This protocol outlines how to isolate, wash, and count nuclei suspensions for use with the Chromium Single Cell ATAC protocol. Cryopreserved primary cells (PBMCs) and cell lines (GM12878 cells; EL4 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.
 | This protocol is only compatible with the Chromium Single Cell ATAC reagent kits. Do not use with Multiome ATAC + Gene Expression or SC3'v3.1 assays. |
FOR USE WITH:
- Chromium Single Cell ATAC Reagent Kits User Guide (v1.1 Chemistry) (CG000209)
- Chromium Single Cell ATAC Reagent Kits User Guide (v1 Chemistry) (CG000168)
- Chromium Next GEM Single Cell ATAC Reagent Kits v2 User Guide (CG000496)