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Dipeptide species are accumulated in the chronic myelogenous leukemia (CML) stem cells [1]. To investigate the molecular mechanisms of the accumulation of dipeptide species in CML stem cells, we performed transcriptome sequencing of long-term stem cells, short-term stem cells, progenitor cells from healthy control and CML-affected mice (GSE70031). The transcriptome data revealed that the expression of a dipeptide transporter (solute carrier family 15, member 2 (SLC15A2)) was elevated only in the CML stem cells. This result indicates that dipeptide species accumulates in CML stem cells through a dipeptide transporter SLC15A2. Keywords: Chronic myelogenous leukemia, CML stem cell, Dipeptide transporter, RNA sequencing, Slc15a2