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Updated: Jun 7, 2025
Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq
Published on: March 12, 2021
Comparative transcriptomic analyses of thymocytes using 10x Genomics and Parse scRNA-seq technologies
Igor Filippov1,2, Chinna Susan Philip3, Leif Schauser4
1Molecular Pathology Research Group, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia. ihor.filippov@ut.ee.
Background:
Single-cell RNA sequencing experiments commonly use 10x Genomics (10x) kits due to their high-throughput capacity and standardized protocols. Recently, Parse Biosciences (Parse) introduced an alternative technology that uses multiple in-situ barcoding rounds within standard 96-well plates. Parse enables the analysis of more cells from multiple samples in a single run without the need for additional reagents or specialized microfluidics equipment. To evaluate the performance of both platforms, we conducted a benchmark study using biological and technical replicates of mouse thymus as a complex immune tissue.
Results:
We found that Parse detected nearly twice the number of genes compared to 10x, with each platform detecting a distinct set of genes. The comparison of multiplexed samples generated from 10x and Parse techniques showed 10x data to have lower technical variability and more precise annotation of biological states in the thymus compared to Parse.
Conclusion:
Our results provide a comprehensive comparison of the suitability of both single-cell platforms for immunological studies.
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