RESEARCH ARTICLE Single-cell transcriptomes and whole-brain projections of serotonin neurons in the mouse dorsal and median raphe nuclei Jing Ren1†*, Alina Isakova2,3†, Drew Friedmann1†, Jiawei Zeng4†, Sophie M Grutzner1, Albert Pun1, Grace Q Zhao5, Sai Saroja Kolluru2,3, Ruiyu Wang4, Rui Lin4, Pengcheng Li6,7, Anan Li6,7, Jennifer L Raymond5, Qingming Luo6, Minmin Luo4,8, Stephen R Quake2,3,9*, Liqun Luo1* 1Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, United States; 2Department of Bioengineering, Stanford University, Stanford, United States; 3Department of Applied Physics, Stanford University, Stanford, United States; 4National Institute of Biological Science, Beijing, China; 5Department of Neurobiology, Stanford University School of Medicine, Stanford, United States; 6Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology (HUST), Wuhan, China; 7HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China; 8School of Life Science, Tsinghua University, Beijing, China; 9Chan Zuckerberg Biohub, San Francisco, United States Abstract Serotonin neurons of the dorsal and median raphe nuclei (DR, MR) collectively innervate the entire forebrain and midbrain, modulating diverse physiology and behavior. To gain a fundamental understanding of their molecular heterogeneity, we used plate-based single-cell RNA- *For correspondence: sequencing to generate a comprehensive dataset comprising eleven transcriptomically distinct
[email protected] (JR);
[email protected] (SRQ); serotonin neuron clusters. Systematic in situ hybridization mapped specific clusters to the principal
[email protected] (LL) DR, caudal DR, or MR. These transcriptomic clusters differentially express a rich repertoire of neuropeptides, receptors, ion channels, and transcription factors.