Identifier Results
| Field | Value |
|---|---|
| Identifier | nemo:dat-ch1nqb7 |
| Dataset Name | A transcriptomic and epigenomic cell atlas of mouse primary motor cortex |
| Version | 1 |
| Release Date | NA |
| DOI | NA |
| Source Data URL | |
| Dataset Collection URL | https://data.nemoarchive.org/publication_release/MOp_MiniAtlas_2020_bdbag_2021_04_28.tgz |
| Description | Single cell transcriptomics has transformed the characterization of brain cell identity by providing quantitative molecular signatures for large, unbiased samples of brain cell populations. With the proliferation of taxonomies based on individual datasets, a major challenge is to integrate and validate results toward defining biologically meaningful cell types. We used a battery of single-cell transcriptome and epigenome measurements generated by the BRAIN Initiative Cell Census Network (BICCN) to comprehensively assess the molecular signatures of cell types in the mouse primary motor cortex (MOp). We further developed computational and statistical methods to integrate these multimodal data and quantitatively validate the reproducibility of the cell types. The reference atlas, based on more than 600,000 high quality single-cell or -nucleus samples assayed by six molecular modalities, is a comprehensive molecular account of the diverse neuronal and non-neuronal cell types in MOp. Collectively, our study indicates that the mouse primary motor cortex contains over 55 neuronal cell types that are highly replicable across analysis methods, sequencing technologies, and modalities. We find many concordant multimodal markers for each cell type, as well as thousands of genes and gene regulatory elements with discrepant transcriptomic and epigenomic signatures. These data highlight the complex molecular regulation of brain cell types and will directly enable design of reagents to target specific MOp cell types for functional analysis. |
| Keywords | |
| Total Files in Collection | 23829 |
| Total Size in Collection (in GB) | 9554.7 |
| Authors | Zizhen Yao, Hanqing Liu, Fangming Xie, Stephan Fischer, A. Sina Booeshaghi, Ricky S Adkins, Andrew I. Aldridge, Seth A. Ament, Antonio Pinto-Duarte, Anna Bartlett, M. Margarita Behrens, Koen Van den Berge, Darren Bertagnolli, Tommaso Biancalani, Héctor Corrada Bravo, Tamara Casper, Carlo Colantuoni, Heather Creasy, Kirsten Crichton, Megan Crow, Nick Dee, Elizabeth L Dougherty, Wayne I. Doyle, Sandrine Dudoit, Rongxin Fang, Victor Felix, Olivia Fong, Michelle Giglio, Jeff Goldy, Mike Hawrylycz, Hector Roux de Bézieux, Brian R. Herb, Ronna Hertzano, Xiaomeng Hou, Qiwen Hu, Jonathan Crabtree, Jayaram Kancherla, Matthew Kroll, Kanan Lathia, Yang Eric Li, Jacinta D. Lucero, Chongyuan Luo, Anup Mahurkar, Delissa McMillen, Naeem Nadaf, Joseph R. Nery, Sheng-Yong Niu, Joshua Orvis, Julia K. Osteen, Thanh Pham, Olivier Poirion, Sebastian Preissl, Elizabeth Purdom, Christine Rimorin, Davide Risso, Angeline C. Rivkin, Kimberly Smith, Kelly Street, Josef Sulc, Thuc Nghi Nguyen, Michael Tieu, Amy Torkelson, Herman Tung, Eeshit Dhaval Vaishnav, Valentine Svensson, Charles R. Vanderburg, Vasilis Ntranos, Cindy van Velthoven, Xinxin Wang, Owen R. White, Z. Josh Huang, Peter V. Kharchenko, Lior Pachter, John Ngai, Aviv Regev, Bosiljka Tasic, Joshua D. Welch, Jesse Gillis, Evan Z. Macosko, Bing Ren, Joseph R. Ecker, Hongkui Zeng and Eran A. Mukamel |
| Organization | Allen Institute for Brain Science; Genomic Analysis Laboratory, The Salk Institute for Biological Studies; Dept. of Physics, University of California, San Diego; Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory; Institute for Genome Sciences, University of Maryland School of Medicine; Genomic Analysis Laboratory, The Salk Institute for Biological Studies; Howard Hughes Medical Institute, The Salk Institute for Biological Studies; Computational Neurobiology Laboratory, The Salk Institute for Biological Studies; Department of Statistics, University of California, Berkeley; Department of Applied Mathematics, Computer Science and Statistics, Ghent University; Broad Institute of MIT and Harvard; California Institute of Technology; Center for Bioinformatics and Computational Biology, University of Maryland; Johns Hopkins School of Medicine; Dept. of Cognitive Science, University of California, San Diego; Bioinformatics and Systems Biology Graduate Program, UC San Diego; Division of Biostatistics, School of Public Health, University of California, Berkeley; Department of Otorhinolaryngology, Anatomy and Neurobiology, University of Maryland School of Medicine; Center for Epigenomics, University of California, San Diego School of Medicine; Department of Biomedical Informatics, Harvard Medical School; Ludwig Institute for Cancer Research; Department of Human Genetics, University of California Los Angeles; UCSF; Dept. of Statistical Sciences, University of Padova; Department of Data Sciences, Dana-Farber Cancer Institute; Department of Molecular and Cell Biology, University of California, Berkeley; Department of Computational Medicine and Bioinformatics, University of Michigan |
| Contact Person | Eran A. Mukamel |
| Contact E-Mail | emukamel@ucsd.edu |
| External Identifier | BICCN_MOp_miniatlas |
| Grant Name | MMA U19 1U19MH114821-01; MMA U19 1U19MH114831-01; MMA U19 1U19MH114830-01 |
| 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 | mouse |
| Protocol ID | 10.17504/protocols.io.pjudknw; 10.17504/protocols.io.bcbrism6; 10.17504/protocols.io.pjvdkn6; 10.17504/protocols.io.2srged6; |
| Field | Value |
|---|---|
| Identifier | nemo:dat-3k8aaar |
| Description | Raw data associated with the publication 'An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types' |
| Source Data URL | https://data.nemoarchive.org/biccn/grant/u19_zeng/zeng/transcriptome/scell/10x_v2/mouse/raw/MOp/ |
| Field | Value |
|---|---|
| Identifier | nemo:dat-a6qizv0 |
| Description | Raw data associated with the publication 'An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types' |
| Source Data URL | https://data.nemoarchive.org/biccn/grant/u19_zeng/zeng/transcriptome/sncell/10x_v2/mouse/raw/MOp |
| Field | Value |
|---|---|
| Identifier | nemo:dat-cb5kiub |
| Description | Raw data associated with the publication 'An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types' |
| Source Data URL | https://data.nemoarchive.org/biccn/grant/u19_cemba/cemba/epigenome/sncell/mCseq/mouse/raw/ |
| Field | Value |
|---|---|
| Identifier | nemo:dat-j3xxa7z |
| Description | Raw data associated with the publications 'An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types' and 'A Multimodal Cell Census and Atlas of the Mammalian Primary Motor Cortex' |
| Source Data URL | https://data.nemoarchive.org/biccn/grant/u19_huang/macosko_regev/transcriptome/sncell/10X_v3/mouse/raw/ |
| Field | Value |
|---|---|
| Identifier | nemo:dat-n5ivyeg |
| Description | Raw data associated with the publication 'An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types' |
| Source Data URL | https://data.nemoarchive.org/biccn/grant/u19_cemba/cemba/epigenome/sncell/ATACseq/mouse/raw/ |
| Field | Value |
|---|---|
| Identifier | nemo:dat-n9ap8cz |
| Description | Raw data associated with the publication 'An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types' |
| Source Data URL | https://data.nemoarchive.org/biccn/grant/u19_zeng/zeng/transcriptome/scell/10x_v3/mouse/raw/MOp/ |
| Field | Value |
|---|---|
| Identifier | nemo:dat-oijbtmc |
| Description | Raw data associated with the publication 'An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types' |
| Source Data URL | https://data.nemoarchive.org/biccn/grant/u19_zeng/zeng/transcriptome/scell/SSv4/mouse/raw/MOp/ |
| Field | Value |
|---|---|
| Identifier | nemo:dat-sv5oe57 |
| Description | Raw data associated with the publication 'An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types' |
| Source Data URL | https://data.nemoarchive.org/biccn/grant/u19_zeng/zeng/transcriptome/sncell/10x_v3/mouse/raw/MOp/ |
| Field | Value |
|---|---|
| Identifier | nemo:dat-t9e8c9u |
| Description | Raw data associated with the publication 'An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types' |
| Source Data URL | https://data.nemoarchive.org/biccn/grant/u19_zeng/zeng/transcriptome/sncell/SSv4/mouse/raw/MOp/ |
| Field | Value |
|---|---|
| Identifier | nemo:dat-15ao5au |
| Description | Processed data associated with the publication 'An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types' |
| Source Data URL | https://data.nemoarchive.org/biccn/grant/u19_cemba/cemba/epigenome/sncell/ATACseq/mouse/processed/analysis/EckerRen_Mouse_MOp_methylation_ATAC/ |
| Field | Value |
|---|---|
| Identifier | nemo:dat-1xp2hje |
| Description | Processed data associated with the publication 'An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types' |
| Source Data URL | https://data.nemoarchive.org/biccn/grant/u19_zeng/zeng/transcriptome/sncell/10x_v3/mouse/processed/analysis/10X_nuclei_v3_AIBS/ |
| Field | Value |
|---|---|
| Identifier | nemo:dat-44czbgu |
| Description | Processed data associated with the publication 'An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types' |
| Source Data URL | https://data.nemoarchive.org/biccn/grant/u19_zeng/zeng/transcriptome/sncell/10x_v3/mouse/processed/analysis/10X_nuclei_v3_Broad/ |
| Field | Value |
|---|---|
| Identifier | nemo:dat-4n3nd9i |
| Description | Processed data associated with the publication 'An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types' |
| Source Data URL | https://data.nemoarchive.org/biccn/grant/u19_zeng/zeng/transcriptome/scell/10x_v2/mouse/processed/analysis/10X_cells_v2_AIBS/ |
| Field | Value |
|---|---|
| Identifier | nemo:dat-55mowp9 |
| Description | Processed data associated with the publication 'An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types' |
| Source Data URL | https://data.nemoarchive.org/biccn/grant/u19_zeng/zeng/transcriptome/sncell/SSv4/mouse/processed/analysis/SMARTer_nuclei_MOp/ |
| Field | Value |
|---|---|
| Identifier | nemo:dat-82b26ty |
| Description | Processed data associated with the publication 'An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types' |
| Source Data URL | http://data.nemoarchive.org/biccn/grant/u19_cemba/cemba/epigenome/sncell/mCseq/mouse/processed/analysis/EckerRen_Mouse_MOp_methylation_ATAC/ |
| Field | Value |
|---|---|
| Identifier | nemo:dat-k7p82j4 |
| Description | Processed data associated with the publication 'An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types' |
| Source Data URL | https://data.nemoarchive.org/biccn/grant/u19_zeng/zeng/transcriptome/scell/SSv4/mouse/processed/analysis/SMARTer_cells_MOp/ |
| Field | Value |
|---|---|
| Identifier | nemo:dat-oxuqvjw |
| Description | Processed data associated with the publication 'An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types' |
| Source Data URL | https://data.nemoarchive.org/biccn/grant/u19_zeng/zeng/transcriptome/scell/10x_v3/mouse/processed/analysis/10X_cells_v3_AIBS/ |
| Field | Value |
|---|---|
| Identifier | nemo:dat-pi7zkyi |
| Description | Processed data associated with the publication 'An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types' |
| Source Data URL | https://data.nemoarchive.org/biccn/grant/u19_zeng/zeng/transcriptome/sncell/10x_v2/mouse/processed/analysis/10X_nuclei_v2_AIBS/ |