Whole Mouse Brain Atlas

The millions to billions of cells that comprise mammalian brains are organized into many highly specialized cell types. Previous studies utilizing high-throughput single-cell sequencing have demonstrated that known and novel cell types can be identified by their single-cell gene expression profiles. However, the actual number of cell types in the brain and the degree of diversity among these cell types has been unknown. The current collection of papers from BICCN researchers reports the first complete cell type atlas of a mammalian brain, with over 30 million cells profiled from the adult mouse brain using a combination of single-cell transcriptomic, epigenomic, and spatial transcriptomic approaches, identifying over 5,300 cell types in the entire mouse brain. These studies achieve brain-wide cross-modality integration between transcriptomic profiles and epigenomic, spatial, or connectional properties, as well as certain aspects of evolutionary conservation and divergence, and uncover multitudes of organizing principles of the extraordinary cell type diversity across the brain. This collective body of work represents the largest effort of its kind to date, completion of the capstone project for BICCN, and a landmark achievement that will have far-reaching impact on understanding cell type-based brain circuit function across the neuroscience field.

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Whole Mouse Brain Atlas Papers

A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain

Zizhen Yao, Cindy T. J. van Velthoven, Michael Kunst, Meng Zhang, Delissa McMillen, Changkyu Lee, Won Jung, Jeff Goldy, Aliya Abdelhak, Matthew Aitken, Katherine Baker, Pamela Baker, Eliza Barkan, Darren Bertagnolli, Ashwin Bhandiwad, Cameron Bielstein, Prajal Bishwakarma, Jazmin Campos, Daniel Carey, Tamara Casper, ..., Hongkui Zeng. (2023) Nature 624, 317–332. doi: 10.1038/s41586-023-06812-z

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nemo:dat-qg7n1b0 (10x scRNAseq)

BIL (merfish)

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ABC Atlas

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Molecularly defined and spatially resolved cell atlas of whole mouse brain

Meng Zhang, Xingjie Pan, Won Jung, Aaron R. Halpern, Stephen W. Eichhorn, Zhiyun Lei, Limor Cohen, Kimberly A. Smith, Bosiljka Tasic, Zizhen Yao, Hongkui Zeng, Xiaowei Zhuang (2023) Nature 624, 317–332 .doi: 10.1038/s41586-023-06808-9

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nemo:dat-qg7n1b0 (10x scRNAseq)‍

cellxgene ‍

BIL (merfish)‍

GSE246919 (bulk RNAseq)

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ABC Atlas

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The molecular cytoarchitecture of the adult mouse brain

Jonah Langlieb, Nina S. Sachdev, Karol S. Balderrama, Naeem M. Nadaf, Mukund Raj, Evan Murray, James T. Webber, Charles Vanderburg, Vahid Gazestani, Daniel Tward, Chris Mezias, Xu Li, Katelyn Flowers, Dylan M. Cable, Tabitha Norton, Partha Mitra, Fei Chen, Evan Z. Macosko. (2023) Nature 624, 333–342. doi: 10.1038/s41586-023-06818-7

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Project (10x)‍

Project (slide-seq)

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nemo:dat-aa0jwmj (10x scRNAseq)

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Brain Cell Data Viewer

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Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain

Liu, H., Zeng, Q., Zhou, J., Bartlett, A., Wang, B.-A., Berube, P., Wei Tian, Mia Kenworthy, Jordan Altshul, Joseph R. Nery, Huaming Chen, Rosa G. Castanon, Songpeng Zu, Yang Eric Li, Jacinta Lucero, Julia K. Osteen, Antonio Pinto-Duarte5, Jasper Lee5, Jon Rink, Silvia Cho, Nora Emerson, Michael Nunn, Carolyn O’Connor, Zizhen Yao, Kimberly A. Smith, Bosiljka Tasic, Hongkui Zeng, Chongyuan Luo, Jesse R. Dixon, Bing Ren, M. Margarita Behrens, Ecker, J. R. (2023). Nature 624, 366–377. DOI: https://doi.org/10.1038/s41586-023-06805-y.

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nemo:dat-sig83t9 (snmC-seq2/3)‍

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Single-cell analysis of chromatin accessibility in adult mouse brain

Songpeng Zu, Yang Eric Li, Kangli Wang, Ethan Armand, Sainath Mamde, Maria Luisa Amaral, Yuelai Wang, Andre Chu, Yang Xie, Michael Miller, Jie Xu, Zhaoning Wang, Kai Zhang, Bojing Jia, Xiaomeng Hou, Lin Lin, Qian Yang, Seoyeon Lee, Bin Li, Samantha Kuan, Hanqing Liu, Jingtian Zhou, Antonio Pinto-Duarte, Jacinta Lucero, Julia Osteen, Michael Nunn, Kimberly A. Smith, Bosiljka Tasic, Zizhen Yao, Hongkui Zeng, Zihan Wang, Jingbo Shang, M. Margarita Behrens, Joseph R. Ecker, Allen Wang, Sebastian Preissl, Bing Ren. (2023) Nature 624, 378–389. doi: https://doi.org/10.1038/s41586-023-06824-9

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nemo:dat-bej4ymm (fastq)

GSE246791 (SnapATAC2)

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CATLAS

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Conserved and divergent gene regulatory programs of the mammalian neocortex

Nathan R Zemke, Ethan J Armand, Wenliang Wang, Seoyeon Lee, Jingtian Zhou, Yang Eric Li, Hanqing Liu, Wei Tian, Joseph R. Nery, Rosa G Castanon, Anna Bartlett, Julia K Osteen, Daofeng Li, Xiaoyu Zhuo, Vincent Xu, Lei Chang, Keyi Dong, Hannah Indralingam, Jonathan A Rink, Yang Xie, Michael Miller, Fenna M Krienen, Qiangge Zhang, Naz Taskin, Jonathan Ting, Guoping Feng, Steven A McCarroll, ..., Bing Ren. (2023) Nature 624, 390–402 (2023). https://doi.org/10.1038/s41586-023-06819-6.

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GSE229169 (10x multiome)

GSE240297 (snm3Cseq)

GSE229169 (paired-tag)

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Comparative Epigenome

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Brain-wide correspondence of neuronal epigenomics and distant projections

Jingtian Zhou, Zhuzhu Zhang, May Wu, Hanqing Liu, Yan Pang, Anna Bartlett, Zihao Peng, Wubin Ding, Angeline Rivkin, Will N. Lagos, Elora Williams, Cheng-Ta Lee, Paula Assakura Miyazaki, Andrew Aldridge, Qiurui Zeng, J. L. Angelo Salinda, Naomi Claffey, Michelle Liem, Conor Fitzpatrick, Lara Boggeman, Zizhen Yao, Kimberly A. Smith, Bosiljka Tasic, Jordan Altshul, Mia A. Kenworthy, Cynthia Valadon, ..., Joseph R. Ecker & Edward M. Callaway. (2023) Nature 624, 355–365. doi: 10.1038/s41586-023-06823-w

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GSE230782 (Epi-Retro-seq)

GSE133912 (Retro-seq)

Mendeley (Act-seq)

snmC-seq and MERFISH

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neomorph

ABC Atlas

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Evolution of neuronal cell classes and types in the vertebrate retina

Joshua Hahn, Aboozar Monavarfeshani, Mu Qiao, Allison Kao, Yvonne Kolsch, Ayush Kumar, Vincent P. Kunze, Ashley M. Rasys, Rose Richardson, Joseph B. Wekselblatt, Herwig Baier, Robert J. Lucas, Wei Li, Markus Meister, Joshua T. Trachtenberg, Wenjun Yan, Yi-Rong Peng, Joshua R. Sanes, and Karthik Shekhar. (2023) Nature 624, 415–424. https://doi.org/10.1038/s41586-023-06638-9

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GSE237215 (snRNA-seq)

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A transcriptomic taxonomy of mouse brain-wide spinal projecting neurons

Carla C. Winter, Anne Jacobi, Junfeng, 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 (2023) Nature 624, 403–414. https://doi.org/10.1038/s41586-023-06817-8

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nemo:dat-76h044v (snRNA-seq)

nemo:dat-qg7n1b0 (10x scRNAseq)

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ABC Atlas

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Spatial Atlas of Molecular Cell Types and AAV Accessibility across the Whole Mouse Brain

Hailing Shi, Yichun He, Yiming Zhou, Jiahao Huang, Kamal Maher, Brandon Wang, Zefang Tang, Shuchen Luo, Peng Tan, Morgan Wu, Zuwan Lin, Jingyi Ren, Yaman Thapa, Xin Tang, Ken Y. Chan, Benjamin E. Deverman, Hao Shen, Albert Liu, Jia Liu & Xiao Wang (2023) Nature 622:552–561. doi: 10.1038/s41586-023-06569-5.

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Zenodo

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Single Cell Portal

Spatial Atlas

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