Molecular Logic of Cellular Diversification in the Mouse Cerebral Cortex (scRNAseq)

The mammalian cerebral cortex has an unparalleled diversity of cell types, which are generated during development through a series of temporally orchestrated events that are under tight evolutionary constraint and are critical for proper cortical assembly and function. However, the molecular logic that governs the establishment and organization of cortical cell types remains elusive, largely due to the large number of cell classes undergoing dynamic cell-state transitions over extended developmental timelines. Here, we have generated a comprehensive single-cell RNA-seq and single-cell ATAC-seq atlas of the developing mouse neocortex, sampled every day throughout embryonic corticogenesis and at early postnatal ages, complemented with a spatial transcriptomics time-course. We computationally reconstruct developmental trajectories across the diversity of cortical cell classes, and infer their spatial organization and the gene regulatory programs that accompany their lineage bifurcation decisions and differentiation trajectories. Finally, we demonstrate how this developmental map pinpoints the origin of lineage-specific developmental abnormalities linked to aberrant corticogenesis in mutant animals. The data provides a global picture of the regulatory mechanisms governing cellular diversification in the neocortex. Single cell RNA-seq (scRNA-Seq) profiles from the full thickness of the developing somatosensory cortex from mouse embryos over the entire period of corticogenesis: E10.5, E11.5 (transition from amplifying to neurogenic progenitors); E12.5 and E13.5 (birthdate of layer 6 and 5 excitatory neurons); E14.5, E15.5 and E16.5 (birthdate of layer 2 to 4 excitatory neurons); and E18.5 and P1 and P4 (transition from neurogenesis to gliogenesis). Overall, 78,503 cells with 4,000 to 10,000 cells per time point were profiled.哺乳动物大脑皮层拥有无与伦比的细胞类型多样性，这些细胞类型在发育过程中通过一系列受严格进化约束、且对皮层正常组装与功能至关重要的时序调控事件产生。然而，调控皮层细胞类型建立与组织的分子逻辑仍不甚明晰，这在很大程度上源于大量细胞类群在漫长的发育时序中经历着动态的细胞状态转变。本研究构建了发育中小鼠新皮层的全面单细胞RNA测序（single-cell RNA-seq, scRNA-seq）与单细胞ATAC测序（single-cell ATAC-seq, scATAC-seq）图谱，在整个胚胎皮层发生期以及出生后早期阶段每日进行采样，并辅以空间转录组时序实验。我们通过计算方法重构了皮层细胞类群多样性背后的发育轨迹，推断了它们的空间组织形式，以及伴随细胞谱系分支决策与分化轨迹的基因调控程序。最后，我们展示了该发育图谱如何精准定位突变动物中异常皮层发生所关联的谱系特异性发育异常的起源。本数据为解析新皮层细胞多样化的调控机制提供了全局视角。本研究的单细胞RNA测序（scRNA-Seq）数据来自小鼠胚胎整个皮层发生期内体感皮层全厚度的样本，采样时间点包括：E10.5、E11.5（从扩增祖细胞向神经源性祖细胞的转变阶段）；E12.5与E13.5（第6层与第5层兴奋性神经元的诞生时期）；E14.5、E15.5及E16.5（第2至4层兴奋性神经元的诞生时期）；以及E18.5、P1与P4（从神经发生向胶质发生的转变阶段）。总计共获取78503个细胞，每个时间点的细胞数介于4000至10000之间。