It depends on the tumor type. There is no universal marker for cancer stem cell.
CD117 also referred to as c-KIT is a well-known marker of neuroendocrine tumor cells and further, MDR1 is one of the ATP-bidnding cassette transporters responsible for drug resistance of cancer cells. By contrast, CD44 and CD133 are widely recognized as cancer stem cell markers. You have to keep in mind, however, that CD133 is difficult to be stained without non-specific signal. That is why CD44, especially CD44 variant, is a great target molecule by IHC.
I would stay away from CD133 as there are CD133 negative glioblastoma CSCs. For IHC generally it can be difficult to get staining to work with some cell surface markers (better used for FACs). I tend to prefer nuclear markers such as SOX2 or Mushashi1 for IHC. Hope that's of use.
Recently (aldh1positive, cd44positive,cd24negative ) lineage found to be of a stem cell because cells of this lineage are known to have self renewable potential. Instead of Single marker we should use combination of markers to identify stem cells properly.
As Sandeep Rajput stated, it completely depends on the type of cancer. You'll have to check the literature to see what is commonly used for your cancer of interest.
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