U19 - Huang 1U19MH114821-01

A Comprehensive Center for Mouse Brain Cell Atlas

An essential step toward a comprehensive understanding of brain function is to establish a cellular-resolution structural framework upon which multiscale and multi-modal information spanning molecules, cells, circuits, systems and behavior can be registered, integrated, interpreted and mined. Dr. Huang and Arlotta will lead the Center to produce two complementary cell atlases integrated within a digital Common Coordinate Framework of the mouse brain: 1) a Brainwide Cell Transcriptome Atlas of unprecedented scale and resolution, integrated with 2) an in-depth Forebrain Projection Neuron Atlas that combines comprehensive anatomic and molecular information. The Center consists of the following research and administrative components: 

  • Molecular Segment: Build a high coverage molecular atlas of the whole brain with in-depth neuronal profiling of the forebrain.
  • Anatomy Segment: Build a high-resolution anatomical atlas of forebrain projection neurons.
  • Cell Tools Segment: Build a comprehensive set of driver and reporter lines to target forebrain projection neurons and rare cell populations brain-wide.
  • Tool and Technology Core: Improve and develop state-of-the-art anatomic, imaging and transcriptomic technologies for rapid and cost-effective brain-wide surveys of integrated gene expression and long-range projections.
  • Data Core: Molecular and anatomic data storage, integration, analysis and display.
  • Administrative Core:  Coordinate research, communication and reporting within the Center, across BICCN, and with NIH.

Project Leadership

Z. Josh Huang, Ph.D. 
Charles Robertson Professor of Neuroscience 
Cold Spring Harbor Laboratory (Co-Investigator, Center Director) 
https://www.cshl.edu/research/faculty-staff/z-josh-huang/

 

Paola Arlotta, Ph.D.  
Professor, Department of Stem Cell and Regenerative Biology 
Harvard University (Co-Investigator, Center Director) 
https://hscrb.harvard.edu/res-fl-arlotta

 

Jesse Gillis, Ph.D. 
Associate Professor, Cold Spring Harbor Laboratory 
https://www.cshl.edu/research/faculty-staff/jesse-gillis/

 

Pavel Osten, Ph.D. 
Associate Professor, Cold Spring Harbor Laboratory 
https://www.cshl.edu/research/faculty-staff/pavel-osten/

 

Partha Mitra, Ph.D. 
Professor, Cold Spring Harbor Laboratory (Data Core Director) 
https://www.cshl.edu/research/faculty-staff/partha-mitra/

 

Anthony Zador, M.D., Ph.D. 
Alle Davis and Maxine Harrison Professor of Neurosciences 
Cold Spring Harbor Laboratory (Technology Core Director) 
https://www.cshl.edu/research/faculty-staff/anthony-zador/

 

Catherine Dulac, Ph.D. 
Howard Hughes Medical Institute Investigator 
Higgins Professor of Molecular and Cellular Biology, Harvard University 
https://www.mcb.harvard.edu/directory/catherine-dulac/

 

Xiaowei Zhuang, Ph.D. 
Howard Hughes Medical Institute Investigator 
David B. Arnold Jr. Professor of Science 
Professor of Chemistry, Chemical Biology, and Physics; Harvard University  
http://zhuang.harvard.edu/

 

Evan Macosko, Ph.D. 
Principal Investigator Stanley Center for Psychiatric Research 
Broad Institute of MIT and Harvard 
Assistant Professor of Psychiatry, Harvard Medical School  
http://macoskolab.com/

 

Anthony Philippakis, M.D., Ph.D. 
Chief Data Officer; Institute Scientist, Broad Institute of MIT and Harvard 
https://www.broadinstitute.org/bios/anthony-philippakis-0

 

Aviv Regev, Ph.D. 
Howard Hughes Medical Institute Investigator 
Director, Klarman Cell Observatory 
Broad Institute of MIT and Harvard 
Professor, Department of Biology, MIT 
https://www.broadinstitute.org/regev-lab

 

Edward Boyden, Ph.D. 
Associate Professor of Biological Engineering and Brain and Cognitive Sciences, MIT 
Media Lab and McGovern Institute 
Y. Eva Tan Professor in Neurotechnology 
https://be.mit.edu/directory/ed-boyden

 

Hong-Wei Dong, Ph.D.  
Professor of Neurology, Director of Center for Integrative Connectomics,  
USC Mark and Mary Stevens Neuroimaging and Informatics Institute 
Keck School of Medicine of University of Southern California 
http://donglab.loni.usc.edu/

 

Michael Miller, Ph.D. 
Professor of Biomedical Engineering 
Director, Center for Imaging Science 
Co-Director, Kavli Neuroscience Discovery Institute 
Johns Hopkins University  
https://www.bme.jhu.edu/faculty_staff/michael-i-miller-phd/

 

John Tilak Ratnanather, Ph.D.  
Associate Research Professor 
Department of Biomedical Engineering  
Johns Hopkins University 
http://www.cis.jhu.edu/~tilak/

 

Qingming Luo, Ph.D. 
Professor of Biomedical Photonics 
School of Engineering Sciences 
Huazhong University of Science and Technology, Wuhan, China 
http://ses.hust.edu.cn/info/1072/1292.htm

 

Hui Gong, Ph.D. 
Professor of Biomedical Photonics 
School of Engineering Sciences 
Huazhong University of Science and Technology, Wuhan, China 
http://ses.hust.edu.cn/info/1072/1313.htm


Project Data Types

  • Over 5 million brain-wide single cell RNAseq libraries - 10x Genomics Chromium v2 snRNA-seq 
  • Over 80,000 high-depth single cell RNAseq libraries - 10x Genomics Chromium v2 snRNA-seq 
  • 60,000 single cell ATACseq libraries 
  • 5 million MERFISH cells 
  • 500 STP brains for cell type distribution 
  • 500 STP brains for rabies trans-synaptic tracing 
  • 400 brains imaged by fMOST with 1,500 single neuron reconstructed 
  • 150 brains mapped using triple anterograde tracing 
  • 250 brains mapped using quadruple retrograde tracing 

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