Human and Non-Human Primate Cell Atlas
The human brain contains more than 100 billion cells, but exactly how these cells are organized into types and how these cell types differ between brain regions and species is an open question. This collection of studies focuses on defining and characterizing the underlying gene expression, gene regulatory, and morphoelectric features of cell types in the human and non-human primate (NHP) brain. These studies employ a range of cellular resolution methods (most notably single cell genomics) for this purpose, marking the beginning of an exciting new era of high-resolution human and NHP analyses. The implications for understanding of human brain function, disease and disease modeling are profound. Studies fall into five categories:
- Adult human single cell atlasing studies, ranging from whole human brain surveys using single cell transcriptomic and epigenomic analyses, to targeted analyses of specific brain regions, to studies of individual variation in cellular and molecular phenotypes. ➔Go to Adult Human Single Cell Atlas
- Adult NHP single cell atlasing studies, focused on similar single cell analyses of marmoset and macaque brain. ➔Go to Adult Non-Human Primate Single Cell Atlas
- Comparative single cell analyses, taking a quantitative comparative approach to understand conserved aspects of cellular and molecular organization and development as well as divergent primate and human specializations. ➔Go to Comparative Single Cell Analyses
- Human and NHP brain development single cell analyses, characterizing developmental dynamics in cellular, molecular and gene regulatory properties in developing human and NHP brain. ➔Go to Human and NHP Brain Development Single Cell Analyses
- Human neuronal cell type functional and anatomical analysis and modeling, including physiological and anatomical characterization of cellular properties in living human tissues, and analyses and modeling of human cell types and specialized cellular properties compared to rodent models. ➔Go to Functional and Anatomical Analysis
Images reprinted with permission from AAAS.
Explore the Collection of Papers
Papers in this collection are published in Science, Science Advances, and Science Translational Medicine, with a few available as preprints at bioRxiv. Papers are listed on this page across all of these journals by the five categories above. Explore the full Science Special Collection with Introduction by Mattia Maroso and Perspective by Alyssa Weniger & Paola Arlotta.
Adult Human Single Cell Atlas
Transcriptomic diversity of cell types across the adult human brain
Siletti, K., Hodge, R., Mossi Albiach, A., Lee, K. W., Ding, S.-L., Hu, L., Lönnerberg, P., ... Linnarsson, S. (2023). Transcriptomic diversity of cell types across the adult human brain. Science. DOI: 10.1126/science.add7046
| Catalog: | Project |
| Data: | NeMO directory |
| Code: | |
| Tools: | cellxgene |
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A comparative atlas of single-cell chromatin accessibility in the human brain
Yang, E. L., Preissl, S., Miller, M., Johnson, N. D., Wang, Z., Jiao, H., ... Ren, B. (2023). A comparative atlas of single-cell chromatin accessibility in the human brain. Science. DOI: 10.1126/science.adf7044
| Catalog: | Project |
| Data: | nemo:dat-d6r90fb |
| Code: | |
| Tools: | CATlas viewer |
Single-cell DNA methylation and 3D genome architecture in the human brain
Tian, W., Zhou, J., Bartlett, A., Zeng, Q., Liu, H., Castanon, R.G., ... Ecker, J. R. (2023). Single-cell DNA methylation and 3D genome architecture in the human brain. Science. DOI: 10.1126/science.adf5357
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| Data: | |
| Protocols: | 3dg dual assay |
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Transcriptomic cytoarchitecture reveals principles of human neocortex organization
Jorstad, N. L., Close, J., Johansen, N., Yanny, A. M., Barkan, E. R., Travaglini, K. J., ... Lein, E. S. (2023). Transcriptomic cytoarchitecture reveals principles of human neocortex organization. Science. DOI: 10.1126/science.adf6812
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| Data: | |
| Portal: | Allen Brain Map |
| Code: | Github analysis code |
Interindividual variation in human cortical cell type abundance and expression
Johansen, N., Somasundaram, S., Travaglini, K. J., Yanny, A. M., Shumyatcher, M., Casper, T., ... Miller, J. A. (2023). Interindividual variation in human cortical cell type abundance and expression. Science. DOI: 10.1126/science.adf2359
| Catalog: | Project |
| Data: | cellxgene |
| Code: | Github analysis code |
A cellular resolution atlas of Broca’s area
Costantini, I., Morgan, L., Yang, J., Balbastre, Y., Varadarajan, D., Pesce, L., ... Hof, P. R. (2023). A cellular resolution atlas of Broca’s area. Science Advances. DOI: 10.1126/sciadv.adg3844
| Catalog: | Project |
| Data: | dandiset/000026 |
| Protocols: |
Adult Non-Human Primate Single Cell Atlas
A marmoset brain cell census reveals regional specialization of cellular identities
Krienen, F. M., Levandowski, K. M., Zaniewski, H., del Rosario, R. C. H., Schroeder, M. E., Goldman, M., ... Feng, G. (2023). A marmoset brain cell census reveals regional specialization of cellular identities. Science Advances. DOI: 10.1126/sciadv.adk3986
A single-cell multi-omic atlas spanning the adult rhesus macaque brain
Chiou, K. L., Huang, X., Bohlen, M. O., Tremblay, S., Decasien, A.R., O’Day, D. R., Spurrell, C. H., ... Snyder-Mackler, N. (2023). A single-cell multi-omic atlas spanning the adult rhesus macaque brain. Science Advances. DOI: 10.1126/sciadv.adh1914
Comparative Single Cell Cell Analyses
Comparative transcriptomics reveals human-specific cortical features
Jorstad, N. L., Song, J. H. T., Exposito-Alonso, D., Suresh, H., Castro, N., Krienen, F. M., ... Bakken, T. E. (2023). Comparative transcriptomics reveals human-specific cortical features. Science. DOI: 10.1126/science.ade9516
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| Data: |
nemo:dat-net1412 (raw)
nemo:dat-swzf4kc (MTG human SSv4)
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| Tools: | |
| Code: | Github analysis code |
Human and NHP Brain Development Single Cell Analyses
Multi-omic profiling of the developing human cerebral cortex at the single cell level
Zhu, K., Bendl, J., Rahman, S., Vicari, J. M., Coleman, C., Clarence, T., Latouche, O., ... Roussos, P. (2023). Multi-omic profiling of the developing human cerebral cortex at the single cell level. Science Advances. DOI: 10.1126/sciadv.adg3754
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| Protocols: | 3dg dual assay |
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A single-cell genomic atlas of postnatal maturation of the human cerebellum during early childhood
Ament, S. A., Cortes-Gutierrez, M., Herb, B. R., Mocci, E., Colantuoni, C., McCarthy, M. M. (2023). A single-cell genomic atlas of postnatal maturation of the human cerebellum during early childhood . Science Translational Medicine. DOI: 10.1126/scitranslmed.ade1283
| Code: | |
| Tools: | NeMO Analytics: 522872b1 |
Comprehensive cell atlas of the first-trimester developing human brain
Braun, E., Danan-Gotthold, M., Borm, L. E., Lee, K. W., Vinsland, E., Lönnerberg, P., ... Linnarsson, S. (2023). Title of the Paper. Science. DOI: 10.1126/science.adf1226
| Data: | |
| Code: | GitHub |
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Spatiotemporal molecular dynamics of the developing human thalamus
Kim, C. N., Shin, D., Wang, A., Nowakowski, T. J. (2023). Comprehensive cell atlas of the first-trimester developing human brain. Science. DOI: 10.1126/science.adf9941
| Data: |
UCSC Cell Browser (scRNAseq)
Dryad (MERFISH)
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Herb, B. R., Glover, H. J., Bhaduri, A., Colantuoni, C., Bale, T. L., Siletti, K., ... Ament, S. A. (2023). Science Advances. DOI: DOI: 10.1126/sciadv.adf6251.
| Catalog: | |
| Data: | nemo:dat-917e9vs |
| Tools | NeMO Analytics: a856c14e |
Single-cell analysis of prenatal and postnatal human cortical development
Velmeshev, D., Perez, Y., Yan, Z., Valencia, J. E., Castaneda-Castellanos, D. R., Wang, L., Schirmer, L., ... Kriegstein, A.R. (2023). Single-cell analysis of prenatal and postnatal human cortical development. Science. DOI: 10.1126/science.adf0834
| Data: | |
| Code: | Zenodo |
Micali, N., Ma, S., Li, M., Kim, S.-K., Mato-Blanco, X., Sindhu, S., ... Rakic, P. (2023). Molecular programs of regional specification and neural stem cell fate progression in macaque telencephalon. Science. DOI: 10.1126/science.adf3786
| Data: |
GEO:GSE226451 (single cell)
GEO:GSE225482 (bulk RNA)
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| Code: | Github |
| Tools: |
Human Neuronal Cell Type Functional and Anatomical Analysis and Modeling
Signature morphoelectric properties of diverse GABAergic interneurons in the human neocortex
Lee, B. R., Dalley, R., Miller, J. A., Chartrand, T., Close, J., Mann, R., ... Ting, J. T. (2023). Signature morphoelectric properties of diverse GABAergic interneurons in the human neocortex. Science. DOI: 10.1126/science.adf6484
Chartrand, T., Dalley, R., Close, J., Goriounova, N. A., Lee, B. R., Mann, R., ... Lein, E.S. (2023). Morphoelectric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex. Science. DOI: 10.1126/science.adf0805
Han, X., Guo, S., Ji, N., Li, T., Liu, J., Ye, X., ... Peng, H. (2023). Whole human-brain mapping of single cortical neurons for profiling morphological diversity and stereotypy. Science Advances. DOI: 10.1126/sciadv.adf3771
Integrated platform for multi-scale molecular imaging and phenotyping of the human brain
Park, J., Wang, J., Guan, W., Kamentsky, L., Evans, N.B., Gjesteby, L. A., Pollack, D., ... Chung, K. (2023). Integrated platform for multi-scale molecular imaging and phenotyping of the human brain. bioRxiv 2022.03.13.484171; doi: https://doi.org/10.1101/2022.03.13.484171
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Rózsa, M., Tóth, M., Oláh, G., Baka, J., Lákovics, R., Barzó, P., ... Tamás, G. (2023). Temporal disparity of action potentials triggered in axon initial segments and distal axons in the neocortex. Science Advances. DOI: 10.1126/sciadv.ade4511
Human voltage-gated Na+ and K+ channel properties underlie sustained fast AP signaling
Wilbers, R., Metodieva, V. D., Duverdin, S., Heyer, D. B., Galakhova, A. A., Mertens, E. J., ... Goriounova, N. A. (2023). Human voltage-gated Na+ and K+ channel properties underlie sustained fast AP signaling. Science Advances. DOI: 10.1126/sciadv.ade3300
Wilbers, R., Galakhova, A. A., Driessens, S. L.W., Heistek, T. S., Metodieva, V. D., Hagemann, J., ... Goriounova, N. A. (2023). Structural and functional specializations of human fast spiking neurons support fast cortical signaling. Science Advances. DOI: 10.1126/sciadv.adf0708
| Data: | DataverseNL |
| Tools: |
Structural complexity supports computational richness in human hippocampal CA1 pyramidal neurons
Mertens, E. J., Leibner, Y., Pie, J., Galakhova, A. A., Waleboer, F., Meijer, J., ... de Kock, C. P.J. (2023). Structural complexity supports computational richness in human hippocampal CA1 pyramidal neurons. bioRxiv. DOI: https://doi.org/10.1101/2023.10.05.561029
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