Identifier Results
| Field | Value |
|---|---|
| Identifier | nemo:dat-p3eei0g |
| Dataset Name | Inter-individual variation in human cortical cell type abundance and expression |
| Version | NA |
| Release Date | NA |
| DOI | NA |
| Source Data URL | NA |
| Dataset Collection URL | https://data.nemoarchive.org/publication_release/Human_Variation-2024-12-17.tgz |
| Description | Single cell transcriptomic studies have identified a conserved set of neocortical cell types from small post-mortem cohorts. We extend these efforts by assessing cell type variation across 75 adult individuals undergoing epilepsy and tumor surgeries. Nearly all nuclei map to one of 125 robust cell types identified in middle temporal gyrus, but with varied abundances and gene expression signatures across donors, particularly in deep layer glutamatergic neurons. A minority of variance is explainable by known factors including donor identity and small contributions from age, sex, ancestry, and disease state. Genomic variation was significantly associated with variable expression of 150-250 genes for most cell types. Thus, human individuals display a highly consistent cellular makeup, but with significant variation reflecting donor characteristics, disease condition, and genetic regulation. |
| Keywords | inter-individual variation, transcriptomics, genetics, snRNA-seq, WGS, human |
| Total Files in Collection | 373 |
| Total Size in Collection (in GB) | 19872.3 |
| Authors | Nelson Johansen, Saroja Somasundaram, Kyle J. Travaglini, Anna Marie Yanny, Maya Shumyatcher, Tamara Casper, Charles Cobbs, Nick Dee, Richard Ellenbogen, Manuel Ferreira, Jeff Goldy, Junitta Guzman, Ryder Gwinn, Daniel Hirschstein, Nikolas L. Jorstad, C. Dirk Keene, Andrew Ko, Boaz P. Levi, Jeffrey G. Ojemann, Thanh Pham, Nadiya Shapovalova, Daniel Silbergeld, Josef Sulc, Amy Torkelson, Herman Tung, Kimberly Smith, Ed S. Lein, Trygve E. Bakken, Rebecca D. Hodge, Jeremy A. Miller |
| Organization | Allen Institute for Brain Science |
| Contact Person | Trygve E. Bakken, Rebecca D. Hodge, Jeremy A. Miller |
| Contact E-Mail | trygveb@alleninstitute.org, rebeccah@alleninstitute.org, jeremym@alleninstitute.org |
| External Identifier | https://doi.org/10.1126/science.adf2359 |
| Grant Name | U01MH114812 |
| Consortium | BICCN |
| Data Repository | NeMO |
| Data Repository RRID | RRID:SCR_016152 |
| Data License | Public data available under CC BY 4.0; controlled access data subject to data use certification |
| Data Access | https://biccn.org/terms-of-use |
| Community Standards | https://biccn.org/standards |
| Study Organism | human |
| Protocol ID | dx.doi.org/10.17504/protocols.io.774hrqw; dx.doi.org/10.17504/protocols.io.bq64mzgw |
| Field | Value |
|---|---|
| Identifier | nemo:dat-0qven3z |
| Description | Controlled (Limited), WGS processed data associated with the following publication: Johansen et al, 2022. Inter-individual variation in human cortical cell type abundance and expression. bioRxiv doi.org/10.1101/2022.10.07.511366. This data can be requested within the following NDA Controlled Access Permission Group: BRAIN/NeMO: A Multimodal atlas of human brain cell types: Human variation RNAseq & WGS, Limited to Brain Health & Disease (Lein) |
| Source Data URL | This is a restricted access dataset. Instructions for controlled access are available at https://nemoarchive.org/resources/accessing-controlled-access-data.php |
| Field | Value |
|---|---|
| Identifier | nemo:dat-2ehy1z6 |
| Description | Controlled (Limited), 10x raw data associated with the following publication: Johansen et al, 2022. Inter-individual variation in human cortical cell type abundance and expression. bioRxiv doi.org/10.1101/2022.10.07.511366. This data can be requested within the following NDA Controlled Access Permission Group: BRAIN/NeMO: A Multimodal atlas of human brain cell types: Human variation RNAseq & WGS, Limited to Brain Health & Disease (Lein) |
| Source Data URL | This is a restricted access dataset. Instructions for controlled access are available at https://nemoarchive.org/resources/accessing-controlled-access-data.php |
| Field | Value |
|---|---|
| Identifier | nemo:dat-nq9eff2 |
| Description | Controlled (GRU), 10x raw data associated with the following publication: Johansen et al, 2022. Inter-individual variation in human cortical cell type abundance and expression. bioRxiv doi.org/10.1101/2022.10.07.511366. This data can be requested within the following NDA Controlled Access Permission Group: BRAIN/NeMO: A Multimodal atlas of human brain cell types: Human variation RNAseq & WGS |
| Source Data URL | This is a restricted access dataset. Instructions for controlled access are available at https://nemoarchive.org/resources/accessing-controlled-access-data.php |
| Field | Value |
|---|---|
| Identifier | nemo:dat-vztjecy |
| Description | Controlled (GRU), WGS raw data associated with the following publication: Johansen et al, 2022. Inter-individual variation in human cortical cell type abundance and expression. bioRxiv doi.org/10.1101/2022.10.07.511366. This data can be requested within the following NDA Controlled Access Permission Group: BRAIN/NeMO: A Multimodal atlas of human brain cell types: Human variation RNAseq & WGS |
| Source Data URL | This is a restricted access dataset. Instructions for controlled access are available at https://nemoarchive.org/resources/accessing-controlled-access-data.php |
| Field | Value |
|---|---|
| Identifier | nemo:dat-5f1u985 |
| Description | Open, processed 10x data associated with the following publication: Johansen et al, 2022. Inter-individual variation in human cortical cell type abundance and expression. bioRxiv doi.org/10.1101/2022.10.07.511366 |
| Source Data URL | https://data.nemoarchive.org/publication_release/Human_Variation_Analysis/ |
| Field | Value |
|---|---|
| Identifier | nemo:dat-c948wqa |
| Description | Controlled (Limited), WGS processed data associated with the following publication: Johansen et al, 2022. Inter-individual variation in human cortical cell type abundance and expression. bioRxiv doi.org/10.1101/2022.10.07.511366. This data can be requested within the following NDA Controlled Access Permission Group: BRAIN/NeMO: A Multimodal atlas of human brain cell types: Human variation RNAseq & WGS, Limited to Brain Health & Disease (Lein) |
| Source Data URL | This is a restricted access dataset. Instructions for controlled access are available at https://nemoarchive.org/resources/accessing-controlled-access-data.php |