Abstract：
:Comparing diverse single-cell RNA sequencing (scRNA-seq) datasets generated by different technologies and in different laboratories remains a major challenge. Here we address the need for guidance in choosing algorithms leading to accurate biological interpretations of varied data types acquired with different platforms. Using two well-characterized cellular reference samples (breast cancer cells and B cells), captured either separately or in mixtures, we compared different scRNA-seq platforms and several preprocessing, normalization and batch-effect correction methods at multiple centers. Although preprocessing and normalization contributed to variability in gene detection and cell classification, batch-effect correction was by far the most important factor in correctly classifying the cells. Moreover, scRNA-seq dataset characteristics (for example, sample and cellular heterogeneity and platform used) were critical in determining the optimal bioinformatic method. However, reproducibility across centers and platforms was high when appropriate bioinformatic methods were applied. Our findings offer practical guidance for optimizing platform and software selection when designing an scRNA-seq study.
journal_name
Nat Biotechnoljournal_title
Nature biotechnologyauthors
Chen W,Zhao Y,Chen X,Yang Z,Xu X,Bi Y,Chen V,Li J,Choi H,Ernest B,Tran B,Mehta M,Kumar P,Farmer A,Mir A,Mehra UA,Li JL,Moos M Jr,Xiao W,Wang Cdoi
10.1038/s41587-020-00748-9subject
Has Abstractpub_date
2020-12-21 00:00:00eissn
1087-0156issn
1546-1696pii
10.1038/s41587-020-00748-9pub_type
杂志文章abstract：:Pollen-mediated movement of transgenes from transplastomic oilseed rape (Brassica napus) into wild relatives will be avoided if chloroplasts are maternally transmitted. We assess the probability of chloroplast exchange between conventional oilseed rape and wild Brassica rapa to model the future behavior of transplasto...
journal_title：Nature biotechnology
pub_type： 杂志文章
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abstract：:We describe a novel approach to design a set of primers selective for large groups of genes. This method is based on the distribution frequency of all nucleotide combinations (octa- to decanucleotides), and the combined ability of primer pairs, based on these oligonucleotides, to detect genes. By analyzing 1000 human ...
journal_title：Nature biotechnology
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journal_title：Nature biotechnology
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abstract：:RNA interference (RNAi) is a conserved sequence-specific, gene-silencing mechanism that is induced by double-stranded RNA. RNAi holds great promise as a novel nucleic acid-based therapeutic against a wide variety of diseases, including cancer, infectious diseases and genetic disorders. Antiviral RNAi strategies have r...
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abstract：:Prediction of HLA epitopes is important for the development of cancer immunotherapies and vaccines. However, current prediction algorithms have limited predictive power, in part because they were not trained on high-quality epitope datasets covering a broad range of HLA alleles. To enable prediction of endogenous HLA ...
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pub_type： 杂志文章,评审
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journal_title：Nature biotechnology
pub_type： 杂志文章
doi：10.1038/nbt.1511
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journal_title：Nature biotechnology
pub_type： 杂志文章
doi：10.1038/6146
更新日期：1999-02-01 00:00:00
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journal_title：Nature biotechnology
pub_type： 杂志文章
doi：10.1038/nbt0498-376
更新日期：1998-04-01 00:00:00
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journal_title：Nature biotechnology
pub_type： 杂志文章
doi：10.1038/nbt1132
更新日期：2005-09-01 00:00:00
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pub_type： 杂志文章
doi：10.1038/nbt0896-1003
更新日期：1996-08-01 00:00:00
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pub_type： 杂志文章
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