15% FBS + 5% DMSO. Optimization of some protocol steps (e.g. lysis time, centrifugation speed/time and filtration steps) may be needed based on cell type.

Caution: RNAse rich samples may need additional optimization. Please see: Can I use RNase-rich tissue samples for single-cell gene expression or Multiome assays?

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.