Abstract：
:The scale and capabilities of single-cell RNA-sequencing methods have expanded rapidly in recent years, enabling major discoveries and large-scale cell mapping efforts. However, these methods have not been systematically and comprehensively benchmarked. Here, we directly compare seven methods for single-cell and/or single-nucleus profiling-selecting representative methods based on their usage and our expertise and resources to prepare libraries-including two low-throughput and five high-throughput methods. We tested the methods on three types of samples: cell lines, peripheral blood mononuclear cells and brain tissue, generating 36 libraries in six separate experiments in a single center. To directly compare the methods and avoid processing differences introduced by the existing pipelines, we developed scumi, a flexible computational pipeline that can be used with any single-cell RNA-sequencing method. We evaluated the methods for both basic performance, such as the structure and alignment of reads, sensitivity and extent of multiplets, and for their ability to recover known biological information in the samples.
journal_name
Nat Biotechnoljournal_title
Nature biotechnologyauthors
Ding J,Adiconis X,Simmons SK,Kowalczyk MS,Hession CC,Marjanovic ND,Hughes TK,Wadsworth MH,Burks T,Nguyen LT,Kwon JYH,Barak B,Ge W,Kedaigle AJ,Carroll S,Li S,Hacohen N,Rozenblatt-Rosen O,Shalek AK,Villani AC,Regevdoi
10.1038/s41587-020-0465-8subject
Has Abstractpub_date
2020-06-01 00:00:00pages
737-746issue
6eissn
1087-0156issn
1546-1696pii
10.1038/s41587-020-0465-8journal_volume
38pub_type
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