The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas

doi:10.1016/j.neuron.2017.10.007

Review

. 2017 Nov 1;96(3):542-557.

doi: 10.1016/j.neuron.2017.10.007.

The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas

Affiliations

¹ Genomic Analysis Laboratory and Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
² Program in Neurogenetics, Departments of Neurology and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
³ Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA.
⁴ Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, QB3 Functional Genomics Laboratory, University of California, Berkeley, Berkeley, CA 94720, USA. Electronic address: jngai@berkeley.edu.
⁵ Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
⁶ Klarman Cell Observatory, Broad Institute of MIT and Harvard, Department of Biology, Koch Institute of Integrative Cancer Research, and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
⁷ Departments of Neuroscience, Genetics, Psychiatry and Comparative Medicine, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale Child Study Center, Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA.
⁸ McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
⁹ Allen Institute for Brain Science, Seattle, WA 98109, USA.

PMID: 29096072
PMCID: PMC5689454
DOI: 10.1016/j.neuron.2017.10.007

Review

The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas

Joseph R Ecker et al. Neuron. 2017.

. 2017 Nov 1;96(3):542-557.

doi: 10.1016/j.neuron.2017.10.007.

Authors

Affiliations

¹ Genomic Analysis Laboratory and Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
² Program in Neurogenetics, Departments of Neurology and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
³ Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA.
⁴ Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, QB3 Functional Genomics Laboratory, University of California, Berkeley, Berkeley, CA 94720, USA. Electronic address: jngai@berkeley.edu.
⁵ Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
⁶ Klarman Cell Observatory, Broad Institute of MIT and Harvard, Department of Biology, Koch Institute of Integrative Cancer Research, and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
⁷ Departments of Neuroscience, Genetics, Psychiatry and Comparative Medicine, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale Child Study Center, Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA.
⁸ McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
⁹ Allen Institute for Brain Science, Seattle, WA 98109, USA.

PMID: 29096072
PMCID: PMC5689454
DOI: 10.1016/j.neuron.2017.10.007

Abstract

A comprehensive characterization of neuronal cell types, their distributions, and patterns of connectivity is critical for understanding the properties of neural circuits and how they generate behaviors. Here we review the experiences of the BRAIN Initiative Cell Census Consortium, ten pilot projects funded by the U.S. BRAIN Initiative, in developing, validating, and scaling up emerging genomic and anatomical mapping technologies for creating a complete inventory of neuronal cell types and their connections in multiple species and during development. These projects lay the foundation for a larger and longer-term effort to generate whole-brain cell atlases in species including mice and humans.

Keywords: BRAIN initiative; anatomy; cell census; connectivity; electrophysiology; human brain; mouse brain; single-cell RNA-seq; single-cell epigenomics; single-cell transcriptomics.

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References

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1. Arendt D, Musser JM, Baker CVH, Bergman A, Cepko C, Erwin DH, Pavlicev M, Schlosser G, Widder S, Laubichler MD, et al. The origin and evolution of cell types. Nat Rev Genet. 2016;17:744–757. - PubMed
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1. Barak T, Kwan KY, Louvi A, Demirbilek V, Saygi S, Tuysuz B, Choi M, Boyaci H, Doerschner K, Zhu Y, et al. Recessive LAMC3 mutations cause malformations of occipital cortical development. Nat Genet. 2011;43:590–594. - PMC - PubMed

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[1] Abrahams BS, Tentler D, Perederiy JV, Oldham MC, Coppola G, Geschwind DH. Genome-wide analyses of human perisylvian cerebral cortical patterning. Proc Natl Acad Sci U S A. 2007;104:17849–17854. - PMC - PubMed

[2] Abrahams BS, Tentler D, Perederiy JV, Oldham MC, Coppola G, Geschwind DH. Genome-wide analyses of human perisylvian cerebral cortical patterning. Proc Natl Acad Sci U S A. 2007;104:17849–17854. - PMC - PubMed

[3] Arendt D, Musser JM, Baker CVH, Bergman A, Cepko C, Erwin DH, Pavlicev M, Schlosser G, Widder S, Laubichler MD, et al. The origin and evolution of cell types. Nat Rev Genet. 2016;17:744–757. - PubMed

[4] Arendt D, Musser JM, Baker CVH, Bergman A, Cepko C, Erwin DH, Pavlicev M, Schlosser G, Widder S, Laubichler MD, et al. The origin and evolution of cell types. Nat Rev Genet. 2016;17:744–757. - PubMed

[5] Arlotta P, Molyneaux BJ, Chen J, Inoue J, Kominami R, Macklis JD. Neuronal subtype-specific genes that control corticospinal motor neuron development in vivo. Neuron. 2005;45:207–221. - PubMed

[6] Arlotta P, Molyneaux BJ, Chen J, Inoue J, Kominami R, Macklis JD. Neuronal subtype-specific genes that control corticospinal motor neuron development in vivo. Neuron. 2005;45:207–221. - PubMed

[7] Bandler RC, Mayer C, Fishell G. Cortical interneuron specification: the juncture of genes, time and geometry. Curr Opin Neurobiol. 2017;42:17–24. - PMC - PubMed

[8] Bandler RC, Mayer C, Fishell G. Cortical interneuron specification: the juncture of genes, time and geometry. Curr Opin Neurobiol. 2017;42:17–24. - PMC - PubMed

[9] Barak T, Kwan KY, Louvi A, Demirbilek V, Saygi S, Tuysuz B, Choi M, Boyaci H, Doerschner K, Zhu Y, et al. Recessive LAMC3 mutations cause malformations of occipital cortical development. Nat Genet. 2011;43:590–594. - PMC - PubMed

[10] Barak T, Kwan KY, Louvi A, Demirbilek V, Saygi S, Tuysuz B, Choi M, Boyaci H, Doerschner K, Zhu Y, et al. Recessive LAMC3 mutations cause malformations of occipital cortical development. Nat Genet. 2011;43:590–594. - PMC - PubMed

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The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas

Affiliations

The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas

Authors

Affiliations

Abstract

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