Cell motility influences the encapsulation process in scRNAseq microfluidics.
Microfluidic isolation methods for single-cell RNA sequencing (scRNA-seq) have primarily been designed for immotile cells, with limited consideration for motile cells, such as those with flagella or cilia. By studying the encapsulation efficiency of the flagellated Trypanosoma brucei using the 10x Genomics platform, we found that maintaining parasites at room temperature results in a low encapsulation yield. We implemented a rapid cooling method to 0C prior to encapsulation, which reduced parasite motility and preventing undesired transcriptomic change. This allowed for a representative scRNA-seq dataset, avoiding the disproportionate loss of the more motile forms. This study highlights the challenges of using motile cells in microfluidic systems and the biases caused by losing specific subpopulations, emphasizing the need for optimized protocols for non-standard mammalian cells.