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  Benchmarking single-cell RNA-sequencing protocols for cell atlas projects

Mereu, E., Lafzi, A., Moutinho, C., Ziegenhain, C., McCarthy, D. J., Álvarez-Varela, A., et al. (2020). Benchmarking single-cell RNA-sequencing protocols for cell atlas projects. Nature Biotechnology. doi:org/10.1038/s41587-020-0469-4.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0006-3B03-5 Version Permalink: http://hdl.handle.net/21.11116/0000-0006-3B04-4
Genre: Journal Article

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 Creators:
Mereu, Elisabetta1, Author
Lafzi, Atefeh1, Author
Moutinho, Catia1, Author
Ziegenhain, Christoph1, Author
McCarthy, Davis J.1, Author
Álvarez-Varela, Adrián1, Author
Batlle, Eduard1, Author
Sagar, Sagar2, Author
Grün, Dominic2, Author              
Lau, Julia K.1, Author
Boutet, Stéphane C.1, Author
Sanada, Chad1, Author
Ooi, Aik1, Author
Jones, Robert C.1, Author
Kaihara, Kelly1, Author
Brampton, Chris1, Author
Talaga, Yasha1, Author
Sasagawa, Yohei1, Author
Tanaka, Kaori1, Author
Hayashi, Tetsutaro1, Author
Braeuning, Caroline1, AuthorFischer, Cornelius1, AuthorSauer, Sascha1, AuthorTrefzer, Timo1, AuthorConrad, Christian1, AuthorAdiconis, Xian1, AuthorNguyen, Lan T.1, AuthorRegev, Aviv1, AuthorLevin, Joshua Z.1, AuthorParekh, Swati1, AuthorJanjic, Aleksandar1, AuthorWange, Lucas E.1, AuthorBagnoli, Johannes W.1, AuthorEnard, Wolfgang1, AuthorGut, Marta1, AuthorSandberg, Rickard1, AuthorNikaido, Itoshi1, AuthorGut, Ivo1, AuthorStegle, Oliver1, AuthorHeyn, Holger1, Author more..
Affiliations:
1External Organizations, ou_persistent22              
2Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society, ou_2243642              

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 Abstract: Single-cell RNA sequencing (scRNA-seq) is the leading technique for characterizing the transcriptomes of individual cells in a sample. The latest protocols are scalable to thousands of cells and are being used to compile cell atlases of tissues, organs and organisms. However, the protocols differ substantially with respect to their RNA capture efficiency, bias, scale and costs, and their relative advantages for different applications are unclear. In the present study, we generated benchmark datasets to systematically evaluate protocols in terms of their power to comprehensively describe cell types and states. We performed a multicenter study comparing 13 commonly used scRNA-seq and single-nucleus RNA-seq protocols applied to a heterogeneous reference sample resource. Comparative analysis revealed marked differences in protocol performance. The protocols differed in library complexity and their ability to detect cell-type markers, impacting their predictive value and suitability for integration into reference cell atlases. These results provide guidance both for individual researchers and for consortium projects such as the Human Cell Atlas.

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Language(s): eng - English
 Dates: 2020-04-06
 Publication Status: Published in print
 Pages: -
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 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: org/10.1038/s41587-020-0469-4
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Title: Nature Biotechnology
Source Genre: Journal
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Publ. Info: New York : Gale Group Inc.
Pages: - Volume / Issue: - Sequence Number: - Start / End Page: - Identifier: ISSN: 1087-0156
CoNE: https://pure.mpg.de/cone/journals/resource/954926980065