To identify genes and signaling pathways associated with the KDM6A-dependent protection of CML cells against imatinib, we carried out comparative transcriptomic analyses of K562 cells and its imatinib-resistant subline K562/G01 both with and without KDM6A depletion. Here, KDM6A is linked to chronic myelogenous leukemia, BCR-ABL1 positive.