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Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation

Ann H. Ryu, Walter L. Eckalbar, Anat Kreimer, Nir Yosef, Nadav Ahituv
doi: https://doi.org/10.1101/130484
Ann H. Ryu
Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USAInstitute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
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Walter L. Eckalbar
Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USAInstitute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
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Anat Kreimer
Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USADepartment of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California Berkeley, Berkeley, CA, USA
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Nir Yosef
Department of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California Berkeley, Berkeley, CA, USARagon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, 02139 Boston, Massachusetts, USA
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Nadav Ahituv
Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USAInstitute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
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  • For correspondence: nadav.ahituv@ucsf.edu
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Abstract

Standard cell culture guidelines often use media supplemented with antibiotics to prevent cell contamination. However, relatively little is known about the effect of antibiotic use in cell culture on gene expression and the extent to which this treatment could confound results. To comprehensively characterize the effect of antibiotic treatment on gene expression, we performed RNA-seq and ChIP-seq for H3K27ac on HepG2 cells, a human liver cell line commonly used for pharmacokinetic, metabolism and genomic studies, cultured in media supplemented with penicillin-streptomycin (PenStrep) or vehicle control. We identified 205 PenStrep-responsive genes, including transcription factors such as ATF3 that are likely to alter the regulation of other genes. Pathway analyses found a significant enrichment for “xenobiotic metabolism signaling” and “PXR/RXR activation” pathways. Our H3K27ac ChIP-seq identified 9,514 peaks that are PenStrep responsive. These peaks were enriched near genes that function in cell differentiation, tRNA modification, nuclease activity and protein dephosphorylation. Our results suggest that PenStrep treatment can significantly alter gene expression and regulation in a common liver cell type such as HepG2, advocating that antibiotic treatment should be taken into account when carrying out genetic, genomic or other biological assays in cultured cells.

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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.
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Posted April 25, 2017.
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Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation
Ann H. Ryu, Walter L. Eckalbar, Anat Kreimer, Nir Yosef, Nadav Ahituv
bioRxiv 130484; doi: https://doi.org/10.1101/130484
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Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation
Ann H. Ryu, Walter L. Eckalbar, Anat Kreimer, Nir Yosef, Nadav Ahituv
bioRxiv 130484; doi: https://doi.org/10.1101/130484

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