Profiling low-mRNA content cells in complex human tissues using BD Rhapsody single-cell analysis
The successful recovery of immune cells, particularly those with low mRNA content, by single-cell RNA sequencing (scRNA-seq) remains a significant challenge. Tissue dissociation and selection of the appropriate scRNA-seq technology are crucial. Our protocol efficiently recovers low-mRNA content immune cells using the BD Rhapsody scRNA-seq platform. It includes optimized tissue dissociation for prostate, lung, and liver tissues, cell labeling with Sample Tag antibodies, microwell-based single-cell capture, cDNA synthesis, library preparation, and data pre-processing with basic quality control analysis. For complete details on the use and execution of this protocol, please refer to Salcher et al.<sup>1</sup>.
Authors
- Rupert Oberhuber (ORCID: https://orcid.org/0000-0003-2752-2557)
- Andreas Pircher (ORCID: https://orcid.org/0000-0002-7747-3012)
- Stefan Salcher (ORCID: https://orcid.org/0000-0003-2391-6954)
- Theresa Hautz (ORCID: https://orcid.org/0000-0003-0388-0202)
- Annabella Pittl
- Dominik Georg Friedrich Wolf (ORCID: https://orcid.org/0000-0002-4761-075X)
- Manuel Trebo (ORCID: https://orcid.org/0000-0001-8597-9729)
- Florian Augustin (ORCID: https://orcid.org/0000-0002-6785-4241)
- Sieghart Sopper (ORCID: https://orcid.org/0000-0003-2265-1974)
- Isabel Heidegger (ORCID: https://orcid.org/0000-0003-1517-5746)
- Alexandra Scheiber (ORCID: https://orcid.org/0009-0005-7759-7807)
- Zlatko Trajanoski (ORCID: https://orcid.org/0000-0002-0636-7351)
Institutions
- Innsbruck Medical University (AT)
- Universität Innsbruck (AT)
- Tyrolean Cancer Research Institute (AT)
Publication Details
- Journal
- STAR Protocols
- Published
- 2024-12-01
- DOI
- https://doi.org/10.1016/j.xpro.2024.103475
- Citations
- 8
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 1.87
Funders
- Austrian Science Fund
- Österreichische Forschungsförderungsgesellschaft