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The Neuroscience Multi-Omic Archive: A BRAIN Initiative resource for single-cell transcriptomic and epigenomic data from the mammalian brain

View ORCID ProfileSeth A. Ament, Ricky S. Adkins, Robert Carter, Elena Chrysostomou, Carlo Colantuoni, Jonathan Crabtree, Heather H. Creasy, Kylee Degatano, Victor Felix, Peter Gandt, Gwenn A. Garden, Michelle Giglio, Brian R. Herb, Farzaneh Khajouei, Elizabeth Kiernan, Carrie McCracken, Kennedy McDaniel, Suvarna Nadendla, Lance Nickel, Dustin Olley, Joshua Orvis, Joseph P. Receveur, Mike Schor, Timothy L. Tickle, Jessica Way, Ronna Hertzano, Anup A. Mahurkar, Owen R White
doi: https://doi.org/10.1101/2022.09.08.505285
Seth A. Ament
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
2Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD
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  • ORCID record for Seth A. Ament
  • For correspondence: sament@som.umaryland.edu rhertzano@som.umaryland.edu amahurkar@som.umaryland.edu owhite@som.umaryland.edu
Ricky S. Adkins
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
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Robert Carter
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
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Elena Chrysostomou
3Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD
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Carlo Colantuoni
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
4Departments of Neurology and Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD
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Jonathan Crabtree
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
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Heather H. Creasy
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
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Kylee Degatano
5Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA
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Victor Felix
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
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Peter Gandt
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
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Gwenn A. Garden
6Department of Neurology, University of North Carolina at Chapel Hill, Chapel Hill, NC
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Michelle Giglio
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
7Department of Medicine, University of Maryland School of Medicine, Baltimore, MD
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Brian R. Herb
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
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Farzaneh Khajouei
5Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA
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Elizabeth Kiernan
5Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA
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Carrie McCracken
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
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Kennedy McDaniel
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
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Suvarna Nadendla
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
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Lance Nickel
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
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Dustin Olley
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
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Joshua Orvis
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
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Joseph P. Receveur
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
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Mike Schor
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
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Timothy L. Tickle
5Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA
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Jessica Way
5Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA
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Ronna Hertzano
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
3Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD
8Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD
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  • For correspondence: sament@som.umaryland.edu rhertzano@som.umaryland.edu amahurkar@som.umaryland.edu owhite@som.umaryland.edu
Anup A. Mahurkar
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
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  • For correspondence: sament@som.umaryland.edu rhertzano@som.umaryland.edu amahurkar@som.umaryland.edu owhite@som.umaryland.edu
Owen R White
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
9Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD
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  • For correspondence: sament@som.umaryland.edu rhertzano@som.umaryland.edu amahurkar@som.umaryland.edu owhite@som.umaryland.edu
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ABSTRACT

Scalable technologies to sequence the transcriptomes and epigenomes of single cells are transforming our understanding of cell types and cell states. The Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative Cell Census Network (BICCN) is applying these technologies at unprecedented scale to map the cell types in the mammalian brain. In an effort to increase data FAIRness (Findable, Accessible, Interoperable, Reusable), the NIH has established repositories to make data generated by the BICCN and related BRAIN Initiative projects accessible to the broader research community. Here, we describe the Neuroscience Multi-Omic Archive (NeMO Archive; nemoarchive.org), which serves as the primary repository for genomics data from the BRAIN Initiative. Working closely with other BRAIN Initiative researchers, we have organized these data into a continually expanding, curated repository, which contains transcriptomic and epigenomic data from over 50 million brain cells, including single-cell genomic data from all of the major regions of the adult and prenatal human and mouse brains, as well as substantial single-cell genomic data from non-human primates. We make available several tools for accessing these data, including a searchable web portal, a cloud-computing interface for large-scale data processing (implemented on Terra, terra.bio), and a visualization and analysis platform, NeMO Analytics (nemoanalytics.org).

KEY POINTS

  • The Neuroscience Multi-Omic Archive serves as the genomics data repository for the BRAIN Initiative.

  • Genomic data from >50 million cells span all the major regions of the brains of humans and mice.

  • We provide a searchable web portal, a cloud-computing interface, and a data visualization platform.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://nemoarchive.org/

  • https://www.nemoanalytics.org/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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The Neuroscience Multi-Omic Archive: A BRAIN Initiative resource for single-cell transcriptomic and epigenomic data from the mammalian brain
Seth A. Ament, Ricky S. Adkins, Robert Carter, Elena Chrysostomou, Carlo Colantuoni, Jonathan Crabtree, Heather H. Creasy, Kylee Degatano, Victor Felix, Peter Gandt, Gwenn A. Garden, Michelle Giglio, Brian R. Herb, Farzaneh Khajouei, Elizabeth Kiernan, Carrie McCracken, Kennedy McDaniel, Suvarna Nadendla, Lance Nickel, Dustin Olley, Joshua Orvis, Joseph P. Receveur, Mike Schor, Timothy L. Tickle, Jessica Way, Ronna Hertzano, Anup A. Mahurkar, Owen R White
bioRxiv 2022.09.08.505285; doi: https://doi.org/10.1101/2022.09.08.505285
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The Neuroscience Multi-Omic Archive: A BRAIN Initiative resource for single-cell transcriptomic and epigenomic data from the mammalian brain
Seth A. Ament, Ricky S. Adkins, Robert Carter, Elena Chrysostomou, Carlo Colantuoni, Jonathan Crabtree, Heather H. Creasy, Kylee Degatano, Victor Felix, Peter Gandt, Gwenn A. Garden, Michelle Giglio, Brian R. Herb, Farzaneh Khajouei, Elizabeth Kiernan, Carrie McCracken, Kennedy McDaniel, Suvarna Nadendla, Lance Nickel, Dustin Olley, Joshua Orvis, Joseph P. Receveur, Mike Schor, Timothy L. Tickle, Jessica Way, Ronna Hertzano, Anup A. Mahurkar, Owen R White
bioRxiv 2022.09.08.505285; doi: https://doi.org/10.1101/2022.09.08.505285

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