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Nuclei Isolation from Complex Tissues for Single Cell Multiome ATAC + Gene Expression Sequencing

Nuclei Isolation from Complex Tissues for Single Cell Multiome ATAC + Gene Expression Sequencing

  • CG000375_DemonstratedProtocol_NucleiIsolationComplexSample_ATAC_GEX_Sequencing_Rev D.pdf

    Demonstrated Protocol, CG000375

    CG000375_DemonstratedProtocol_NucleiIsolationComplexSample_ATAC_GEX_Sequencing_Rev D.pdf

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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). Fresh frozen human malignant lymphoma, glioblastoma, and normal brain tissue were used to develop this protocol. 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

  • 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

Document Type
Demonstrated Protocol
Last Modified
April 20, 2026