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  • A multimodal cell census and atlas of the mammalian primary motor cortex NATURE Callaway, E. M., Dong, H., Ecker, J. R., Hawrylycz, M. J., Huang, Z., Lein, E. S., Ngai, J., Osten, P., Ren, B., Tolias, A., White, O., Zeng, H., Zhuang, X., Ascoli, G. A., Behrens, M., Chun, J., Feng, G., Gee, J. C., Ghosh, S. S., Halchenko, Y. O., Hertzano, R., Lim, B., Martone, M. E., Ng, L., Pachter, L., Ropelewski, A. J., Tickle, T. L., Yang, X., Zhang, K., Bakken, T. E., Berens, P., Daigle, T. L., Harris, J. A., Jorstad, N. L., Kalmbach, B. E., Kobak, D., Li, Y., Liu, H., Matho, K. S., Mukamel, E. A., Naeemi, M., Scala, F., Tan, P., Ting, J. T., Xie, F., Zhang, M., Zhang, Z., Zhou, J., Zingg, B., Bertagnolli, D., Casper, T., Crichton, K., Dee, N., Diep, D., Ding, S., Dong, W., Dougherty, E. L., Fong, O., Goldman, M., Goldy, J., Hodge, R. D., Hu, L., Keene, C., Krienen, F. M., Kroll, M., Lake, B. B., Lathia, K., Linnarsson, S., Liu, C. S., Macosko, E. Z., McCarroll, S. A., McMillen, D., Nadaf, N. M., Thuc Nghi Nguyen, Palmer, C. R., Thanh Pham, Plongthongkum, N., Reed, N. M., Regev, A., Rimorin, C., Romanow, W. J., Savoia, S., Siletti, K., Smith, K., Sulc, J., Tasic, B., Tieu, M., Torkelson, A., Tung, H., van Velthoven, C. J., Vanderburg, C. R., Yanny, A., Fang, R., Hou, X., Lucero, J. D., Osteen, J. K., Pinto-Duarte, A., Poirion, O., Preissl, S., Wang, X., Aldridge, A., Bartlett, A., Boggeman, L., O'Connor, C., Castanon, R. G., Chen, H., Fitzpatrick, C., Luo, C., Nery, J. R., Nunn, M., Rivkin, A. C., Tian, W., Dominguez, B., Ito-Cole, T., Jacobs, M., Jin, X., Lee, C., Lee, K., Miyazaki, P., Pang, Y., Rashid, M., Smith, J. B., Vu, M., Williams, E., Armand, E., Biancalani, T., Booeshaghi, A., Crow, M., Dudoit, S., Fischer, S., Gillis, J., Hu, Q., Kharchenko, P., Niu, S., Ntranos, V., Purdom, E., Risso, D., de Bezieux, H., Somasundaram, S., Street, K., Svensson, V., Vaishnav, E., Van den Berge, K., Welch, J. D., Yao, Z., An, X., Bateup, H. S., Bowman, I., Chance, R. K., Foster, N. N., Galbavy, W., Gong, H., Gou, L., Hatfield, J. T., Hintiryan, H., Hirokawa, K. E., Kim, G., Kramer, D. J., Li, A., Li, X., Luo, Q., Munoz-Castaneda, R., Stafford, D. A., Feng, Z., Jia, X., Jiang, S., Jiang, T., Kuang, X., Larsen, R., Lesnar, P., Li, Y., Li, Y., Liu, L., Peng, H., Qu, L., Ren, M., Ruan, Z., Shen, E., Song, Y., Wakeman, W., Wang, P., Wang, Y., Wang, Y., Yin, L., Yuan, J., Zhao, S., Zhao, X., Narasimhan, A., Palaniswamy, R., Banerjee, S., Ding, L., Huilgol, D., Huo, B., Kuo, H., Laturnus, S., Li, X., Mitra, P. P., Mizrachi, J., Wang, Q., Xie, P., Xiong, F., Yu, Y., Eichhorn, S. W., Berg, J., Bernabucci, M., Bernaerts, Y., Cadwell, C., Castro, J., Dalley, R., Hartmanis, L., Horwitz, G. D., Jiang, X., Ko, A. L., Miranda, E., Mulherkar, S., Nicovich, P. R., Owen, S. F., Sandberg, R., Sorensen, S. A., Tan, Z., Allen, S., Hockemeyer, D., Lee, A. Y., Veldman, M. B., Adkins, R. S., Ament, S. A., Bravo, H., Carter, R., Chatterjee, A., Colantuoni, C., Crabtree, J., Creasy, H., Felix, V., Giglio, M., Herb, B. R., Kancherla, J., Mahurkar, A., McCracken, C., Nickel, L., Olley, D., Orvis, J., Schor, M., Hood, G., Dichter, B., Grauer, M., Helba, B., Bandrowski, A., Barkas, N., Carlin, B., D'Orazi, F. D., Degatano, K., Gillespie, T. H., Khajouei, F., Konwar, K., Thompson, C., Kelly, K., Mok, S., Sunkin, S., BRAIN Initiative Cell Census Netwo 2021; 598 (7879): 86-102

    Abstract

    Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input-output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1-5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.

    View details for DOI 10.1038/s41586-021-03950-0

    View details for Web of Science ID 000705847500002

    View details for PubMedID 34616075

    View details for PubMedCentralID PMC8494634

  • Super-resolution light-sheet fluorescence microscopy by SOFI bioRxiv Mizrachi, J., Narasimhan, A., Qi, X., Drewes, R., Palaniswamy, R., Wu, Z., Osten, P. 2020
  • OLST protocol v1 (protocols.io.smwec7e) protocols.io Narasimhan, A., Umadevi Venkataraju, K., Mizrachi, J., Albeanu, D. F., Osten, P. 2018
  • SOFIA FORCAST Grism Study of the Mineralogy of Dust in the Winds of Proto-planetary Nebulae: RV Tauri Stars and SRd Variables ASTROPHYSICAL JOURNAL Arneson, R. A., Gehrz, R. D., Woodward, C. E., Helton, L. A., Shenoy, D., Evans, A., Keller, L. D., Hinkle, K. H., Jura, M., Lebzelter, T., Lisse, C. M., Rushton, M. T., Mizrachi, J. 2017; 843 (1)
  • Oblique light-sheet tomography: fast and high resolution volumetric imaging of mouse brains bioRxiv Narasimhan, A., Umadevi Venkataraju, K., Mizrachi, J., Albeanu, D. F., Osten, P. 2017

    View details for DOI 10.1101/132423

  • MRI in Practice, 4th ed.MRI in Practice, 4th ed. By Catherine Westbrook, Carolyn Kaut Roth, and John Talbot. West Sussex, UK: Wiley-Blackwell, 456 pp., 2011. $51.99 softcover (ISBN: 978-1444337433) American Journal of Roentgenology Stoffey, R. D., Mizrachi, J. S. 2012

    View details for DOI 10.2214/ajr.11.8252