Nuclei Concentration

  • See the nuclei input concentration for Individual Transposition . The entire volume of nuclei after Individual Transposition is used for GEM Generation.

  • The optimal input nuclei concentration depends upon the desired nuclei recovery target. For details, see the Transposition and GEM Generation steps.

    Optimal Input Concentration

    Nuclei Recovery Target
    700-1,200 nuclei/ μl 500-20,000 nuclei
    1,300-1,600 nuclei/ μl 10,000-20,000 nuclei

  • The presence of debris in the suspension may reduce the recovery rate. Consult the following documents for more information on preparing cells:

    • 10x Genomics Single Cell Protocols Cell Preparation Handbook (Documents CG00053)

    • Best Practices to Minimize Chromium Next GEM Chip Clogs and Wetting Failure (Document CG000479)

    Multiplet Rate (%)

    # of Nuclei Loaded

    # of Nuclei Recovered

    ~0.20%

    ~725

    ~500

    ~0.40%

    ~1,450

    ~1,000

    ~0.80%

    ~2,900

    ~2,000

    ~1.20%

    ~4,350

    ~3,000

    ~1.60%

    ~5,800

    ~4,000

    ~2.00%

    ~7,250

    ~5,000

    ~2.40%

    ~8,700

    ~6,000

    ~2.80%

    ~10,150

    ~7,000

    ~3.20%

    ~11,600

    ~8,000

    ~3.60%

    ~13,050

    ~9,000

    ~4.00%

    ~14,500

    ~10,000

    ~4.40%

    ~15,950

    ~11,000

    ~4.80%

    ~17,400

    ~12,000

    ~5.20%

    ~18,850

    ~13,000

    ~5.60%

    ~20,300

    ~14,000

    ~6.00%

    ~21,750

    ~15,000

    ~6.40%

    ~23,200

    ~16,000

    ~6.80%

    ~24,650

    ~17,000

    ~7.20%

    ~26,100

    ~18,000

    ~7.60%

    ~27,550

    ~19,000

    ~8.00%

    ~29,000

    ~20,000