Identifier Results
| Field | Value |
|---|---|
| Identifier | nemo:dat-jb2f34y |
| Dataset Name | A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation |
| Version | 2 |
| Release Date | NA |
| DOI | NA |
| Source Data URL | |
| Dataset Collection URL | https://data.nemoarchive.org/publication_release/Zeng_Transcriptomic_Allen_SMARTer_10X_cells_Cortex_Hippocampus_2021.tgz |
| 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 | 4 |
| 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 | https://doi.org/10.1016/j.cell.2021.04.021 |
| Grant Name | R01EY023173, U01MH105982, U19MH114830 |
| Consortium | BICCN |
| Data Repository | NeMO |
| Data Repository RRID | NA |
| Data License | NA |
| Data Access | https://biccn.org/terms-of-use |
| Community Standards | https://biccn.org/standards |
| Study Organism | mouse |
| Protocol ID | NA |
| Field | Value |
|---|---|
| Identifier | nemo:dat-swf6xv3 |
| Description | Raw 10X data associated with the publication 'A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation' |
| Source Data URL | https://data.nemoarchive.org/biccn/grant/u19_zeng/zeng/transcriptome/scell/10x_v2/mouse/raw |
| Field | Value |
|---|---|
| Identifier | nemo:dat-v39m5v1 |
| Description | Raw SMARTSeq data associated with the publication 'A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation' |
| Source Data URL | https://data.nemoarchive.org/biccn/grant/u19_zeng/zeng/transcriptome/scell/SSv4/mouse/raw/ |
| Field | Value |
|---|---|
| Identifier | nemo:dat-iye7gkp |
| Description | Processed SMARTSeq data associated with the publication 'A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation' |
| Source Data URL | http://data.nemoarchive.org/biccn/grant/u19_zeng/zeng/transcriptome/scell/SSv4/mouse/processed/YaoHippo2020/ |
| Field | Value |
|---|---|
| Identifier | nemo:dat-v8hcynz |
| Description | Processed 10X data associated with the publication 'A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation' |
| Source Data URL | http://data.nemoarchive.org/biccn/grant/u19_zeng/zeng/transcriptome/scell/10x_v2/mouse/processed/YaoHippo2020/ |