Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing

Demonstrated Protocol, For use with cell lines and PBMCs, Last Modified on July 12, 2022, Permalink

CG000365_DemonstratedProtocol_NucleiIsolation_ATAC_GEX_Sequencing_RevC.pdf

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."}

FOR USE WITH:

• 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