Application protocol

Pre-enrichment of mouse hematopoietic stem and progenitor cells

This application protocol describes the pre-enrichment of lineage marker-negative, bone marrow-derived cells and their phenotypic analysis using flow cytometry. 


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This protocol includes detailed instructions for preparing necessary reagents and materials and then carrying out each step.


The following is a listing of reagents, instruments, and consumables needed for each step of this protocol. These products are for research use only.

General reagent and instrument requirements

  • PBE buffer: Prepare a solution containing phosphate-buffered saline (PBS), pH 7.2, 0.5 % bovine serum albumin (BSA), and 2 mM EDTA by diluting MACS® BSA Stock Solution (# 130-091-376) 1:20 with autoMACS® Rinsing Solution (# 130-091-222). Keep buffer cold (2−8 °C). Degas buffer before use, as air bubble could block the column.

For mononuclear cell isolation

  • MACS SmartStrainers (30 µm) (# 130-098-458)
  • Neubauer chamber or other cell counting device

For lineage cell depletion

  • Lineage Cell Depletion Kit, mouse (# 130-090-858) or Direct Lineage Cell Depletion Kit, mouse (# 130-110-470)
    ▲ Note: Use the Direct Lineage Cell Depletion Kit for a high cell yield or the Linear Cell Depletion Kit for a more stringent depletion.
  • (Optional) Hematopoietic Lineage Labeling Cocktail, anti-mouse, Biotin (# 130-092-613)
  • (Optional) Fluorochrome-conjugated antibodies for flow cytometry analysis, e.g., Biotin Antibody, anti-mouse, APC, CD117 Antibody, anti-mouse, PE, or CD117 Antibody, anti-mouse, APC. For more information about antibodies refer to
  • (Optional) Propidium Iodide Solution (# 130-093-233) or 7-AAD Staining Solution (# 130-111-568) for flow cytometric exclusion of dead cells.
  • (Optional) Dead Cell Removal Kit (# 130-090-101) for the depletion of dead cells.
  • (Optional) Pre-Separation Filters (30 µm) (# 130-041-407) to remove cell clumps.
  • MACS Columns and MACS Separators: Choose the appropriate MACS Separator and MACS Columns according to the number of labeled cells and the number of total cells. Use autoMACS for automated magnetic cell separation. 
    ▲ Note: Use LS Columns for the Direct Lineage Cell Depletion Kit, mouse. The kit can be additionally used with the MultiMACS™ Cell24 Separator Plus, and includes a completely automated cell isolation protocol for use with the autoMACS Pro. 
ColumnMax. number of labeled cellsMax. number of total cellsSeparator
Positive or negative selection
MS1×1072×10⁸MiniMACS™, OctoMACS™,
LS1×1082×109MidiMACS™, QuadroMACS™,
LS or Multi-24 Column Block (per column)1×1081×109MultiMACS Cell24 Separator Plus
XS1×1092×1010SuperMACS II
Positive or negative selection
autoMACS2×1084×109autoMACS Pro, autoMACS

Note: Column adapters are required to insert certain columns into SuperMACS™ II Separators. For details refer to the respective MACS Separator data sheet.

▲ Note: When using the Direct Lineage Cell Depletion Kit, the unwanted cell fraction is labeled and the target
cells remain unlabeled. Depending on the target cell frequency, the labeled fraction can represent the majority of the total cells. To avoid blocking of the column, do not exceed the maximum number of labeled cells per column. Estimate the number of labeled cells in the sample, split the sample if necessary and use the appropriate number of separation columns.

Note: If separating with LS Columns and the MultiMACS Cell24 Separator Plus, use the Single-Column Adapter. Refer to the user manual for details.

For expansion of lineage marker-negative cells or LSK cells

  • Mouse SCF, research grade (# 130-094-079)
  • Mouse Flt3-Ligand, research grade (# 130-094-038)
  • Mouse Thrombopoietin (TPO), research grade (# 130-094-083)
  • Mouse IL-3 IS, research grade (# 130-096-687)
  • Mouse IL-6, research grade (# 130-094-065)

For flow cytometry analysis

  • Sca-1 Antibody, anti-mouse, FITC
  • CD117 Antibody, anti-mouse, PE
  • Labeling Check Reagent, APC (# 130-122-219) or Streptavidin, APC (# 130-106-792)
  • FcR Blocking Reagent, mouse (# 130-092-575)
  • MACSQuant® Analyzer 10 (# 130-096-343)
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