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.
Important
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)