Comparative transcriptomic analyses of thymocytes using 10x Genomics and Parse scRNA-seq technologies
Abstract 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-we...
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BMC
2024-11-01
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| Online Access: | https://doi.org/10.1186/s12864-024-10976-x |
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| author | Igor Filippov Chinna Susan Philip Leif Schauser Pärt Peterson |
| author_facet | Igor Filippov Chinna Susan Philip Leif Schauser Pärt Peterson |
| author_sort | Igor Filippov |
| collection | DOAJ |
| description | Abstract 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. |
| format | Article |
| id | doaj-art-aac5f50fc29348b5bb61a38fddfc938e |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-aac5f50fc29348b5bb61a38fddfc938e2024-11-17T12:11:42ZengBMCBMC Genomics1471-21642024-11-0125111310.1186/s12864-024-10976-xComparative transcriptomic analyses of thymocytes using 10x Genomics and Parse scRNA-seq technologiesIgor Filippov0Chinna Susan Philip1Leif Schauser2Pärt Peterson3Molecular Pathology Research Group, Institute of Biomedicine and Translational Medicine, University of TartuMolecular Pathology Research Group, Institute of Biomedicine and Translational Medicine, University of TartuQIAGEN Aarhus A/SMolecular Pathology Research Group, Institute of Biomedicine and Translational Medicine, University of TartuAbstract 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.https://doi.org/10.1186/s12864-024-10976-xTranscriptomics10xParsescRNA-seqThymus |
| spellingShingle | Igor Filippov Chinna Susan Philip Leif Schauser Pärt Peterson Comparative transcriptomic analyses of thymocytes using 10x Genomics and Parse scRNA-seq technologies BMC Genomics Transcriptomics 10x Parse scRNA-seq Thymus |
| title | Comparative transcriptomic analyses of thymocytes using 10x Genomics and Parse scRNA-seq technologies |
| title_full | Comparative transcriptomic analyses of thymocytes using 10x Genomics and Parse scRNA-seq technologies |
| title_fullStr | Comparative transcriptomic analyses of thymocytes using 10x Genomics and Parse scRNA-seq technologies |
| title_full_unstemmed | Comparative transcriptomic analyses of thymocytes using 10x Genomics and Parse scRNA-seq technologies |
| title_short | Comparative transcriptomic analyses of thymocytes using 10x Genomics and Parse scRNA-seq technologies |
| title_sort | comparative transcriptomic analyses of thymocytes using 10x genomics and parse scrna seq technologies |
| topic | Transcriptomics 10x Parse scRNA-seq Thymus |
| url | https://doi.org/10.1186/s12864-024-10976-x |
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