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

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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.

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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

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Single nucleus RNAseq

Postmortem brain processing

Isolation of Nuclei

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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

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epiformer deep learning

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CATlas viewer

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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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Human Brain Atlas Code

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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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Allen Brain Map

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

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cellxgene

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Github analysis code

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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

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dandiset/000026

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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

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NeMO‍BIL

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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

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nemo:dat-rtmm5q2 cellxgene

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sci-RNA-seq3 demultiplex

sci-ATAC-seq3 demultiplex

sci-RNA-seq3 preprocess

sci-ATAC-seq3 preprocess

analysis

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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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nemo:dat-net1412 (raw)

nemo:dat-swzf4kc (MTG human SSv4)

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Github analysis code

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Cytosplore Viewer

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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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GEO:GSE204684

cellxgene

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UCSC Genome Browser

Single Cell Portal:SCP1859

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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

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R scripts gene networks

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NeMO Analytics: 522872b1

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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

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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

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UCSC Cell Browser (scRNAseq)

Dryad (MERFISH)

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Single-cell genomics reveals region-specific developmental trajectories underlying neuronal diversity in the human hypothalamus

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.

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nemo:dat-917e9vs

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NeMO Analytics: a856c14e

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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

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Molecular programs of regional specification and neural stem cell fate progression in macaque telencephalon

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

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nemo:dat-fjx1jbr

GEO:GSE226451 (single cell)

GEO:GSE225482 (bulk RNA)

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Github

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Viewer

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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

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GitHub (Electrophysiology)

GitHub (Morphology)

GitHub (Transcriptomics)

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Morphoelectric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex

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

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Human Collections

Mouse Collections

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analysis code

ipfx (electrophysiology)

neuron morphology

skeleton keys (morphology)

transcriptomics

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Whole human-brain mapping of single cortical neurons for profiling morphological diversity and stereotypy

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

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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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Multi-round alignment

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Chung Lab Neuroglancer

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Temporal disparity of action potentials triggered in axon initial segments and distal axons in the neocortex

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

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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

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DataverseNL

Synaptic Physiology Coarse Matrix

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Allen Cell Types Database

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Structural and functional specializations of human fast spiking neurons support fast cortical signaling

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

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DataverseNL

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Allen Cell Types Database

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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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MIES

Morphys

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