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bioRxiv · 10.64898/2026.04.20.719117

Comparative benchmarking of single-cell transcriptomes and immune repertoires across technologies

King, C.·Iqbal, M.·Shokati, E.·Man Ying Li, C.·Li, R.·Tomita, Y.·Smith, E.·Kawecka, J. A.·Wang, S.·Fenix, K.
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Abstract

Immune receptor profiling enables tracking of individual T or B cell clones across time and tissues, providing insight into immune responses, cancer, and autoimmunity. When combined with single-cell transcriptomics, it links clonotype identity to cellular function, revealing the diversity and dynamics of immune cell populations. This study presents a head-to-head benchmarking comparison of two single-cell immune profiling technologies: droplet-based microfluidics from 10x Genomics (10x) and combinatorial barcoding from Parse Biosciences (Parse). Using matched human samples from PBMCs, the analysis evaluates performance across transcriptomic and T cell immune receptor features to assess data quality, reproducibility, and chain-specific recovery. The findings provide a framework for interpreting single-cell immune profiling platforms and emphasize the importance of accounting for technology-specific biases in bioinformatic analyses.

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King, C., Iqbal, M., Shokati, E., Man Ying Li, C., Li, R., Tomita, Y., Smith, E., Kawecka, J. A., Wang, S., Fenix, K.. 2026-04-22. Comparative benchmarking of single-cell transcriptomes and immune repertoires across technologies. https://doi.org/10.64898/2026.04.20.719117

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