A Unified Comparison of 10X Genomics and Parse Biosciences scRNA-seq Technologies

Droplet-based and split-pool barcoding are the two dominant high-throughput single-cell RNA-seq paradigms, yet their systematic biases remain incompletely characterized. We compared seven matched 10X Genomics Chromium and Parse Biosciences Evercode WT sample pairs from five studies spanning multiple tissues and species focusing on gene counts and compositional differences rather than cell-type resolution. By separating Parse reads by priming strategy, we distinguished biases arising from priming chemistry from platform-level effects. These effects were largely independent, with platform-level differences substantially larger. Priming strategy introduced a GC-content bias within Parse, whereas the two platforms showed a consistent compositional shift across priming strategies, supported by differential capture of nuclear- and cytoplasmic-enriched transcripts. We interpret this shift as a relative enrichment of nuclear RNA in Parse. Finally, using contamination measures that do not assume a droplet-specific model, we found background RNA contamination in Parse to be comparable in magnitude to that in 10X, contrary to claims of substantially lower contamination. Together, these results indicate that expression measurements and cell-type composition are not directly interchangeable between the two platforms.