Comparative cellular analysis of motor cortex in human, marmoset and mouse
Open accessPublished version of a preprint
Abstract
. 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.
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Human single nucleus RNA sequencing data from Bakken and colleagues were obtained from the Human Protein Atlas.
“Human single nucleus RNA sequencing data from Bakken and colleagues [11] were obtained from the Human Protein Atlas (proteinatlas.org).”
From Selective suppression of oligodendrocyte-derived amyloid beta rescues neuronal dysfunction in Alzheimer’s disease (2024) · cites this paper as [11]
Apart from PSEN2, oligodendrocytes had elevated expression of all genes involved in amyloid beta production in human single-nucleus RNA sequencing datasets.
“We found that, apart from PSEN2 (which is not essential for gamma secretase function when PSEN1 is present [13]), oligodendrocytes had elevated expression of all of these genes (Fig 1A–1D).”
From Selective suppression of oligodendrocyte-derived amyloid beta rescues neuronal dysfunction in Alzheimer’s disease (2024) · cites this paper as [11]
The citation is attached to the parenthetical claim that PSEN2 is not essential for gamma-secretase function when PSEN1 is present. Our copy’s Methods > SNARE–seq2 and Consensus M1 taxonomy across species passages discuss oligodendrocyte profiling, but do not address PSEN1, PSEN2, gamma-secretase function, or elevated expression of amyloid-beta-production genes. Searches for those terms found no decisive passage. (LLM, conf=0.75)
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Cites
Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp616 · Cited by 41,364 · see citing works
Wickham, H. (2016) · Use R! · doi:10.1007/978-3-319-24277-4 · Cited by 33,612 · see citing works
Comprehensive Integration of Single-Cell Data
Stuart, T., Butler, A., Hoffman, P., Hafemeister, C., Papalexi, E., Mauck, W. M., Hao, Y., Stoeckius, M., Smibert, P., & Satija, R. (2019) · Cell · doi:10.1016/j.cell.2019.05.031 · Cited by 15,453 · see citing works
Gene selection for cancer classification using support vector machines
Guyon, I., Weston, J., Barnhill, S., & Vapnik, V. (2002) · Machine Learning · doi:10.1023/a:1012487302797 · Cited by 9,954 · see citing works
SCANPY: large-scale single-cell gene expression data analysis
Wolf, F. A., Angerer, P., & Theis, F. J. (2018) · Genome Biology · doi:10.1186/s13059-017-1382-0 · Cited by 8,881 · see citing works
deepTools2: a next generation web server for deep-sequencing data analysis
Ramírez, F., Ryan, D. P., Grüning, B., Bhardwaj, V., Kilpert, F., Richter, A. S., Heyne, S., Dündar, F., & Manke, T. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw257 · Cited by 8,096 · see citing works
From Louvain to Leiden: guaranteeing well-connected communities
Traag, V. A., Waltman, L., & van Eck, N. J. (2019) · Scientific Reports · doi:10.1038/s41598-019-41695-z · Cited by 5,635 · see citing works
La Manno, G., Soldatov, R., Zeisel, A., Braun, E., Hochgerner, H., Petukhov, V., Lidschreiber, K., Kastriti, M. E., Lönnerberg, P., Furlan, A., et al. (2018) · Nature · doi:10.1038/s41586-018-0414-6 · Cited by 4,118 · see citing works
Self-citationCell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq
Zeisel, A., Muñoz-Manchado, A. B., Codeluppi, S., Lönnerberg, P., La Manno, G., Juréus, A., Marques, S., Munguba, H., He, L., Betsholtz, C., et al. (2015) · Science · doi:10.1126/science.aaa1934 · Cited by 3,124 · see citing works
Self-citationImaging Neuronal Subsets in Transgenic Mice Expressing Multiple Spectral Variants of GFP
Feng, G., Mellor, R. H., Bernstein, M., Keller-Peck, C., Nguyen, Q. T., Wallace, M., Nerbonne, J. M., Lichtman, J. W., & Sanes, J. R. (2000) · Neuron · doi:10.1016/s0896-6273(00)00084-2 · Cited by 3,042 · see citing works
Self-citationMi, H., Muruganujan, A., Ebert, D., Huang, X., & Thomas, P. D. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1038 · Cited by 2,950 · see citing works
Imbalanced-learn: A Python Toolbox to Tackle the Curse of Imbalanced Datasets in Machine LearningPreprint
Lemaître, G., Nogueira, F., & Aridas, C. K. (2016) · Journal of machine learning research · doi:10.48550/arxiv.1609.06570 · Cited by 2,733 · see citing works
Single-cell chromatin accessibility reveals principles of regulatory variation
Buenrostro, J. D., Wu, B., Litzenburger, U. M., Ruff, D., Gonzales, M. L., Snyder, M. P., Chang, H. Y., & Greenleaf, W. J. (2015) · Nature · doi:10.1038/nature14590 · Cited by 2,308 · see citing works
Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis
Levine, J. H., Simonds, E. F., Bendall, S. C., Davis, K. L., Amir, E.-A. D., Tadmor, M. D., Litvin, O., Fienberg, H. G., Jager, A., Zunder, E. R., et al. (2015) · Cell · doi:10.1016/j.cell.2015.05.047 · Cited by 2,303 · see citing works
Molecular diversity and specializations among the cells of the adult mouse brain
Saunders, A., Macosko, E. Z., Wysoker, A., Goldman, M., Krienen, F. M., de Rivera, H., Bien, E., Baum, M., Bortolin, L., Wang, S., et al. (2018) · Cell · doi:10.1016/j.cell.2018.07.028 · Cited by 1,847 · see citing works
Self-citationThe ENCODE Blacklist: Identification of Problematic Regions of the Genome
Amemiya, H. M., Kundaje, A., & Boyle, A. P. (2019) · Scientific Reports · doi:10.1038/s41598-019-45839-z · Cited by 1,831 · see citing works
The Balanced Accuracy and Its Posterior Distribution
Brodersen, K. H., Ong, C. S., Stephan, K. E., & Buhmann, J. M. (2010) · 2010 20th International Conference on Pattern Recognition · doi:10.1109/icpr.2010.764 · Cited by 1,816 · see citing works
A comparative encyclopedia of DNA elements in the mouse genome
Yue, F., Cheng, Y., Breschi, A., Vierstra, J., Wu, W., Ryba, T., Sandstrom, R., Ma, Z., Davis, C., Pope, B. D., et al. (2014) · Nature · doi:10.1038/nature13992 · Cited by 1,781 · see citing works
Self-citationConserved cell types with divergent features in human versus mouse cortex
Hodge, R. D., Bakken, T. E., Miller, J. A., Smith, K. A., Barkan, E. R., Graybuck, L. T., Close, J. L., Long, B., Johansen, N., Penn, O., et al. (2019) · Nature · doi:10.1038/s41586-019-1506-7 · Cited by 1,775 · see citing works
Self-citationJASPAR 2020: update of the open-access database of transcription factor binding profiles
Fornes, O., Castro-Mondragon, J. A., Khan, A., van der Lee, R., Zhang, X., Richmond, P. A., Modi, B. P., Correard, S., Gheorghe, M., Baranašić, D., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1001 · Cited by 1,763 · see citing works
Shared and distinct transcriptomic cell types across neocortical areas
Tasic, B., Yao, Z., Graybuck, L. T., Smith, K. A., Nguyen, T. N., Bertagnolli, D., Goldy, J., Garren, E., Economo, M. N., Viswanathan, S., et al. (2018) · Nature · doi:10.1038/s41586-018-0654-5 · Cited by 1,746 · see citing works
Self-citationAdult mouse cortical cell taxonomy revealed by single cell transcriptomics
Tasic, B., Menon, V., Nguyen, T. N., Kim, T. K., Jarsky, T., Yao, Z., Levi, B., Gray, L. T., Sorensen, S. A., Dolbeare, T., et al. (2016) · Nature Neuroscience · doi:10.1038/nn.4216 · Cited by 1,714 · see citing works
Self-citationchromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data
Schep, A. N., Wu, B., Buenrostro, J. D., & Greenleaf, W. J. (2017) · Nature Methods · doi:10.1038/nmeth.4401 · Cited by 1,680 · see citing works
Descending Pathways in Motor Control
Lemon, R. N. (2008) · Annual Review of Neuroscience · doi:10.1146/annurev.neuro.31.060407.125547 · Cited by 1,599 · see citing works
Chan, K. Y., Jang, M. J., Yoo, B. B., Greenbaum, A., Ravi, N., Wu, W.-L., Sánchez-Guardado, L., Lois, C., Mazmanian, S. K., Deverman, B. E., et al. (2017) · Nature Neuroscience · doi:10.1038/nn.4593 · Cited by 1,578 · see citing works
Uniquely Hominid Features of Adult Human Astrocytes
Oberheim, N. A., Takano, T., Han, X., He, W., Lin, J. H. C., Wang, F., Xu, Q., Wyatt, J. D., Pilcher, W., Ojemann, J. G., et al. (2009) · The Journal of Neuroscience · doi:10.1523/jneurosci.4707-08.2009 · Cited by 1,488 · see citing works
Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing
Cusanovich, D. A., Daza, R., Adey, A., Pliner, H. A., Christiansen, L., Gunderson, K. L., Steemers, F. J., Trapnell, C., & Shendure, J. (2015) · Science · doi:10.1126/science.aab1601 · Cited by 1,248 · see citing works
Die Cytoarchitektonik der Hirnrinde des erwachsenen Menschen
Economo, C. V., & Koskinas, G. N. (1925) · Springer eBooks · Cited by 1,234 · see citing works
Lun, A. T. L., Riesenfeld, S. J., Andrews, T. S., Dao, T. P., Gomes, T., Jamboree, P. I. T. 1. H. C. A., & Marioni, J. C. (2019) · Genome biology · doi:10.1186/s13059-019-1662-y · Cited by 1,042 · see citing works
Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain
Lake, B. B., Chen, S., Sos, B. C., Fan, J., Kaeser, G. E., Yung, Y. C., Duong, T. E., Gao, D., Chun, J., Kharchenko, P. V., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4038 · Cited by 983 · see citing works
Self-citationNeuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain
Lake, B. B., Ai, R., Kaeser, G. E., Salathia, N. S., Yung, Y. C., Liu, R., Wildberg, A., Gao, D., Fung, H.-L., Chen, S., et al. (2016) · Science · doi:10.1126/science.aaf1204 · Cited by 957 · see citing works
Self-citationSynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse
Koopmans, F., van Nierop, P., Andres-Alonso, M., Byrnes, A., Cijsouw, T., Coba, M. P., Cornelisse, L. N., Farrell, R. J., Goldschmidt, H. L., Howrigan, D. P., et al. (2019) · Neuron · doi:10.1016/j.neuron.2019.05.002 · Cited by 938 · see citing works
Self-citationVisualizing Genomic Data Using Gviz and Bioconductor
Hahne, F., & Ivánek, R. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-3578-9_16 · Cited by 893 · see citing works
Efficient integration of heterogeneous single-cell transcriptomes using Scanorama
Hie, B., Bryson, B. D., & Berger, B. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0113-3 · Cited by 853 · see citing works
Molecular diversity of midbrain development in mouse, human, and stem cells
La Manno, G., Gyllborg, D., Codeluppi, S., Nishimura, K., Salto, C., Zeisel, A., Borm, L. E., Stott, S. R. W., Toledo, E. M., Villaescusa, J. C., et al. (2016) · Cell · doi:10.1016/j.cell.2016.09.027 · Cited by 835 · see citing works
High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell
Chen, S., Lake, B. B., & Zhang, K. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0290-0 · Cited by 810 · see citing works
Self-citationCicero predicts cis-regulatory DNA interactions from single-cell chromatin accessibility data
Pliner, H. A., Packer, J. S., McFaline-Figueroa, J. L., Cusanovich, D. A., Daza, R. M., Aghamirzaie, D., Srivatsan, S., Qiu, X., Jackson, D., Minkina, A., et al. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.06.044 · Cited by 789 · see citing works
Kv3 channels: voltage-gated K+ channels designed for high-frequency repetitive firing
Rudy, B., & McBain, C. J. (2001) · Trends in Neurosciences · doi:10.1016/s0166-2236(00)01892-0 · Cited by 781 · see citing works
The origin and evolution of cell types
Arendt, D., Musser, J. M., Baker, C. V. H., Bergman, A., Cepko, C., Erwin, D. H., Pavlicev, M., Schlosser, G., Widder, S., Laubichler, M. D., et al. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.127 · Cited by 764 · see citing works
Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data
McLeay, R. C., & Bailey, T. L. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-165 · Cited by 687 · see citing works
Microstructure of the neocortex: comparative aspects
DeFelipe, J., Alonso-Nanclares, L., & Arellano, J. I. (2002) · Journal of Neurocytology · doi:10.1023/a:1024130211265 · Cited by 686 · see citing works
Amyloid β oligomers constrict human capillaries in Alzheimer's disease via signaling to pericytes
Nortley, R., Korte, N., Izquierdo, P., Hirunpattarasilp, C., Mishra, A., Jaunmuktane, Z., Kyrargyri, V., Pfeiffer, T., Khennouf, L., Madry, C., et al. (2019) · Science · doi:10.1126/science.aav9518 · Cited by 682 · see citing works
Ting, J. T., Daigle, T. L., Chen, Q., & Feng, G. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-1096-0_14 · Cited by 631 · see citing works
Self-citationSingle-nucleus and single-cell transcriptomes compared in matched cortical cell types
Bakken, T. E., Hodge, R. D., Miller, J. A., Yao, Z., Nguyen, T. N., Aevermann, B., Barkan, E., Bertagnolli, D., Casper, T., Dee, N., et al. (2018) · PLoS ONE · doi:10.1371/journal.pone.0209648 · Cited by 608 · see citing works
Self-citationDisease-specific oligodendrocyte lineage cells arise in multiple sclerosis
Falcão, A. M., van Bruggen, D., Marques, S., Meijer, M., Jäkel, S., Agirre, E., Samudyata, Floriddia, E. M., Vanichkina, D. P., ffrench-Constant, C., et al. (2018) · Nature Medicine · doi:10.1038/s41591-018-0236-y · Cited by 579 · see citing works
Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex
Luo, C., Keown, C. L., Kurihara, L., Zhou, J., He, Y., Li, J., Castanon, R., Lucero, J., Nery, J. R., Sandoval, J. P., et al. (2017) · Science · doi:10.1126/science.aan3351 · Cited by 545 · see citing works
Self-citationIntegrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells
Gouwens, N. W., Sorensen, S. A., Baftizadeh, F., Budzillo, A., Lee, B. R., Jarsky, T., Alfiler, L., Baker, K., Barkan, E., Berry, K., et al. (2020) · Cell · doi:10.1016/j.cell.2020.09.057 · Cited by 538 · see citing works
Self-citationThe Primate Premotor Cortex: Past, Present, and Preparatory
Wise, S. P. (1985) · Annual Review of Neuroscience · doi:10.1146/annurev.ne.08.030185.000245 · Cited by 531 · see citing works
Tosches, M. A., Yamawaki, T. M., Naumann, R. K., Jacobi, A. A., Tushev, G., & Laurent, G. (2018) · Science · doi:10.1126/science.aar4237 · Cited by 506 · see citing works
Classification of electrophysiological and morphological neuron types in the mouse visual cortex
Gouwens, N. W., Sorensen, S. A., Berg, J., Lee, C., Jarsky, T., Ting, J., Sunkin, S. M., Feng, D., Anastassiou, C. A., Barkan, E., et al. (2019) · Nature Neuroscience · doi:10.1038/s41593-019-0417-0 · Cited by 456 · see citing works
Self-citationTranscriptional Architecture of Synaptic Communication Delineates GABAergic Neuron Identity
Paul, A., Crow, M., Raudales, R., He, M., Gillis, J., & Huang, Z. J. (2017) · Cell · doi:10.1016/j.cell.2017.08.032 · Cited by 421 · see citing works
Self-citationA transcriptomic and epigenomic cell atlas of the mouse primary motor cortex
Yao, Z., Liu, H., Xie, F., Fischer, S., Adkins, R. S., Aldridge, A. I., Ament, S. A., Bartlett, A., Behrens, M. M., Van den Berge, K., et al. (2021) · Nature · doi:10.1038/s41586-021-03500-8 · Cited by 398 · see citing works
Self-citationAn integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types
Yao, Z., Liu, H., Xie, F., Fischer, S., Booeshaghi, A. S., Adkins, R. S., Aldridge, A. I., Ament, S. A., Pinto-Duarte, A., Bartlett, A., et al. (2020) · doi:10.1101/2020.02.29.970558 · Cited by 397 · see citing works
Self-citationThe axo-axonic interneuron in the cerebral cortex of the rat, cat and monkey
Somogyi, P., Freund, T. F., & Cowey, A. (1982) · Neuroscience · doi:10.1016/0306-4522(82)90086-0 · Cited by 392 · see citing works
5th International Conference on Pattern Recognition
(1979) · IEEE Transactions on Computers · doi:10.1109/tc.1979.1675255 · Cited by 392 · see citing works
Innovations present in the primate interneuron repertoire
Krienen, F. M., Goldman, M., Zhang, Q., C. H. del Rosario, R., Florio, M., Machold, R., Saunders, A., Levandowski, K., Zaniewski, H., Schuman, B., et al. (2020) · Nature · doi:10.1038/s41586-020-2781-z · Cited by 381 · see citing works
Self-citationInnovations in Primate Interneuron Repertoire
Krienen, F. M., Goldman, M., Zhang, Q., del Rosario, R., Florio, M., Machold, R., Saunders, A., Levandowski, K., Zaniewski, H., Schuman, B., et al. (2019) · doi:10.1101/709501 · Cited by 372 · see citing works
Self-citationCrow, M., Paul, A., Ballouz, S., Huang, Z. J., & Gillis, J. (2018) · Nature Communications · doi:10.1038/s41467-018-03282-0 · Cited by 365 · see citing works
Self-citationOrganization of corticospinal neurons in the monkey
Murray, E. A., & Coulter, J. D. (1981) · Journal of Comparative Neurology · doi:10.1002/cne.901950212 · Cited by 344 · see citing works
Simultaneous profiling of 3D genome structure and DNA methylation in single human cells
Lee, D.-S., Luo, C., Zhou, J., Chandran, S., Rivkin, A., Bartlett, A., Nery, J. R., Fitzpatrick, C., O’Connor, C., Dixon, J. R., et al. (2019) · Nature Methods · doi:10.1038/s41592-019-0547-z · Cited by 340 · see citing works
Self-citationTranscriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type
Boldog, E., Bakken, T. E., Hodge, R. D., Novotny, M., Aevermann, B. D., Baka, J., Bordé, S., Close, J. L., Diez-Fuertes, F., Ding, S.-L., et al. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0205-2 · Cited by 291 · see citing works
Self-citationDNA methylation atlas of the mouse brain at single-cell resolution
Liu, H., Zhou, J., Tian, W., Luo, C., Bartlett, A., Aldridge, A., Lucero, J., Osteen, J. K., Nery, J. R., Chen, H., et al. (2021) · Nature · doi:10.1038/s41586-020-03182-8 · Cited by 289 · see citing works
Self-citationHuman neocortical expansion involves glutamatergic neuron diversification
Berg, J., Sorensen, S. A., Ting, J. T., Miller, J. A., Chartrand, T., Buchin, A., Bakken, T. E., Budzillo, A., Dee, N., Ding, S.-L., et al. (2021) · Nature · doi:10.1038/s41586-021-03813-8 · Cited by 285 · see citing works
Self-citationRELATION OF DISCHARGE FREQUENCY TO CONDUCTION VELOCITY IN PYRAMIDAL TRACT NEURONS
Evarts, E. V. (1965) · Journal of Neurophysiology · doi:10.1152/jn.1965.28.2.216 · Cited by 238 · see citing works
Selective functional, regional, and neuronal vulnerability in frontotemporal dementia
Seeley, W. W. (2008) · Current Opinion in Neurology · doi:10.1097/wco.0b013e3283168e2d · Cited by 235 · see citing works
Structure of the human sensorimotor system. I: Morphology and cytoarchitecture of the central sulcus
WHITE, L. E. (1997) · Cerebral Cortex · doi:10.1093/cercor/7.1.18 · Cited by 234 · see citing works
Herculano‐Houzel, S., Catania, K. C., Manger, P. R., & Kaas, J. H. (2015) · Brain Behavior and Evolution · doi:10.1159/000437413 · Cited by 227 · see citing works
Transcriptional Architecture of the Primate Neocortex
Bernard, A., Lubbers, L. S., Tanis, K. Q., Luo, R., Podtelezhnikov, A. A., Finney, E. M., McWhorter, M. M. E., Serikawa, K., Lemon, T., Morgan, R., et al. (2012) · Neuron · doi:10.1016/j.neuron.2012.03.002 · Cited by 224 · see citing works
Self-citationConservation of trans-acting circuitry during mammalian regulatory evolution
Stergachis, A. B., Neph, S., Sandstrom, R., Haugen, E., Reynolds, A. P., Zhang, M., Byron, R., Canfield, T., Stelhing-Sun, S., Lee, K., et al. (2014) · Nature · doi:10.1038/nature13972 · Cited by 212 · see citing works
Robust single-cell DNA methylome profiling with snmC-seq2
Luo, C., Rivkin, A., Zhou, J., Sandoval, J. P., Kurihara, L., Lucero, J., Castanon, R., Nery, J. R., Pinto-Duarte, A., Bui, B., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06355-2 · Cited by 189 · see citing works
Self-citationBaker, A. L., Kalmbach, B. E., Morishima, M., Kim, J., Juavinett, A., Li, N., & Dembrow, N. C. (2018) · Journal of Neuroscience · doi:10.1523/jneurosci.0150-18.2018 · Cited by 187 · see citing works
Self-citationVigneswaran, G., Kraskov, A., & Lemon, R. (2011) · Journal of Neuroscience · doi:10.1523/jneurosci.3142-11.2011 · Cited by 175 · see citing works
Fetz, E. E., Cheney, P. D., Mewes, K., & Palmer, S. S. (1989) · Progress in brain research · doi:10.1016/s0079-6123(08)62241-4 · Cited by 172 · see citing works
Single nucleus multi-omics identifies human cortical cell regulatory genome diversity
Luo, C., Liu, H., Xie, F., Armand, E. J., Siletti, K., Bakken, T. E., Fang, R., Doyle, W. I., Stuart, T., Hodge, R. D., et al. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100107 · Cited by 167 · see citing works
Self-citationTranscriptional Programs of Circuit Assembly in the Drosophila Visual System
Kurmangaliyev, Y. Z., Yoo, J., Valdes-Aleman, J., Sanfilippo, P., & Zipursky, S. L. (2020) · Neuron · doi:10.1016/j.neuron.2020.10.006 · Cited by 166 · see citing works
Shared and distinct transcriptomic cell types across neocortical areasPreprint
Tasic, B., Yao, Z., Smith, K. A., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/229542 · Cited by 163 · see citing works
Self-citationGroh, A., Meyer, H. S., Schmidt, E. F., Heintz, N., Sakmann, B. J., & Krieger, P. (2009) · Cerebral Cortex · doi:10.1093/cercor/bhp152 · Cited by 162 · see citing works
Spatiotemporal DNA methylome dynamics of the developing mouse fetus
He, Y., Hariharan, M., Gorkin, D. U., Dickel, D. E., Luo, C., Castanon, R., Nery, J. R., Lee, A. Y., Zhao, Y., Huang, H., et al. (2020) · Nature · doi:10.1038/s41586-020-2119-x · Cited by 162 · see citing works
Self-citationHof, P. R., Nimchinsky, E. A., & Morrison, J. H. (1995) · Journal of Comparative Neurology · doi:10.1002/cne.903620107 · Cited by 159 · see citing works
Self-citationMotor cortex — to act or not to act?
Ebbesen, C. L., & Brecht, M. (2017) · Nature reviews. Neuroscience · doi:10.1038/nrn.2017.119 · Cited by 152 · see citing works
A genuine layer 4 in motor cortex with prototypical synaptic circuit connectivity
Yamawaki, N., Borges, K., Suter, B. A., Harris, K. D., & Shepherd, G. M. G. (2014) · eLife · doi:10.7554/elife.05422 · Cited by 141 · see citing works
Krimer, L. S., Zaitsev, A. V., Czanner, G., Kröner, S., González‐Burgos, G., Povysheva, N. V., Iyengar, S., Barrionuevo, G., & Lewis, D. A. (2005) · Journal of Neurophysiology · doi:10.1152/jn.00156.2005 · Cited by 135 · see citing works
The homeostatic astroglia emerges from evolutionary specialization of neural cells
Verkhratsky, A., & Nedergaard, M. (2016) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2015.0428 · Cited by 133 · see citing works
Rivara, C., Sherwood, C. C., Bouras, C., & Hof, P. R. (2003) · The Anatomical Record Part A Discoveries in Molecular Cellular and Evolutionary Biology · doi:10.1002/ar.a.10015 · Cited by 127 · see citing works
Self-citationCastro-Mondragon, J. A., Jaeger, S., Thieffry, D., Thomas‐Chollier, M., & van Helden, J. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx314 · Cited by 126 · see citing works
Tsang, Y. M., Chiong, F., Kuznetsov, D., Kasarskis, E. J., & Geula, C. (2000) · Brain Research · doi:10.1016/s0006-8993(00)01954-5 · Cited by 125 · see citing works
Integrative single-cell analysis by transcriptional and epigenetic states in human adult brainPreprint
Lake, B. B., Chen, S., Sos, B. C., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/128520 · Cited by 122 · see citing works
Self-citationControl of species-dependent cortico-motoneuronal connections underlying manual dexterity
Gu, Z., Kalambogias, J., Yoshioka, S., Han, W., Li, Z., Kawasawa, Y. I., Pochareddy, S., Li, Z., Liu, F., Xu, X., et al. (2017) · Science · doi:10.1126/science.aan3721 · Cited by 118 · see citing works
Ting, J. T., Kalmbach, B. E., Chong, P., de Frates, R. A., Keene, C. D., Gwinn, R. P., Cobbs, C., Cobbs, C., Ko, A. L., Ojemann, J. G., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-26803-9 · Cited by 116 · see citing works
Self-citationSome aspects of the morphology of Betz cells in the cerebral cortex of the cat
Kaiserman‐Abramof, I. R., & Peters, A. (1972) · Brain Research · doi:10.1016/0006-8993(72)90406-4 · Cited by 101 · see citing works
Hodge, R. D., Miller, J. A., Novotny, M. A., Kalmbach, B. E., Ting, J. T., Bakken, T. E., Aevermann, B. D., Barkan, E. R., Berkowitz-Cerasano, M. L., Cobbs, C., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-14952-3 · Cited by 92 · see citing works
Self-citationSpain, W. J., Schwindt, P. C., & Crill, W. E. (1991) · The Journal of Physiology · doi:10.1113/jphysiol.1991.sp018489 · Cited by 87 · see citing works
Self-citationGayoso, A., Shor, J. D., Carr, A., et al. (2019) · Figshare · doi:10.5281/zenodo.2678041 · Cited by 85 · see citing works
Area 4 has layer <scp>IV</scp> in adult primates
García‐Cabezas, M. Á., & Barbas, H. (2014) · European Journal of Neuroscience · doi:10.1111/ejn.12585 · Cited by 81 · see citing works
The RacGAP β2-Chimaerin Selectively Mediates Axonal Pruning in the Hippocampus
Riccomagno, M. M., Hurtado, A., Wang, H., Macopson, J. G. J., Griner, E., Betz, A., Brose, N., Kazanietz, M. G., & Kolodkin, A. L. (2012) · Cell · doi:10.1016/j.cell.2012.05.018 · Cited by 76 · see citing works
Chen, W., Zhang, J.-J., Hu, G., & Wu, C.-P. (1996) · Neuroscience · doi:10.1016/0306-4522(96)00009-7 · Cited by 76 · see citing works
THE HUMAN PYRAMIDAL TRACT: II. A NUMERICAL INVESTIGATION OF THE BETZ CELLS OF THE MOTOR AREA
Lassek, A. M. (1941) · Archives of Neurology And Psychiatry · doi:10.1001/archneurpsyc.1940.02280100020002 · Cited by 76 · see citing works
Gray, L. T., Yao, Z., Nguyen, T. N., Kim, T. K., Zeng, H., & Tasic, B. (2017) · eLife · doi:10.7554/elife.21883 · Cited by 72 · see citing works
Self-citationMultiple divisions of macaque precentral motor cortex identified with neurofilament antibody SMI-32
Preuss, T. M., Stepniewska, I., Jain, N., & Kaas, J. H. (1997) · Brain Research · doi:10.1016/s0006-8993(97)00704-x · Cited by 71 · see citing works
Neocortical calretinin neurons in primates: increase in proportion and microcircuitry structure
aja, D. D. ⁄., Hladnik, A., Bičanić, I., Baković, M., & Petanjek, Z. (2014) · Frontiers in Neuroanatomy · doi:10.3389/fnana.2014.00103 · Cited by 69 · see citing works
Evolution of Specialized Pyramidal Neurons in Primate Visual and Motor Cortex
Sherwood, C. C., Lee, P. W. H., Rivara, C., Holloway, R. L., Gilissen, E., Simmons, R. M. T., Hakeem, A. Y., Allman, J. M., ERWIN, J. M., & Hof, P. R. (2003) · Brain Behavior and Evolution · doi:10.1159/000068879 · Cited by 66 · see citing works
Self-citationNeuronal population of area 4 during the life span of the rhesus monkey
Tigges, J., Herndon, J. G., & Peters, A. (1990) · Neurobiology of Aging · doi:10.1016/0197-4580(90)90546-c · Cited by 64 · see citing works
Cell type discovery using single-cell transcriptomics: implications for ontological representation
Aevermann, B. D., Novotny, M. A., Bakken, T. E., Miller, J. A., Diehl, A. D., Osumi-Sutherland, D., Lasken, R. S., Lein, E. S., & Scheuermann, R. H. (2018) · Human Molecular Genetics · doi:10.1093/hmg/ddy100 · Cited by 63 · see citing works
Self-citationRegion-Specific Spike-Frequency Acceleration in Layer 5 Pyramidal Neurons Mediated by Kv1 Subunits
Miller, M. N., Okaty, B. W., & Nelson, S. B. (2008) · Journal of Neuroscience · doi:10.1523/jneurosci.2940-08.2008 · Cited by 60 · see citing works
Cell type discovery and representation in the era of high-content single cell phenotyping
Bakken, T., Cowell, L., Aevermann, B. D., Novotny, M., Hodge, R., Miller, J. A., Lee, A., Chang, I., McCorrison, J., Pulendran, B., et al. (2017) · BMC Bioinformatics · doi:10.1186/s12859-017-1977-1 · Cited by 55 · see citing works
Self-citationComparative morphology of gigantopyramidal neurons in primary motor cortex across mammals
Jacobs, B., Garcia, M. E., Shea‐Shumsky, N. B., Tennison, M. E., Schall, M., Saviano, M. S., Tummino, T. A., Bull, A. J., Driscoll, L. L., Raghanti, M. A., et al. (2017) · The Journal of Comparative Neurology · doi:10.1002/cne.24349 · Cited by 50 · see citing works
Self-citationPlongthongkum, N., Diep, D. H., Chen, S., Lake, B. B., & Zhang, K. (2021) · Nature Protocols · doi:10.1038/s41596-021-00507-3 · Cited by 48 · see citing works
Self-citationBasilar dendrite bundles of giant pyramidal cells
Scheibel, M. E., Davies, T. L., Lindsay, R. D., & Scheibel, A. B. (1974) · Experimental Neurology · doi:10.1016/0014-4886(74)90028-4 · Cited by 36 · see citing works
Berg, J., Sorensen, S. A., Ting, J. T., Miller, J. A., Chartrand, T., Buchin, A., Bakken, T. E., Budzillo, A., Dee, N., Ding, S., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.03.31.018820 · Cited by 35 · see citing works
Self-citationLassek, A. M. (1942) · Archives of Neurology And Psychiatry · doi:10.1001/archneurpsyc.1942.02290100061006 · Cited by 31 · see citing works
Graybuck (2019) · doi:10.1101/525014 · Cited by 31 · see citing works
Luo, C., Liu, H., Xie, F.-M., et al. (2019) · bioRxiv · doi:10.1101/2019.12.11.873398 · Cited by 27 · see citing works
Self-citationThe interlaminar glia: from serendipity to hypothesis
Colombo, J. A. (2016) · Brain Structure and Function · doi:10.1007/s00429-016-1332-8 · Cited by 25 · see citing works
Spatiotemporal DNA Methylome Dynamics of the Developing Mammalian FetusPreprint
He, Y., Hariharan, M., Gorkin, D. U., et al. (2017) · bioRxiv · doi:10.1101/166744 · Cited by 22 · see citing works
Hof, P. R., & Perl, D. P. (2002) · Neuroscience Letters · doi:10.1016/s0304-3940(02)00523-2 · Cited by 15 · see citing works
Self-citationFunctional properties of GABA synaptic inputs onto GABA neurons in monkey prefrontal cortex
Rotaru, D. C., Olezene, C. S., Miyamae, T., Povysheva, N. V., Zaitsev, A. V., Lewis, D. A., & González‐Burgos, G. (2014) · Journal of Neurophysiology · doi:10.1152/jn.00799.2014 · Cited by 15 · see citing works
Hodge, R. D., Miller, J. A., Novotny, M. A., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/627505 · Cited by 9 · see citing works
Self-citationThe Human Pyramidal Tract II. A Numerical Investigation of the Betz Cells of the Motor Area.
Lassek, A. M. (1941) · The Journal of Nervous and Mental Disease · doi:10.1097/00005053-194108000-00026 · Cited by 4 · see citing works
Overview and critique of Chapters 35–37
Hoffer, J. A. (1989) · Progress in brain research · doi:10.1016/s0079-6123(08)62239-6 · Cited by 2 · see citing works
Nuclei Isolation for SNARE-seq2 v1Preprint
Palmer, C. R., Liu, C. S., & Chun, J. (2019) · protocols.io · doi:10.17504/protocols.io.8tvhwn6 · Cited by 1 · see citing works
Self-citationSNARE-seq2 v2Preprint
Plongthongkum, N., Diep, D., Chen, S., et al. (2021) · doi:10.17504/protocols.io.bzcvp2w6 · Cited by 1 · see citing works
Self-citation
Flagged first, then by citations
Research works printed but not linked: 2
- [15]Evarts, E. V. in Neurophysiological Basis of Normal and Abnormal Motor Activities 215–253 (Raven Press, New York, 1967).
- [57]Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2016).
Cited by
Sorted by citations
SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks
Bravo González-Blas, C., De Winter, S., Hulselmans, G., Hecker, N., Matetovici, I., Christiaens, V., Poovathingal, S., Wouters, J., Aibar, S., & Aerts, S. (2023) · Nature Methods · doi:10.1038/s41592-023-01938-4 · Cited by 778 · see citing works
Schwartzentruber, J., Cooper, S., Liu, J. Z., Barrio-Hernandez, I., Bello, E., Kumasaka, N., Young, A. M. H., Franklin, R. J. M., Johnson, T., Estrada, K., et al. (2021) · Nature Genetics · doi:10.1038/s41588-020-00776-w · Cited by 532 · see citing works
Maturation and circuit integration of transplanted human cortical organoids
Revah, O., Gore, F., Kelley, K. W., Andersen, J., Sakai, N., Chen, X., Li, M.-Y., Birey, F., Yang, X., Saw, N. L., et al. (2022) · Nature · doi:10.1038/s41586-022-05277-w · Cited by 504 · see citing works
Mathys, H., Peng, Z., Boix, C. A., Victor, M. B., Leary, N., Babu, S., Abdelhady, G., Jiang, X., Ng, A. P., Ghafari, K., et al. (2023) · Cell · doi:10.1016/j.cell.2023.08.039 · Cited by 495 · see citing works
What is a cell type and how to define it?
Zeng, H. (2022) · Cell · doi:10.1016/j.cell.2022.06.031 · Cited by 439 · see citing works
Integrated multimodal cell atlas of Alzheimer’s disease
Gabitto, M. I., Travaglini, K. J., Rachleff, V. M., Kaplan, E. S., Long, B., Ariza, J., Ding, Y., Mahoney, J. T., Dee, N., Goldy, J., et al. (2024) · Nature Neuroscience · doi:10.1038/s41593-024-01774-5 · Cited by 397 · see citing works
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Fang, R., Xia, C., Close, J. L., Zhang, M., He, J., Huang, Z., Halpern, A. R., Long, B., Miller, J. A., Lein, E. S., et al. (2022) · Science · doi:10.1126/science.abm1741 · Cited by 277 · see citing works
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Armand, E. J., Li, J., Xie, F., Luo, C., & Mukamel, E. A. (2021) · Neuron · doi:10.1016/j.neuron.2020.12.010 · Cited by 241 · see citing works
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“( b ) Data from Bakken and colleagues [11] was generated using tissue from the motor cortex of 5 control subjects.”
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Vance, K., Alitinok, A., Winfree, S., Jensen-Smith, H., Swanson, B. J., Grandgenett, P. M., Klute, K. A., Crichton, D. J., & Hollingsworth, M. A. (2022) · Cancer Biomarkers · doi:10.3233/cbm-210308 · Cited by 14 · see citing works
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- Authors
- Bakken, T. E., Jorstad, N. L., Hu, Q., Lake, B. B., Tian, W., Kalmbach, B. E., Crow, M., Hodge, R. D., Krienen, F. M., Sorensen, S. A., Eggermont, J., Yao, Z., Aevermann, B. D., Aldridge, A. I., Bartlett, A., Bertagnolli, D., Casper, T., Castanon, R. G., Crichton, K., Daigle, T. L., Dalley, R., Dee, N., Dembrow, N., Diep, D., Ding, S.-L., Dong, W., Fang, R., Fischer, S., Goldman, M., Goldy, J., Graybuck, L. T., Herb, B. R., Hou, X., Kancherla, J., Kroll, M., Lathia, K., van Lew, B., Li, Y. E., Liu, C. S., Liu, H., Lucero, J. D., Mahurkar, A., McMillen, D., Miller, J. A., Moussa, M., Nery, J. R., Nicovich, P. R., Niu, S.-Y., Orvis, J., Osteen, J. K., Owen, S., Palmer, C. R., Pham, T., Plongthongkum, N., Poirion, O., Reed, N. M., Rimorin, C., Rivkin, A., Romanow, W. J., Sedeño-Cortés, A. E., Siletti, K., Somasundaram, S., Sulc, J., Tieu, M., Torkelson, A., Tung, H., Wang, X., Xie, F., Yanny, A. M., Zhang, R., Ament, S. A., Behrens, M. M., Bravo, H. C., Chun, J., Dobin, A., Gillis, J., Hertzano, R., Hof, P. R., Höllt, T., Horwitz, G. D., Keene, C. D., Kharchenko, P. V., Ko, A. L., Lelieveldt, B. P., Luo, C., Mukamel, E. A., Pinto-Duarte, A., Preissl, S., Regev, A., Ren, B., Scheuermann, R. H., Smith, K., Spain, W. J., White, O. R., Koch, C., Hawrylycz, M., Tasic, B., Macosko, E. Z., McCarroll, S. A., Ting, J. T., Zeng, H., Zhang, K., Feng, G., Ecker, J. R., Linnarsson, S., & Lein, E. S.
- Affiliations
- Allen Institute for Brain Science (US)
- Harvard University (US)
- University of California San Diego (US)
- Salk Institute for Biological Studies (US)
- Cold Spring Harbor Laboratory (US)
- Leiden University Medical Center (NL)
- J. Craig Venter Institute (US)
- University of Washington (US)
- University of Maryland, Baltimore (US)
- University of Maryland, College Park (US)
- Sanford Burnham Prebys Medical Discovery Institute (US)
- University of Connecticut (US)
- Karolinska Institutet (SE)
- Washington University in St. Louis (US)
- Icahn School of Medicine at Mount Sinai (US)
- Delft University of Technology (NL)
- University of California, Los Angeles (US)
- Broad Institute (US)
- Corresponding author
- Bakken, Trygve E.
- Lein, Ed S.
- ORCID
- Bakken, Trygve E.
- Jorstad, Nikolas L.
- Hu, Qiwen
- Lake, Blue B.
- Kalmbach, Brian E.
- Crow, Megan
- Hodge, Rebecca D.
- Krienen, Fenna M.
- Sorensen, Staci A.
- Eggermont, Jeroen
- Yao, Zizhen
- Aevermann, Brian D.
- Aldridge, Andrew I.
- Bartlett, Anna
- Bertagnolli, Darren
- Casper, Tamara
- Castanon, Rosa G.
- Crichton, Kirsten
- Daigle, Tanya L.
- Dalley, Rachel
- Dee, Nick
- Dembrow, Nikolai
- Diep, Dinh
- Ding, Song-Lin
- Dong, Weixiu
- Fang, Rongxin
- Fischer, Stephan
- Goldman, Melissa
- Goldy, Jeff
- Graybuck, Lucas T.
- Herb, Brian R.
- Hou, Xiaomeng
- Kancherla, Jayaram
- Kroll, Matthew
- Lathia, Kanan
- van Lew, Baldur
- Li, Yang Eric
- Liu, Christine S.
- Liu, Hanqing
- Lucero, Jacinta D.
- Mahurkar, Anup
- McMillen, Delissa
- Miller, Jeremy A.
- Moussa, Marmar
- Nery, Joseph R.
- Nicovich, Philip R.
- Niu, Sheng-Yong
- Orvis, Joshua
- Osteen, Julia K.
- Owen, Scott
- Palmer, Carter R.
- Pham, Thanh
- Plongthongkum, Nongluk
- Poirion, Olivier
- Reed, Nora M.
- Rimorin, Christine
- Rivkin, Angeline
- Romanow, William J.
- Sedeño-Cortés, Adriana E.
- Siletti, Kimberly
- Somasundaram, Saroja
- Tieu, Michael
- Torkelson, Amy
- Tung, Herman
- Wang, Xinxin
- Xie, Fangming
- Yanny, Anna Marie
- Ament, Seth A.
- Behrens, M. Margarita
- Chun, Jerold
- Dobin, Alexander
- Gillis, Jesse
- Hertzano, Ronna
- Hof, Patrick R.
- Höllt, Thomas
- Horwitz, Gregory D.
- Keene, C. Dirk
- Kharchenko, Peter V.
- Ko, Andrew L.
- Lelieveldt, Boudewijn P.
- Luo, Chongyuan
- Mukamel, Eran A.
- Pinto-Duarte, António
- Preissl, Sebastian
- Regev, Aviv
- Ren, Bing
- Scheuermann, Richard H.
- Smith, Kimberly
- Spain, William J.
- White, Owen R.
- Koch, Christof
- Hawrylycz, Michael
- Tasic, Bosiljka
- Macosko, Evan Z.
- McCarroll, Steven A.
- Ting, Jonathan T.
- Zeng, Hongkui
- Zhang, Kun
- Feng, Guoping
- Ecker, Joseph R.
- Linnarsson, Sten
- Lein, Ed S.
- Venue
- Nature
- Published
- 2021-10-06
- Volume
- 598
- Issue
- 7879
- Pages
- 111-119
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC8494640
- OpenAlex
- W3204443805
- Cited by
- 812
- References
- 122
- Citations by year
- 2026: 134 · 2025: 159 · 2024: 157 · 2023: 180 · 2022: 114 · 2021: 50 · 2020: 17 · 2018: 1
- FWCI
- 40.67
- Type
- journal article
- Language
- en
- Update notices
- correction (2022-03-22)
- Open access
- hybrid
- doi.org
- Locations
- Nature (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Research Repository (Delft University of Technology) (publishedVersion)
- Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
- Digital Commons@Becker (Washington University School of Medicine) (submittedVersion, cc-by)
- Data Archiving and Networked Services (DANS) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- Leiden Repository (Leiden University) (submittedVersion, cc-by)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Funders
- National Science Foundation (CAREER, 1846559)
- Howard Hughes Medical Institute
- California Institute for Regenerative Medicine (GC1R-06673, GC1R-06673-B)
- Silicon Valley Community Foundation (2018-182730)
- Nancy and Buster Alvord Endowment
- University of Washington (UL1 TR000423)
- National Alliance for Research on Schizophrenia and Depression
- Institute of Translational Health Sciences (UL1 TR000423)
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (024.004.012, 17126)
- National Institutes of Health (5u01mh114812-03, UL1TR000423, 1rf1mh123220-01, U01 MH114812-02, MH114812-02, MH114821, P51OD010425)
- National Institute on Aging (P30AG066509)
- National Institute of Mental Health (U01MH114828, U19MH114821, U01 MH114812-02, U19MH114831, RF1 MH123220, U01MH114812, U01MH114819, RF1MH114126, U01MH121282, R24MH114815, U19MH114830, MH114821, R24MH114788, MH114831)
- National Institute on Drug Abuse (R01DA036909)
- National Human Genome Research Institute (R01HG009318)
- National Institute on Deafness and Other Communication Disorders (R01DC019370, U01DC013817)
- National Institute of Neurological Disorders and Stroke (R01NS044163)
- National Center for Advancing Translational Sciences
- Office of Research Infrastructure Programs, National Institutes of Health (P51OD010425)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neuroscience and Neuropharmacology Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- motor cortex, single-nucleus transcriptomics, DNA methylation, chromatin state, layer 5, Patch-seq, marmoset, non-human primates, mice, cell type markers, species-specific adaptation
- MeSH terms
- Animals, Atlases as Topic, Callithrix, Female, Glutamates, Humans, Male, Middle Aged, Motor Cortex, Neurons, Organ Specificity, Phylogeny, Species Specificity, In Situ Hybridization, Fluorescence, Gene Expression Profiling, Epigenesis, Genetic, Mice, Epigenomics, Single-Cell Analysis, GABAergic Neurons, Transcriptome
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