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Article

Enzymatic Dissociation Induces Transcriptional and Proteotype Bias in Brain Cell Populations

1
Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, CH-8057 Zurich, Switzerland
2
Core Unit Bioinformatics, Berlin Institute of Health, Charité-Universitaetsmedizin, 10117 Berlin, Germany
3
Institute of Molecular Systems Biology and Department for Health Sciences and Technology, ETH Zürich, 8092 Zurich, Switzerland
4
Institute of Laboratory Animal Science, University of Zurich, 8952 Schlieren, Switzerland
5
Neuroscience Centre Zurich, University of Zurich and ETH Zurich, 8092 Zurich, Switzerland
6
Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
7
Department of Biomedical Sciences, University of Lausanne, Rue du Bugnon 7, 1005 Lausanne, Switzerland
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this study.
Shared senior authorship.
Int. J. Mol. Sci. 2020, 21(21), 7944; https://doi.org/10.3390/ijms21217944
Received: 21 September 2020 / Revised: 18 October 2020 / Accepted: 20 October 2020 / Published: 26 October 2020
(This article belongs to the Special Issue Molecular, Cellular and Systemic Signature of Microglia)
Different cell isolation techniques exist for transcriptomic and proteotype profiling of brain cells. Here, we provide a systematic investigation of the influence of different cell isolation protocols on transcriptional and proteotype profiles in mouse brain tissue by taking into account single-cell transcriptomics of brain cells, proteotypes of microglia and astrocytes, and flow cytometric analysis of microglia. We show that standard enzymatic digestion of brain tissue at 37 °C induces profound and consistent alterations in the transcriptome and proteotype of neuronal and glial cells, as compared to an optimized mechanical dissociation protocol at 4 °C. These findings emphasize the risk of introducing technical biases and biological artifacts when implementing enzymatic digestion-based isolation methods for brain cell analyses. View Full-Text
Keywords: microglia; astrocytes; neurons; enzymatic digestion; single-cell sequencing; protocol; microglia isolation microglia; astrocytes; neurons; enzymatic digestion; single-cell sequencing; protocol; microglia isolation
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MDPI and ACS Style

Mattei, D.; Ivanov, A.; van Oostrum, M.; Pantelyushin, S.; Richetto, J.; Mueller, F.; Beffinger, M.; Schellhammer, L.; vom Berg, J.; Wollscheid, B.; Beule, D.; Paolicelli, R.C.; Meyer, U. Enzymatic Dissociation Induces Transcriptional and Proteotype Bias in Brain Cell Populations. Int. J. Mol. Sci. 2020, 21, 7944. https://doi.org/10.3390/ijms21217944

AMA Style

Mattei D, Ivanov A, van Oostrum M, Pantelyushin S, Richetto J, Mueller F, Beffinger M, Schellhammer L, vom Berg J, Wollscheid B, Beule D, Paolicelli RC, Meyer U. Enzymatic Dissociation Induces Transcriptional and Proteotype Bias in Brain Cell Populations. International Journal of Molecular Sciences. 2020; 21(21):7944. https://doi.org/10.3390/ijms21217944

Chicago/Turabian Style

Mattei, Daniele, Andranik Ivanov, Marc van Oostrum, Stanislav Pantelyushin, Juliet Richetto, Flavia Mueller, Michal Beffinger, Linda Schellhammer, Johannes vom Berg, Bernd Wollscheid, Dieter Beule, Rosa Chiara Paolicelli, and Urs Meyer. 2020. "Enzymatic Dissociation Induces Transcriptional and Proteotype Bias in Brain Cell Populations" International Journal of Molecular Sciences 21, no. 21: 7944. https://doi.org/10.3390/ijms21217944

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