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| Status |
Public on Jul 25, 2019 |
| Title |
DMSO cryopreservation: the method of choice for droplet-based single-cell RNA sequencing of preserved cells [Drop-Seq] |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Recently, combining single-cell RNA sequencing (scRNA-seq) with upstream cell preservation procedures such as cryopreservation or methanol fixation has become more common. By separating cell handling and preparation, from downstream library generation, scRNA-seq workflows are more flexible and manageable. However, the inherent transcriptomics 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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| Overall design |
Examination of 3 different cell preservation protocols in two different cell matrices and different timepoints: 11 samples
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| Contributor(s) |
Wohnhaas CT, Leparc GG, Fernandez-Albert F, Kind D, Gantner F, Viollet C, Hildebrandt T, Baum P |
| Citation(s) |
31337793 |
| Submission date |
Feb 27, 2019 |
| Last update date |
Jul 25, 2019 |
| Contact name |
Christian Thaddaeus Wohnhaas |
| Organization name |
Boehringer Ingelheim
|
| Street address |
Birkendorfer Straße 65
|
| City |
Biberach |
| ZIP/Postal code |
88397 |
| Country |
Germany |
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| Platforms (2) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL19415 |
Illumina NextSeq 500 (Homo sapiens; Mus musculus) |
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| Samples (11)
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| This SubSeries is part of SuperSeries: |
| GSE127249 |
DMSO cryopreservation: the method of choice for droplet-based single-cell RNA sequencing of preserved cells |
|
| Relations |
| BioProject |
PRJNA524475 |
| SRA |
SRP186997 |
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