New Results
The Human Cell Atlas
Aviv Regev, Sarah A. Teichmann, Eric S. Lander, Ido Amit, Christophe Benoist, Ewan Birney, Bernd Bodenmiller, Peter Campbell, Piero Carninci, Menna Clatworthy, Hans Clevers, Bart Deplancke, Ian Dunham, James Eberwine, Roland Eils, Wolfgang Enard, Andrew Farmer, Lars Fugger, Berthold Göttgens, Nir Hacohen, Muzlifah Haniffa, Martin Hemberg, Seung Kim, Paul Klenerman, Arnold Kriegstein, Ed Lein, Sten Linnarsson, Joakim Lundeberg, Partha Majumder, John C. Marioni, Miriam Merad, Musa Mhlanga, Martijn Nawijn, Mihai Netea, Garry Nolan, Dana Pe’er, Anthony Phillipakis, Chris P. Ponting, Steve Quake, Wolf Reik, Orit Rozenblatt-Rosen, Joshua Sanes, Rahul Satija, Ton N. Schumacher, Alex Shalek, Ehud Shapiro, Padmanee Sharma, Jay W. Shin, Oliver Stegle, Michael Stratton, Michael J. T. Stubbington, Alexander van Oudenaarden, Allon Wagner, Fiona Watt, Jonathan Weissman, Barbara Wold, Ramnik Xavier, Nir Yosef, the Human Cell Atlas Meeting Participants
doi: https://doi.org/10.1101/121202
Aviv Regev
1Broad Institute of MIT and Harvard, Cambridge MA 02138, USA
2Department of Biology, Massachusetts Institute of Technology, Cambridge MA 02138 USA
3Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
Sarah A. Teichmann
4Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
5EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
6Cavendish Laboratory, Physics Department, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
Eric S. Lander
1Broad Institute of MIT and Harvard, Cambridge MA 02138, USA
2Department of Biology, Massachusetts Institute of Technology, Cambridge MA 02138 USA
7Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
Ido Amit
8Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
Christophe Benoist
9Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
Ewan Birney
5EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Bernd Bodenmiller
10Institute of Molecular Life Sciences, University of Zürich, CH-8057 Zürich, Switzerland
Peter Campbell
4Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
11Department of Haematology, University of Cambridge, Cambridge CB2 0XY, UK
Piero Carninci
12RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
Menna Clatworthy
13Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH UK
Hans Clevers
14Hubrecht Institute, Princess Maxima Center for Pediatric Oncology and University Medical Center Utrecht 3584 CT, the Netherlands
Bart Deplancke
15Institute of Bioengineering, School of Life Sciences, Bldg. AI 1147, Station 19, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
Ian Dunham
5EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
James Eberwine
16Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
Roland Eils
17Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
18Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, D-69120 Heidelberg, Germany
Wolfgang Enard
19Department of Biology II, Ludwig Maximilian University Munich, 82152 Martinsried, Germany
Andrew Farmer
20Takara Bio USA, Inc., Mountain View, CA 94043, USA
Lars Fugger
21Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, and MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
Berthold Göttgens
11Department of Haematology, University of Cambridge, Cambridge CB2 0XY, UK
22Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
Nir Hacohen
1Broad Institute of MIT and Harvard, Cambridge MA 02138, USA
23Massachusetts General Hospital Cancer Center, Boston, MA, 02114, USA
Muzlifah Haniffa
24Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
Martin Hemberg
4Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Seung Kim
25Departments of Developmental Biology and of Medicine, Stanford University School of Medicine, Stanford, CA 94305-5329 USA
Paul Klenerman
26Peter Medawar Building for Pathogen Research and Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX1 3SY, UK
27Oxford NIHR Biomedical Research Centre, The John Radcliffe Hospital, Oxford OX3 9DU, UK
Arnold Kriegstein
28Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, 35 Medical Center Way, San Francisco, California 94143-0525, USA
Ed Lein
29Allen Institute for Brain Science, Seattle, WA 98109 USA
Sten Linnarsson
30Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
Joakim Lundeberg
31Science for Life Laboratory, Department of Gene Technology, Royal Institute of Technology, SE-106 91 Stockholm, Sweden
Partha Majumder
32National Institute of Biomedical Genomics, Kalyani, West Bengal 741251, India
John C. Marioni
4Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
5EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
33University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
Miriam Merad
34Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Musa Mhlanga
35Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine (IDM), Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
Martijn Nawijn
36Department of Pathology and Medical Biology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
Mihai Netea
37Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
Garry Nolan
38Department of Microbiology and Immunology, Stanford University, Palo Alto, CA 94304 USA
Dana Pe’er
39Computational and Systems Biology Program, Sloan Kettering Institute, New York, NY, 10065
Anthony Phillipakis
1Broad Institute of MIT and Harvard, Cambridge MA 02138, USA
Chris P. Ponting
40MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU UK
Steve Quake
41Department of Applied Physics, Stanford University, Stanford, CA 94305; Department of Bioengineering, Stanford University, Stanford, CA 9430 USA
42Chan Zuckerberg Biohub, San Francisco, CA 94158 USA
Wolf Reik
4Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
43Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
44Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
Orit Rozenblatt-Rosen
1Broad Institute of MIT and Harvard, Cambridge MA 02138, USA
Joshua Sanes
45Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge MA, 02138 USA
Rahul Satija
46Department of Biology, New York University, New York, NY 10003, USA
47New York Genome Center, New York University, New York, NY 10013, USA
Ton N. Schumacher
48Division of Immunology, The Netherlands Cancer Institute, 1066 CX, Amsterdam, the Netherlands
Alex Shalek
1Broad Institute of MIT and Harvard, Cambridge MA 02138, USA
49Institute for Medical Engineering & Science (IMES) and Department of Chemistry, MIT, Cambridge, MA 02139 USA
50Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139 USA
Ehud Shapiro
51Department of Computer Science and Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
Padmanee Sharma
52Department of Genitourinary Medical Oncology, Department of Immunology, MD Anderson Cancer Center, University of Texas, Houston, TX 77030 USA
Jay W. Shin
12RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan
Oliver Stegle
5EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Michael Stratton
4Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Michael J. T. Stubbington
4Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Alexander van Oudenaarden
53Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
Allon Wagner
54Department of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California, Berkeley, CA, 94720-1770 USA
Fiona Watt
55Centre for Stem Cells and Regenerative Medicine, King’s College London, London WC2R 2LS UK
Jonathan Weissman
3Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
56Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158 USA
57California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158 USA
58Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158 USA
Barbara Wold
59Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125 USA
Ramnik Xavier
1Broad Institute of MIT and Harvard, Cambridge MA 02138, USA
60Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114 USA
61Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA 02114 USA
62Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
Nir Yosef
50Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139 USA
54Department of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California, Berkeley, CA, 94720-1770 USA
Abstract
The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body, by undertaking a Human Cell Atlas Project as an international collaborative effort. The aim would be to define all human cell types in terms of distinctive molecular profiles (e.g., gene expression) and connect this information with classical cellular descriptions (e.g., location and morphology). A comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, as well as provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas.
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 4.0 International license.
Posted May 08, 2017.
The Human Cell Atlas
Aviv Regev, Sarah A. Teichmann, Eric S. Lander, Ido Amit, Christophe Benoist, Ewan Birney, Bernd Bodenmiller, Peter Campbell, Piero Carninci, Menna Clatworthy, Hans Clevers, Bart Deplancke, Ian Dunham, James Eberwine, Roland Eils, Wolfgang Enard, Andrew Farmer, Lars Fugger, Berthold Göttgens, Nir Hacohen, Muzlifah Haniffa, Martin Hemberg, Seung Kim, Paul Klenerman, Arnold Kriegstein, Ed Lein, Sten Linnarsson, Joakim Lundeberg, Partha Majumder, John C. Marioni, Miriam Merad, Musa Mhlanga, Martijn Nawijn, Mihai Netea, Garry Nolan, Dana Pe’er, Anthony Phillipakis, Chris P. Ponting, Steve Quake, Wolf Reik, Orit Rozenblatt-Rosen, Joshua Sanes, Rahul Satija, Ton N. Schumacher, Alex Shalek, Ehud Shapiro, Padmanee Sharma, Jay W. Shin, Oliver Stegle, Michael Stratton, Michael J. T. Stubbington, Alexander van Oudenaarden, Allon Wagner, Fiona Watt, Jonathan Weissman, Barbara Wold, Ramnik Xavier, Nir Yosef, the Human Cell Atlas Meeting Participants
bioRxiv 121202; doi: https://doi.org/10.1101/121202
The Human Cell Atlas
Aviv Regev, Sarah A. Teichmann, Eric S. Lander, Ido Amit, Christophe Benoist, Ewan Birney, Bernd Bodenmiller, Peter Campbell, Piero Carninci, Menna Clatworthy, Hans Clevers, Bart Deplancke, Ian Dunham, James Eberwine, Roland Eils, Wolfgang Enard, Andrew Farmer, Lars Fugger, Berthold Göttgens, Nir Hacohen, Muzlifah Haniffa, Martin Hemberg, Seung Kim, Paul Klenerman, Arnold Kriegstein, Ed Lein, Sten Linnarsson, Joakim Lundeberg, Partha Majumder, John C. Marioni, Miriam Merad, Musa Mhlanga, Martijn Nawijn, Mihai Netea, Garry Nolan, Dana Pe’er, Anthony Phillipakis, Chris P. Ponting, Steve Quake, Wolf Reik, Orit Rozenblatt-Rosen, Joshua Sanes, Rahul Satija, Ton N. Schumacher, Alex Shalek, Ehud Shapiro, Padmanee Sharma, Jay W. Shin, Oliver Stegle, Michael Stratton, Michael J. T. Stubbington, Alexander van Oudenaarden, Allon Wagner, Fiona Watt, Jonathan Weissman, Barbara Wold, Ramnik Xavier, Nir Yosef, the Human Cell Atlas Meeting Participants
bioRxiv 121202; doi: https://doi.org/10.1101/121202
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