Identifier Results
| Field | Value |
|---|---|
| Identifier | nemo:dat-ek5dbmu |
| Dataset Name | Comparative cellular analysis of motor cortex in human, marmoset and mouse |
| Version | 2 |
| Release Date | NA |
| DOI | NA |
| Source Data URL | |
| Dataset Collection URL | |
| Description | The primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals1. Here, using high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei in humans, marmoset monkeys and mice, we demonstrate a broadly conserved cellular makeup of this region, with similarities that mirror evolutionary distance and are consistent between the transcriptome and epigenome. The core conserved molecular identities of neuronal and non-neuronal cell types allow us to generate a cross-species consensus classification of cell types, and to infer conserved properties of cell types across species. Despite the overall conservation, however, many species-dependent specializations are apparent, including differences in cell-type proportions, gene expression, DNA methylation and chromatin state. Few cell-type marker genes are conserved across species, revealing a short list of candidate genes and regulatory mechanisms that are responsible for conserved features of homologous cell types, such as the GABAergic chandelier cells. This consensus transcriptomic classification allows us to use patch–seq (a combination of whole-cell patch-clamp recordings, RNA sequencing and morphological characterization) to identify corticospinal Betz cells from layer 5 in non-human primates and humans, and to characterize their highly specialized physiology and anatomy. These findings highlight the robust molecular underpinnings of cell-type diversity in M1 across mammals, and point to the genes and regulatory pathways responsible for the functional identity of cell types and their species-specific adaptations. |
| Keywords | snmC-seq2, snRNA-seq, 10x, SSv4, SNARE-seq2, DNA methylation, RNA-sequencing, ATAC-seq, human, macaque, marmoset, mouse, brain, primary motor cortex, M1, Mop |
| Total Files in Collection | 0 |
| Total Size in Collection (in GB) | 0.0 |
| Authors | Bakken, T.E., Jorstad, N.L., Hu, Q. et al. |
| Organization | Allen Institute for Brain Science |
| Contact Person | Trygve Bakken |
| Contact E-Mail | trygveb@alleninstitute.org |
| External Identifier | https://doi.org/10.1038/s41586-021-03465-8 |
| Grant Name | Allen Institute for Brain Science and by US National Institutes of Health (NIH) grant U01 MH114812-02 |
| 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 | Human (Homo sapiens), Macaque (Macaca mulatta), Marmoset (Callithrix jacchus), Mouse (Mus musculus) |
| Protocol ID | snRNA-seq SMART-seq V4 (dx.doi.org/10.17504/protocols.io.7aehibe, dx.doi.org/10.17504/protocols.io.ztqf6mw), snRNA-seq 10x Cv3 (dx.doi.org/10.17504/protocols.io.y6rfzd6, dx.doi.org/10.17504/protocols.io.nx3dfqn), marmoset nuclei preparation (https://www.protocols.io/view/extraction-of-nuclei-from-brain-tissue-2srged6), SNARE-seq2 (https://dx.doi.org/10.17504/protocols.io.8tvhwn6, https://dx.doi.org/10.17504/protocols.io.be5gjg3w), mouse prep for 10x Cv3 nuclei (doi:10.17504/protocols.io.bcbrism6), mouse snmC-seq2 bisulfite conversion and library preparation (doi:10.17504/protocols.io.pjvdkn6), mouse snATAC-seq (doi:10.17504/protocols.io.pjudknw) |
| Field | Value |
|---|---|
| Identifier | nemo:dat-2mwt2hg |
| Description | Raw SNAREseq data from marmoset, generated by the Zhang lab, associated with the following publication: Bakken et al, 2021. Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature doi.org/10.1038/s41586-021-03465-8 |
| Source Data URL | http://data.nemoarchive.org/biccn/grant/u01_zhangk/zhang/multimodal/sncell/ |
| Field | Value |
|---|---|
| Identifier | nemo:dat-9arp1vk |
| Description | Raw, open access mCseq data from human, generated by the Lein lab, associated with the publication, Comparative cellular analysis of motor cortex in human, marmoset and mouse |
| Source Data URL | https://data.nemoarchive.org/biccn/grant/u01_ecker/ecker/epigenome/sncell/mCseq/human/raw/ |
| Field | Value |
|---|---|
| Identifier | nemo:dat-bx7hnbd |
| Description | Raw, open access 10X data from human, generated by the Linnarsson lab, associated with the publication, Comparative cellular analysis of motor cortex in human, marmoset and mouse |
| Source Data URL | http://data.nemoarchive.org/biccn/grant/u01_lein/linnarsson/transcriptome/sncell/10x_v3/human/raw/ |
| Field | Value |
|---|---|
| Identifier | nemo:dat-cg2cf8j |
| Description | Raw 10X data from marmoset, generated by the Feng lab, associated with the following publication: Bakken et al, 2021. Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature doi.org/10.1038/s41586-021-03465-8 |
| Source Data URL | http://data.nemoarchive.org/biccn/grant/u01_feng/mccarroll/transcriptome/sncell/10Xv3/marmoset/raw/ |
| Field | Value |
|---|---|
| Identifier | nemo:dat-f1g21to |
| Description | Raw ATACseq data from mouse, generated by the Tasic lab, associated with the publication, Comparative cellular analysis of motor cortex in human, marmoset and mouse |
| Source Data URL | http://data.nemoarchive.org/biccn/grant/rf1_tasic/tasic/epigenome/scell/ATACseq/mouse/raw/ |
| Field | Value |
|---|---|
| Identifier | nemo:dat-gf9tvdo |
| Description | Raw 10X data from mouse, generated by the Macosko & Regev labs, associated with the publication, Comparative cellular analysis of motor cortex in human, marmoset and mouse |
| Source Data URL | http://data.nemoarchive.org/biccn/grant/u19_huang/macosko_regev/transcriptome/sncell/10X_v3/mouse/raw/ |
| Field | Value |
|---|---|
| Identifier | nemo:dat-mhvbd8b |
| Description | Raw, consented open access SS4 data from human, generated by the Lein lab, associated with the following publication: Bakken et al, 2021. Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature doi.org/10.1038/s41586-021-03465-8 |
| Source Data URL | This dataset is included within NDA Permissions Group "BRAIN/NeMO: A multimodal atlas of human brain cell types: Human Cortex". Instructions for requesting controlled access are available at https://nemoarchive.org/resources/accessing-controlled-access-data.php |
| Field | Value |
|---|---|
| Identifier | nemo:dat-u3ajbhg |
| Description | Raw mCseq data from marmoset, generated within the CEMBA project, associated with the following publication: Bakken et al, 2021. Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature doi.org/10.1038/s41586-021-03465-8 |
| Source Data URL | http://data.nemoarchive.org/biccn/grant/u19_cemba/cemba/epigenome/sncell/mCseq/marmoset/raw/ |
| Field | Value |
|---|---|
| Identifier | nemo:dat-wosa3hn |
| Description | Raw, consented open access SNAREseq data from human, generated by the Zhang lab, associated with the following publication: Bakken et al, 2021. Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature doi.org/10.1038/s41586-021-03465-8 |
| Source Data URL | http://data.nemoarchive.org/biccn/grant/u01_zhangk/zhang/multimodal/sncell/ |
| Field | Value |
|---|---|
| Identifier | nemo:dat-a8at9ih |
| Description | Processed analysis files associated with the publication: Bakken et al, 2021. Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature doi.org/10.1038/s41586-021-03465-8 |
| Source Data URL | https://data.nemoarchive.org/publication_release/Lein_2020_M1_study_analysis |