2015
DOI: 10.1093/nar/gkv136
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Assessing the prevalence of mycoplasma contamination in cell culture via a survey of NCBI's RNA-seq archive

Abstract: Mycoplasmas are notorious contaminants of cell culture and can have profound effects on host cell biology by depriving cells of nutrients and inducing global changes in gene expression. Over the last two decades, sentinel testing has revealed wide-ranging contamination rates in mammalian culture. To obtain an unbiased assessment from hundreds of labs, we analyzed sequence data from 9395 rodent and primate samples from 884 series in the NCBI Sequence Read Archive. We found 11% of these series were contaminated … Show more

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Cited by 91 publications
(80 citation statements)
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“…We investigated the correspondence between gene expression levels and Mycoplasma concentrations in the samples and identified genes potentially associated with the infection (Additional file 1: Fig. S6A); however, significant GO terms were not detected, which is consistent with the findings of a previous report [9]. Remarkably, the DG-75 samples were heavily contaminated with multiple microbes (Fig 5B), and the gene expression levels exhibited diverse correlation patterns with the concentrations of other microbes (Additional file 1: Fig.…”
Section: Resultssupporting
confidence: 85%
“…We investigated the correspondence between gene expression levels and Mycoplasma concentrations in the samples and identified genes potentially associated with the infection (Additional file 1: Fig. S6A); however, significant GO terms were not detected, which is consistent with the findings of a previous report [9]. Remarkably, the DG-75 samples were heavily contaminated with multiple microbes (Fig 5B), and the gene expression levels exhibited diverse correlation patterns with the concentrations of other microbes (Additional file 1: Fig.…”
Section: Resultssupporting
confidence: 85%
“…A recent paper using publicly available RNA-Seq datasets evaluated the prevalence of mycoplasma contamination in published studies (Olarerin-George and Hogenesch 2015). Of the datasets, 11% featured one or more contaminated samples, defined as 100 reads million − 1 mapping to mycoplasma.…”
Section: Supporting Informationmentioning
confidence: 99%
“…RNA-seq data was also used to check for mycoplasma contamination, as performed in [80]. All libraries were aligned to the genomes of four common mycoplasma species known to contaminate mammalian cell culture: Mycoplasma hominis ATCC 23114 (NC_013511.1), M. hyorhinis MCLD (NC_017519.1), Mycoplasma fermentans M64 (NC_014921.1) and Acholeplasma laidlawii PG-8A (NC_010163.1).…”
Section: Rna-seq Analysismentioning
confidence: 99%