Kantonsspital St. Gallen 1 article published in JoVE Cancer Research Harnessing the DNA Dye-triggered Side Population Phenotype to Detect and Purify Cancer Stem Cells from Biological Samples Maximilian Boesch*1,2,3, Elisabeth Hoflehner2,3, Dominik Wolf2,3,4, Guenther Gastl2, Sieghart Sopper*2,3 1Institute of Immunobiology, Kantonsspital St. Gallen, 2Internal Medicine V, Medical University of Innsbruck, 3Tyrolean Cancer Research Institute (TKFI), 4Medical Clinic III, Oncology, Hematology, Immunoncology and Rheumatology, University Clinic Bonn (UKB) Methods allowing the characterization and isolation of stem cell populations from biological samples are critical for the advance of stem cell-targeted treatments in cancer and beyond. Here, we provide a detailed protocol for cancer stem cell isolation using the dye-triggered side population phenotype.