Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
Tsinghua-Peking Center for Life Sciences, Tsinghua University, School of Medicine, Tsinghua University, Beijing, 100084, China.
Nat Commun. 2017 Nov 30;8(1):1856. doi: 10.1038/s41467-017-01860-2.
Single-cell RNA sequencing (scRNA-seq) is a powerful method for dissecting intercellular heterogeneity during development. Conventional trajectory analysis provides only a pseudotime of development, and often discards cell-cycle events as confounding factors. Here using matched cell population RNA-seq (cpRNA-seq) as a reference, we developed an "iCpSc" package for integrative analysis of cpRNA-seq and scRNA-seq data. By generating a computational model for reference "biological differentiation time" using cell population data and applying it to single-cell data, we unbiasedly associated cell-cycle checkpoints to the internal molecular timer of single cells. Through inferring a network flow from cpRNA-seq to scRNA-seq data, we predicted a role of M phase in controlling the speed of neural differentiation of mouse embryonic stem cells, and validated it through gene knockout (KO) experiments. By linking temporally matched cpRNA-seq and scRNA-seq data, our approach provides an effective and unbiased approach for identifying developmental trajectory and timing-related regulatory events.
单细胞 RNA 测序 (scRNA-seq) 是解析发育过程中细胞间异质性的强大方法。传统的轨迹分析仅提供发育的伪时间，并且经常将细胞周期事件视为混杂因素而丢弃。在这里，我们使用匹配的细胞群体 RNA-seq (cpRNA-seq) 作为参考，开发了一个“iCpSc”包，用于 cpRNA-seq 和 scRNA-seq 数据的综合分析。通过使用细胞群体数据生成参考“生物分化时间”的计算模型，并将其应用于单细胞数据，我们将细胞周期检查点与单细胞内部分子计时器无偏关联。通过从 cpRNA-seq 到 scRNA-seq 数据推断网络流，我们预测了 M 期在控制小鼠胚胎干细胞神经分化速度中的作用，并通过基因敲除 (KO) 实验进行了验证。通过将时间匹配的 cpRNA-seq 和 scRNA-seq 数据联系起来，我们的方法为识别发育轨迹和与时间相关的调节事件提供了一种有效且无偏的方法。
