Comparative analysis of 10X Chromium vs. BD Rhapsody whole transcriptome single-cell sequencing technologies in complex human tissues
The development of single-cell omics tools has enabled scientists to study the tumor microenvironment (TME) in unprecedented detail. However, each of the different techniques may have its unique strengths and limitations. Here we directly compared two commercially available high-throughput single-ce...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2024-04-01
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| Series: | Heliyon |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2405844024043895 |
| _version_ | 1797237982186438656 |
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| author | Stefan Salcher Isabel Heidegger Gerold Untergasser Georgios Fotakis Alexandra Scheiber Agnieszka Martowicz Asma Noureen Anne Krogsdam Christoph Schatz Georg Schäfer Zlatko Trajanoski Dominik Wolf Sieghart Sopper Andreas Pircher |
| author_facet | Stefan Salcher Isabel Heidegger Gerold Untergasser Georgios Fotakis Alexandra Scheiber Agnieszka Martowicz Asma Noureen Anne Krogsdam Christoph Schatz Georg Schäfer Zlatko Trajanoski Dominik Wolf Sieghart Sopper Andreas Pircher |
| author_sort | Stefan Salcher |
| collection | DOAJ |
| description | The development of single-cell omics tools has enabled scientists to study the tumor microenvironment (TME) in unprecedented detail. However, each of the different techniques may have its unique strengths and limitations. Here we directly compared two commercially available high-throughput single-cell RNA sequencing (scRNA-seq) technologies - droplet-based 10X Chromium vs. microwell-based BD Rhapsody - using paired samples from patients with localized prostate cancer (PCa) undergoing a radical prostatectomy.Although high technical consistency was observed in unraveling the whole transcriptome, the relative abundance of cell populations differed. Cells with low mRNA content such as T cells were underrepresented in the droplet-based system, at least partly due to lower RNA capture rates. In contrast, microwell-based scRNA-seq recovered less cells of epithelial origin. Moreover, we discovered platform-dependent variabilities in mRNA quantification and cell-type marker annotation. Overall, our study provides important information for selection of the appropriate scRNA-seq platform and for the interpretation of published results. |
| first_indexed | 2024-04-24T17:28:24Z |
| format | Article |
| id | doaj.art-9c6a43d55fa142b582569e65d4b2b953 |
| institution | Directory Open Access Journal |
| issn | 2405-8440 |
| language | English |
| last_indexed | 2024-04-24T17:28:24Z |
| publishDate | 2024-04-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Heliyon |
| spelling | doaj.art-9c6a43d55fa142b582569e65d4b2b9532024-03-28T06:38:25ZengElsevierHeliyon2405-84402024-04-01107e28358Comparative analysis of 10X Chromium vs. BD Rhapsody whole transcriptome single-cell sequencing technologies in complex human tissuesStefan Salcher0Isabel Heidegger1Gerold Untergasser2Georgios Fotakis3Alexandra Scheiber4Agnieszka Martowicz5Asma Noureen6Anne Krogsdam7Christoph Schatz8Georg Schäfer9Zlatko Trajanoski10Dominik Wolf11Sieghart Sopper12Andreas Pircher13Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck (MUI), Innsbruck, AustriaDepartment of Urology, Medical University of Innsbruck, Innsbruck, AustriaDepartment of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck (MUI), Innsbruck, AustriaBiocenter, Institute of Bioinformatics, Medical University of Innsbruck, AustriaDepartment of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck (MUI), Innsbruck, AustriaDepartment of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck (MUI), Innsbruck, AustriaBiocenter, Institute of Bioinformatics, Medical University of Innsbruck, AustriaBiocenter, Institute of Bioinformatics, Medical University of Innsbruck, AustriaDepartment of Pathology, Medical University Innsbruck, Innsbruck, AustriaDepartment of Pathology, Medical University Innsbruck, Innsbruck, AustriaBiocenter, Institute of Bioinformatics, Medical University of Innsbruck, AustriaDepartment of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck (MUI), Innsbruck, AustriaDepartment of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck (MUI), Innsbruck, Austria; Corresponding author.Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck (MUI), Innsbruck, Austria; Corresponding author.The development of single-cell omics tools has enabled scientists to study the tumor microenvironment (TME) in unprecedented detail. However, each of the different techniques may have its unique strengths and limitations. Here we directly compared two commercially available high-throughput single-cell RNA sequencing (scRNA-seq) technologies - droplet-based 10X Chromium vs. microwell-based BD Rhapsody - using paired samples from patients with localized prostate cancer (PCa) undergoing a radical prostatectomy.Although high technical consistency was observed in unraveling the whole transcriptome, the relative abundance of cell populations differed. Cells with low mRNA content such as T cells were underrepresented in the droplet-based system, at least partly due to lower RNA capture rates. In contrast, microwell-based scRNA-seq recovered less cells of epithelial origin. Moreover, we discovered platform-dependent variabilities in mRNA quantification and cell-type marker annotation. Overall, our study provides important information for selection of the appropriate scRNA-seq platform and for the interpretation of published results.http://www.sciencedirect.com/science/article/pii/S2405844024043895Single-cell RNA sequencingLow-mRNA content cellsNeutrophils10X ChromiumBD RhapsodyProstate cancer |
| spellingShingle | Stefan Salcher Isabel Heidegger Gerold Untergasser Georgios Fotakis Alexandra Scheiber Agnieszka Martowicz Asma Noureen Anne Krogsdam Christoph Schatz Georg Schäfer Zlatko Trajanoski Dominik Wolf Sieghart Sopper Andreas Pircher Comparative analysis of 10X Chromium vs. BD Rhapsody whole transcriptome single-cell sequencing technologies in complex human tissues Heliyon Single-cell RNA sequencing Low-mRNA content cells Neutrophils 10X Chromium BD Rhapsody Prostate cancer |
| title | Comparative analysis of 10X Chromium vs. BD Rhapsody whole transcriptome single-cell sequencing technologies in complex human tissues |
| title_full | Comparative analysis of 10X Chromium vs. BD Rhapsody whole transcriptome single-cell sequencing technologies in complex human tissues |
| title_fullStr | Comparative analysis of 10X Chromium vs. BD Rhapsody whole transcriptome single-cell sequencing technologies in complex human tissues |
| title_full_unstemmed | Comparative analysis of 10X Chromium vs. BD Rhapsody whole transcriptome single-cell sequencing technologies in complex human tissues |
| title_short | Comparative analysis of 10X Chromium vs. BD Rhapsody whole transcriptome single-cell sequencing technologies in complex human tissues |
| title_sort | comparative analysis of 10x chromium vs bd rhapsody whole transcriptome single cell sequencing technologies in complex human tissues |
| topic | Single-cell RNA sequencing Low-mRNA content cells Neutrophils 10X Chromium BD Rhapsody Prostate cancer |
| url | http://www.sciencedirect.com/science/article/pii/S2405844024043895 |
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