Identifier Results
| Field | Value |
|---|---|
| Identifier | nemo:dat-yc7wcpv |
| Dataset Name | A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types |
| Version | NA |
| Release Date | NA |
| DOI | NA |
| Source Data URL | Analysis data and additional raw SSv4 data will be made available on July 7, 2025. |
| Dataset Collection URL | https://data.nemoarchive.org/publication_release/Cortical_Tools_2024.tgz |
| Description | The mammalian cortex is comprised of cells with different morphological, physiological, and molecular properties, classified according to shared properties into distinct cell types. Defining the contribution of each cell type to the computational and cognitive processes guided by the cortex is essential for understanding its function in health and disease. We used transcriptomic and epigenomic cortical cell type taxonomies from mice and humans to define marker genes and putative enhancers and created a large toolkit of transgenic lines and enhancer AAVs for selective targeting of cortical populations. We report evaluation of fifteen new transgenic driver lines, two new reporter lines, and over 680 different enhancer AAVs covering all major subclasses of cortical cells, with many achieving a high degree of specificity comparable with existing transgenic lines. The tools reported here as well as the scaled process of tool creation enable diverse experimental strategies towards understanding mammalian cortex and brain function. |
| Keywords | scRNA,10X multiome, 10X, SMARTER, SSv4, cortex, AAV, tools, enhancers |
| Total Files in Collection | 24974 |
| Total Size in Collection (in GB) | 4355.5 |
| Authors | Yoav Ben-Simon, Marcus Hooper, Sujatha Narayan, Tanya Daigle, Deepanjali Dwivedi, Sharon W. Way, Aaron Oster, David A. Stafford, John K. Mich, Michael J. Taormina, Refugio A. Martinez, Ximena Opitz-Araya, Jada R. Roth, Shona Allen, Angela Ayala, Trygve E. Bakken, Tyler Barcelli, Stuard Barta, Jacqueline Bendrick, Darren Bertagnolli, Jessica Bowlus, Gabriella Boyer, Krissy Brouner, Brittny Casian, Tamara Casper, Anish B. Chakka, Rushil Chakrabarty, Rebecca K. Chance, Sakshi Chavan, Maxwell Departee, Nicholas Donadio, Nadezhda Dotson, Tom Egdorf, Mariano Gabitto, Jazmin Garcia, Amanda Gary, Molly Gasperini, Jeff Goldy, Bryan B. Gore, Lucas Graybuck, Noah Greisman, Francoise Haeseleer, Carliana Halterman, Olivia Helback, Dirk Hockemeyer, Cindy Huang, Sydney Huff, Avery Hunker, Nelson Johansen, Zoe Juneau, Brian Kalmbach, Shannon Khem, Emily Kussick, Rana Kutsal, Rachael Larsen, Changkyu Lee, Angus Y. Lee, Madison Leibly, Garreck H. Lenz, Elizabeth Liang, Nicholas Lusk, Jocelin Malone, Tyler Mollenkopf, Elyse Morin, Dakota Newman, Lydia Ng, Kiet Ngo, Victoria Omstead, Alana Oyama, Trangthanh Pham, Christina A. Pom, Lydia Potekhina, Shea Ransford, Dean Rette, Christine Rimorin, Dana Rocha, Augustin Ruiz, Raymond E.A. Sanchez, Adriana Sedeno-Cortes, Joshua P. Sevigny, Nadiya Shapovalova, Lyudmila Shulga, Ana R. Sigler, La’ Akea Siverts, Saroja Somasundaram, Kaiya Stewart, Eric Szelenyi, Michael Tieu, Cameron Trader, Cindy T.J. van Velthoven, Miranda Walker, Natalie Weed, Morgan Wirthlin, Toren Wood, Brooke Wynalda, Zizhen Yao, Thomas Zhou, Jeanelle Ariza, Nick Dee, Melissa Reding, Kara Ronellenfitch, Shoaib Mufti, Susan M. Sunkin, Kimberly A. Smith, Luke Esposito, Jack Waters, Bargavi Thyagarajan, Shenqin Yao, Ed S. Lein, Hongkui Zeng, Boaz P. Levi, John Ngai, Jonathan Ting, Bosiljka Tasic |
| Organization | Allen Institute for Brain Science |
| Contact Person | Yoav Ben-Simon, Bosiljka Tasic |
| Contact E-Mail | yoav.ben-simon@alleninstitute.org, bosiljkat@alleninstitute.org |
| External Identifier | https://doi.org/10.1101/2024.06.10.597244 |
| Grant Name | U19MH114830,RF1MH121274,RF1MH114126,UG3MH120095 |
| Consortium | BICCN |
| Data Repository | NeMO |
| Data Repository RRID | RRID:SCR_016152 |
| Data License | CC BY 4.0 |
| Data Access | https://biccn.org/terms-of-use |
| Community Standards | https://biccn.org/standards |
| Study Organism | Mus musculus |
| Protocol ID | dx.doi.org/10.17504/protocols.io.4r3l22n5pl1y/v1 |
| Field | Value |
|---|---|
| Identifier | nemo:dat-1c0d8ut |
| Description | Raw scATAC-seq data from mouse associated with the following publication: Ben-Simon Y, Hooper M, Narayan S et al. A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types. bioRxiv [Preprint]. 2024 Jun 11:2024.06.10.597244. doi: 10.1101/2024.06.10.597244 |
| Source Data URL | https://data.nemoarchive.org/biccn/grant/u19_zeng/zeng/multimodal/sncell/10xMultiome_ATACseq/mouse/raw/ |
| Field | Value |
|---|---|
| Identifier | nemo:dat-7ch0teh |
| Description | Raw scRNA-seq data from mouse associated with the following publication: Ben-Simon Y, Hooper M, Narayan S et al. A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types. bioRxiv [Preprint]. 2024 Jun 11:2024.06.10.597244. doi: 10.1101/2024.06.10.597244 |
| Source Data URL | https://data.nemoarchive.org/biccn/grant/u19_zeng/zeng/multimodal/sncell/10xMultiome_RNAseq/mouse/raw/ |
| Field | Value |
|---|---|
| Identifier | nemo:dat-oqm6pmh |
| Description | Raw SSv4 data from mouse associated with the following publication: Ben-Simon Y, Hooper M, Narayan S et al. A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types. bioRxiv [Preprint]. 2024 Jun 11:2024.06.10.597244. doi: 10.1101/2024.06.10.597244 |
| Source Data URL | https://data.nemoarchive.org/biccn/grant/rf1_tasic/tasic/transcriptome/scell/SSv4/mouse/raw/ |
This identifier does not have sub-identifiers with "analysis" data associated