Assessing the prevalence of mycoplasma contamination in cell culture via a survey of NCBI's RNA-seq archive

Olarerin-George, Anthony O.; Hogenesch, John B.

doi:10.1093/nar/gkv136

Cited by 84 publications

(69 citation statements)

References 27 publications

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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%

A systematic NGS-based approach for contaminant detection and functional inference

Park

Onizuka

Seki

et al. 2019

Preprint

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BackgroundMicrobial contamination impedes successful biological and biomedical research. Computational approaches utilizing next-generation sequencing (NGS) data offer promising diagnostics to assess the presence of contaminants. However, as host cells are often contaminated by multiple microorganisms, these approaches require careful attention to intra- and interspecies sequence similarities, which have not yet been fully addressed.ResultsWe present a computational approach that rigorously investigates the genomic origins of sequenced reads, including those mapped to multiple species that have been discarded in previous studies. Through the analysis of large-scale synthetic and public NGS samples, we approximated that 1,000−100,000 microbial reads prevail when one million host reads are sequenced by RNA-seq. The microbe catalog we established included Cutibacterium as a prevalent contaminant, suggesting that contamination mostly originates from the laboratory environment. Importantly, by applying a systematic method to infer the functional impact of contamination, we revealed that host-contaminant interactions cause profound changes in the host molecular landscapes, as exemplified by changes in inflammatory and apoptotic pathways during Mycoplasma infection.ConclusionsThese findings reinforce the concept that precise determination of the origins and functional impacts of contamination is imperative for quality research and illustrate the usefulness of the proposed approach to comprehensively characterize contamination landscapes.

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Section: Resultssupporting

confidence: 85%

A systematic NGS-based approach for contaminant detection and functional inference

Park

Onizuka

Seki

et al. 2019

Preprint

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“…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%

Pooled analysis of radiation hybrids identifies loci for growth and drug action in mammalian cells

Lin

Wang

et al. 2019

Preprint

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Genetic screens in mammalian cells commonly focus on loss-of-function approaches. To evaluate the phenotypic consequences of extra gene copies, we used bulk segregant analysis (BSA) of radiation hybrid (RH) cells. We constructed six pools of RH cells, each consisting of ∼2500 independent clones, and placed the pools under selection in media with or without paclitaxel. Low pass sequencing identified 859 growth loci, 38 paclitaxel loci, 62 interaction loci and 3 loci for mitochondrial abundance at genome-wide significance. Resolution was measured as ∼30 kb, close to single-gene. Divergent properties were displayed by the RH-BSA growth genes compared to those from loss-of-function screens, refuting the balance hypothesis. In addition, enhanced retention of human centromeres in the RH pools suggests a new approach to functional dissection of these chromosomal elements. Pooled analysis of RH cells showed high power and resolution and should be a useful addition to the mammalian genetic toolkit.

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“…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%

TNF-α differentially regulates cell cycle genes in promyelocytic and granulocytic HL-60/S4 cells

Jacobson

Perry

Vickers

et al. 2018

Preprint

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Tumor necrosis factor alpha (TNF-α) is a potent cytokine involved in systemic inflammation and immune modulation. Signaling responses that involve TNF-α are context dependent and capable of stimulating pathways promoting both cell death and survival. TNF-α treatment has been investigated as part of a combined therapy for acute myeloid leukemia due to its modifying effects on all-trans retinoic acid (ATRA) mediated differentiation into granulocytes.To investigate the interaction between cellular differentiation and TNF-α, we performed RNA-sequencing on two forms of the human HL-60/S4 promyelocytic leukemia cell line treated with TNF-α. The ATRA-differentiated granulocytic form of HL-60/S4 cells had an enhanced transcriptional response to TNF-α treatment compared to the undifferentiated promyelocytes. The observed TNF-α responses included differential expression of cell cycle gene sets, which were generally upregulated in TNF-α treated promyelocytes, and downregulated in TNF-α treated granulocytes. This is consistent with TNF-α induced cell cycle repression in granulocytes and cell cycle progression in promyelocytes. Moreover, comparisons with gene expression changes associated with differentiation indicated that TNF-α treatment of granulocytes shifts the transcriptome towards that of a macrophage.We conclude that TNF-α treatment promotes a divergent transcriptional program in promyelocytes and granulocytes. TNF-α promotes cell cycle associated gene expression in promyelocytes. In contrast, TNF-α stimulated granulocytes have reduced cell cycle gene expression, and a macrophage-like transcriptional program.

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Assessing the prevalence of mycoplasma contamination in cell culture via a survey of NCBI's RNA-seq archive

Cited by 84 publications

References 27 publications

A systematic NGS-based approach for contaminant detection and functional inference

A systematic NGS-based approach for contaminant detection and functional inference

Pooled analysis of radiation hybrids identifies loci for growth and drug action in mammalian cells

TNF-α differentially regulates cell cycle genes in promyelocytic and granulocytic HL-60/S4 cells

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