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.

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

Nature Methods

NATURE METHODS 是一个发表新方法和显着改进生命科学中久经考验的基础研究技术的论坛。该月刊面向广泛的跨学科受众，包括积极参与实验室实践的学术和行业研究人员。它为他们提供了进行研究的新工具，并强调所提出的工作的直接实际相关性。该杂志发表主要研究论文以及最近技术和方法发展的概述。我们正在积极寻找与生物和生物医学科学相关的主要方法论文，包括以化学为基础的方法，这些方法在生物学问题的研究中具有实际应用。

NATURE METHODS is a journal dedicated to publishing new methods and significant improvements in established research techniques within the life sciences. This monthly publication targets a broad interdisciplinary audience, including academic and industry researchers actively engaged in laboratory practices. It provides researchers with new tools for conducting studies and emphasizes the direct practical relevance of the work presented. The journal publishes primary research articles as well as reviews on recent developments in technologies and methods. We are actively seeking major method papers related to biological and biomedical sciences, particularly those based on chemistry that have practical applications in the study of biological questions.

NATURE METHODS 是一个专注于发表生命科学领域新方法和显著改进的基础研究技术的期刊。该月刊面向广泛的跨学科受众，包括积极参与实验室实践的学术和行业研究人员。它为研究人员提供了新的研究工具，并强调所提出工作的直接实际相关性。该杂志发表主要研究论文以及最近技术和方法发展的综述。我们积极寻找与生物和生物医学科学相关的主要方法论文，特别是那些在生物学研究中具有实际应用的化学基础方法。

Nat Methods

Considerations for building and using integrated single-cell atlases

构建和使用综合单细胞图谱的考虑因素

Category	Quartile
生物学	1
生物学, 生化研究方法	1

Considerations for building and using integrated single-cell atlases

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