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...

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Vydané v:Heliyon Ročník 10; číslo 7; s. e28358
Hlavní autori: Salcher, Stefan, Heidegger, Isabel, Untergasser, Gerold, Fotakis, Georgios, Scheiber, Alexandra, Martowicz, Agnieszka, Noureen, Asma, Krogsdam, Anne, Schatz, Christoph, Schäfer, Georg, Trajanoski, Zlatko, Wolf, Dominik, Sopper, Sieghart, Pircher, Andreas
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: England Elsevier Ltd 15.04.2024
Elsevier
Predmet:
10X Chromium
BD Rhapsody
chromium
epithelium
humans
Low-mRNA content cells
Neutrophils
Prostate cancer
prostatic neoplasms
RNA
Single-cell RNA sequencing
transcriptome
10X Chromium
BD Rhapsody
Low-mRNA content cells
Single-cell RNA sequencing
Prostate cancer
Neutrophils
ISSN:2405-8440, 2405-8440
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Shrnutí: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. [Display omitted] •Comparison of scRNA-seq protocols uncovers disparities in RNA-to-library conversion.•Microwell-based scRNA-seq technology excels in capturing low-mRNA content cells.•Biased transcriptomes due to gene specific RNA detection efficacies by both platforms.•The study guides in informed scRNA-seq platform selection and data interpretation.
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These authors contributed equally.
ISSN:2405-8440
2405-8440
DOI:10.1016/j.heliyon.2024.e28358