Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain [snDrop-seq]

Detailed characterization of the cell types in the human brain requires scalable experimental approaches to examine multiple aspects of the molecular state of individual cells, as well as computational integration of the data to produce unified cell-state annotations. Here we report improved high-throughput methods for single-nucleus droplet-based sequencing (snDrop-seq) and single-cell transposome hypersensitive site sequencing (scTHS-seq). We used each method to acquire nuclear transcriptomic and DNA accessibility maps for >60,000 single cells from human adult visual cortex, frontal cortex, and cerebellum. Integration of these data revealed regulatory elements and transcription factors that underlie cell-type distinctions, providing a basis for the study of complex processes in the brain, such as genetic programs that coordinate adult remyelination. We also mapped disease-associated risk variants to specific cellular populations, which provided insights into normal and pathogenic cellular processes in the human brain. This integrative multi-omics approach permits more detailed single-cell interrogation of complex organs and tissues. Single DAPI+ nuclei (according to the Samples list) were isolated from the visual cortex (BA17), frontal cortex (BA6 or BA10), and cerebellar hemisphere from 6 different postmortem adult human brains and were processed for single-nucleus Drop-seq (snDrop-seq). This series contains data only for snDrop-Seq.

对人类大脑细胞类型进行精准表征，需要采用可规模化的实验手段以检测单个细胞分子状态的多个维度，同时还需通过计算方法整合数据，以获得统一的细胞状态注释。本研究报道了两种经过优化的高通量方法：单核液滴测序（single-nucleus droplet-based sequencing, snDrop-seq）与单细胞转座酶超敏位点测序（single-cell transposome hypersensitive site sequencing, scTHS-seq）。我们分别采用这两种方法，对来自成人人类视觉皮层、前额叶皮层与小脑的超过6万个单细胞获取了核转录组与DNA开放性染色质图谱。整合这些数据后，我们鉴定出了驱动细胞类型差异的调控元件与转录因子，为研究大脑复杂生物学过程（如协调成人髓鞘再生的遗传程序）提供了坚实基础。此外，我们将疾病相关风险变异定位至特定细胞群，为解析人类大脑的正常与致病细胞过程提供了全新视角。这种整合式多组学方法可实现对复杂器官与组织更精细的单细胞解析。本研究从6例成人死后捐献的人类大脑中，分离得到视觉皮层（BA17区）、前额叶皮层（BA6或BA10区）以及小脑半球的单个DAPI阳性细胞核（详见样本列表），并对其进行单核液滴测序（snDrop-seq）处理。本数据集仅包含snDrop-seq相关数据。