Fig. 4

Results of the Mycoplasma prevalence analysis and the functional impacts on host cells. a Twenty-two out of 432 public RNA-seq datasets contained significant Mycoplasma-mapped reads (red-colored bar) that were normalized to RPMHs (blue-colored line); the x-axis labels are colored black for DRA001846, gray for IHBM2, blue for ENCODE, and red for Mycoplasma-positive samples. b Gene expression correlation plots between Mycoplasma-positive (Myco+) and Mycoplasma-negative (Myco-) MSCs; Myco(+) hPDL-MSCs are Mycoplasma spike-in cells (2000 CFU × 7 species, 3 days cultured without antibiotics), FPKMs were transformed onto the log₁₀ scale by adding one, and the black-labeled genes are the 13 genes listed in d. c Highly enriched Gene Ontology terms and Reactome pathways (q value after Bonferroni correction < 0.001). d Venn diagram showing unique or shared differentially upregulated genes (DUGs) in MSCs, including 13 out of 967 DUGs unique to Myco(+) MSCs. e Expression levels of the 13 genes in Myco(+) ESCs and MSCs; the values are expressed as relative TPM (transcripts per million)