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Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain
Blue B. Lake, Rizi Ai, Gwendolyn E. Kaeser, Neeraj S. Salathia, Yun C. Yung, Rui Liu, Andre Wildberg, Derek Gao, Ho Lim Fung, Song Chen, Raakhee Vijayaraghavan, Julian Wong, Allison Chen, Xiaoyan Sheng, Fiona Kaper, Richard Shen, Mostafa Ronaghi, Jian Bing Fan, Wei Wang, Jerold Chun, Kun Zhang
The human brain has enormously complex cellular diversity and connectivities fundamental to our neural functions, yet difficulties in interrogating individual neurons has impeded understanding of the underlying transcriptional landscape. We developed a scalable approach to sequence and quantify RNA molecules in isolated neuronal nuclei from a postmortem brain, generating 3227 sets of single-neuron data from six distinct regions of the cerebral cortex. Using an iterative clustering and classification approach, we identified 16 neuronal subtypes that were further annotated on the basis of known markers and cortical cytoarchitecture. These data demonstrate a robust and scalable method for identifying and categorizing single nuclear transcriptomes, revealing shared genes sufficient to distinguish previously unknown and orthologous neuronal subtypes as well as regional identity and transcriptomic heterogeneity within the human brain.