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| Status |
Public on Oct 26, 2020 |
| Title |
Enzymatic dissociation induces transcriptional and proteotype bias in brain cell populations |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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 artefacts when implementing enzymatic digestion-based isolation methods for brain cell analyses.
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| Overall design |
Adult male mice hippocampi where dissociated via either enzymatic digestion for 30 min at 37°C or via mechanical dissociation at 4°C. The resulting cell suspensions were analysed via 10X Genomics single cell sequencing.
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| Contributor(s) |
Mattei D, Ivanov A, van Oostrum M, Pantelyushin S, Richetto J, Mueller F, Beffinger MM, Schellhammer L, vom Berg J, Wollscheid B, Beule D, Paolicelli RC, Meyer U |
| Citation(s) |
33114694, 32398717, 37717033 |
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| Submission date |
Jan 16, 2020 |
| Last update date |
Sep 27, 2023 |
| Contact name |
Ge Tan |
| E-mail(s) |
ge_tan@outlook.com
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| Organization name |
University of Zurich
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| Department |
Functional Genomics Center Zurich
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| Street address |
Winterthurerstrasse 190
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| City |
Zurich |
| ZIP/Postal code |
8057 |
| Country |
Switzerland |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA601729 |
| SRA |
SRP242212 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE143796_RAW.tar |
72.5 Mb |
(http)(custom) |
TAR (of MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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