Discussion
Single-cell RNA sequencing (scRNAseq) using microfluidic systems, such as 10XGenomics, is a prevailing trend to study cell states and identities. This method involves encapsulation of the single cells in drops of oil, called GEMs (Gel Bead-in-Emulsion).
Whether motility of cells, specifically extracellular parasites like
Trypanosoma brucei, affects encapsulation efficiency remains unknown.
We conducted experiments to investigate the effects of adding motile and non-motile parasites to the encapsulation process of 10XGenomics at both the transcriptional and microscopy levels.
Following encapsulation, we observed that these parasites did not incur any damage during the encapsulation process and retained their high motility, potentially causing rupture of droplets, and releasing the parasites into the interspaces of the GEMs. The posterior analysis revealed that a significant proportion of immotile parasites persisted in the final data, while the highly motile ones nearly disappeared by the end of the analysis.
This data highlights the importance of considering cell motility in microfluidic-dependent setups and the fact that valuable information from highly motile cells may be lost.
