使用单细胞 RNA 测序数据的人类胚胎综合参考工具。

IF 36.1 1区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS
Cheng Zhao, Alvaro Plaza Reyes, John Paul Schell, Jere Weltner, Nicolás M Ortega, Yi Zheng, Åsa K Björklund, Laura Baqué-Vidal, Joonas Sokka, Ras Torokovic, Brian Cox, Janet Rossant, Jianping Fu, Sophie Petropoulos, Fredrik Lanner
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引用次数: 0

摘要

以干细胞为基础的胚胎模型为研究人类早期发育提供了前所未有的实验工具。胚胎模型的实用性取决于其分子、细胞和结构是否与体内模型一致。为了验证人类胚胎模型,单细胞 RNA 测序已被用于无偏见的转录剖析。然而,作为人类胚胎模型基准的通用参考,一个有组织的综合人类单细胞 RNA 测序数据集仍然不可用。在这里,我们整合了六个已发表的人类数据集,涵盖了从胚胎到胃的发育过程,从而建立了这样一个参考。系谱注释与现有的人类和非人灵长类数据集进行了对比和验证。我们利用稳定的均匀簇逼近和投影技术,构建了一个早期胚胎发生预测工具,可将查询数据集投影到参考工具上,并用预测的细胞身份进行注释。利用这一参考工具,我们对已发表的人类胚胎模型进行了检查,发现如果不利用相关参考资料进行基准测试和认证,就有可能造成错误标注。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
A comprehensive human embryo reference tool using single-cell RNA-sequencing data.

Stem cell-based embryo models offer unprecedented experimental tools for studying early human development. The usefulness of embryo models hinges on their molecular, cellular and structural fidelities to their in vivo counterparts. To authenticate human embryo models, single-cell RNA sequencing has been utilized for unbiased transcriptional profiling. However, an organized and integrated human single-cell RNA-sequencing dataset, serving as a universal reference for benchmarking human embryo models, remains unavailable. Here we developed such a reference through the integration of six published human datasets covering development from the zygote to the gastrula. Lineage annotations are contrasted and validated with available human and nonhuman primate datasets. Using stabilized Uniform Manifold Approximation and Projection, we constructed an early embryogenesis prediction tool, where query datasets can be projected on the reference and annotated with predicted cell identities. Using this reference tool, we examined published human embryo models, highlighting the risk of misannotation when relevant references are not utilized for benchmarking and authentication.

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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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