To model the effect of TKI treatment, we isolated and cultured patient-derived CML CD34+ cells in physiological culture medium, in the absence or presence of imatinib-mediated BCR::ABL1 inhibition and subjected them to RNA-seq and LC-MS mediated metabolomics to generate paired multi-omics datasets. Here, CD34 is linked to chronic myelogenous leukemia, BCR-ABL1 positive.