A single-cell RNA labeling strategy for measuring stress response upon tissue dissociation

Tissue dissociation, a crucial step in single-cell sample preparation, can alter the transcriptional state of a sample through the intrinsic cellular stress response. Here we demonstrate a general approach for measuring transcriptional response during sample preparation. In our method, transcripts made during dissociation are labeled for later identification upon sequencing. We found general as well as cell-type-specific dissociation response programs in zebrafish larvae, and we observed sample-to-sample variation in the dissociation response of mouse cardiomyocytes despite well-controlled experimental conditions. Finally, we showed that dissociation of the mouse hippocampus can lead to the artificial activation of microglia. In summary, our approach facilitates experimental optimization of dissociation procedures as well as computational removal of transcriptional perturbation response.

Automated summary

Tissue dissociation during single-cell sample preparation can induce transcriptional changes due to cellular stress response. We developed a method to measure this response by labeling dissociation-induced transcripts for sequencing identification. Our study revealed general and cell-type-specific dissociation response programs in zebrafish larvae, and sample-to-sample variation in mouse cardiomyocyte dissociation response despite controlled conditions. Additionally, we demonstrated the artificial activation of microglia in the mouse hippocampus upon dissociation. Our approach enables experimental optimization and computational removal of transcriptional perturbation response.