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Identifier nemo:dat-jb2f34y
Dataset Name A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation
Version 1
Release Date NA
DOI NA
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Description The isocortex and hippocampal formation (HPF) in the mammalian brain play critical roles in perception, cognition, emotion, and learning. We profiled approximately 1.3 million cells covering the entire adult mouse isocortex and HPF and derived a transcriptomic cell-type taxonomy revealing a comprehensive repertoire of glutamatergic and GABAergic neuron types. Contrary to the traditional view of HPF as having a simpler cellular organization, we discover a complete set of glutamatergic types in HPF homologous to all major subclasses found in the six-layered isocortex, suggesting that HPF and the isocortex share a common circuit organization. We also identify large-scale continuous and graded variations of cell types along isocortical depth, across the isocortical sheet, and in multiple dimensions in hippocampus and subiculum. Overall, our study establishes a molecular architecture of the mammalian isocortex and hippocampal formation and begins to shed light on its underlying relationship with the development, evolution, connectivity, and function of these two brain structures
Keywords GABAergic; cell type; cortex; excitatory neuron; glutamatergic; hippocampus; interneuron; single-cell RNA sequencing; single-cell transcriptomics
Total Files in Collection 0
Total Size in Collection (in GB) 0.0
Authors Zizhen Yao, Cindy T J van Velthoven, Thuc Nghi Nguyen, Jeff Goldy, Adriana E Sedeno-Cortes, Fahimeh Baftizadeh, Darren Bertagnolli, Tamara Casper, Megan Chiang, Kirsten Crichton, Song-Lin Ding, Olivia Fong, Emma Garren, Alexandra Glandon, Nathan W Gouwens, James Gray, Lucas T Graybuck, Michael J Hawrylycz, Daniel Hirschstein, Matthew Kroll, Kanan Lathia, Changkyu Lee, Boaz Levi, Delissa McMillen, Stephanie Mok, Thanh Pham, Qingzhong Ren, Christine Rimorin, Nadiya Shapovalova, Josef Sulc, Susan M Sunkin, Michael Tieu, Amy Torkelson, Herman Tung, Katelyn Ward, Nick Dee, Kimberly A Smith, Bosiljka Tasic, Hongkui Zeng
Organization Allen Institute for Brain Science
Contact Person Hongkui Zeng
Contact E-Mail HongkuiZ@alleninstitute.org
External Identifier Zeng_Transcriptomic_Allen_SMARTer_10X_cells_Cortex_Hippocampus
Grant Name R01EY023173, U01MH105982, U19MH114830
Consortium NA
Data Repository BICCN
Data Repository RRID NA
Data License NA
Data Access
Community Standards
Study Organism mouse
Protocol ID NA
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Description Raw data associated with publication 'A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation'
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Description Raw data associated with publication 'A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation'
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Description Processed data associated with publication 'A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation'
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Description Processed data associated with publication 'A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation'
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