UNIT 9.23 Flow Cytometry of the Side Population (SP)

  1. Jordi Petriz

Published Online: 1 JAN 2007

DOI: 10.1002/0471142956.cy0923s39

Current Protocols in Cytometry

Current Protocols in Cytometry

How to Cite

Petriz, J. 2007. Flow Cytometry of the Side Population (SP). Current Protocols in Cytometry. 39:9.23:9.23.1–9.23.14.

Author Information

  1. Institut de Recerca Hospital Universitari Vall d'Hebron, Barcelona, Spain

Publication History

  1. Published Online: 1 JAN 2007
  2. Published Print: JAN 2007

This is not the most recent version of the article. View current version (1 APR 2013)


The side population (SP) has become an important hallmark for the definition of the stem-cell compartment, especially for the detection of stem cells and for their physical isolation by fluorescence-activated cell sorting (FACS). SP cells are CD34 and were discovered using ultraviolet excitation based on the efflux of Hoechst 33342 (Ho342). Although the method works as originally described, the protocol is difficult for most investigators to perform: first, because the ability to discriminate SP cells is based on the differential retention of Ho342 during a functional assay; second, because of the difficulties in setting the right experimental and acquisition conditions; and third, because analysis of the acquired data requires extensive expertise in flow cytometry to accurately detect the SP events. This unit is packed with helpful pointers to aid the user in obtaining the best possible results.


  • side population;
  • stem cells;
  • CD34 negative;
  • Hoechst 33342;
  • flow cytometry