构建和使用集成单细胞图谱的注意事项。

IF 36.1 1区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS
Karin Hrovatin, Lisa Sikkema, Vladimir A. Shitov, Graham Heimberg, Maiia Shulman, Amanda J. Oliver, Michaela F. Mueller, Ignacio L. Ibarra, Hanchen Wang, Ciro Ramírez-Suástegui, Peng He, Anna C. Schaar, Sarah A. Teichmann, Fabian J. Theis, Malte D. Luecken
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引用次数: 0

摘要

单细胞技术的快速采用创造了建立单细胞“地图集”的机会,整合了许多实验室的不同数据集。这种地图集可以作为分析和解释当前和未来数据的参考。然而,很明显,绘制地图的方法不同,而这些差异的影响往往不清楚。在这里,我们回顾了目前的地图集文献,并提出了建立和使用地图集的考虑。重要的是,我们发现不存在一个适用于地图集构建的通用协议,而是讨论了特定于上下文的考虑因素和工作流程,包括地图集概念化,数据收集,管理和集成,地图集评估和地图集共享。我们进一步强调了综合地图集在分析新数据集和获得超越单个数据集的生物学见解方面的好处。我们对当前实践和相关建议的概述将提高未来地图集的质量,促进向统一的、基于参考的单细胞生物学理解的转变。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Considerations for building and using integrated single-cell atlases

Considerations for building and using integrated single-cell atlases
The rapid adoption of single-cell technologies has created an opportunity to build single-cell ‘atlases’ integrating diverse datasets across many laboratories. Such atlases can serve as a reference for analyzing and interpreting current and future data. However, it has become apparent that atlasing approaches differ, and the impact of these differences are often unclear. Here we review the current atlasing literature and present considerations for building and using atlases. Importantly, we find that no one-size-fits-all protocol for atlas building exists, but rather we discuss context-specific considerations and workflows, including atlas conceptualization, data collection, curation and integration, atlas evaluation and atlas sharing. We further highlight the benefits of integrated atlases for analyses of new datasets and deriving biological insights beyond what is possible from individual datasets. Our overview of current practices and associated recommendations will improve the quality of atlases to come, facilitating the shift to a unified, reference-based understanding of single-cell biology. This Review provides a comprehensive and detailed discussion about how to build and use single-cell atlases.
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来源期刊
Nature Methods
Nature Methods 生物-生化研究方法
CiteScore
58.70
自引率
1.70%
发文量
326
审稿时长
1 months
期刊介绍: Nature Methods is a monthly journal that focuses on publishing innovative methods and substantial enhancements to fundamental life sciences research techniques. Geared towards a diverse, interdisciplinary readership of researchers in academia and industry engaged in laboratory work, the journal offers new tools for research and emphasizes the immediate practical significance of the featured work. It publishes primary research papers and reviews recent technical and methodological advancements, with a particular interest in primary methods papers relevant to the biological and biomedical sciences. This includes methods rooted in chemistry with practical applications for studying biological problems.
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