Cancer stem cells (CSCs) are the most malignant subpopulation of tumor cells that possess a tumorigenic potential and resistantance to chemotherapy. These properties make CSCs a promising target for the development of targeted antitumor therapy which is especially in demand in highly aggressive cancers. However, the correct identification of cancer cells with stem properties remains a challenge. A newly developed lentivirus-based reporter SORE6 allows to directly identify CSCs by measuring gene expression of the embryonic stem cell factors SOX2 and OCT4. In the current study the reporter was modified to enable isolation of SOX2⁺/OCT4⁺ cells by immunomagnetic separation and then was used to transduce HCC1806 and MDA-MB-453 triple-negative breast cancer (TNBC) cell lines. To validate the modified reporter, SOX2⁺/OCT4⁺ populations were isolated and analyzed for the content of NANOG, a key transcription factor of pluropotency which expression is regulated by SOX2/OCT4. The percentage of SOX2⁺/OCT4⁺ cells was assessed for each cell line. An increased content of NANOG protein was found in isolated SOX2⁺/OCT4⁺ cell fractions indicating that the modified reporter is suitable for further studying the CSC subset.