Performance comparison of high throughput single-cell RNA-Seq platforms in complex tissues.

Colino-Sanguino, Y; Rodriguez de la Fuente, L; Gloss, B; Law, AMK; Handler, K; Pajic, M; Salomon, R; Gallego-Ortega, D; Valdes-Mora, F

Performance comparison of high throughput single-cell RNA-Seq platforms in complex tissues.

Colino-Sanguino, Y Rodriguez de la Fuente, L Gloss, B Law, AMK Handler, K Pajic, M Salomon, R

Gallego-Ortega, D Valdes-Mora, F

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Publisher:: CELL PRESS
Publication Type:: Journal Article
Citation:: Heliyon, 2024, 10, (17), pp. e37185
Issue Date:: 2024-09-15

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Field	Value	Language
dc.contributor.author	Colino-Sanguino, Y
dc.contributor.author	Rodriguez de la Fuente, L
dc.contributor.author	Gloss, B
dc.contributor.author	Law, AMK
dc.contributor.author	Handler, K
dc.contributor.author	Pajic, M
dc.contributor.author	Salomon, R https://orcid.org/0000-0003-4504-2901
dc.contributor.author	Gallego-Ortega, D
dc.contributor.author	Valdes-Mora, F
dc.date.accessioned	2024-11-05T12:18:07Z
dc.date.available	2024-08-28
dc.date.available	2024-11-05T12:18:07Z
dc.date.issued	2024-09-15
dc.identifier.citation	Heliyon, 2024, 10, (17), pp. e37185
dc.identifier.issn	2405-8440
dc.identifier.issn	2405-8440
dc.identifier.uri	http://hdl.handle.net/10453/181763
dc.description.abstract	Single-cell transcriptomics has emerged as the preferred tool to define cell identity through the analysis of gene expression signatures. However, there are limited studies that have comprehensively compared the performance of different scRNAseq systems in complex tissues. Here, we present a systematic comparison of two well-established high throughput 3'-scRNAseq platforms: 10× Chromium and BD Rhapsody, using tumours that present high cell diversity. Our experimental design includes both fresh and artificially damaged samples from the same tumours, which also provides a comparable dataset to examine their performance under challenging conditions. The performance metrics used in this study consist of gene sensitivity, mitochondrial content, reproducibility, clustering capabilities, cell type representation and ambient RNA contamination. These analyses showed that BD Rhapsody and 10× Chromium have similar gene sensitivity, while BD Rhapsody has the highest mitochondrial content. Interestingly, we found cell type detection biases between platforms, including a lower proportion of endothelial and myofibroblast cells in BD Rhapsody and lower gene sensitivity in granulocytes for 10× Chromium. Moreover, the source of the ambient noise was different between plate-based and droplet-based platforms. In conclusion, our reported platform differential performance should be considered for the selection of the scRNAseq method during the study experimental designs.
dc.format	Electronic-eCollection
dc.language	eng
dc.publisher	CELL PRESS
dc.relation	National Breast Cancer FoundationIIRS- 21-096
dc.relation.ispartof	Heliyon
dc.relation.isbasedon	10.1016/j.heliyon.2024.e37185
dc.rights	info:eu-repo/semantics/openAccess
dc.title	Performance comparison of high throughput single-cell RNA-Seq platforms in complex tissues.
dc.type	Journal Article
utslib.citation.volume	10
utslib.location.activity	England
pubs.organisational-group	University of Technology Sydney
pubs.organisational-group	University of Technology Sydney/Faculty of Engineering and Information Technology
pubs.organisational-group	University of Technology Sydney/Faculty of Science
pubs.organisational-group	University of Technology Sydney/Faculty of Science/School of Mathematical and Physical Sciences
pubs.organisational-group	University of Technology Sydney/Faculty of Engineering and Information Technology/School of Biomedical Engineering
utslib.copyright.status	open_access	*
dc.rights.license	This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND 4.0). To view a copy of this license, visit https://creativecommons.org/licenses/by-nc-nd/4.0/
dc.date.updated	2024-11-05T12:17:51Z
pubs.issue	17
pubs.publication-status	Published online
pubs.volume	10
utslib.citation.issue	17

Abstract:

Single-cell transcriptomics has emerged as the preferred tool to define cell identity through the analysis of gene expression signatures. However, there are limited studies that have comprehensively compared the performance of different scRNAseq systems in complex tissues. Here, we present a systematic comparison of two well-established high throughput 3'-scRNAseq platforms: 10× Chromium and BD Rhapsody, using tumours that present high cell diversity. Our experimental design includes both fresh and artificially damaged samples from the same tumours, which also provides a comparable dataset to examine their performance under challenging conditions. The performance metrics used in this study consist of gene sensitivity, mitochondrial content, reproducibility, clustering capabilities, cell type representation and ambient RNA contamination. These analyses showed that BD Rhapsody and 10× Chromium have similar gene sensitivity, while BD Rhapsody has the highest mitochondrial content. Interestingly, we found cell type detection biases between platforms, including a lower proportion of endothelial and myofibroblast cells in BD Rhapsody and lower gene sensitivity in granulocytes for 10× Chromium. Moreover, the source of the ambient noise was different between plate-based and droplet-based platforms. In conclusion, our reported platform differential performance should be considered for the selection of the scRNAseq method during the study experimental designs.

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http://hdl.handle.net/10453/181763