Identifier Results

Field Value
Identifier nemo:dat-76h044v
Dataset Name A transcriptomic taxonomy of mouse brain-wide spinal projecting neurons
Version NA
Release Date NA
Source Data URL NA
Dataset Collection URL
Description The brain controls nearly all bodily functions via spinal projecting neurons (SPNs) that carry command signals from the brain to the spinal cord. However, a comprehensive molecular characterization of brain-wide SPNs is still lacking. Here, we transcriptionally profiled a total of 65,002 SPNs, identified 76 region-specific SPN types, and mapped these types into a companion atlas of the whole mouse brain. This taxonomy reveals a three-component organization of SPNs: (1) molecularly homogeneous excitatory SPNs from the cortex, red nucleus, and cerebellum with somatotopic spinal terminations suitable for point-to-point communication; (2) heterogeneous populations in the reticular formation with broad spinal termination patterns, suitable for relaying commands related to the activities of the entire spinal cord; and (3) modulatory neurons expressing slow-acting neurotransmitters and/or neuropeptides in the hypothalamus, midbrain, and reticular formation for gain control of brain-spinal signals. Further, this atlas revealed a LIM homeobox transcription factor code that parcellates the reticulospinal neurons into five molecularly distinct and spatially segregated populations.Finally, we found transcriptional signatures of a subset of SPNs with large soma size and correlated these with fast-firing electrophysiological properties. Together, this study establishes a comprehensive taxonomy of brain-wide SPNs and provides insight into the functional organization of SPNs in mediating brain control of bodily functions.
Keywords single nucleus RNA-seq, transcriptome, mouse, spinal projecting neuron, corticospinal, rubrospinal, reticulospinal
Total Files in Collection 4453
Total Size in Collection (in GB) 818.0
Authors Carla C. Winter, Anne Jacobi, Junfeng Su, Leeyup Chung, Cindy T. J. van Velthoven, Zizhen Yao, Changkyu Lee, Zicong Zhang, Shuguang Yu, Kun Gao, Geraldine Duque Salazar, Evgenii Kegeles, Yu Zhang, Makenzie C. Tomihiro, Yiming Zhang, Zhiyun Yang, Junjie Zhu, Jing Tang, Xuan Song, Ryan J. Donahue, Qing Wang, Delissa McMillen, Michael Kunst, Ning Wang, Kimberly A. Smith, Gabriel E. Romero, Michelle M. Frank, Alexandra Krol, Riki Kawaguchi, Daniel H. Geschwind, Guoping Feng, Lisa V. Goodrich, Yuanyuan Liu, Bosiljka Tasic, Hongkui Zeng, Zhigang He
Organization Boston Children's Hospital, Harvard Medical School, Allen Institute for Brain Science
Contact Person Carla C. Winter, Hongkui Zeng, Zhigang He
Contact E-Mail,,
External Identifier NA
Grant Name This work was supported by the National Institutes of Health (F30AG074598, U19MH114830, R01NS109947 and R01AT010779); Allen Institute for Brain Science; Wings for Life Spinal Cord Research Foundation; Department of Public Health of Massachusetts; Dr. Miriam and Sheldon G. Adelson Medical Research Foundation
Consortium BICCN
Data Repository NeMO
Data Repository RRID RRID:SCR_016152
Data License CC BY 4.0
Data Access
Community Standards
Study Organism Mus musculus
Protocol ID;;
Field Value
Description Raw sn-RNAseq data (10x and SSv4) from mouse, generated by the He lab, associated with the following publication: Winter et al. 2023. A transcriptomic taxonomy of mouse brain-wide spinal projecting neurons
Source Data URL
Field Value
Description Analysis bag contains processed data associated with the following publication: Winter et al. A transcriptomic taxonomy of mouse brain-wide spinal projecting neurons
Source Data URL
HOWTO: Download BDBag Data