Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

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

Anthony O. Olarerin-George, John B. Hogenesch
doi: https://doi.org/10.1101/007054
Anthony O. Olarerin-George
1Department of Pharmacology and the Institute for Translational Medicine and Therapeutics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
John B. Hogenesch
1Department of Pharmacology and the Institute for Translational Medicine and Therapeutics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: hogenesc@mail.med.upenn.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

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. Because they are small, they can escape filtration in culture media. Because they lack cell walls, they are resistant to commonly used antibiotics. 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 (or projects) in the NCBI Sequence Read Archive. We found 11% of these series were contaminated (defined as ≥ 100 reads/million mapping to mycoplasma in one or more samples). Ninety percent of mycoplasma-mapped reads aligned to ribosomal RNA. Interestingly, series using poly(A)-selection, which should bias against mycoplasma detection, had comparable contamination rates as non-poly(A)-selected series. We also examined the relationship between mycoplasma contamination and host gene expression in a single cell RNA-seq dataset and found 61 host genes (P < 0.001) were significantly associated with mycoplasma-mapped read counts. Lastly, to estimate the potential economic cost of this widespread contamination, we queried NIH RePORTER to find grants with the terms “cell culture” or “cell lines”. Funding for these totaled over $3 billion, suggesting hundreds of millions of dollars in research are potentially affected. In all, this study suggests mycoplasma contamination is still prevalent today and poses substantial risk to research quality, with considerable financial consequences.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Back to top
PreviousNext
Posted July 11, 2014.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Assessing the prevalence of mycoplasma contamination in cell culture via a survey of NCBI’s RNA-seq archive
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Assessing the prevalence of mycoplasma contamination in cell culture via a survey of NCBI’s RNA-seq archive
Anthony O. Olarerin-George, John B. Hogenesch
bioRxiv 007054; doi: https://doi.org/10.1101/007054
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
Assessing the prevalence of mycoplasma contamination in cell culture via a survey of NCBI’s RNA-seq archive
Anthony O. Olarerin-George, John B. Hogenesch
bioRxiv 007054; doi: https://doi.org/10.1101/007054

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Genomics
Subject Areas
All Articles
  • Animal Behavior and Cognition (4683)
  • Biochemistry (10360)
  • Bioengineering (7675)
  • Bioinformatics (26336)
  • Biophysics (13528)
  • Cancer Biology (10686)
  • Cell Biology (15440)
  • Clinical Trials (138)
  • Developmental Biology (8497)
  • Ecology (12821)
  • Epidemiology (2067)
  • Evolutionary Biology (16857)
  • Genetics (11399)
  • Genomics (15478)
  • Immunology (10617)
  • Microbiology (25217)
  • Molecular Biology (10223)
  • Neuroscience (54468)
  • Paleontology (401)
  • Pathology (1668)
  • Pharmacology and Toxicology (2897)
  • Physiology (4342)
  • Plant Biology (9247)
  • Scientific Communication and Education (1586)
  • Synthetic Biology (2558)
  • Systems Biology (6781)
  • Zoology (1466)