Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing

This protocol outlines how to isolate, wash, and count nuclei suspensions for use with GEM-X Epi Multiome for ATAC + Gene Expression protocol (CG001689) or 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?

Important

This protocol is only compatible with the Chromium Single Cell Multiome ATAC + Gene Expression reagent kits. Do not use with standalone Epi ATAC or Universal 3’ assays.

FOR USE WITH:

GEM-X Epi Multiome applications

GEM-X Epi Multiome, 16 samples PN-1000979 | 4 samples PN-1000980
- GEM-X Epi Multiome GEM Kit, 16 rxns PN-1000945 | 4 rxns PN-1000946
- GEM-X Epi Multiome Amp Kit, 16 rxns PN-1000947 | 4 rxns PN-1000948
- GEM-X Epi Multiome Gel Bead Kit 16 rxns PN-1000943 | 4 rxns PN-1000944
- GEM-X Epi Multiome ATAC Kit 16 rxns PN-1000949 | 4 rxns PN-1000950
- Library Construction Kit C, 16 rxns PN-1000694 | 4 rxns PN-1000689
- Dynabeads™ MyOne™ SILANE
GEM-X Epi Multiome Chip Kit, 4 chips, PN-1000951
Single Index Kit N Set A, 96 rxns, PN-1000212
Dual Index Kit TT Set A, 96 rxns, PN-1000215

Next GEM Epi Multiome applications

Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 16 rxns PN-1000283, includes:
- Chromium Next GEM Single Cell Multiome ATAC Kit A, 16 rxns PN-1000280
- Chromium Next GEM Single Cell Multiome Reagent Kit A, 16 rxns PN-1000232
- Library Construction Kit, 16 rxns PN-1000190
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 4 rxns PN-1000285, includes:
- Chromium Next GEM Single Cell Multiome ATAC Kit A, 4 rxns PN-1000281
- Chromium Next GEM Single Cell Multiome Reagent Kit A, 4 rxns PN-1000236
- Library Construction Kit B, 4 rxns PN-1000279
Chromium Next GEM Chip J Single Cell Kit, 48 rxns PN-1000234
Chromium Next GEM Chip J Single Cell Kit, 16 rxns PN-1000230
Single Index Kit N Set A, 96 rxns PN-1000212
Dual Index Kit TT Set A, 96 rxns PN-1000215

Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing

Demonstrated Protocol, CG000365

CG000365_DemonstratedProtocol_NucleiIsolation_ATAC_GEX_Sequencing-Rev_F.pdf