A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain.
A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain.
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DOI：
10.1038/s41586-023-06812-z
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发表时间：
2023-12
期刊：
影响因子：
64.8
通讯作者：
Zeng, Hongkui
中科院分区：
文献类型：
--
作者：
Yao, Zizhen;van Velthoven, Cindy T. J.;Kunst, Michael;Zhang, Meng;Mcmillen, Delissa;Lee, Changkyu;Jung, Won;Goldy, Jeff;Abdelhak, Aliya;Aitken, Matthew;Baker, Katherine;Baker, Pamela;Barkan, Eliza;Bertagnolli, Darren;Bhandiwad, Ashwin;Bielstein, Cameron;Bishwakarma, Prajal;Campos, Jazmin;Carey, Daniel;Casper, Tamara;Chakka, Anish Bhaswanth;Chakrabarty, Rushil;Chavan, Sakshi;Chen, Min;Clark, Michael;Close, Jennie;Crichton, Kirsten;Daniel, Scott;Divalentin, Peter;Dolbeare, Tim;Ellingwood, Lauren;Fiabane, Elysha;Fliss, Timothy;Gee, James;Gerstenberger, James;Glandon, Alexandra;Gloe, Jessica;Gould, Joshua;Gray, James;Guilford, Nathan;Guzman, Junitta;Hirschstein, Daniel;Ho, Windy;Hooper, Marcus;Huang, Mike;Hupp, Madie;Jin, Kelly;Kroll, Matthew;Lathia, Kanan;Leon, Arielle;Li, Su;Long, Brian;Madigan, Zach;Malloy, Jessica;Malone, Jocelin;Maltzer, Zoe;Martin, Naomi;Mccue, Rachel;Mcginty, Ryan;Mei, Nicholas;Melchor, Jose;Meyerdierks, Emma;Mollenkopf, Tyler;Moonsman, Skyler;Nguyen, Thuc Nghi;Otto, Sven;Pham, Trangthanh;Rimorin, Christine;Ruiz, Augustin;Sanchez, Raymond;Sawyer, Lane;Shapovalova, Nadiya;Shepard, Noah;Slaughterbeck, Cliff;Sulc, Josef;Tieu, Michael;Torkelson, Amy;Tung, Herman;Valera Cuevas, Nasmil;Vance, Shane;Wadhwani, Katherine;Ward, Katelyn;Levi, Boaz;Farrell, Colin;Young, Rob;Staats, Brian;Wang, Ming-Qiang Michael;Thompson, Carol L.;Mufti, Shoaib;Pagan, Chelsea M.;Kruse, Lauren;Dee, Nick;Sunkin, Susan M.;Esposito, Luke;Hawrylycz, Michael J.;Waters, Jack;Ng, Lydia;Smith, Kimberly;Tasic, Bosiljka;Zhuang, Xiaowei;Zeng, Hongkui
哺乳动物的大脑由数百万到数十亿个细胞组成，这些细胞被组织成特定的空间分布模式以及结构和功能特性。通过组合大约700万个细胞的单细胞RNA-severing（SCRNA-SEQ），创建了细胞类型的地图质量控制），以及使用多重误差荧光原位杂交的大约430万个单元的空间转录组数据集（Merfish）。我们提出一个在线平台，艾伦脑细胞地图RNA-sequering和Merfish数据集。不同的大脑区域 - 尤其是大脑的背侧和腹侧部分之间的二分法。类型，腹侧部分包含更多的神经元类型，这些类型彼此之间更加紧密相关。是细胞类型分类的主要决定剂，并确定了组合转录因子代码，该代码定义了整个大脑的所有部分小鼠脑脑转录组和空间细胞类型地图集建立了基准参考地图集和基础资源，用于整合细胞和电路功能，哺乳动物大脑的发育和进化。
整个成年小鼠大脑的转录组细胞类型图集具有约5,300个簇，该簇由单细胞和空间转录组数据集构建，具有超过800万个细胞的细胞数据集揭示了整个大脑的细胞类型多样性以及不同大脑区域的独特细胞类型特征。
The mammalian brain consists of millions to billions of cells that are organized into many cell types with specific spatial distribution patterns and structural and functional properties. Here we report a comprehensive and high-resolution transcriptomic and spatial cell-type atlas for the whole adult mouse brain. The cell-type atlas was created by combining a single-cell RNA-sequencing (scRNA-seq) dataset of around 7 million cells profiled (approximately 4.0 million cells passing quality control), and a spatial transcriptomic dataset of approximately 4.3 million cells using multiplexed error-robust fluorescence in situ hybridization (MERFISH). The atlas is hierarchically organized into 4 nested levels of classification: 34 classes, 338 subclasses, 1,201 supertypes and 5,322 clusters. We present an online platform, Allen Brain Cell Atlas, to visualize the mouse whole-brain cell-type atlas along with the single-cell RNA-sequencing and MERFISH datasets. We systematically analysed the neuronal and non-neuronal cell types across the brain and identified a high degree of correspondence between transcriptomic identity and spatial specificity for each cell type. The results reveal unique features of cell-type organization in different brain regions—in particular, a dichotomy between the dorsal and ventral parts of the brain. The dorsal part contains relatively fewer yet highly divergent neuronal types, whereas the ventral part contains more numerous neuronal types that are more closely related to each other. Our study also uncovered extraordinary diversity and heterogeneity in neurotransmitter and neuropeptide expression and co-expression patterns in different cell types. Finally, we found that transcription factors are major determinants of cell-type classification and identified a combinatorial transcription factor code that defines cell types across all parts of the brain. The whole mouse brain transcriptomic and spatial cell-type atlas establishes a benchmark reference atlas and a foundational resource for integrative investigations of cellular and circuit function, development and evolution of the mammalian brain. A transcriptomic cell-type atlas of the whole adult mouse brain with ~5,300 clusters built from single-cell and spatial transcriptomic datasets with more than eight million cells reveals remarkable cell type diversity across the brain and unique cell type characteristics of different brain regions.
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影响因子：
4.7
作者：
Downs, Anthony M.;McElligott, Zoe A.
通讯作者：
McElligott, Zoe A.
影响因子：
64.5
作者：
Daigle TL;Madisen L;Hage TA;Valley MT;Knoblich U;Larsen RS;Takeno MM;Huang L;Gu H;Larsen R;Mills M;Bosma-Moody A;Siverts LA;Walker M;Graybuck LT;Yao Z;Fong O;Nguyen TN;Garren E;Lenz GH;Chavarha M;Pendergraft J;Harrington J;Hirokawa KE;Harris JA;Nicovich PR;McGraw MJ;Ollerenshaw DR;Smith KA;Baker CA;Ting JT;Sunkin SM;Lecoq J;Lin MZ;Boyden ES;Murphy GJ;da Costa NM;Waters J;Li L;Tasic B;Zeng H
通讯作者：
Zeng H
影响因子：
16.2
作者：
Ecker JR;Geschwind DH;Kriegstein AR;Ngai J;Osten P;Polioudakis D;Regev A;Sestan N;Wickersham IR;Zeng H
通讯作者：
Zeng H
影响因子：
--
作者：
Campbell, Christine E.;Piper, Michael;Gronostajski, Richard M.
通讯作者：
Gronostajski, Richard M.
影响因子：
5.4
作者：
Srivastava M;Larroux C;Lu DR;Mohanty K;Chapman J;Degnan BM;Rokhsar DS
通讯作者：
Rokhsar DS