Massively parallel single-cell RNA sequencing can precisely resolve cellular diversity in a high-throughput manner at low cost, but unbiased isolation of intact single cells from complex tissues such as adult mammalian brains is challenging. Here, we integrate sucrose-gradient-assisted purification of nuclei with droplet microfluidics to develop a highly scalable single-nucleus RNA-seq approach (sNucDrop-seq), which is free of enzymatic dissociation and nucleus sorting. By profiling ∼18,000 nuclei isolated from cortical tissues of adult mice, we demonstrate that sNucDrop-seq not only accurately reveals neuronal and non-neuronal subtype composition with high sensitivity but also enables in-depth analysis of transient transcriptional states driven by neuronal activity, at single-cell resolution, in vivo.

大规模并行的单细胞RNA测序可以以高通量的方式低成本准确地解析细胞多样性，但是完整无缺的单细胞与复杂组织（如成年哺乳动物的大脑）的无偏分离是一个挑战。在这里，我们将蔗糖梯度辅助的核与液滴微流控技术集成在一起，以开发高度可扩展的单核RNA-seq方法（sNucDrop-seq），该方法无需酶解离和核排序。通过对成年小鼠皮质组织中分离出的约18,000个核进行分析，我们证明了sNucDrop-seq不仅可以高灵敏度准确地揭示神经元和非神经元亚型的成分，而且还能够深入分析由神经元活性驱动的瞬时转录状态。体内单细胞分辨率。