Cross-contamination with ambient RNA is common in single-cell RNA sequencing droplet-based platforms. In this study, we demonstrate that mouse kidney cells were less susceptible to ambient RNA contamination when analyzed with the Parse Evercode WT v2 hardware-free method than with Chromium Next GEM 3’ v3.1.
The study evaluates gene detection and cell type clusters. Evercode detected 79 percent more genes than Chromium. Annotation of the two datasets showed a large cluster of seemingly RBCs in the Chromium data, and hemoglobin RNA was found across all clusters, absent in the Evercode data. When minor tubule cells were subclustered, Evercode data showed a clear resolution of two types of collecting duct cells, while there is a single cluster in the Chromium data, further illustrating the negative impact of ambient RNA. These results demonstrate that Evercode detected more genes per cell, had substantially less ambient RNA contamination, and demonstrated higher cluster resolution.
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