RNA sequencing data from STS-109 human undifferentiated pleomorphic sarcoma (UPS) cells deficient in DNMT3A or DNMT3B expression

DNA methylation is frequently disrupted in sarcoma but little is known about the specific roles of DNA methyltransferases (DNMTs) in this process. Using an shRNA lentivirus-mediated genetic depletion approach, we found that reduction of DNMT3A or DNMT3B expression potently reduced UPS cell proliferation. Therefore, we performed RNA sequencing to identify global gene expression changes in DNMT3A- or DNMT3B-depleted cells. STS-109 cells recently derived from a human UPS tumor were infected with one of two independent shRNAs targeting either DNMT3A (shDNMT3A) or DNMT3B (shDNMT3B), or a scrambled control shRNA (shSCR). Cells were selected with 3 µg/mL of puromycin 48 hours after infection, and harvested for RNA isolation 96 hours after infection. All cells were harvested at 50% confluency.