DMSO cryopreservation is the method of choice to preserve cells for droplet-based single-cell RNA sequencing

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2019
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Leparc, Germán G.
Fernandez-Albert, Francesc
Kind, David
Viollet, Coralie
Hildebrandt, Tobias
Baum, Patrick
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Combining single-cell RNA sequencing (scRNA-seq) with upstream cell preservation procedures such as cryopreservation or methanol fixation has recently become more common. By separating cell handling and preparation, from downstream library generation, scRNA-seq workflows are more flexible and manageable. However, the inherent transcriptomic changes associated with cell preservation and how they may bias further downstream analysis remain unknown. Here, we present a side-by-side droplet-based scRNA-seq analysis, comparing the gold standard - fresh cells - to three different cell preservation workflows: dimethyl sulfoxide based cryopreservation, methanol fixation and CellCover reagent. Cryopreservation proved to be the most robust protocol, maximizing both cell integrity and low background ambient RNA. Importantly, gene expression profiles from fresh cells correlated most with those of cryopreserved cells. Such similarities were consistently observed across the tested cell lines (R ≥ 0.97), monocyte-derived macrophages (R = 0.97) and immune cells (R = 0.99). In contrast, both methanol fixation and CellCover preservation showed an increased ambient RNA background and an overall lower gene expression correlation to fresh cells. Thus, our results demonstrate the superiority of cryopreservation over other cell preservation methods. We expect our comparative study to provide single-cell omics researchers invaluable support when integrating cell preservation into their scRNA-seq studies.

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570 Biowissenschaften, Biologie
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Transcriptomics
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ISO 690WOHNHAAS, Christian T., Germán G. LEPARC, Francesc FERNANDEZ-ALBERT, David KIND, Florian GANTNER, Coralie VIOLLET, Tobias HILDEBRANDT, Patrick BAUM, 2019. DMSO cryopreservation is the method of choice to preserve cells for droplet-based single-cell RNA sequencing. In: Scientific reports. 2019, 9(1), 10699. eISSN 2045-2322. Available under: doi: 10.1038/s41598-019-46932-z
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@article{Wohnhaas2019-07-23cryop-48019,
  year={2019},
  doi={10.1038/s41598-019-46932-z},
  title={DMSO cryopreservation is the method of choice to preserve cells for droplet-based single-cell RNA sequencing},
  number={1},
  volume={9},
  journal={Scientific reports},
  author={Wohnhaas, Christian T. and Leparc, Germán G. and Fernandez-Albert, Francesc and Kind, David and Gantner, Florian and Viollet, Coralie and Hildebrandt, Tobias and Baum, Patrick},
  note={Article Number: 10699}
}
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